NCBI Conserved Domain Search

PDZ domain 1 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467245 [Multi-domain] Cd Length: 95 Bit Score: 198.78 E-value: 1.91e-59

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  615 EWETEVVEFERETEDIDLKALGFDMAEGVNEPCFPGDCGIFVTKVDKGSIADGRLRVNDWLLRINDVDLINKDKKQAIKA 694
Cdd:cd06764     1 EWETETVEFEKVRDDMDLKALGFDIAGGVNDPQFPGDCSIFVTKVDKGSIADGRLRVNDCLLRINDVDLTNKDKKQAIQA 80

                          90
                  ....*....|....*
gi 767964249  695 LLNGEGAINMVVRRR 709
Cdd:cd06764    81 VLNGGGVINMVVRRR 95

PDZ domain 3 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467248 [Multi-domain] Cd Length: 82 Bit Score: 169.81 E-value: 2.21e-49

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1346 EEPRHVKVQKGSEPLGISIVSGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITILA 1425
Cdd:cd06767     1 EEPRHVSIEKGSEPLGISIVSGENGGIFVSSVTEGSLAHQAGLEYGDQLLEVNGINLRNATEQQAALILRQCGDTITMLV 80


                  ..
gi 767964249 1426 QY 1427
Cdd:cd06767    81 QY 82

PDZ domain 4 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467247 [Multi-domain] Cd Length: 81 Bit Score: 167.95 E-value: 7.84e-49

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1499 EPRVVFIKKSQLELGVHLCGGNLHGVFVAEVEDDSPAKGPDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRDGVRLKV 1578
Cdd:cd06766     1 EPRLVFLKKSQVELGIQLCGGNLHGIFVEDVEDDSPAKGPDGLVPGDLILEYNSVDMRNKTAEEAYLEMLKPAETVTLKV 80


                  .
gi 767964249 1579 Q 1579
Cdd:cd06766    81 Q 81

PDZ domain 2 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PSZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467246 [Multi-domain] Cd Length: 77 Bit Score: 151.34 E-value: 4.88e-43

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  721 HINLSGQKDSGISLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLKVFP 797
Cdd:cd06765     1 HINLSGQKDSGISLENGVFISRIVPGSPAAKEGSLTVGDRIIAINGIALDNKSLSECEALLRSCRDSLSLSLMKVFP 77

Src homology 3 domain of Disks Large homolog 5; DLG5 is a multifunctional scaffold protein that is located at sites of cell-cell contact and is involved in the maintenance of cell shape and polarity. Mutations in the DLG5 gene are associated with Crohn's disease (CD) and inflammatory bowel disease (IBD). DLG5 is a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. DLG5 contains 4 PDZ domains as well as an N-terminal domain of unknown function. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212794 Cd Length: 63 Bit Score: 122.06 E-value: 5.32e-33

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1597 YIRALYDRLADVEQELSFKKDDILYVDDTLPQGTFGSWMAWQLDENAQKIQRGQIPSKYV 1656
Cdd:cd11860     1 YVRALFDRSAENEDELSFKKDDILYVDNTMFNGVFGQWRAWLVDEEGRKRKCGIIPSKYK 60

Takusan; This domain is named takusan, which is a Japanese word meaning 'many'. Members of this family regulate synaptic activity.

Pssm-ID: 461445 Cd Length: 85 Bit Score: 114.28 E-value: 6.25e-30

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   129 KAPSPPPLLTDQQVNEKVENLSIQLRLMTRERNELRKRLAFATHGTAFDkRPYHRLNPDYERLKIQCVRAMSDLQSLQNQ 208
Cdd:pfam04822    2 ASSSPPTILSKEQRKKELERLKFELQLITNERNELRDILALYTEGDLND-RPYHRLNPEYEILKLQHEKVMSDLQKLENE 80


                   ....*
gi 767964249   209 HTNAL 213
Cdd:pfam04822   81 ISEAL 85

Unstructured region between two PDZ domains on Dlg5; dbPDZ_assoc is found on higher eukaryote Dlg5, Disks large homolog 5, proteins, lying between the second pair of PDZ domains. The sequence is natively unstructured but may just be long extensions of the PDZs on these sequences in this position. The function is not known.

Pssm-ID: 465197 Cd Length: 81 Bit Score: 100.74 E-value: 3.48e-25

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  1427 YNPHVHQLSSHSRSSSHLDPAGTHSTLQGSGTTTPEHPSVIDPLMEQDEGPSTPPAKQS--------SSRIAGDANKKTL 1498
Cdd:pfam16610    1 YNPHMYQLGNHSRSSSRLEPVSNHSTPQGSGATTPDNHSTIDTLSEQDEGTMTPPSKQTtpatsphnSFRMPGDANKRVP 80


                   .
gi 767964249  1499 E 1499
Cdd:pfam16610   81 E 81

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

Pssm-ID: 214570 [Multi-domain] Cd Length: 85 Bit Score: 82.81 E-value: 6.45e-19

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   1347 EPRHVKVQKGSEPLGISIVSG--EKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITIL 1424
Cdd:smart00228    1 EPRLVELEKGGGGLGFSLVGGkdEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLT 80


                    ....*
gi 767964249   1425 AQYNP 1429
Cdd:smart00228   81 VLRGG 85

PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila Dlg1, human Dlg1, 2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197; SAP-97), Dlg2 (also known as channel-associated protein of synapse-110; postsynaptic density protein 93, PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95; synapse-associated protein 90, SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling, regulating surface expression of NMDA receptors in dorsal horn neurons of the spinal cord; it interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. The Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development; postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467257 [Multi-domain] Cd Length: 91 Bit Score: 82.40 E-value: 1.06e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1347 EPRHVKVQKGSEPLGISIVSGEKG-GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITIL 1424
Cdd:cd06795     1 EPRKIVLHKGSTGLGFNIVGGEDGeGIFISFILAGGPADLSGeLRRGDQILSVNGVDLRNATHEQAAAALKNAGQTVTII 80


                  ....*
gi 767964249 1425 AQYNP 1429
Cdd:cd06795    81 AQYKP 85

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 89.73 E-value: 1.32e-17

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   338 LEQLGEENQRLLKQTEMLTQQRDTAIQLQHQCALSLRRFEAIH----HELNKATAQNKDLQWEMELLQSELTELRTtqvk 413
Cdd:TIGR02168  700 LAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVeqleERIAQLSKELTELEAEIEELEERLEEAEE---- 775

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   414 TAKESEKYREERDAVYSEYKlimSERDQVISELDKLQTEVEL-------AESKLKSSTSEKKAANEEMEALRQIKDTVTM 486
Cdd:TIGR02168  776 ELAEAEAEIEELEAQIEQLK---EELKALREALDELRAELTLlneeaanLRERLESLERRIAATERRLEDLEEQIEELSE 852

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   487 DAGRANKEVEILRKQCKALCQELKEALqeadvakcrrdwafQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLD 566
Cdd:TIGR02168  853 DIESLAAEIEELEELIEELESELEALL--------------NERASLEEALALLRSELEELSEELRELESKRSELRRELE 918

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249   567 DTRKQKNDVSRELKELKEQMESQLEK--EARFRQLMAHSSHDSAIDTDSMEWETEVVEFEREtedidLKALG 636
Cdd:TIGR02168  919 ELREKLAQLELRLEGLEVRIDNLQERlsEEYSLTLEEAEALENKIEDDEEEARRRLKRLENK-----IKELG 985

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467153 [Multi-domain] Cd Length: 81 Bit Score: 76.81 E-value: 7.04e-17

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1350 HVKVQKGS-EPLGISIVSGE--KGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITIL 1424
Cdd:cd00136     1 TVTLEKDPgGGLGFSIRGGKdgGGGIFVSRVEPGGPAARDGrLRVGDRILEVNGVSLEGLTHEEAVELLKSAGGEVTLT 79

PDZ domain 4 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467247 [Multi-domain] Cd Length: 81 Bit Score: 75.50 E-value: 2.07e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1347 EPRHVKVQKGSEPLGISIVSGEKGGIYVSKVTVGSIAHQA-GLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITILA 1425
Cdd:cd06766     1 EPRLVFLKKSQVELGIQLCGGNLHGIFVEDVEDDSPAKGPdGLVPGDLILEYNSVDMRNKTAEEAYLEMLKPAETVTLKV 80


                  .
gi 767964249 1426 Q 1426
Cdd:cd06766    81 Q 81

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467153 [Multi-domain] Cd Length: 81 Bit Score: 75.27 E-value: 2.50e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  702 INMVVRRRKSLGgkvvtplhINLSGQKDSGIslenGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLL 781
Cdd:cd00136     2 VTLEKDPGGGLG--------FSIRGGKDGGG----GIFVSRVEPGGPAARDGRLRVGDRILEVNGVSLEGLTHEEAVELL 69


                  ....*....
gi 767964249  782 RSCQDSLTL 790
Cdd:cd00136    70 KSAGGEVTL 78

PDZ domain 1 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Dlg1, human Dlg1,2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197 or SAP-97), Dlg2 (also known as channel-associated protein of synapse-110, postsynaptic density protein 93, or PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95, synapse-associated protein 90, or SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling. It regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord, and it also interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467206 [Multi-domain] Cd Length: 89 Bit Score: 74.27 E-value: 7.76e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  628 EDIDL----KALGFDMAEGVNEPCFPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGA 701
Cdd:cd06723     2 EEITLergnSGLGFSIAGGTDNPHIGDDPSIYITKIIPGGAAaaDGRLRVNDIILRVNDVDVRNVTHSVAVEALKEAGSI 81


                  ....*...
gi 767964249  702 INMVVRRR 709
Cdd:cd06723    82 VRLYVKRR 89

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467153 [Multi-domain] Cd Length: 81 Bit Score: 71.42 E-value: 6.29e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  620 VVEFERETEdidlKALGFDMAEGVNepcfpGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd00136     1 TVTLEKDPG----GGLGFSIRGGKD-----GGGGIFVSRVEPGGPAarDGRLRVGDRILEVNGVSLEGLTHEEAVELLKS 71

                          90
                  ....*....|
gi 767964249  698 GEGAINMVVR 707
Cdd:cd00136    72 AGGEVTLTVR 81

PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467220 [Multi-domain] Cd Length: 82 Bit Score: 70.43 E-value: 1.50e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1356 GSEPLGISIVSG--EKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIgQQCDTITI 1423
Cdd:cd06738    11 GTRGLGCSISSGptQKPGIFISNVKPGSLAEEVGLEVGDQIVEVNGTSFTNVDHKEAVMAL-KSSRHLTI 79

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 78.95 E-value: 2.37e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   297 EILNKLYDTA--MDKLEVV----KKDYDALRK------RYSE-KVAIHNADLS----RLEQLGEENQRLLKQTEMLTQQR 359
Cdd:TIGR02168  176 ETERKLERTRenLDRLEDIlnelERQLKSLERqaekaeRYKElKAELRELELAllvlRLEELREELEELQEELKEAEEEL 255

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   360 DTAIQLQHQCALSLRRFEAIHHELNKataqnkdlqwEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSER 439
Cdd:TIGR02168  256 EELTAELQELEEKLEELRLEVSELEE----------EIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQL 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   440 DQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKdtvtmdagrankeveilrkqckalcQELKEALQEADV- 518
Cdd:TIGR02168  326 EELESKLDELAEELAELEEKLEELKEELESLEAELEELEAEL-------------------------EELESRLEELEEq 380

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   519 ---AKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDdtRKQKNDVSRELKELKEQMESQLEKEAR 595
Cdd:TIGR02168  381 letLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLE--EAELKELQAELEELEEELEELQEELER 458


                   ...
gi 767964249   596 FRQ 598
Cdd:TIGR02168  459 LEE 461

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 77.80 E-value: 5.05e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   231 SRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMK-RLHE------EDQKEIGDLRAQQQQVLK-HNGSSEILNKL 302
Cdd:TIGR02169  663 RGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIEnRLDElsqelsDASRKIGEIEKEIEQLEQeEEKLKERLEEL 742

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   303 yDTAMDKLEVVKKDYDALRKRYSEKVAIHNADLSRLE-QLGEENQRLLKQTEMLTQQRDTAIQLQHQcalSLR-RFEAIH 380
Cdd:TIGR02169  743 -EEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEeALNDLEARLSHSRIPEIQAELSKLEEEVS---RIEaRLREIE 818

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   381 HELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKL 460
Cdd:TIGR02169  819 QKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQL 898

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   461 KSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKcrrdwafqERDKIVAErdsI 540
Cdd:TIGR02169  899 RELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKGEDEEIPEEELSLEDVQA--------ELQRVEEE---I 967

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249   541 RTLCD-NLrrerdRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMEsQLEKEAR 595
Cdd:TIGR02169  968 RALEPvNM-----LAIQEYEEVLKRLDELKEKRAKLEEERKAILERIE-EYEKKKR 1017

Src homology 3 domain of the Tight junction proteins, Zonula occludens (ZO) proteins; ZO proteins are scaffolding proteins that associate with each other and with other proteins of the tight junction, zonula adherens, and gap junctions. They play roles in regulating cytoskeletal dynamics at these cell junctions. They are considered members of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. Vertebrates contain three ZO proteins (ZO-1, ZO-2, and ZO-3) with redundant and non-redundant roles. They contain three PDZ domains, followed by SH3 and GuK domains; in addition, ZO-1 and ZO-2 contains a proline-rich (PR) actin binding domain at the C-terminus while ZO-3 contains this PR domain between the second and third PDZ domains. The C-terminal regions of the three ZO proteins are unique. The SH3 domain of ZO-1 has been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212793 Cd Length: 62 Bit Score: 67.31 E-value: 8.96e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1597 YIRALYDRLADVEQELSFKKDDILYVDDTLPQGTFGSWMAWQLDENAQKIQRGQIPSK 1654
Cdd:cd11859     1 YIRTHFDYEKPAKGELSFKKGEVFHVVDTLYQGTVGSWQAVRVGRNHQELERGVIPNK 58

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

Pssm-ID: 214570 [Multi-domain] Cd Length: 85 Bit Score: 67.79 E-value: 1.25e-13

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   1499 EPRVVFIKKSQLELGVHLCGG--NLHGVFVAEVEDDSPAKGpDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRDGVRL 1576
Cdd:smart00228    1 EPRLVELEKGGGGLGFSLVGGkdEGGGVVVSSVVPGSPAAK-AGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTL 79


                    ....*.
gi 767964249   1577 KVQYRP 1582
Cdd:smart00228   80 TVLRGG 85

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 76.25 E-value: 1.35e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   248 RRENGQLLRERNL--LQQSWEDMKRLHEEDQKEIGDLRAQQQQVLKhngSSEILNKLYDTAMDKLEVVKKDYDALRKRyS 325
Cdd:TIGR02168  667 KTNSSILERRREIeeLEEKIEELEEKIAELEKALAELRKELEELEE---ELEQLRKELEELSRQISALRKDLARLEAE-V 742

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   326 EKVAihnadlSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQCALSLRRFEAihhELNKATAQNKDLQWEMELLQSELT 405
Cdd:TIGR02168  743 EQLE------ERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEA---QIEQLKEELKALREALDELRAELT 813

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   406 ELRTTQvkTAKESEKYREERDAVYSEYKLIMSE------RDQVIS---ELDKLQTEVELAESKLKSSTSEKKAANEEMEA 476
Cdd:TIGR02168  814 LLNEEA--ANLRERLESLERRIAATERRLEDLEeqieelSEDIESlaaEIEELEELIEELESELEALLNERASLEEALAL 891

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   477 LRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDwAFQER----------------DKIVAERDSI 540
Cdd:TIGR02168  892 LRSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGLEVRID-NLQERlseeysltleeaealeNKIEDDEEEA 970

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249   541 RTLCDNLRRERDR-------AVSELAEALRSLDDTRKQKNDVSRELKELKEQMEsQLEKEARFR 597
Cdd:TIGR02168  971 RRRLKRLENKIKElgpvnlaAIEEYEELKERYDFLTAQKEDLTEAKETLEEAIE-EIDREARER 1033

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 75.87 E-value: 2.24e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   240 LKDDVDMLRRENGQLLRERNLLqqswedmKRLHEEDQ----KEIGDLRAQQQQVLKhngssEIlnklyDTAMDKLEVVKK 315
Cdd:TIGR02169  196 KRQQLERLRREREKAERYQALL-------KEKREYEGyellKEKEALERQKEAIER-----QL-----ASLEEELEKLTE 258

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   316 DYDALRKRYSEKVAIHNADLSRLEQLGEENQRLLkQTEMLtqqrdtaiQLQHQCALSLRRFEAIHHELNKATAQNKDLQW 395
Cdd:TIGR02169  259 EISELEKRLEEIEQLLEELNKKIKDLGEEEQLRV-KEKIG--------ELEAEIASLERSIAEKERELEDAEERLAKLEA 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   396 EMELLQSELTELRttqvktaKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEME 475
Cdd:TIGR02169  330 EIDKLLAEIEELE-------REIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREIN 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   476 ALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAV 555
Cdd:TIGR02169  403 ELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVE 482

                          330       340       350
                   ....*....|....*....|....*....|..
gi 767964249   556 SELAEALRSLDDTRKQKNDVSRELKELKEQME 587
Cdd:TIGR02169  483 KELSKLQRELAEAEAQARASEERVRGGRAVEE 514

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

Pssm-ID: 214570 [Multi-domain] Cd Length: 85 Bit Score: 65.48 E-value: 8.38e-13

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249    715 KVVTPLHINLSGQKDSGisleNGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:smart00228    9 KGGGGLGFSLVGGKDEG----GGVVVSSVVPGSPAAKAG-LRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVL 82

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 73.18 E-value: 1.23e-12

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   183 RLNPDYERLKIQCVRAMSDLQSLQNqHTNALKRCEEVAKETdfyhtlHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQ 262
Cdd:TIGR02169  678 RLRERLEGLKRELSSLQSELRRIEN-RLDELSQELSDASRK------IGEIEKEIEQLEQEEEKLKERLEELEEDLSSLE 750

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   263 QSWEDMKRLHEEDQKEIGDLRAQQQQVlkhngsSEILNKLYDT-AMDKLEVVKKDYDALRKRYSEKVAIhnadLSRLEQl 341
Cdd:TIGR02169  751 QEIENVKSELKELEARIEELEEDLHKL------EEALNDLEARlSHSRIPEIQAELSKLEEEVSRIEAR----LREIEQ- 819

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   342 gEENQRLLKQtEMLTQQRDTAIQLQHQCALSLRRFEAIHHELNkatAQNKDLQWEMELLQSELTELRTTQVKTAKEseky 421
Cdd:TIGR02169  820 -KLNRLTLEK-EYLEKEIQELQEQRIDLKEQIKSIEKEIENLN---GKKEELEEELEELEAALRDLESRLGDLKKE---- 890

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   422 REERDAVYSEYKlimserdqviSELDKLQTEVELAESKLKSSTSEKKAANEEmeaLRQIKDTVTMDAGRANKE--VEILR 499
Cdd:TIGR02169  891 RDELEAQLRELE----------RKIEELEAQIEKKRKRLSELKAKLEALEEE---LSEIEDPKGEDEEIPEEElsLEDVQ 957

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249   500 KQCKALCQELKE-------ALQEADVAKCRRDWAFQERDKIVAERDSIRTL---CDNLRRE 550
Cdd:TIGR02169  958 AELQRVEEEIRAlepvnmlAIQEYEEVLKRLDELKEKRAKLEEERKAILERieeYEKKKRE 1018

PDZ domain 2 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Dlg1, human Dlg1,2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197 or SAP-97), Dlg2 (also known as channel-associated protein of synapse-110, postsynaptic density protein 93, or PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95, synapse-associated protein 90, or SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling. It regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord, and it also interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467207 [Multi-domain] Cd Length: 85 Bit Score: 64.98 E-value: 1.35e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249  629 DIDL----KALGFDMAEGVNEPCFPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd06724     1 EIKLvkgpKGLGFSIAGGVGNQHIPGDNGIYVTKIIEGGAAqkDGRLQVGDKLLAVNDVSLEEVTHEEAVAALKN 75

PDZ domain 2 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467169 [Multi-domain] Cd Length: 89 Bit Score: 63.79 E-value: 3.83e-12

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767964249  743 VLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06681    37 VRPGGPADREGTIKPGDRLLSVDGISLHGATHAEAMSILKQCGQEATL 84

DNA double-strand break repair Rad50 ATPase;

Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 70.84 E-value: 5.38e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  147 ENLSIQLRLMTRERNELRKRLAFATHGTAFDkrpyhrlNPDYERLKIQcvraMSDLQslqnqhtnalKRCEEVAKETDFY 226
Cdd:PRK02224  275 EELAEEVRDLRERLEELEEERDDLLAEAGLD-------DADAEAVEAR----REELE----------DRDEELRDRLEEC 333

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  227 HTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQVLKHNGSSEILnklYDTA 306
Cdd:PRK02224  334 RVAAQAHNEEAESLREDADDLEERAEELREEAAELESELEEAREAVEDRREEIEELEEEIEELRERFGDAPVD---LGNA 410

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  307 MDKLEVVKKDYDALRkrysEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDTAiQLQHQCALSLRRfeaihHELNKA 386
Cdd:PRK02224  411 EDFLEELREERDELR----EREAELEATLRTARERVEEAEALLEAGKCPECGQPVE-GSPHVETIEEDR-----ERVEEL 480

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  387 TAQNKDLQWEMELLQSELTELrTTQVKTAKESEKYREERDAV---YSEYKLIMSERDQVISEL----DKLQTEVELAESK 459
Cdd:PRK02224  481 EAELEDLEEEVEEVEERLERA-EDLVEAEDRIERLEERREDLeelIAERRETIEEKRERAEELreraAELEAEAEEKREA 559

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  460 LKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILrkqckALCQELKEALQEadVAKCRRDWAF---QERDKIVAE 536
Cdd:PRK02224  560 AAEAEEEAEEAREEVAELNSKLAELKERIESLERIRTLL-----AAIADAEDEIER--LREKREALAElndERRERLAEK 632

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  537 RDSIRTLCDNL--------RRERDRAVSELAEALRSLDDTRKQKND-------VSRELKELKEQMESQLEKEARFRQLma 601
Cdd:PRK02224  633 RERKRELEAEFdearieeaREDKERAEEYLEQVEEKLDELREERDDlqaeigaVENELEELEELRERREALENRVEAL-- 710

                         490
                  ....*....|...
gi 767964249  602 HSSHDSAIDTDSM 614
Cdd:PRK02224  711 EALYDEAEELESM 723

PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467186 [Multi-domain] Cd Length: 89 Bit Score: 63.04 E-value: 6.14e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1351 VKVQKGSEPLGISIVSG----------EKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDT 1420
Cdd:cd06702     3 IHLVKAGGPLGLSIVGGsdhsshpfgvDEPGIFISKVIPDGAAAKSGLRIGDRILSVNGKDLRHATHQEAVSALLSPGQE 82


                  ....*.
gi 767964249 1421 ITILAQ 1426
Cdd:cd06702    83 IKLLVR 88

PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of human PTPN13, and related domains. PTPN13, also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1), negatively regulates FAS-mediated apoptosis and NGFR-mediated pro-apoptotic signaling, and may also regulate phosphoinositide 3-kinase (PI3K) signaling. It contains 5 PDZ domains; interaction partners of its second PDZ domain (PDZ2) include the Fas receptor (TNFRSF6) and thyroid receptor-interacting protein 6 (TRIP6). The second PDZ (PDZ2) domain, but not PDZ1 or PDZ3, of FRMPD2 binds to GluN2A and GluN2B, two subunits of N-methyl-d-aspartic acid (NMDA) receptors. Other binding partners of the FRMPDZ2 PDZ2 domain include NOD2, and catenin family members, delta catenin (CTNND2), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) and p0071 (also known as plakophilin 4; PKP4). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467254 [Multi-domain] Cd Length: 87 Bit Score: 62.23 E-value: 1.15e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249  720 LHINLSGQKDSGISLeNGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSL 792
Cdd:cd06792    14 LGISVTGGINTSVRH-GGIYVKSLVPGGAAEQDGRIQKGDRLLEVNGVSLEGVTHKQAVECLKNAGQVVTLVL 85

Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.

Pssm-ID: 464943 [Multi-domain] Cd Length: 1112 Bit Score: 69.76 E-value: 1.65e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   197 RAMSDLQ-SLQNQHTNALKRCEEVAKetdfyhtLHSRL---LSDQTRLKDDVDMLRRENGQL------LRERN----LLQ 262
Cdd:pfam15921  496 RTVSDLTaSLQEKERAIEATNAEITK-------LRSRVdlkLQELQHLKNEGDHLRNVQTECealklqMAEKDkvieILR 568

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   263 QSWEDMKRLHEEDQKEIGDLRAQQQQVLKhngssEILNKLYDtaMDKLEVVKKDYDA----LRKRYS----EKVAIHNAD 334
Cdd:pfam15921  569 QQIENMTQLVGQHGRTAGAMQVEKAQLEK-----EINDRRLE--LQEFKILKDKKDAkireLEARVSdlelEKVKLVNAG 641

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   335 LSRL---EQLGEENQRLLKQTEmltQQRDTAIQLQHQCALSLRRFEAIHHELNKATaqNKdLQWEMELLQSELTELRTTq 411
Cdd:pfam15921  642 SERLravKDIKQERDQLLNEVK---TSRNELNSLSEDYEVLKRNFRNKSEEMETTT--NK-LKMQLKSAQSELEQTRNT- 714

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   412 VKTAKESEKYREErdAVYSEYKLIMSERDQViselDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRA 491
Cdd:pfam15921  715 LKSMEGSDGHAMK--VAMGMQKQITAKRGQI----DALQSKIQFLEEAMTNANKEKHFLKEEKNKLSQELSTVATEKNKM 788

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|..
gi 767964249   492 NKEVEILRKQCKalcqELKEALQEADVAKCRRDWAFQERDKIV--AERDSIR 541
Cdd:pfam15921  789 AGELEVLRSQER----RLKEKVANMEVALDKASLQFAECQDIIqrQEQESVR 836

PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467211 [Multi-domain] Cd Length: 82 Bit Score: 61.43 E-value: 1.87e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1347 EPRHVKVQKGSEpLGISIVSGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIG--QQCDTITIL 1424
Cdd:cd06729     1 DTRLVSFRKGGS-VGLRLAGGNDVGIFVAGVQEGSPAEKQGLQEGDQILKVNGVDFRNLTREEAVLFLLdlPKGEEVTIL 79


                  ...
gi 767964249 1425 AQY 1427
Cdd:cd06729    80 AQS 82

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.

Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 69.43 E-value: 1.88e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   215 RCEEVAKETDFYHTLHSRLLSDQTRLKDDVDmlrRENGQLLRERNLLQQSWEDM-KRLHE-EDQKeigdlRAQQQQVLKH 292
Cdd:pfam01576  626 RAEAEAREKETRALSLARALEEALEAKEELE---RTNKQLRAEMEDLVSSKDDVgKNVHElERSK-----RALEQQVEEM 697

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   293 NGSSEILNKLYDTAMD---KLEVvkkDYDALRkrysekvAIHNADLSRLEQLGEENQR-LLKQT-EMLTQ------QRDT 361
Cdd:pfam01576  698 KTQLEELEDELQATEDaklRLEV---NMQALK-------AQFERDLQARDEQGEEKRRqLVKQVrELEAElederkQRAQ 767

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   362 AIQLQHQCALSLRRFEAIHHELNK----ATAQNKDLQWEMELLQSELTELRTTQ---VKTAKESEKYRE--ERDAVYSEY 432
Cdd:pfam01576  768 AVAAKKKLELDLKELEAQIDAANKgreeAVKQLKKLQAQMKDLQRELEEARASRdeiLAQSKESEKKLKnlEAELLQLQE 847

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   433 KLIMSER--DQVISELDKLQTEVELAESKlKSSTSEKKaaneemealRQIKDTVTMdagrankeveilrkqckaLCQELK 510
Cdd:pfam01576  848 DLAASERarRQAQQERDELADEIASGASG-KSALQDEK---------RRLEARIAQ------------------LEEELE 899

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   511 EALQEADVAKCRRDWAFQERDKIVAERDSIRTLC---DNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELK-EQM 586
Cdd:pfam01576  900 EEQSNTELLNDRLRKSTLQVEQLTTELAAERSTSqksESARQQLERQNKELKAKLQEMEGTVKSKFKSSIAALEAKiAQL 979

                          410
                   ....*....|...
gi 767964249   587 ESQLEKEARFRQL 599
Cdd:pfam01576  980 EEQLEQESRERQA 992

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 68.81 E-value: 2.92e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  248 RRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQVLKhngsseilnklydtamdKLEVVKKDYDALRKRYSEK 327
Cdd:COG1196   224 ELEAELLLLKLRELEAELEELEAELEELEAELEELEAELAELEA-----------------ELEELRLELEELELELEEA 286

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  328 VAIHNADLSRLEQLGEENQRllkQTEMLTQQRDTAIQLQHQCALSLRRFEAIHHELNKATAQNKDLQWEMELLQSELTEL 407
Cdd:COG1196   287 QAEEYELLAELARLEQDIAR---LEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEA 363

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  408 RTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMD 487
Cdd:COG1196   364 EEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEA 443

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  488 AGRANKEVEILRKQCKALCQELKEALQEADvakcrrdwafQERDKIvaerdsirtlcDNLRRERDRAVSELaEALRSLDD 567
Cdd:COG1196   444 LEEAAEEEAELEEEEEALLELLAELLEEAA----------LLEAAL-----------AELLEELAEAAARL-LLLLEAEA 501

                         330
                  ....*....|....*...
gi 767964249  568 TRKQKNDVSRELKELKEQ 585
Cdd:COG1196   502 DYEGFLEGVKAALLLAGL 519

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 68.56 E-value: 3.42e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   317 YDALRKRYSEKVAihnaDLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQCALSL-----------RRFEAIHHELNK 385
Cdd:TIGR02169  659 SRAPRGGILFSRS----EPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELsdasrkigeieKEIEQLEQEEEK 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   386 ATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREE----RDAVYS-EYKLIMSERDQVISELDKLQTEV------- 453
Cdd:TIGR02169  735 LKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDlhklEEALNDlEARLSHSRIPEIQAELSKLEEEVsriearl 814

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   454 ELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEalqeadvakcrrdwafqerdKI 533
Cdd:TIGR02169  815 REIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEE--------------------LE 874

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   534 VAERDSIRTLCDnLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMAHSSHDSAIDTDS 613
Cdd:TIGR02169  875 AALRDLESRLGD-LKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKGEDEEIPEEELSL 953

                          330       340
                   ....*....|....*....|....
gi 767964249   614 MEWETEVVEFERET---EDIDLKA 634
Cdd:TIGR02169  954 EDVQAELQRVEEEIralEPVNMLA 977

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467153 [Multi-domain] Cd Length: 81 Bit Score: 60.25 E-value: 4.25e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1501 RVVFIKKSQLELGVHLCGGNLH--GVFVAEVEDDSPAKgPDG-LVPGDLILEYGSLDVRNKTVEEVyVEMLK-PRDGVRL 1576
Cdd:cd00136     1 TVTLEKDPGGGLGFSIRGGKDGggGIFVSRVEPGGPAA-RDGrLRVGDRILEVNGVSLEGLTHEEA-VELLKsAGGEVTL 78


                  ...
gi 767964249 1577 KVQ 1579
Cdd:cd00136    79 TVR 81

PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form domain-swapping dimers; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467210 [Multi-domain] Cd Length: 79 Bit Score: 59.54 E-value: 9.33e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  729 DSGISLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLK 794
Cdd:cd06728    13 EYGLRLGSRIFVKEITPDSLAAKDGNLQEGDIILKINGTPVENLSLSEAKKLIEKSKDKLQLVVLR 78

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNJ2BP-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467193 [Multi-domain] Cd Length: 86 Bit Score: 59.61 E-value: 1.03e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  628 EDIDLK----ALGFDMAEGVNEPCFPGDCGIFVTKV-DKGSIA-DGRLRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd06709     1 EEITLKrgpsGLGFNIVGGTDQPYIPNDSGIYVAKIkEDGAAAiDGRLQEGDKILEINGQSLENLTHQDAVELFRN 76

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 67.02 E-value: 1.14e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   306 AMDKLEVVKKDYDALRKRYSEKvaihnadLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQhqcalsLRRFEAIHHELNK 385
Cdd:TIGR02169  175 ALEELEEVEENIERLDLIIDEK-------RQQLERLRREREKAERYQALLKEKREYEGYEL------LKEKEALERQKEA 241

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   386 ATAQNKDLQWEMELLQSELTELrttqvktAKESEKYREERDAVYSEYKLIMSERD-QVISELDKLQTEVELAESKLKsst 464
Cdd:TIGR02169  242 IERQLASLEEELEKLTEEISEL-------EKRLEEIEQLLEELNKKIKDLGEEEQlRVKEKIGELEAEIASLERSIA--- 311

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   465 sekkaaneemEALRQIKDtvtMDAGRANKEVEILRKQCKAlcQELKEALQEADVakcrrdwafqERDKIVAERDSIRTLC 544
Cdd:TIGR02169  312 ----------EKERELED---AEERLAKLEAEIDKLLAEI--EELEREIEEERK----------RRDKLTEEYAELKEEL 366

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   545 DNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMAHsshdsaIDTDSMEWETEVVEFE 624
Cdd:TIGR02169  367 EDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELAD------LNAAIAGIEAKINELE 440


                   ....*....
gi 767964249   625 RETEDIDLK 633
Cdd:TIGR02169  441 EEKEDKALE 449

PDZ domain of afadin (AFDN), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of afadin (AFDN, also known as ALL1-fused gene from chromosome 6 protein (AF6) and MLLT4), and related domains. AFDN belongs to the adhesion system, probably together with the E-cadherin-catenin system, that plays a role in the organization of homotypic, interneuronal, and heterotypic cell-cell adherens junctions. The AFDN PDZ domain interaction partners include poliovirus receptor-related protein PRR2/nectin, the junctional adhesion molecule (JAM), the breakpoint-cluster-region protein (BCR), connexin36 (Cx36), and a subset of Eph-related receptor tyrosine kinases; it can also bind low molecular weight ligands, in competition with a natural peptide ligand. Other AFDN-binding proteins have been identified. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This AFDN family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467251 [Multi-domain] Cd Length: 89 Bit Score: 59.22 E-value: 1.32e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1351 VKVQKGSEPLGISIVSG-----EKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITI 1423
Cdd:cd06789     6 VTLKKVGNGMGLSIVAAkgagqDKLGIYIKSVVKGGAADLDGrLQAGDQLLSVDGHSLVGLSQERAAELMTKTGSVVTL 84

PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange factor 6, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Rap guanine nucleotide exchange factor 2 (RapGEF2, also named RA-GEF-1, PDZ-GEF1, CNrasGEF and nRapGEP) and Rap guanine nucleotide exchange factor 6 (RapGEF6, also named RA-GEF-2 and PDZ-GEF2). RapGEF2 and RapGEF6 constitute a subfamily of guanine nucleotide exchange factors (GEFs) for RAP small GTPases that is characterized by the possession of the PDZ and Ras/Rap-associating domains. They activate Rap small GTPases, by catalyzing the release of GDP from the inactive GDP-bound forms, thereby accelerating GTP loading to yield the active GTP-bound forms. The PDZ domain of RapGEF6 (also known as PDZ-GEF2) binds junctional adhesion molecule A (JAM-A). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RapGEF2 and RapGEF6 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467237 [Multi-domain] Cd Length: 83 Bit Score: 59.20 E-value: 1.33e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1349 RHVKVQKGS--EPLGISIVSG-EKG-GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06755     1 RTVTLTRPSreSPLHFSLLGGsEKGfGIFVSKVEKGSKAAEAGLKRGDQILEVNGQNFENITLKKALEIL 70

PDZ domain 4 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467174 [Multi-domain] Cd Length: 99 Bit Score: 59.67 E-value: 1.53e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  727 QKDSGISLENGVYAAAVL----------PGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLR 782
Cdd:cd06686    17 LKGFGIQLQGGVFATETLsspplisfiePDSPAERCGVLQVGDRVLSINGIPTEDRTLEEANQLLR 82

Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.

Pssm-ID: 114219 [Multi-domain] Cd Length: 787 Bit Score: 66.28 E-value: 1.57e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   136 LLTDQQVNEKVENLSIQLRLMTRERNELRKRLAFATHGTAFDKRPYHRLNPDYERLKIQCVRAMSDLQSLQNQHTNALKR 215
Cdd:pfam05483  246 LIQITEKENKMKDLTFLLEESRDKANQLEEKTKLQDENLKELIEKKDHLTKELEDIKMSLQRSMSTQKALEEDLQIATKT 325

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   216 CEEVAKE-------------------TDFYHT---LHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQ---------- 263
Cdd:pfam05483  326 ICQLTEEkeaqmeelnkakaahsfvvTEFEATtcsLEELLRTEQQRLEKNEDQLKIITMELQKKSSELEEmtkfknnkev 405

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   264 SWEDMKRLHEEDQKEIGDLRAQQQQVLKHNGSSEILNKLYDT---AMDKLEVVKKDYDALRKRYSEKVA-----IHNADL 335
Cdd:pfam05483  406 ELEELKKILAEDEKLLDEKKQFEKIAEELKGKEQELIFLLQArekEIHDLEIQLTAIKTSEEHYLKEVEdlkteLEKEKL 485

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   336 SRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQcalslrrfeaiHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTA 415
Cdd:pfam05483  486 KNIELTAHCDKLLLENKELTQEASDMTLELKKH-----------QEDIINCKKQEERMLKQIENLEEKEMNLRDELESVR 554

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   416 KESEKYREE---------RDAVYSEYKLIMSERDQVISEL--DKLQTEVE---------LAESKL--KSSTSEKKAANE- 472
Cdd:pfam05483  555 EEFIQKGDEvkckldkseENARSIEYEVLKKEKQMKILENkcNNLKKQIEnknknieelHQENKAlkKKGSAENKQLNAy 634

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   473 ---------EMEALRQIKDTVTmdaGRANKEVEILRKQCKALCQELKEALQEADVA---------KCRRDWA----FQER 530
Cdd:pfam05483  635 eikvnklelELASAKQKFEEII---DNYQKEIEDKKISEEKLLEEVEKAKAIADEAvklqkeidkRCQHKIAemvaLMEK 711

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   531 -----DKIVAERDSIRTLCDNLRRERDRAVSELAEALrslddtrkqkNDVSRELKELKEQMEsqLEKEARfRQLMAHSSH 605
Cdd:pfam05483  712 hkhqyDKIIEERDSELGLYKNKEQEQSSAKAALEIEL----------SNIKAELLSLKKQLE--IEKEEK-EKLKMEAKE 778


                   ....*..
gi 767964249   606 DSAIDTD 612
Cdd:pfam05483  779 NTAILKD 785

PDZ domain; PDZ domains are found in diverse signaling proteins.

Pssm-ID: 395476 [Multi-domain] Cd Length: 81 Bit Score: 58.83 E-value: 1.62e-10

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  1356 GSEPLGISIVSGEKG---GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITILAQ 1426
Cdd:pfam00595    8 GRGGLGFSLKGGSDQgdpGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLTIL 81

PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467211 [Multi-domain] Cd Length: 82 Bit Score: 58.73 E-value: 1.65e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1499 EPRVV-FIKKSQLelGVHLCGGNLHGVFVAEVEDDSPAKGpDGLVPGDLILEYGSLDVRNKTVEEV--YVEMLKPRDGVR 1575
Cdd:cd06729     1 DTRLVsFRKGGSV--GLRLAGGNDVGIFVAGVQEGSPAEK-QGLQEGDQILKVNGVDFRNLTREEAvlFLLDLPKGEEVT 77


                  ....*
gi 767964249 1576 LKVQY 1580
Cdd:cd06729    78 ILAQS 82

PDZ domain of densin, erbin, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of densin, erbin, and related domains. Densin (also known as leucine-rich repeat-containing protein 7, LRRC7, densin-180, protein LAP1) and erbin (also known as densin-180-like protein, Erbb2-interacting protein, protein LAP2) belong to the LAP (leucine-rich repeat and PDZ domain) family of scaffolding proteins that play roles in the maintenance of cell shape and apical-basal polarity. Densin and erbin are components of the excitatory postsynaptic compartment and are regulators of dendritic morphology and postsynaptic structure. The densin PDZ domain binds CaV1.3 alpha1 subunit, delta-catenin, and MAGUIN-1. Binding partners of the erbin PDZ domain include ErbB receptor tyrosine kinase ErbB2, HTLV-1 Tax1, Cav1.3 Ca2+channels, and constituents of the cadherin:catenin cell adhesion complex, in particular delta-catenin, p0071 and ARVCF. The erbin PDZ domain binds Smad3, a transductor of the TGFbeta pathway, possibly by a novel interface of binding. Erbin and two other LAP proteins (scribble and lano) redundantly regulate epithelial polarity and apical adhesion complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This densin and erbin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467231 [Multi-domain] Cd Length: 87 Bit Score: 58.49 E-value: 2.51e-10

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  635 LGFDMAEGVN---EPCFPGDCGIFVTKVDKGSIADGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRR 708
Cdd:cd06749    11 LGFSISGGIGsqgNPFRPDDDGIFVTKVQPDGPASKLLQPGDKILEVNGYDFVNIEHGQAVSLLKSFQNTVDLVVER 87

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 63.01 E-value: 3.92e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  322 KRYSEKVAIHNADLSRLEqlgEENQRLLKQTEMLTQQRDTAIQLQHQCALSLRRFEAIHHELNKATAQNKDLQWEmelLQ 401
Cdd:COG1340    11 EELEEKIEELREEIEELK---EKRDELNEELKELAEKRDELNAQVKELREEAQELREKRDELNEKVKELKEERDE---LN 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  402 SELTELRttqvktaKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEV-------ELAEsKLKSSTSEKKAANEEM 474
Cdd:COG1340    85 EKLNELR-------EELDELRKELAELNKAGGSIDKLRKEIERLEWRQQTEVlspeeekELVE-KIKELEKELEKAKKAL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  475 EALRQIKDTVTmdagrankEVEILRKQCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDS-------IRTLCDNL 547
Cdd:COG1340   157 EKNEKLKELRA--------ELKELRKEAEEIHKKIKELAEEAQELHEEMIELYKEADELRKEADElhkeiveAQEKADEL 228

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 767964249  548 RRERDRAVSELAEALRSLDDTRKQKNDVSR-----ELKELKEQMESQLEK 592
Cdd:COG1340   229 HEEIIELQKELRELRKELKKLRKKQRALKRekekeELEEKAEEIFEKLKK 278

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.

Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 65.20 E-value: 3.95e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   239 RLKDDVDMLRRENGQLLRERNLLQQSWEDMK-RLHEEDQK--EIGDLRAQQQQVLkhngsSEILNKLYDTAMDKLEVVKk 315
Cdd:pfam01576  135 KLEEDILLLEDQNSKLSKERKLLEERISEFTsNLAEEEEKakSLSKLKNKHEAMI-----SDLEERLKKEEKGRQELEK- 208

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   316 dydALRKRYSEKVAIHN--ADL-SRLEQLG-------EENQRLLKQTEMLTQQRDTAI----QLQHQCALSLRRFEAIHH 381
Cdd:pfam01576  209 ---AKRKLEGESTDLQEqiAELqAQIAELRaqlakkeEELQAALARLEEETAQKNNALkkirELEAQISELQEDLESERA 285

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   382 ELNKATAQNKDLQWEMELLQselTELRTTQVKTAKESEkYREERDAVYSEYKLIMSER----DQVISELDKLQTEV---- 453
Cdd:pfam01576  286 ARNKAEKQRRDLGEELEALK---TELEDTLDTTAAQQE-LRSKREQEVTELKKALEEEtrshEAQLQEMRQKHTQAleel 361

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   454 --ELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRAnkEVEILRKQCKALCQELKEALQEADVAKCRRdwafQER- 530
Cdd:pfam01576  362 teQLEQAKRNKANLEKAKQALESENAELQAELRTLQQAKQ--DSEHKRKKLEGQLQELQARLSESERQRAEL----AEKl 435

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249   531 DKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTR-------KQKNDVSRELKELKEQ---MESQLEKEARFRQ 598
Cdd:pfam01576  436 SKLQSELESVSSLLNEAEGKNIKLSKDVSSLESQLQDTQellqeetRQKLNLSTRLRQLEDErnsLQEQLEEEEEAKR 513

Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.

Pssm-ID: 462303 [Multi-domain] Cd Length: 488 Bit Score: 64.15 E-value: 4.07e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   217 EEVAKETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQ----QQVLKH 292
Cdd:pfam07888   55 RQREKEKERYKRDREQWERQRRELESRVAELKEELRQSREKHEELEEKYKELSASSEELSEEKDALLAQRaaheARIREL 134

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   293 NGSSEILNK---LYDTAMDKL-EVVKKDYDALRKRYSEKVAIHnadlSRLEQLGEENQRLLKQTEMLTQ---QRDT-AIQ 364
Cdd:pfam07888  135 EEDIKTLTQrvlERETELERMkERAKKAGAQRKEEEAERKQLQ----AKLQQTEEELRSLSKEFQELRNslaQRDTqVLQ 210

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   365 LQHQCAlslrrfeAIHHELNkaTAQNKDLqwEMELLQSELTELRTTQVKTAKESEKYREERDAVyseykliMSERDQVIS 444
Cdd:pfam07888  211 LQDTIT-------TLTQKLT--TAHRKEA--ENEALLEELRSLQERLNASERKVEGLGEELSSM-------AAQRDRTQA 272

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   445 ELDKL-----QTEVELAESKLKssTSEKKAA-NEEMEALRQikdtvtmdagRANKEVEILRKQCKALcQELKEALQEADV 518
Cdd:pfam07888  273 ELHQArlqaaQLTLQLADASLA--LREGRARwAQERETLQQ----------SAEADKDRIEKLSAEL-QRLEERLQEERM 339

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   519 akcrrdwafqERDKIVAE----RDSIRTLCDNLRRErdraVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEA 594
Cdd:pfam07888  340 ----------EREKLEVElgreKDCNRVQLSESRRE----LQELKASLRVAQKEKEQLQAEKQELLEYIRQLEQRLETVA 405

                          410       420
                   ....*....|....*....|....*
gi 767964249   595 RFRQLMAHSSHDSAIDTDSMEWETE 619
Cdd:pfam07888  406 DAKWSEAALTSTERPDSPLSDSEDE 430

PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GOPC-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467261 [Multi-domain] Cd Length: 83 Bit Score: 57.77 E-value: 4.48e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1349 RHVKVQKG-SEPLGISIVSGEKGG--IYVSKVTVGSIAHQ-AGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITIL 1424
Cdd:cd06800     1 RKVLLSKEpHEGLGISITGGKEHGvpILISEIHEGQPADRcGGLYVGDAILSVNGIDLRDAKHKEAVTILSQQRGEITLE 80


                  ...
gi 767964249 1425 AQY 1427
Cdd:cd06800    81 VVY 83

Src homology 3 domain of the Tight junction protein, Zonula occludens protein 1; ZO-1 is a scaffolding protein that associates with other ZO proteins and other proteins of the tight junction, zonula adherens, and gap junctions. ZO proteins play roles in regulating cytoskeletal dynamics at these cell junctions. ZO-1 plays an essential role in embryonic development. It regulates the assembly and dynamics of the cortical cytoskeleton at cell-cell junctions. It is considered a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. The C-terminal region of ZO-1 is the largest of the three ZO proteins and contains an actin-binding region and domains of unknown function designated alpha and ZU5. The SH3 domain of ZO-1 has been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212959 Cd Length: 65 Bit Score: 57.01 E-value: 5.36e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1594 DSFYIRALYDRLADVEQELSFKKDDILYVDDTLPQGTFGSWMAWQLDENAQKIQRGQIPSK 1654
Cdd:cd12026     1 DSFYIRTHFEYEKESPYGLSFNKGEVFRVVDTLYNGKLGSWLAIRIGKNHKEVERGIIPNK 61

Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.

Pssm-ID: 464943 [Multi-domain] Cd Length: 1112 Bit Score: 64.75 E-value: 5.50e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   140 QQVNEKVENLSIQLRLMTR---ERNELRKRLAFATHGTAFDkrpyhrLNPDYERLKIQcVRAMSDLQSLQNQHTNALK-R 215
Cdd:pfam15921   74 EHIERVLEEYSHQVKDLQRrlnESNELHEKQKFYLRQSVID------LQTKLQEMQME-RDAMADIRRRESQSQEDLRnQ 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   216 CEEVAKETDFYHTLHSRLLSDQTrlkDDVDMLRRengQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQVLKHNGS 295
Cdd:pfam15921  147 LQNTVHELEAAKCLKEDMLEDSN---TQIEQLRK---MMLSHEGVLQEIRSILVDFEEASGKKIYEHDSMSTMHFRSLGS 220

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   296 --SEILNKLyDTAMDKLE----VVKKDYDALRKRYSEKVAI---HNADlsRLEQLGEENQ-RLLKQTEMLTQQRDTAIQL 365
Cdd:pfam15921  221 aiSKILREL-DTEISYLKgrifPVEDQLEALKSESQNKIELllqQHQD--RIEQLISEHEvEITGLTEKASSARSQANSI 297

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   366 QHQcalslrrFEAIHHELNKATA----QNKDLQWEMELLQSELTELRTTQVKTAKESEKY-----------REERDAVYS 430
Cdd:pfam15921  298 QSQ-------LEIIQEQARNQNSmymrQLSDLESTVSQLRSELREAKRMYEDKIEELEKQlvlanselteaRTERDQFSQ 370

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   431 EYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRankeVEILRKQCKALCQELK 510
Cdd:pfam15921  371 ESGNLDDQLQKLLADLHKREKELSLEKEQNKRLWDRDTGNSITIDHLRRELDDRNMEVQR----LEALLKAMKSECQGQM 446

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   511 EalqeadvakcRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQL 590
Cdd:pfam15921  447 E----------RQMAAIQGKNESLEKVSSLTAQLESTKEMLRKVVEELTAKKMTLESSERTVSDLTASLQEKERAIEATN 516


                   ....*..
gi 767964249   591 EKEARFR 597
Cdd:pfam15921  517 AEITKLR 523

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 64.69 E-value: 5.68e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   408 RTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMD 487
Cdd:TIGR02168  669 NSSILERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEER 748

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   488 AGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDD 567
Cdd:TIGR02168  749 IAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLES 828

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249   568 TRKQKNDVSRELKELKEQMESQLEKEARfrqlMAHSSHDSAIDTDSMEWETEVVEFERETEDIDLKALGFDMAE 641
Cdd:TIGR02168  829 LERRIAATERRLEDLEEQIEELSEDIES----LAAEIEELEELIEELESELEALLNERASLEEALALLRSELEE 898

PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of human PTPN13, and related domains. PTPN13, also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1), negatively regulates FAS-mediated apoptosis and NGFR-mediated pro-apoptotic signaling, and may also regulate phosphoinositide 3-kinase (PI3K) signaling. It contains 5 PDZ domains; interaction partners of its second PDZ domain (PDZ2) include the Fas receptor (TNFRSF6) and thyroid receptor-interacting protein 6 (TRIP6). The second PDZ (PDZ2) domain, but not PDZ1 or PDZ3, of FRMPD2 binds to GluN2A and GluN2B, two subunits of N-methyl-d-aspartic acid (NMDA) receptors. Other binding partners of the FRMPDZ2 PDZ2 domain include NOD2, and catenin family members, delta catenin (CTNND2), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) and p0071 (also known as plakophilin 4; PKP4). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467254 [Multi-domain] Cd Length: 87 Bit Score: 57.22 E-value: 5.93e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1351 VKVQKGSEPLGISIVSG-----EKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITIL 1424
Cdd:cd06792     5 VELSKKDGSLGISVTGGintsvRHGGIYVKSLVPGGAAEQDGrIQKGDRLLEVNGVSLEGVTHKQAVECLKNAGQVVTLV 84

PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467223 [Multi-domain] Cd Length: 84 Bit Score: 57.27 E-value: 6.34e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249 1351 VKVQKGSePLGISIVSG-EKG-GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06741     6 LVVEDGQ-SLGLMIRGGaEYGlGIYVTGVDPGSVAENAGLKVGDQILEVNGRSFLDITHDEAVKIL 70

PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467187 [Multi-domain] Cd Length: 92 Bit Score: 57.27 E-value: 6.95e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  631 DLKALGFDMAEGVNEPCF-PGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVR 707
Cdd:cd06703    10 DGKGLGFSIAGGKGSTPFrDGDEGIFISRITEGGAAdrDGKLQVGDRVLSINGVDVTEARHDQAVALLTSSSPTITLVVE 89


                  .
gi 767964249  708 R 708
Cdd:cd06703    90 R 90

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

Pssm-ID: 275316 [Multi-domain] Cd Length: 745 Bit Score: 63.89 E-value: 7.90e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   136 LLTDQQVNEKVENLSIQLRLMTRERNELRKRLafathgtafdkrpyHRLNPDYERLKIQCVRAMSDLQSLQNQHTNALKR 215
Cdd:TIGR04523  203 LSNLKKKIQKNKSLESQISELKKQNNQLKDNI--------------EKKQQEINEKTTEISNTQTQLNQLKDEQNKIKKQ 268

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   216 CEEVAKETDfyhtLHSRLLSDqtrLKDDVDMLrreNGQLLRERNLLQQSWedMKRLHEEDQKEIGDLRAQQQQVLKHNgs 295
Cdd:TIGR04523  269 LSEKQKELE----QNNKKIKE---LEKQLNQL---KSEISDLNNQKEQDW--NKELKSELKNQEKKLEEIQNQISQNN-- 334

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   296 sEILNKLydtaMDKLEVVKKDYDALRKRYSEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQ-RDTAIQLQHQcalslr 374
Cdd:TIGR04523  335 -KIISQL----NEQISQLKKELTNSESENSEKQRELEEKQNEIEKLKKENQSYKQEIKNLESQiNDLESKIQNQ------ 403

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   375 rfeaihHELNKATAQN-KDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEV 453
Cdd:TIGR04523  404 ------EKLNQQKDEQiKKLQQEKELLEKEIERLKETIIKNNSEIKDLTNQDSVKELIIKNLDNTRESLETQLKVLSRSI 477

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   454 ELAESKLKSSTSEKKAANEEMEALrqikdtvtmdagraNKEVEILRKQCKALCQELKEALQEADVAKCRRDwafQERDKI 533
Cdd:TIGR04523  478 NKIKQNLEQKQKELKSKEKELKKL--------------NEEKKELEEKVKDLTKKISSLKEKIEKLESEKK---EKESKI 540

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   534 VAERDSIRTLCDNLRR--------ERDRAVSELAEALRSLDDTRKQKNDV----SRELKELKEQME------SQLEKEAR 595
Cdd:TIGR04523  541 SDLEDELNKDDFELKKenlekeidEKNKEIEELKQTQKSLKKKQEEKQELidqkEKEKKDLIKEIEekekkiSSLEKELE 620

Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.

Pssm-ID: 464943 [Multi-domain] Cd Length: 1112 Bit Score: 63.98 E-value: 7.98e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   200 SDLQSLQNQ--HTNALKRCEEVAKETDFYHtLHSRLLSDQTRLKDDVDMLRRE----NGQLLRERNLLQQSWEDMKRLHE 273
Cdd:pfam15921  299 SQLEIIQEQarNQNSMYMRQLSDLESTVSQ-LRSELREAKRMYEDKIEELEKQlvlaNSELTEARTERDQFSQESGNLDD 377

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   274 EDQKEIGDLRAQQQQVlkhNGSSEILNKLYDTAMDKLEVVkkdyDALRKRYSEKvaihNADLSRLEQLgeenqrllkqte 353
Cdd:pfam15921  378 QLQKLLADLHKREKEL---SLEKEQNKRLWDRDTGNSITI----DHLRRELDDR----NMEVQRLEAL------------ 434

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   354 MLTQQRDTAIQLQHQCAlslrRFEAIHHELNKATAQNKDLQWEMELLQSELTELrttqvkTAKESEKYREERdaVYSEYK 433
Cdd:pfam15921  435 LKAMKSECQGQMERQMA----AIQGKNESLEKVSSLTAQLESTKEMLRKVVEEL------TAKKMTLESSER--TVSDLT 502

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   434 LIMSERDQVI----SELDKLQTEVELAESKLKSSTSEK---KAANEEMEALRqikdtvtMDAGRANKEVEILRKQCKALC 506
Cdd:pfam15921  503 ASLQEKERAIeatnAEITKLRSRVDLKLQELQHLKNEGdhlRNVQTECEALK-------LQMAEKDKVIEILRQQIENMT 575

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   507 Q------------ELKEALQEADVAKCRRDwaFQERDKIVAERDS-IRTL---CDNLRRERDRAVSELAEALRSLDDTRK 570
Cdd:pfam15921  576 QlvgqhgrtagamQVEKAQLEKEINDRRLE--LQEFKILKDKKDAkIRELearVSDLELEKVKLVNAGSERLRAVKDIKQ 653

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249   571 QKNDVSRELKELKEQMESQLEKEARFRQLMAHSSHDSAIDTDSMEWETEVVEFERETEDIDLKAL 635
Cdd:pfam15921  654 ERDQLLNEVKTSRNELNSLSEDYEVLKRNFRNKSEEMETTTNKLKMQLKSAQSELEQTRNTLKSM 718

PDZ domain of Ras-associating and dilute domain-containing protein (Radil) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Radil (also known as protein KIAA1849) and related domains. Radil is required for cell adhesion and migration of neural crest precursors during development. Radil is a component of a Rasip1-Radil-ARHGAP29 complex at endothelial cell-cell junctions. Rap1, via its effectors Radil and Rasip1 and their binding partner ArhGAP29, controls the endothelial barrier by decreasing Rho-mediated radial tension on cell-cell junctions. ArhGAP29 binds the Radil PDZ domain. The Radil PDZ domain also binds kinesin family protein 14 (KIF14); KIF14 negatively regulates Rap1-mediated inside-out integrin activation by tethering Radil on microtubules. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Radil-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467177 [Multi-domain] Cd Length: 88 Bit Score: 56.92 E-value: 8.03e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06690    29 SPGIYIRTLVPDSPAARDGRLRLGDRILAVNGTSLVGADYQSAMDLIRTSGDKLRF 84

PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467269 [Multi-domain] Cd Length: 84 Bit Score: 56.67 E-value: 9.83e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249 1351 VKVQKGS-EPLGISIVSG-EKG-GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd10833     4 VTVEKSPdGSLGFSVRGGsEHGlGIFVSKVEEGSAAERAGLCVGDKITEVNGVSLENITMSSA 66

Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

Pssm-ID: 214620 [Multi-domain] Cd Length: 56 Bit Score: 55.62 E-value: 1.02e-09

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249   1594 DSFYIRALYDRLADVEQELSFKKDDILYVDDTLPQGtfgsWMAWQLDENaqkiQRGQIPSKYVK 1657
Cdd:smart00326    1 EGPQVRALYDYTAQDPDELSFKKGDIITVLEKSDDG----WWKGRLGRG----KEGLFPSNYVE 56

DNA double-strand break repair Rad50 ATPase;

Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 63.52 E-value: 1.15e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  329 AIHNADL-SRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQCALSLRRFEaihhelnkataqnkDLQWEMELLQSELTEL 407
Cdd:PRK02224  198 EKEEKDLhERLNGLESELAELDEEIERYEEQREQARETRDEADEVLEEHE--------------ERREELETLEAEIEDL 263

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  408 RTTQVKTAKESEKYREErdavyseykliMSERDQVISELDKLQTEVeLAESKLKSSTSEKKAA-----NEEMEALRQIKD 482
Cdd:PRK02224  264 RETIAETEREREELAEE-----------VRDLRERLEELEEERDDL-LAEAGLDDADAEAVEArreelEDRDEELRDRLE 331

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  483 TVTMDAGRANKEVEILRKQCKALCQELKEALQEA-----DVAKCRRDWAfQERDKIVAERDSIRTL---CDNLRRERDRA 554
Cdd:PRK02224  332 ECRVAAQAHNEEAESLREDADDLEERAEELREEAaelesELEEAREAVE-DRREEIEELEEEIEELrerFGDAPVDLGNA 410

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  555 VSELAEALRSLDDTRKQKNDVSRELKELKEQMEsqlEKEARFR--------QLMAHSSHDSAIDtdsmEWETEVVEFERE 626
Cdd:PRK02224  411 EDFLEELREERDELREREAELEATLRTARERVE---EAEALLEagkcpecgQPVEGSPHVETIE----EDRERVEELEAE 483


                  ....*..
gi 767964249  627 TEDIDLK 633
Cdd:PRK02224  484 LEDLEEE 490

PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila Dlg1, human Dlg1, 2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197; SAP-97), Dlg2 (also known as channel-associated protein of synapse-110; postsynaptic density protein 93, PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95; synapse-associated protein 90, SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling, regulating surface expression of NMDA receptors in dorsal horn neurons of the spinal cord; it interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. The Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development; postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467257 [Multi-domain] Cd Length: 91 Bit Score: 56.59 E-value: 1.27e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1499 EPRVVFIKKSQLELGVHLCGG-NLHGVFVAEVEDDSPAKGPDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRDGVRLK 1577
Cdd:cd06795     1 EPRKIVLHKGSTGLGFNIVGGeDGEGIFISFILAGGPADLSGELRRGDQILSVNGVDLRNATHEQAAAALKNAGQTVTII 80


                  ....*...
gi 767964249 1578 VQYRPEEF 1585
Cdd:cd06795    81 AQYKPEEY 88

PDZ domain of protein Lin-7 and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Lin-7 (also known as LIN-7 or LIN7), and related domains. Lin-7 targets and organize protein complexes to epithelial and synaptic plasma membranes. There are three mammalian Lin-7 homologs: Lin-7A (protein lin-7 homolog A, also known as mammalian lin-seven protein 1 (MALS-1), vertebrate lin-7 homolog 1 (Veli-1), tax interaction protein 33); Lin-7B (also known as MALS-2, Veli-2); and Lin-7C (also known as MALS-3, Veli-3). Lin-7 is involved in localization of the Let-23 growth factor receptor to the basolateral membrane of epithelial cells, in tight junction localization of insulin receptor substrate p53 (IRSp53), in retaining gamma-aminobutyric (GABA) transporter (BGT-1) at the basolateral surface of epithelial cells, and in regulating recruitment of neurotransmitter receptors to the postsynaptic density (PSD). The Lin7 PDZ domain binds Let-23, BGT and beta-catenin, and NMDA (N-methyl-D-aspartate) receptor NR2B. Lin-7 also binds to the PDZ binding motif located in the C-terminal tail of Rhotekin, an effector protein for small GTPase Rho. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Lin-7-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467258 [Multi-domain] Cd Length: 86 Bit Score: 56.29 E-value: 1.39e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1348 PRHVKVQKGSEPLGISIVSG--EKGGIYVSKVTVGSIA-HQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITIL 1424
Cdd:cd06796     2 PRVVELPKTEEGLGFNVMGGkeQNSPIYISRIIPGGVAdRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAAQGSVKLV 81


                  ....*
gi 767964249 1425 AQYNP 1429
Cdd:cd06796    82 VRYTP 86

PDZ domain 3 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP, Drosophila Bazooka) and related domains. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par-3 and the Par complex include Par3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467272 [Multi-domain] Cd Length: 103 Bit Score: 56.91 E-value: 1.45e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  651 DCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKAL-------LNGEGAINMVVRRR 709
Cdd:cd23059    36 DLGIFIKSIIHGGAAskDGRLRVNDQLIAVNGESLLGLTNSEAMETLrramsteGNIRGMIQLVVARR 103

PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13),FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467180 [Multi-domain] Cd Length: 92 Bit Score: 56.63 E-value: 1.48e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  733 SLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06694    27 SLDLGIFVKSIIPGGPADKDGRIKPGDRIIAINGQSLEGKTHHAAVEIIQNAPDKVEL 84

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 62.09 E-value: 2.71e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  218 EVAKETdFYHTLHSRLLSdqtRLKDDVDMLRRENGQL----LRERNLLQQSWEDMKRLHEE---DQKEIGDLRAQQQQVl 290
Cdd:COG4717    33 EAGKST-LLAFIRAMLLE---RLEKEADELFKPQGRKpelnLKELKELEEELKEAEEKEEEyaeLQEELEELEEELEEL- 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  291 khngssEILNKLYDTAMDKLEVVKKDYDALRKRysEKVAIHNADL-SRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQC 369
Cdd:COG4717   108 ------EAELEELREELEKLEKLLQLLPLYQEL--EALEAELAELpERLEELEERLEELRELEEELEELEAELAELQEEL 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  370 ALSLRRF-EAIHHELNKATAQNKDLQWEMELLQSELTELR-------------TTQVKTAKESEKYREER---------- 425
Cdd:COG4717   180 EELLEQLsLATEEELQDLAEELEELQQRLAELEEELEEAQeeleeleeeleqlENELEAAALEERLKEARlllliaaall 259

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  426 ------DAVYSEYKLIM---------------------SERDQVISELDKLQTEVELAESKLKS-----STSEKKAANEE 473
Cdd:COG4717   260 allglgGSLLSLILTIAgvlflvlgllallflllarekASLGKEAEELQALPALEELEEEELEEllaalGLPPDLSPEEL 339

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  474 MEALRQIKDTVTMDAGRANKEVEIlrkQCKALCQELKEALQEADV-------AKCRRdwaFQERDKIVAERDSIRTLCDN 546
Cdd:COG4717   340 LELLDRIEELQELLREAEELEEEL---QLEELEQEIAALLAEAGVedeeelrAALEQ---AEEYQELKEELEELEEQLEE 413

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249  547 LRRERDRAVS---------ELAEALRSLDDTRKQKNDVSRELKELKEQMEsQLEKEARFRQLMAH 602
Cdd:COG4717   414 LLGELEELLEaldeeeleeELEELEEELEELEEELEELREELAELEAELE-QLEEDGELAELLQE 477

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

Pssm-ID: 214570 [Multi-domain] Cd Length: 85 Bit Score: 55.46 E-value: 3.01e-09

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249    617 ETEVVEFERETEDidlkaLGFDMAEGVNEpcfpgDCGIFVTKVDKGSIADGR-LRVNDWLLRINDVDLINKDKKQAIKAL 695
Cdd:smart00228    1 EPRLVELEKGGGG-----LGFSLVGGKDE-----GGGVVVSSVVPGSPAAKAgLRVGDVILEVNGTSVEGLTHLEAVDLL 70

                            90
                    ....*....|....*
gi 767964249    696 LNGEGAINMVVRRRK 710
Cdd:smart00228   71 KKAGGKVTLTVLRGG 85

PDZ domain 7 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 6 of PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of MUPP1 and PDZ domain 6 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467159 [Multi-domain] Cd Length: 96 Bit Score: 55.40 E-value: 3.40e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1347 EPRHVKVQK-GSEPLGISIVSG-----------EKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLI 1413
Cdd:cd06671     1 PPRRVELWRePGKSLGISIVGGrvmgsrlsngeEIRGIFIKHVLEDSPAGRNGtLKTGDRILEVNGVDLRNATHEEAVEA 80

                          90
                  ....*....|...
gi 767964249 1414 IGQQCDTITILAQ 1426
Cdd:cd06671    81 IRNAGNPVVFLVQ 93

DNA double-strand break repair ATPase Rad50;

Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 61.23 E-value: 5.65e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  140 QQVNEKVENLSIQLRLMTRERNELRKRLAfathgtafDKRPYHRLnpdYERLK--------IQCVRAMSDLQSLQNQHTN 211
Cdd:PRK03918  327 EERIKELEEKEERLEELKKKLKELEKRLE--------ELEERHEL---YEEAKakkeelerLKKRLTGLTPEKLEKELEE 395

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  212 ALKRCEEVAKETDFYHTLHSRLLSDQTRLKDDVDMLRREN------GQLLRE---RNLLQQSWEDMKRLhEEDQKEIG-- 280
Cdd:PRK03918  396 LEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKgkcpvcGRELTEehrKELLEEYTAELKRI-EKELKEIEek 474

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  281 --DLRAQQQQVLKHNGSSEILNKLYDTA--------------MDKLEVVKKDYDALRKRYSE---KVAIHNADLSRLEQL 341
Cdd:PRK03918  475 erKLRKELRELEKVLKKESELIKLKELAeqlkeleeklkkynLEELEKKAEEYEKLKEKLIKlkgEIKSLKKELEKLEEL 554

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  342 GEENQRLLKQ--------TEMLTQQRDTAIQLQHQCALSLRRFEAIHHELNKATAQNKDLQW---EMELLQSELTELRTT 410
Cdd:PRK03918  555 KKKLAELEKKldeleeelAELLKELEELGFESVEELEERLKELEPFYNEYLELKDAEKELEReekELKKLEEELDKAFEE 634

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  411 QVKTAKESEKYREERDAV---YS--EYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVT 485
Cdd:PRK03918  635 LAETEKRLEELRKELEELekkYSeeEYEELREEYLELSRELAGLRAELEELEKRREEIKKTLEKLKEELEEREKAKKELE 714

                         410       420       430
                  ....*....|....*....|....*....|.
gi 767964249  486 mDAGRANKEVEILRKQCKALCQELKE-ALQE 515
Cdd:PRK03918  715 -KLEKALERVEELREKVKKYKALLKErALSK 744

PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467253 [Multi-domain] Cd Length: 89 Bit Score: 54.55 E-value: 6.17e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1351 VKVQKGSEPLGISIV-------SGEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06791     5 VELVKDEQGLGITIAgyvgekaSGELSGIFVKSIIPGSAADQDGrIQVNDQIIAVDGVNLQGFTNQEA 72

Src homology 3 domain of the Tight junction protein, Zonula occludens protein 3; ZO-3 is a scaffolding protein that associates with other ZO proteins and other proteins of the tight junction, zonula adherens, and gap junctions. ZO proteins play roles in regulating cytoskeletal dynamics at these cell junctions. ZO-3 is critical for epidermal barrier function. It regulates cyclin D1-dependent cell proliferation. It is considered a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. The C-terminal region of ZO-3 is the smallest of the three ZO proteins. The SH3 domain of the related protein ZO-1 has been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212961 Cd Length: 65 Bit Score: 53.72 E-value: 7.08e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1594 DSFYIRALYDRLADVEQELSFKKDDILYVDDTLPQGTFGSWMAWQLDENAQKIQRGQIPSK 1654
Cdd:cd12028     1 DSFYIRTHFDYEPDPPSGLSFTRGEVFHVLDTMHRGKLGSWLAVRMGRDLREMEKGIIPNQ 61

PDZ domain 4 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467216 [Multi-domain] Cd Length: 84 Bit Score: 53.77 E-value: 9.71e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767964249  743 VLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06734    33 IIPGSPADRCGQLKVGDRILAVNGISILNLSHGDIVNLIKDSGLSVTL 80

PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467222 [Multi-domain] Cd Length: 82 Bit Score: 53.52 E-value: 1.21e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1349 RHV--KVQKGSEPLGISIVSG-EKG-GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06740     2 RQVtlKRSKSHEGLGFSIRGGaEHGvGIYVSLVEPGSLAEKEGLRVGDQILRVNDVSFEKVTHAEAVKIL 71

PDZ domain 2 of PDZ domain containing 2 (PDZD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains, and is expressed at exceptionally high levels in the pancreas and certain cancer tissues such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467239 [Multi-domain] Cd Length: 88 Bit Score: 53.51 E-value: 1.26e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249  650 GDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRRR 709
Cdd:cd06758    27 GDIGIFVAGVEEGGSAdrDGRLKKGDELLMINGQSLIGLSHQEAVAILRSSASPVQLVIASK 88

PDZ domain 1 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467165 [Multi-domain] Cd Length: 89 Bit Score: 53.40 E-value: 1.70e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1347 EPRHVKVQKGS--EPLGISIVSGEK---GGIYVSKV-TVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDT 1420
Cdd:cd06677     2 EITTIEIHRSDpyEELGISIVGGNDtplINIVIQEVyRDGVIARDGRLLPGDQILEVNGVDISNVTHSQARSVLRQPCPV 81


                  ....*.
gi 767964249 1421 --ITIL 1424
Cdd:cd06677    82 lrLTVL 87

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 59.70 E-value: 1.72e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   141 QVNEKVENLSI-------QLRLMTRERN------ELRKRLAfathgtafDKRPYHRLNpDYERLKIQCVRAMSDLQSLQN 207
Cdd:TIGR02169  181 EVEENIERLDLiidekrqQLERLRREREkaeryqALLKEKR--------EYEGYELLK-EKEALERQKEAIERQLASLEE 251

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   208 QHTNALKRCEEVAKEtdfYHTLHSRLLSDQTRLKDdvdMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQ 287
Cdd:TIGR02169  252 ELEKLTEEISELEKR---LEEIEQLLEELNKKIKD---LGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLA 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   288 QvlkhnGSSEILNKLYD-TAMDK-LEVVKKDYDALRKRYSEKVAIHNADLSRLEQLGEENQRLL-------KQTEMLTQQ 358
Cdd:TIGR02169  326 K-----LEAEIDKLLAEiEELEReIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRdelkdyrEKLEKLKRE 400

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   359 RDTAIQLQHQCALSLRRFEA----IHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKL 434
Cdd:TIGR02169  401 INELKRELDRLQEELQRLSEeladLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDR 480

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*
gi 767964249   435 IMSERDQVISELDKLQTEVELAESKLKSStsekKAANEEMEALRQ 479
Cdd:TIGR02169  481 VEKELSKLQRELAEAEAQARASEERVRGG----RAVEEVLKASIQ 521

PDZ domain 1 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467176 [Multi-domain] Cd Length: 102 Bit Score: 53.79 E-value: 1.72e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  625 RETEDIDL-----KALGFDMAeGVNEPCfPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDL-INKDKKQAIKALL 696
Cdd:cd06689    13 RQVEYIELekpesGGLGFSVV-GLKSEN-RGELGIFVQEIQPGSVAarDGRLKENDQILAINGQPLdQSISHQQAIAILQ 90

                          90
                  ....*....|..
gi 767964249  697 NGEGAINMVVRR 708
Cdd:cd06689    91 QAKGSVELVVAR 102

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 59.69 E-value: 1.92e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   145 KVENLSIQLRLMTRERNELRKRLAFATHGTAFDKRPYHRLNPDYERLKIQCVRAMSDLQSLQNQHTNALKRCEEVAKETd 224
Cdd:TIGR02168  678 EIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKEL- 756

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   225 fyhtlhSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQvlkhngsseiLNKLYD 304
Cdd:TIGR02168  757 ------TELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTL----------LNEEAA 820

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   305 TAMDKLEVVKKDYDALRKRY----------SEKVAIHNADLSRLEQLGEEnqrLLKQTEMLTQQRDtaiQLQHQCALSLR 374
Cdd:TIGR02168  821 NLRERLESLERRIAATERRLedleeqieelSEDIESLAAEIEELEELIEE---LESELEALLNERA---SLEEALALLRS 894

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   375 RFEAIHHELNKATAQNKDLQWEMELLQSELTELRT----TQVKTAKESEKYREErdavYS-EYKLIMSERDQVISELDKL 449
Cdd:TIGR02168  895 ELEELSEELRELESKRSELRRELEELREKLAQLELrlegLEVRIDNLQERLSEE----YSlTLEEAEALENKIEDDEEEA 970

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 767964249   450 QTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVT 485
Cdd:TIGR02168  971 RRRLKRLENKIKELGPVNLAAIEEYEELKERYDFLT 1006

PDZ domain 5 of Danio rerio tyrosine-protein phosphatase non-receptor type 13 (Ptpn13) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of Danio rerio Ptpn13, and related domains. Protein-tyrosine phosphatases (PTPs) dephosphorylate phosphotyrosyl residues in proteins that are phosphorylated by protein tyrosine kinases (PTKs). Danio rerio Ptpn13 is a classical non-receptor-like PTP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467273 [Multi-domain] Cd Length: 80 Bit Score: 52.74 E-value: 2.19e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1356 GSEPLGISIVSGEKG-GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd23060     8 ANGGLGFSLVGGEGGsGIFVKSISPGGVADRDGrLQVGDRLLQVNGESVIGLSHSKAVNIL 68

PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467219 [Multi-domain] Cd Length: 85 Bit Score: 53.03 E-value: 2.24e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1349 RHVKVQK-GSEPLGISIVSG-EKG-GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQcDTITI 1423
Cdd:cd06737     3 RLVRLDRrGPESLGFSVRGGlEHGcGLFVSHVSPGSQADNKGLRVGDEIVRINGYSISQCTHEEVINLIKTK-KTVSL 79

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

Pssm-ID: 129694 [Multi-domain] Cd Length: 1311 Bit Score: 59.29 E-value: 2.57e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   138 TDQQVNEKVENLSIQLRLMTRERNELRKRLA--------FATHGTAFDKRpYHRLNPDYERLKIQCVRAMSDLQSLQNQ- 208
Cdd:TIGR00606  299 TDEQLNDLYHNHQRTVREKERELVDCQRELEklnkerrlLNQEKTELLVE-QGRLQLQADRHQEHIRARDSLIQSLATRl 377

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   209 HTNALKRCEEVAKETDFYHTLHSRLLSDQTR--------LKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIG 280
Cdd:TIGR00606  378 ELDGFERGPFSERQIKNFHTLVIERQEDEAKtaaqlcadLQSKERLKQEQADEIRDEKKGLGRTIELKKEILEKKQEELK 457

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   281 DLRAQQQQVlkHNGSSEILNKLYDTAMDKLEVVKKDYDAL---RKRYSEKVAIHNADLSR-LEQLGEENQRL------LK 350
Cdd:TIGR00606  458 FVIKELQQL--EGSSDRILELDQELRKAERELSKAEKNSLtetLKKEVKSLQNEKADLDRkLRKLDQEMEQLnhhtttRT 535

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   351 QTEMLTQQRDTA------IQLQHQCALS--------LRRFEAIHHELNKATAQNKDlqwEMELLQSELTELRTTQVKTAK 416
Cdd:TIGR00606  536 QMEMLTKDKMDKdeqirkIKSRHSDELTsllgyfpnKKQLEDWLHSKSKEINQTRD---RLAKLNKELASLEQNKNHINN 612

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   417 EsEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESK---LKSSTSEKKAANEEMEALRQIKDTVTMDAGRANK 493
Cdd:TIGR00606  613 E-LESKEEQLSSYEDKLFDVCGSQDEESDLERLKEEIEKSSKQramLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEA 691

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   494 EVEILRKQCKALCQELKEALQEADvakcrrdwafQERDKIVAERDSIRTLCDNLRRERDRAVSELAEalrslddTRKQKN 573
Cdd:TIGR00606  692 ELQEFISDLQSKLRLAPDKLKSTE----------SELKKKEKRRDEMLGLAPGRQSIIDLKEKEIPE-------LRNKLQ 754

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249   574 DVSRELKELKEQMEsqlEKEARFRQLMA--HSSHDSAIDTDSME-WETEVVEFERETEDIDLKALGFDMAEGVNE 645
Cdd:TIGR00606  755 KVNRDIQRLKNDIE---EQETLLGTIMPeeESAKVCLTDVTIMErFQMELKDVERKIAQQAAKLQGSDLDRTVQQ 826

PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZD11, and related domains. PDZD11 (also known as ATPase-interacting PDZ protein, plasma membrane calcium ATPase-interacting single-PDZ protein, PMCA-interacting single-PDZ protein, PISP) is involved in the dynamic assembly of apical junctions (AJs). It is recruited by PLEKHA7 to AJs to promote the efficient junctional recruitment and stabilization of nectins, and the efficient early phases of assembly of AJs in epithelial cells. The PDZD11 PDZ domain binds nectin-1 and nectin-3. PDZD11 also binds to a PDZ binding motif located in the C-terminal tail of the human sodium-dependent multivitamin transporter, to the cytoplasmic tail of the Menkes copper ATPase ATP7A, and to the cytoplasmic tail of all plasma membrane Ca2+-ATPase b-splice variants. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD11-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467234 [Multi-domain] Cd Length: 83 Bit Score: 52.32 E-value: 3.11e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1355 KGSEPLGISIVSGEKG--GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIgQQCDTITILAQYNP 1429
Cdd:cd06752     8 PPGEQLGFNIRGGKASglGIFISKVIPDSDAHRLGLKEGDQILSVNGVDFEDIEHSEAVKVL-KTAREIQMRVRYFP 83

PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467188 [Multi-domain] Cd Length: 87 Bit Score: 52.67 E-value: 3.19e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  620 VVEFERETedidlKALGFDMAEGVNEPCFPG-DCGIFVTKVDKGSIAD-GRLRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd06704     2 TITIERQT-----GGLGISIAGGKGSTPYKGdDEGIFISRVTEGGPAAkAGVRVGDKLLEVNGVDLVDADHHEAVEALKN 76

                          90
                  ....*....|.
gi 767964249  698 GEGAINMVVRR 708
Cdd:cd06704    77 SGNTVTMVVLR 87

PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467188 [Multi-domain] Cd Length: 87 Bit Score: 52.28 E-value: 3.80e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1360 LGISIVSGeKG---------GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06704    12 LGISIAGG-KGstpykgddeGIFISRVTEGGPAAKAGVRVGDKLLEVNGVDLVDADHHEA 70

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 58.44 E-value: 3.88e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   299 LNKLYDTAMDKLEV------VKKDYDALRKRysEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQhqcALS 372
Cdd:pfam02463  175 LKKLIEETENLAELiidleeLKLQELKLKEQ--AKKALEYYQLKEKLELEEEYLLYLDYLKLNEERIDLLQELL---RDE 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   373 LRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDavysEYKLIMSERDQVISELDKLQTE 452
Cdd:pfam02463  250 QEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELL----KLERRKVDDEEKLKESEKEKKK 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   453 VELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVakcRRDWAFQERDK 532
Cdd:pfam02463  326 AEKELKKEKEEIEELEKELKELEIKREAEEEEEEELEKLQEKLEQLEEELLAKKKLESERLSSAAK---LKEEELELKSE 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   533 IVAERDSI----RTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKEL------KEQMESQLEKEARFRQLMAH 602
Cdd:pfam02463  403 EEKEAQLLlelaRQLEDLLKEEKKEELEILEEEEESIELKQGKLTEEKEELEKQelkllkDELELKKSEDLLKETQLVKL 482

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249   603 SSHDSAIDTDSMEWETEVVEFERETEDIDLKALGFDMAEGVNEPCFP--GDCGIFVTKVD-KGSIADGRLRVND 673
Cdd:pfam02463  483 QEQLELLLSRQKLEERSQKESKARSGLKVLLALIKDGVGGRIISAHGrlGDLGVAVENYKvAISTAVIVEVSAT 556

PDZ domain of Rab3-interacting molecule 1 (RIM), RIM2, piccolo and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RIM, RIM2, piccolo and related domains. RIM proteins and Gallus gallus protein piccolo (also called aczonin) are involved in neurotransmitter release at presynaptic active zones, the site of vesicle fusion. A protein complex containing RIM proteins positions synaptic vesicles containing synaptotagmin at the active zone. RIM proteins simultaneously activate docking and priming of synaptic vesicles and recruit Ca2+-channels to active zones, thereby connecting primed synaptic vesicles to Ca2+-channels. RIM binding to vesicular Rab proteins (Rab3 and Rab27 isoforms) mediates vesicle docking; RIM binding to Munc13 activates vesicle priming; RIM binding to the Ca2+-channel, both directly and indirectly via RIM-BP, recruits the Ca2+-channels. The RIM PDZ domain interacts with the C-termini of N- and P/Q-type voltage-gated Ca2+-channels. RIM1, RIM2 and piccolo also participate in regulated exocytosis through binding cAMP-GEFII (cAMP-binding protein-guanidine nucleotide exchange factor II). The piccolo PDZ domain binds cAMP-GEFII. RIM2 also plays a role in dendrite formation by melanocytes. Caenorhabditis elegans RIM (also known as unc-10) may be involved in the regulation of defecation and daumone response. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467198 [Multi-domain] Cd Length: 95 Bit Score: 52.56 E-value: 3.93e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1347 EPRHVKVQKGSEP-------LGISIVSGEKG-----GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLI 1413
Cdd:cd06714     3 LIGRIILQRDPKDgsvsgngLGLKVVGGKMTesgrlGAYVTKVKPGSVADTVGhLREGDEVLEWNGISLQGKTFEEVQDI 82

                          90
                  ....*....|.
gi 767964249 1414 IGQQCDTITIL 1424
Cdd:cd06714    83 ISQSKGEVELV 93

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 58.53 E-value: 3.95e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   142 VNEKVENLSIQLRLMTR------ERNELRKRLAfATHGTAFDKRpYHRLNPDYERLKIQCVRAMSDLQSLQNQHTNALKR 215
Cdd:TIGR02168  198 LERQLKSLERQAEKAERykelkaELRELELALL-VLRLEELREE-LEELQEELKEAEEELEELTAELQELEEKLEELRLE 275

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   216 CEEVAKETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQVLKhngS 295
Cdd:TIGR02168  276 VSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKE---E 352

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   296 SEILNKLYDTAMDKLEVVKKDYDALRKRYSEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQcalslrr 375
Cdd:TIGR02168  353 LESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEE------- 425

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   376 feaihHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVEL 455
Cdd:TIGR02168  426 -----LLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQARLDSLERLQEN 500

                          330       340       350
                   ....*....|....*....|....*....|....
gi 767964249   456 AESKLKSSTSEKKAANEEMEALRQIKDTVTMDAG 489
Cdd:TIGR02168  501 LEGFSEGVKALLKNQSGLSGILGVLSELISVDEG 534

PDZ domain; PDZ domains are found in diverse signaling proteins.

Pssm-ID: 395476 [Multi-domain] Cd Length: 81 Bit Score: 51.90 E-value: 4.73e-08

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249   719 PLHINLSGQKDSGIsleNGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:pfam00595   11 GLGFSLKGGSDQGD---PGIFVSEVLPGGAAEAGG-LKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLTIL 81

PDZ domain 6 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467171 [Multi-domain] Cd Length: 85 Bit Score: 51.92 E-value: 4.98e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  719 PLHINLSGQKDsgisLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLK 794
Cdd:cd06683    14 PLGITISGTEE----PFDPIVISGLTEGGLAERTGAIHVGDRILAINGESLRGKPLSEAIHLLQNAGDTVTLKISR 85

PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SHANK1, SHANK2, SHANK3, and related domains. SHANK family proteins, SHANK1 (also known as somatostatin receptor-interacting protein, SSTR-interacting protein, SSTRIP), SHANK2 (also known as cortactin-binding protein 1, proline-rich synapse-associated protein 1), and SHANK3 (proline-rich synapse-associated protein 2) are synaptic scaffolding proteins which are highly enriched in the post-synaptic densities of excitatory synapses. They have been implicated in synaptic transmission, synapse formation, synaptic plasticity, and cytoskeletal remodeling, and are regulators of Cav1 calcium current and CREB target expression. Many protein ligands have been identified for the Shank PDZ domain, such as GKAP (also known as SAPAP), betaPIX (a guanine nucleotide exchange factor used by Rho GTPase family members Rac1 and Cdc42), alpha-latrotoxin, neuroligin, group I metabotropic glutamate receptors (mGluRs), and L-type calcium channels. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SHANK-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F.

Pssm-ID: 467228 [Multi-domain] Cd Length: 101 Bit Score: 52.21 E-value: 5.17e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1373 YVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITI 1423
Cdd:cd06746    45 YLESVDPGGVADKAGLKKGDFLLEINGEDVVKASHEQVVNLIRQSGNTLVL 95

PDZ domain 3 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467248 [Multi-domain] Cd Length: 82 Bit Score: 51.56 E-value: 5.83e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1499 EPRVVFIKKSQLELGVHLCGGNLHGVFVAEVEDDSPAKgPDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRDGVRLKV 1578
Cdd:cd06767     2 EPRHVSIEKGSEPLGISIVSGENGGIFVSSVTEGSLAH-QAGLEYGDQLLEVNGINLRNATEQQAALILRQCGDTITMLV 80


                  ..
gi 767964249 1579 QY 1580
Cdd:cd06767    81 QY 82

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 56.07 E-value: 6.31e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  387 TAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSE 466
Cdd:COG1340     7 SSSLEELEEKIEELREEIEELKEKRDELNEELKELAEKRDELNAQVKELREEAQELREKRDELNEKVKELKEERDELNEK 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  467 KKAANEEMEALRQIKDTvtmdAGRANKEVEILRKQCKAL-------------------------------------CQEL 509
Cdd:COG1340    87 LNELREELDELRKELAE----LNKAGGSIDKLRKEIERLewrqqtevlspeeekelvekikelekelekakkalekNEKL 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  510 KEALQEADVAKCRRDWAFQ-------ERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKEL 582
Cdd:COG1340   163 KELRAELKELRKEAEEIHKkikelaeEAQELHEEMIELYKEADELRKEADELHKEIVEAQEKADELHEEIIELQKELREL 242

                         250
                  ....*....|..
gi 767964249  583 KEQMESQLEKEA 594
Cdd:COG1340   243 RKELKKLRKKQR 254

PDZ domain 2 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZRN4-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467200 [Multi-domain] Cd Length: 88 Bit Score: 51.51 E-value: 6.51e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  651 DCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDkkQAIKALLNGEGAINMVVRR 708
Cdd:cd06716    30 DTGIYVSEVDPNSIAakDGRIREGDQILQINGVDVQNRE--EAIALLSEEEKSITLLVAR 87

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467235 [Multi-domain] Cd Length: 79 Bit Score: 51.38 E-value: 6.80e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249  724 LSGQKDSGISLengvYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLK 794
Cdd:cd06753    14 LQGGKDFNQPL----TISRVTPGGKAAQAN-LRPGDVILAINGESTEGMTHLEAQNKIKAATGSLSLTLER 79

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 57.08 E-value: 7.54e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  282 LRAQQQQVLKHNGSSEILNKlydTAMDKLEVVKKDYDALRKRYSEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDT 361
Cdd:COG4717    51 LEKEADELFKPQGRKPELNL---KELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQL 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  362 AIQLQHQCALS---------LRRFEAIHHELNKATAQNKDLQWEMELLQSELTEL-RTTQVKTAKESEKYREERDAVYSE 431
Cdd:COG4717   128 LPLYQELEALEaelaelperLEELEERLEELRELEEELEELEAELAELQEELEELlEQLSLATEEELQDLAEELEELQQR 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  432 YKLIMSERDQVISELDKLQTEVELAESKLKS------------------------------------------------- 462
Cdd:COG4717   208 LAELEEELEEAQEELEELEEELEQLENELEAaaleerlkearlllliaaallallglggsllsliltiagvlflvlglla 287

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  463 -----STSEKKAANEEMEA--------------LRQIKDTVTMDAGRANKEVEILRKQCKALCQ---ELKEALQEADVAK 520
Cdd:COG4717   288 llfllLAREKASLGKEAEElqalpaleeleeeeLEELLAALGLPPDLSPEELLELLDRIEELQEllrEAEELEEELQLEE 367

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  521 CRRDW-------------AFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDT--RKQKNDVSRELKELKEQ 585
Cdd:COG4717   368 LEQEIaallaeagvedeeELRAALEQAEEYQELKEELEELEEQLEELLGELEELLEALDEEelEEELEELEEELEELEEE 447

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  586 MESQLEKEARFRQLMAHSSHDSAIDTDSMEWETEVVEFERETEDIDLKALGFDMAE 641
Cdd:COG4717   448 LEELREELAELEAELEQLEEDGELAELLQELEELKAELRELAEEWAALKLALELLE 503

PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467186 [Multi-domain] Cd Length: 89 Bit Score: 51.49 E-value: 8.71e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  628 EDIDLK----ALGFDMAEGVNEPCFP---GDCGIFVTKVDKGSIAdGR--LRVNDWLLRINDVDLINKDKKQAIKALLNG 698
Cdd:cd06702     1 EEIHLVkaggPLGLSIVGGSDHSSHPfgvDEPGIFISKVIPDGAA-AKsgLRIGDRILSVNGKDLRHATHQEAVSALLSP 79

                          90
                  ....*....|
gi 767964249  699 EGAINMVVRR 708
Cdd:cd06702    80 GQEIKLLVRH 89

PDZ domain 4 of PDZ domain containing 2 (PDZD2), PDZ domain 2 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the second PDZ domain (PDZ2) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467241 [Multi-domain] Cd Length: 90 Bit Score: 51.12 E-value: 9.39e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249  727 QKDSGISL------------ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQ 785
Cdd:cd06760    10 NKEPGVGLgiglcclplendIPGIFIHHLSPGSVAHMDGRLRRGDQILEINGTSLRNVTLNEAYAILSQCK 80

PDZ domain 2 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Dlg1, human Dlg1,2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197 or SAP-97), Dlg2 (also known as channel-associated protein of synapse-110, postsynaptic density protein 93, or PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95, synapse-associated protein 90, or SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling. It regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord, and it also interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467207 [Multi-domain] Cd Length: 85 Bit Score: 51.11 E-value: 9.45e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1350 HVKVQKGSEPLGISIVSGeKG--------GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDT 1420
Cdd:cd06724     1 EIKLVKGPKGLGFSIAGG-VGnqhipgdnGIYVTKIIEGGAAQKDGrLQVGDKLLAVNDVSLEEVTHEEAVAALKNTSDV 79


                  ....
gi 767964249 1421 ITIL 1424
Cdd:cd06724    80 VYLK 83

PDZ domain 5 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family domain PDZ5 is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467170 [Multi-domain] Cd Length: 85 Bit Score: 51.19 E-value: 9.78e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767964249  742 AVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLK 794
Cdd:cd06682    33 DVKKGSVAHRTGTLEPGDKLLAIDNIRLDNCSMEDAAQILQQAEDIVKLKIRK 85

PDZ domain 2 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467166 [Multi-domain] Cd Length: 82 Bit Score: 51.09 E-value: 9.86e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1350 HVKVQK-GSEPLGISIVS-GEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06678     2 HVTLNKrDGEQLGIKLVRkKDEPGVFILDLLEGGLAARDGrLKSDDRVLAINGQDLRHGTPEQAAQII 69

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.

Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 57.11 E-value: 1.01e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   187 DYERLKIQCVRAMSDLQSLQNQHTNALKRCEEVAketdfyHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWE 266
Cdd:pfam01576  423 ESERQRAELAEKLSKLQSELESVSSLLNEAEGKN------IKLSKDVSSLESQLQDTQELLQEETRQKLNLSTRLRQLED 496

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   267 DMKRLHEEDQKEIGDLRAQQQQVLKHNGS-SEILNKLYDTA--MDKLEVVKK----DYDALRKRYSEKVAIHnadlsrlE 339
Cdd:pfam01576  497 ERNSLQEQLEEEEEAKRNVERQLSTLQAQlSDMKKKLEEDAgtLEALEEGKKrlqrELEALTQQLEEKAAAY-------D 569

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   340 QLGEENQRLLKQTEMLTQQRDTAIQLQHQCALSLRRFEAIHHELNKATAQNKDlqwEMELLQSELTELRTTQVKTAKESE 419
Cdd:pfam01576  570 KLEKTKNRLQQELDDLLVDLDHQRQLVSNLEKKQKKFDQMLAEEKAISARYAE---ERDRAEAEAREKETRALSLARALE 646

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   420 KYREERDAVYSEYKLIMSERDQVISELDKLQTEV-ELAESK--LKSSTSEKKAANEEME-ALRQIKDT-----VTMDAGR 490
Cdd:pfam01576  647 EALEAKEELERTNKQLRAEMEDLVSSKDDVGKNVhELERSKraLEQQVEEMKTQLEELEdELQATEDAklrleVNMQALK 726

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   491 ANKEVEILRK------QCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSEL------ 558
Cdd:pfam01576  727 AQFERDLQARdeqgeeKRRQLVKQVRELEAELEDERKQRAQAVAAKKKLELDLKELEAQIDAANKGREEAVKQLkklqaq 806

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   559 -AEALRSLDDTRKQKNDV---SRE----LKELKEQM---------------ESQLEKEARFRQLMAHSSHDSAIDTDSME 615
Cdd:pfam01576  807 mKDLQRELEEARASRDEIlaqSKEsekkLKNLEAELlqlqedlaaserarrQAQQERDELADEIASGASGKSALQDEKRR 886

                          490
                   ....*....|....
gi 767964249   616 WETEVVEFERETED 629
Cdd:pfam01576  887 LEARIAQLEEELEE 900

PDZ domain 2 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP, Drosophila Bazooka) and related domains. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par3 and the Par complex include Par3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467271 [Multi-domain] Cd Length: 93 Bit Score: 51.10 E-value: 1.08e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  728 KDSGISLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:cd23058    24 RDNPTGGSGPIYIKNILPKGAAIQDGRLKAGDRLLEVNGVDVTGKTQEEVVSLLRSTKLGGTVSLV 89

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442439 [Multi-domain] Cd Length: 687 Bit Score: 56.56 E-value: 1.34e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  398 ELLQSELTELRTTQVKTAKESEKYREERDAVYSEyklimSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEAL 477
Cdd:COG3206   178 EFLEEQLPELRKELEEAEAALEEFRQKNGLVDLS-----EEAKLLLQQLSELESQLAEARAELAEAEARLAALRAQLGSG 252

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  478 RQIKDTVTmdagrANKEVEILRKQCKALCQELKEALQEadvakcrrdwaFQERD-KIVAERDSIRTLCDNLRRERDRAVS 556
Cdd:COG3206   253 PDALPELL-----QSPVIQQLRAQLAELEAELAELSAR-----------YTPNHpDVIALRAQIAALRAQLQQEAQRILA 316

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 767964249  557 ELAEALRSLddtRKQKNDVSRELKELKEQMESQLEKEARFRQLM 600
Cdd:COG3206   317 SLEAELEAL---QAREASLQAQLAQLEARLAELPELEAELRRLE 357

PDZ domain 3 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP, Drosophila Bazooka) and related domains. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par-3 and the Par complex include Par3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467272 [Multi-domain] Cd Length: 103 Bit Score: 51.13 E-value: 1.45e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  720 LHINLSGQ---KDSGISLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLR 782
Cdd:cd23059    18 LGVSVKGKtskEDNGGKADLGIFIKSIIHGGAASKDGRLRVNDQLIAVNGESLLGLTNSEAMETLR 83

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 56.46 E-value: 1.58e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  352 TEMLTQQR--DTAIQLQHQcalsLRRFEAIHHELNKATAQnkdlqweMELLQsELTELRTTQVKTAKESEKYREERDAVy 429
Cdd:COG4913   215 EYMLEEPDtfEAADALVEH----FDDLERAHEALEDAREQ-------IELLE-PIRELAERYAAARERLAELEYLRAAL- 281

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  430 sEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKdtvtmdAGRANKEVEILRKQCKALCQEL 509
Cdd:COG4913   282 -RLWFAQRRLELLEAELEELRAELARLEAELERLEARLDALREELDELEAQI------RGNGGDRLEQLEREIERLEREL 354

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  510 KEALQEAD--VAKCRR-DWAF-QERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELK 583
Cdd:COG4913   355 EERERRRArlEALLAAlGLPLpASAEEFAALRAEAAALLEALEEELEALEEALAEAEAALRDLRRELRELEAEIASLE 432

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CPP (also known as tail-specific protease, PRC protein, Protease Re, and Photosystem II D1 protein processing peptidase), and related domains. CPP belongs to the peptidase S41A family. It cleaves a C-terminal 11 residue peptide from the precursor form of penicillin-binding protein 3, and may have a role in protecting bacterium from thermal and osmotic stresses. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This CPP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467623 [Multi-domain] Cd Length: 88 Bit Score: 50.56 E-value: 1.75e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 767964249  742 AVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLR 782
Cdd:cd06782    20 SPIPGGPAEKAG-IKPGDVIVAVDGESVRGMSLDEVVKLLR 59

PDZ domain of membrane palmitoylated proteins (MPPs), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP1-7 (also known as MAGUK p55 subfamily members 1-7), and related domains. MPPs comprise a subfamily of a larger group of multidomain proteins, namely, membrane-associated guanylate kinases (MAGUKs). MPPs form diverse protein complexes at the cell membranes, which are involved in a wide range of cellular processes, including establishing proper cell structure, polarity and cell adhesion. MPPs have only one PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467208 [Multi-domain] Cd Length: 80 Bit Score: 49.96 E-value: 2.08e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1349 RHVKVQKG-SEPLGISIvSGEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITI 1423
Cdd:cd06726     1 RLVEFEKArDEPLGATI-KMEEDSVIVARILHGGMAHRSGlLHVGDEILEINGIPVSGKTVDELQKLLSSLSGSVTF 76

Src homology 3 domain of the Tight junction protein, Zonula occludens protein 2; ZO-2 is a scaffolding protein that associates with other ZO proteins and other proteins of the tight junction, zonula adherens, and gap junctions. ZO proteins play roles in regulating cytoskeletal dynamics at these cell junctions. ZO-2 plays an essential role in embryonic development. It is critical for the blood-testis barrier integrity and male fertility. It also regulates the expression of cyclin D1 and cell proliferation. It is considered a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. The C-terminal region of ZO-2 contains an actin-binding region and a domain of unknown function designated beta. The SH3 domain of the related protein ZO-1 has been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212960 Cd Length: 63 Bit Score: 49.53 E-value: 2.12e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249 1593 GDSFYIRALYDRLADVEQELSFKKDDILYVDDTLPQGTFGSWMAWQLdenAQKIQRGQIPSK 1654
Cdd:cd12027     1 GDSFFIRTHFEYEKELPQSLAFTRGEIFRVVDTLYDGKLGNWLAVRI---GNELEKGLIPNK 59

PDZ domain of PICK1 (protein interacting with C-kinase 1) and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PICK1, and related domains. PICK1 (also known as PRKCA-binding protein and protein kinase C-alpha-binding protein) plays a key role in regulating trafficking of binding partners by altering either their subcellular targeting and/or surface expression. PICK1 plays a role in synaptic plasticity by regulating the trafficking and internalization of amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors; the PICK1-PDZ domain binds the AMPA receptor subunits. The PICK1 PDZ domain also binds glutamate transporters, Eph receptors, metabotropic glutamate receptors, and ASICs (acid-sensing ion channels), among others. Clustering and synaptic targeting of PICK1 requires direct interaction between the PDZ domain and lipid membranes. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PICK-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F.

Pssm-ID: 467205 [Multi-domain] Cd Length: 84 Bit Score: 50.11 E-value: 2.16e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  727 QKDS----GISLENG------VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLK 794
Cdd:cd06722     6 KKDAqnliGISIGGGapycpcLYIVQVFDNTPAAKDGTLAAGDEIVGVNGKSVKGKTKVEVAKMIQAVKGEVTIHYNK 83

PDZ domain of membrane palmitoylated proteins (MPPs), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP1-7 (also known as MAGUK p55 subfamily members 1-7), and related domains. MPPs comprise a subfamily of a larger group of multidomain proteins, namely, membrane-associated guanylate kinases (MAGUKs). MPPs form diverse protein complexes at the cell membranes, which are involved in a wide range of cellular processes, including establishing proper cell structure, polarity and cell adhesion. MPPs have only one PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467208 [Multi-domain] Cd Length: 80 Bit Score: 49.96 E-value: 2.36e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:cd06726    21 EDSVIVARILHGGMAHRSGLLHVGDEILEINGIPVSGKTVDELQKLLSSLSGSVTFKLI 79

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 55.71 E-value: 2.43e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  140 QQVNEKVENLSIQLRLMTRERNELRKRLAFATHGTAFDKRPYHRLNPDYERLKIQCVRAMSDLQSLQNQHTNALKRCEEV 219
Cdd:COG1196   361 AEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEE 440

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  220 AKETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQVLKHNGSSEiL 299
Cdd:COG1196   441 EEALEEAAEEEAELEEEEEALLELLAELLEEAALLEAALAELLEELAEAAARLLLLLEAEADYEGFLEGVKAALLLAG-L 519

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  300 NKLYDTAMDKLEVVKKDYDALRKRYSEK-VAIHNADLSRLEQLGEE--NQRLLKQTE--MLTQQRDTAIQLQHQCALSLR 374
Cdd:COG1196   520 RGLAGAVAVLIGVEAAYEAALEAALAAAlQNIVVEDDEVAAAAIEYlkAAKAGRATFlpLDKIRARAALAAALARGAIGA 599

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  375 RFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYRE---ERDAVYSEYKLIMSERDQVISELDKLQT 451
Cdd:COG1196   600 AVDLVASDLREADARYYVLGDTLLGRTLVAARLEAALRRAVTLAGRLREvtlEGEGGSAGGSLTGGSRRELLAALLEAEA 679

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  452 EVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQckaLCQELKEALQEADVAKCRRDWAFQERD 531
Cdd:COG1196   680 ELEELAERLAEEELELEEALLAEEEEERELAEAEEERLEEELEEEALEEQ---LEAEREELLEELLEEEELLEEEALEEL 756

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  532 KIVAERDSIRTLCDNLRRERDR-------AVSELAEALRSLDDTRKQKNDVSRELKELKEQMEsQLEKEARfRQLMA 601
Cdd:COG1196   757 PEPPDLEELERELERLEREIEAlgpvnllAIEEYEELEERYDFLSEQREDLEEARETLEEAIE-EIDRETR-ERFLE 831

PDZ domain of FERM and PDZ domain-containing protein 1 (FRMPD1), FRMPD3, FRMPD4, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of FRMPD1, FRMPD3, FRMPD4, and related domains. FRMPD1 (also known as FERM domain-containing protein 2, FRMD2), inhibits the malignant phenotype of lung cancer by activating the Hippo pathway via interaction with WWC3; the FRMPD1 PDZ domain binds WWC3. FRMPD3 is a target gene of the neuron-specific transcription factor NPAS4 that is involved in synaptic plasticity. FRMPD4 (also known as PDZ domain-containing protein 10, PDZD10, PDZK10, PSD-95-interacting regulator of spine morphogenesis, and Preso) regulates dendritic spine morphogenesis, and mGluR1/5 signaling; the FRMPD4 PDZ domain binds PAK-interacting exchange factor-beta (betaPix). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This FRMPD1,3,4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467250 [Multi-domain] Cd Length: 75 Bit Score: 49.55 E-value: 2.52e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249  732 ISLENGVYAAAVLPGSPAakEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:cd06769    16 AGSERPVVVRSVTPGGPS--EGKLLPGDQILKINNEPVEDLPRERVIDLIRECKDSIVLTVL 75

PDZ domain 1 of amyloid-beta A4 precursor protein-binding family A member 1 (APBA1), APBA2, APBA3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of APBA1, APBA2, APBA3, and related domains. The APBA/X11/Mint protein family includes three members: neuron specific APBA1 (also known as X11alpha and Mint1) and APBA2 (also known as X11beta and Mint2), and the ubiquitously expressed APBA3 (also known as (X12gamma and Mint3). They are involved in regulating neuronal signaling, trafficking and plasticity. They contain two PDZ domains (PDZ1 and PDZ2) which bind a variety of proteins: Arf GTPases (APBA1 and APBA2 PDZ2) and neurexin (APBA1 and APBA2 PDZ1 and 2), which are involved in vesicle docking and exocytosis; alpha1B subunit of N-type Ca2+ channel (APBA1 PDZ1) that is involved in ion channels; KIF17 (APBA1 PDZ1) that is involved in transport and traffic; and Alzheimer's disease related proteins such as APP (APBA3 PDZ2), CCS (APBA1 PDZ2), NF-kappa-B/p65 (APBA2 PDZ2), presenilin-1 (APBA1 and APBA2 PDZ1 and PDZ2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This APBA1,2,3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F.

Pssm-ID: 467203 [Multi-domain] Cd Length: 86 Bit Score: 49.95 E-value: 2.78e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767964249  738 VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSC 784
Cdd:cd06720    29 VVVANMMPGGPAARSGKLNIGDQIMSINGTSLVGLPLSTCQAIIKNL 75

PDZ domain 5 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family domain PDZ5 is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467170 [Multi-domain] Cd Length: 85 Bit Score: 49.65 E-value: 2.92e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1350 HVKVQKGSEP-LGISIVSGEK----GGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIgQQCDTITI 1423
Cdd:cd06682     2 HVKLPKRSGVgLGITISAPKNrkpgDPLIISDVKKGSVAHRTGtLEPGDKLLAIDNIRLDNCSMEDAAQIL-QQAEDIVK 80


                  .
gi 767964249 1424 L 1424
Cdd:cd06682    81 L 81

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 55.71 E-value: 2.92e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  136 LLTDQQVNEKVENLSIQLRLMTRERNELRKRLAfathgtafdkrpyhRLNPDYERLKIQCVRAMSDLQSLQNQHTNALKR 215
Cdd:COG1196   231 LLKLRELEAELEELEAELEELEAELEELEAELA--------------ELEAELEELRLELEELELELEEAQAEEYELLAE 296

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  216 CEEVAKETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQVLKhnGS 295
Cdd:COG1196   297 LARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEA--EL 374

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  296 SEILNKLYDTAMDKLEVVKKDYDALRKRYSEKVAIHNAdLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQCALSLRR 375
Cdd:COG1196   375 AEAEEELEELAEELLEALRAAAELAAQLEELEEAEEAL-LERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAE 453

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  376 FEAihhELNKATAQNKDLQWEMELLQSELTELRTtQVKTAKESEKYREERDAVYSEY---------KLIMSERDQVISEL 446
Cdd:COG1196   454 LEE---EEEALLELLAELLEEAALLEAALAELLE-ELAEAAARLLLLLEAEADYEGFlegvkaallLAGLRGLAGAVAVL 529

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  447 DKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRAN--------------------------KEVEILRK 500
Cdd:COG1196   530 IGVEAAYEAALEAALAAALQNIVVEDDEVAAAAIEYLKAAKAGRATflpldkiraraalaaalargaigaavDLVASDLR 609

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  501 QCKALCQELKEALQEADVAKCRRDWAFQERDKIVAE------------------RDSIRTLCDNLRRERDRAVSELAEAL 562
Cdd:COG1196   610 EADARYYVLGDTLLGRTLVAARLEAALRRAVTLAGRlrevtlegeggsaggsltGGSRRELLAALLEAEAELEELAERLA 689

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  563 RSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMAHSSHDSAI----------------------DTDSMEWETEV 620
Cdd:COG1196   690 EEELELEEALLAEEEEERELAEAEEERLEEELEEEALEEQLEAEREElleelleeeelleeealeelpePPDLEELEREL 769

                         570
                  ....*....|....*.
gi 767964249  621 VEFEREtedidLKALG 636
Cdd:COG1196   770 ERLERE-----IEALG 780

PDZ1 domain of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, and related domains. Gallus gallus STXBP4 isoform X1 contains 2 PDZ domains (PDZ1 and PDZ2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This STXBP4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467179 [Multi-domain] Cd Length: 88 Bit Score: 49.91 E-value: 3.06e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1357 SEPLGISIV------SGEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06692     7 SKGLGIKIIggyrenTGEEFGIFIKRILPGGLAATDGrLKEGDLILEVNGESLQGVTNERA 67

DNA double-strand break repair ATPase Rad50;

Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 55.46 E-value: 3.09e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  303 YDTAMDKLEVVKKDYDALRKRYsEKVAIHNADLSrlEQLGEENQRLLKQTEMLTQQRDTAIQLQHQCAL---SLRRFEAI 379
Cdd:PRK03918  160 YENAYKNLGEVIKEIKRRIERL-EKFIKRTENIE--ELIKEKEKELEEVLREINEISSELPELREELEKlekEVKELEEL 236

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  380 HHELNKATAQNKDLQWEMELLQSELTELRT-------------TQVKTAKESEKYREERDAVYSEYKLIMSERDQVISEL 446
Cdd:PRK03918  237 KEEIEELEKELESLEGSKRKLEEKIRELEErieelkkeieeleEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRL 316

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  447 DKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTM---------DAGRANKEVEILRKQCKalCQELKEALQEAD 517
Cdd:PRK03918  317 SRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEEleerhelyeEAKAKKEELERLKKRLT--GLTPEKLEKELE 394

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  518 VAKCRRDWAFQERDKIVAERDSIRtlcdNLRRERDRAVSELAEAL-------RSLDDTRKQK---------NDVSRELKE 581
Cdd:PRK03918  395 ELEKAKEEIEEEISKITARIGELK----KEIKELKKAIEELKKAKgkcpvcgRELTEEHRKElleeytaelKRIEKELKE 470

                         330
                  ....*....|....
gi 767964249  582 LKEQmESQLEKEAR 595
Cdd:PRK03918  471 IEEK-ERKLRKELR 483

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 54.52 E-value: 3.12e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  382 ELNKATAQNKDLQWEMELLQSELTELrttqvktakesekyREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLK 461
Cdd:COG4372    32 QLRKALFELDKLQEELEQLREELEQA--------------REELEQLEEELEQARSELEQLEEELEELNEQLQAAQAELA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  462 SSTSEKKAANEEMEALRQikdtvtmDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDwafQERDKIVAERDSIR 541
Cdd:COG4372    98 QAQEELESLQEEAEELQE-------ELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELK---ELEEQLESLQEELA 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  542 TLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMAHSSHDSAIDTDSMEWETEVV 621
Cdd:COG4372   168 ALEQELQALSEAEAEQALDELLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEED 247

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  622 EFERETEDIDLKALGFDMAEGVNEPCFPGDCGIFVTKVDKGSIADGRLRVNDWLLRINDVDLINKDKKQAIKALLNG 698
Cdd:COG4372   248 KEELLEEVILKEIEELELAILVEKDTEEEELEIAALELEALEEAALELKLLALLLNLAALSLIGALEDALLAALLEL 324

PDZ domain 10 of multi-PDZ-domain protein 1 (MUPP1), domain 8 of PATJ (protein-associated tight junction) and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 10 of MUPP1, PDZ domain 8 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ10 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467161 [Multi-domain] Cd Length: 86 Bit Score: 49.60 E-value: 3.18e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1351 VKVQKGSEPLGISIVSGEK---GGIYVSKV-TVGSIAHQAGLEYGDQLLEFNGINLRSATEQQArliigqqcdtITILAQ 1426
Cdd:cd06673     6 IEINKGKKGLGLSIVGGSDtllGAIIIHEVyEDGAAAKDGRLWAGDQILEVNGEDLRKATHDEA----------INVLRQ 75


                  ....*...
gi 767964249 1427 YNPHVHQL 1434
Cdd:cd06673    76 TPQKVRLL 83

PDZ domain 1 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins, and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467209 [Multi-domain] Cd Length: 87 Bit Score: 49.58 E-value: 3.53e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249  722 INLSGQKDS--GISLENGVYAAAVLPGSPAakEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06727    15 IAVSGGRDNphFQSGDTSIVISDVLKGGPA--EGKLQENDRVVSVNGVSMENVEHSFAVQILRKCGKTANI 83

Weak chloroplast movement under blue light; WEMBL consists of several plant proteins required for the chloroplast avoidance response under high intensity blue light. This avoidance response consists in the relocation of chloroplasts on the anticlinal side of exposed cells. Acts in association with PMI2 to maintain the velocity of chloroplast photo-relocation movement via the regulation of cp-actin filaments. Thus several member-sequences are described as "myosin heavy chain-like".

Pssm-ID: 461718 [Multi-domain] Cd Length: 562 Bit Score: 55.03 E-value: 3.62e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   439 RDQVISELDKLQTEVelAESKLKSSTSE--KKAANEEMEALRQIKDTVTMDAGRANKEvEILRKQCKALCQ-ELKE---- 511
Cdd:pfam05701   37 RKLVELELEKVQEEI--PEYKKQSEAAEaaKAQVLEELESTKRLIEELKLNLERAQTE-EAQAKQDSELAKlRVEEmeqg 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   512 --------ALQEADVAKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELK 583
Cdd:pfam05701  114 iadeasvaAKAQLEVAKARHAAAVAELKSVKEELESLRKEYASLVSERDIAIKRAEEAVSASKEIEKTVEELTIELIATK 193

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 767964249   584 EQMESqlekearfrqlmAHSSHDSA----------IDTDSMEWETEVVEFERE 626
Cdd:pfam05701  194 ESLES------------AHAAHLEAeehrigaalaREQDKLNWEKELKQAEEE 234

The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.

Pssm-ID: 153280 [Multi-domain] Cd Length: 218 Bit Score: 52.74 E-value: 4.04e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  417 ESEKYREERDAVySEYKLIMSERDQVISELDKLQTEV-----ELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRA 491
Cdd:cd07596     2 EDQEFEEAKDYI-LKLEEQLKKLSKQAQRLVKRRRELgsalgEFGKALIKLAKCEEEVGGELGEALSKLGKAAEELSSLS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  492 NKEVeilRKQCKALCQELKEALQEADVAKCrrdwAFQERDKIVAERDSIRTLCDNLRRERDRAVS-------ELAEALRS 564
Cdd:cd07596    81 EAQA---NQELVKLLEPLKEYLRYCQAVKE----TLDDRADALLTLQSLKKDLASKKAQLEKLKAapgikpaKVEELEEE 153

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 767964249  565 LDDTRKQKNDVSRELKELKEQMESQLE--KEARFRQLMA 601
Cdd:cd07596   154 LEEAESALEEARKRYEEISERLKEELKrfHEERARDLKA 192

PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the second PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467270 [Multi-domain] Cd Length: 85 Bit Score: 49.31 E-value: 4.32e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1350 HVKVQKGSEPLGISIVSG-EKG-GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQA-RLIIGQQCDTITI 1423
Cdd:cd10834     5 HLYTTSDDYCLGFNIRGGsEYGlGIYVSKVDPGGLAEQNGIKVGDQILAVNGVSFEDITHSKAvEVLKSQTHLMLTI 81

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440556 [Multi-domain] Cd Length: 341 Bit Score: 53.72 E-value: 4.44e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249  712 LGGKVVTPLHINLSGQKDS-GISL---ENGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLR 782
Cdd:COG0793    43 LDPEEYEDFQESTSGEFGGlGAELgeeDGKVVVVSVIPGSPAEKAG-IKPGDIILAIDGKSVAGLTLDDAVKLLR 116

PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13),FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467180 [Multi-domain] Cd Length: 92 Bit Score: 49.32 E-value: 5.11e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1354 QKGsepLGISIVSGEKG-----GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITILA 1425
Cdd:cd06694    12 QKG---LGFTIVGGENSgsldlGIFVKSIIPGGPADKDGrIKPGDRIIAINGQSLEGKTHHAAVEIIQNAPDKVELII 86

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 53.38 E-value: 5.45e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  248 RRE-NGQLLRERNLLQQswedMKRLHEEDQKEIGDLRAQQQQVLkhngssEILNKLYDTA------MDKLEVVKKDYDAL 320
Cdd:COG1340    45 RDElNAQVKELREEAQE----LREKRDELNEKVKELKEERDELN------EKLNELREELdelrkeLAELNKAGGSIDKL 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  321 RKRYsekvaihnadlsrlEQLgEENQrllkQTEMLTQQRDTAIQLQhqcalsLRRFEAIHHELNKATAQNKDLQW---EM 397
Cdd:COG1340   115 RKEI--------------ERL-EWRQ----QTEVLSPEEEKELVEK------IKELEKELEKAKKALEKNEKLKElraEL 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  398 ELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEAL 477
Cdd:COG1340   170 KELRKEAEEIHKKIKELAEEAQELHEEMIELYKEADELRKEADELHKEIVEAQEKADELHEEIIELQKELRELRKELKKL 249

                         250       260       270
                  ....*....|....*....|....*....|...
gi 767964249  478 RQIKdtvtmDAGRANKEVEILRKQCKALCQELK 510
Cdd:COG1340   250 RKKQ-----RALKREKEKEELEEKAEEIFEKLK 277

PDZ domain of syntrophins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of syntrophins (including alpha-1-syntrophin, beta-1-syntrophin, beta-2-syntrophin, gamma-1-syntrophin, and gamma-2-syntrophin), and related domains. Syntrophins play a role in recruiting various signaling molecules into signaling complexes and help provide appropriate spatiotemporal regulation of signaling pathways. They function in cytoskeletal organization and maintenance; as components of the dystrophin-glycoprotein complex (DGC), they help maintain structural integrity of skeletal muscle fibers. They link voltage-gated sodium channels to the actin cytoskeleton and the extracellular matrix, and control the localization and activity of the actin reorganizing proteins such as PI3K, PI(3,4)P2 and TAPP1. Through association with various cytoskeletal proteins within the cells, they are involved in processes such as regulation of focal adhesions, myogenesis, calcium homeostasis, and cell migration. They also have roles in synapse formation and in the organization of utrophin, acetylcholine receptor, and acetylcholinesterase at the neuromuscular synapse. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This syntrophin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467262 [Multi-domain] Cd Length: 83 Bit Score: 48.72 E-value: 5.55e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249 1349 RHVKVQKgsEP---LGISIvsgeKGG------IYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06801     1 RTVRVVK--QDvggLGISI----KGGaehkmpILISKIFKGQAADQTGqLFVGDAILSVNGENLEDATHDEA 66

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

Pssm-ID: 275316 [Multi-domain] Cd Length: 745 Bit Score: 54.64 E-value: 5.89e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   231 SRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQ---QVLKHNgssEILNKLYDTam 307
Cdd:TIGR04523  338 SQLNEQISQLKKELTNSESENSEKQRELEEKQNEIEKLKKENQSYKQEIKNLESQINdleSKIQNQ---EKLNQQKDE-- 412

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   308 dKLEVVKKDYDALRKRY---SEKVAIHNADLSRLEqlgEENQRLLKQTEMLTQQRDtaiQLQHQCALSLRRFEAIHH--- 381
Cdd:TIGR04523  413 -QIKKLQQEKELLEKEIerlKETIIKNNSEIKDLT---NQDSVKELIIKNLDNTRE---SLETQLKVLSRSINKIKQnle 485

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   382 -----------ELNKATAQNKDLQWEMELLQSELTELRTTQVK------------TAKESEKYREERDAVYSEYKLIMSE 438
Cdd:TIGR04523  486 qkqkelkskekELKKLNEEKKELEEKVKDLTKKISSLKEKIEKlesekkekeskiSDLEDELNKDDFELKKENLEKEIDE 565

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   439 RDQVISEL----DKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQCKALcQELKEALQ 514
Cdd:TIGR04523  566 KNKEIEELkqtqKSLKKKQEEKQELIDQKEKEKKDLIKEIEEKEKKISSLEKELEKAKKENEKLSSIIKNI-KSKKNKLK 644


                   .
gi 767964249   515 E 515
Cdd:TIGR04523  645 Q 645

PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of human PTPN13, and related domains. PTPN13, also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1), negatively regulates FAS-mediated apoptosis and NGFR-mediated pro-apoptotic signaling, and may also regulate phosphoinositide 3-kinase (PI3K) signaling. It contains 5 PDZ domains; interaction partners of its second PDZ domain (PDZ2) include the Fas receptor (TNFRSF6) and thyroid receptor-interacting protein 6 (TRIP6). The second PDZ (PDZ2) domain, but not PDZ1 or PDZ3, of FRMPD2 binds to GluN2A and GluN2B, two subunits of N-methyl-d-aspartic acid (NMDA) receptors. Other binding partners of the FRMPDZ2 PDZ2 domain include NOD2, and catenin family members, delta catenin (CTNND2), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) and p0071 (also known as plakophilin 4; PKP4). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467254 [Multi-domain] Cd Length: 87 Bit Score: 48.75 E-value: 5.90e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  622 EFERETEDIDlKALGFDMAEGVNEPCFPGdcGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGE 699
Cdd:cd06792     2 VFEVELSKKD-GSLGISVTGGINTSVRHG--GIYVKSLVPGGAAeqDGRIQKGDRLLEVNGVSLEGVTHKQAVECLKNAG 78


                  ....*....
gi 767964249  700 GAINMVVRR 708
Cdd:cd06792    79 QVVTLVLER 87

PDZ domain 7 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 6 of PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of MUPP1 and PDZ domain 6 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467159 [Multi-domain] Cd Length: 96 Bit Score: 49.24 E-value: 5.96e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  705 VVRR-RKSLGgkvvtplhINLSGQKDSGISLEN-----GVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECE 778
Cdd:cd06671     7 LWREpGKSLG--------ISIVGGRVMGSRLSNgeeirGIFIKHVLEDSPAGRNGTLKTGDRILEVNGVDLRNATHEEAV 78


                  ....*...
gi 767964249  779 SLLRSCQD 786
Cdd:cd06671    79 EAIRNAGN 86

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 53.61 E-value: 6.25e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  400 LQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALR- 478
Cdd:COG4942    25 AEAELEQLQQEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRAELEAQKe 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  479 ----QIKDTVTM-------------DAGRANKEVEILR---KQCKALCQELKEALQEADvakcrrdwafQERDKIVAERD 538
Cdd:COG4942   105 elaeLLRALYRLgrqpplalllspeDFLDAVRRLQYLKylaPARREQAEELRADLAELA----------ALRAELEAERA 174

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  539 SIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQmESQLEKEAR 595
Cdd:COG4942   175 ELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQE-AEELEALIA 230

PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467187 [Multi-domain] Cd Length: 92 Bit Score: 48.80 E-value: 6.49e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1347 EPRHVKVQKGSEPLGISIVSGeKG---------GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQ 1416
Cdd:cd06703     1 ETITTTLIRDGKGLGFSIAGG-KGstpfrdgdeGIFISRITEGGAADRDGkLQVGDRVLSINGVDVTEARHDQAVALLTS 79

                          90
                  ....*....|
gi 767964249 1417 QCDTITILAQ 1426
Cdd:cd06703    80 SSPTITLVVE 89

PDZ domain 5 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), Protein-tyrosine phosphatase 1E (PTP-E1), and Protein-tyrosine phosphatase (PTPL1)] and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467183 [Multi-domain] Cd Length: 87 Bit Score: 48.88 E-value: 6.67e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249  719 PLHINLSGQKDSgisLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06697    14 QLGLKLTGGSDS---KYQVIYVLEIVPGSAAAEEGSLQPLDIIHYINGVSTQGMTLEDAVRALEASLPTVVL 82

PDZ domain 1 of FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of FRMPD2 (also known as PDZ domain-containing protein 4, and related domains. FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467284 [Multi-domain] Cd Length: 92 Bit Score: 48.64 E-value: 7.84e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249  726 GQKDSGiSLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd23071    21 GGENTG-KLDLGIFIASIIPGGPAEKDGRIKPGGRLISLNNISLEGVTFNTAVKILQNSPDEVEL 84

DNA double-strand break repair ATPase Rad50;

Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 54.30 E-value: 7.97e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  214 KRCEEVAKETDFYHTLhSRLLSDqtrLKDDVDMLRRENGQLLRERNLLQQSWEDMkrlhEEDQKEIGDLRAQQQQVLKHN 293
Cdd:PRK03918  283 KELKELKEKAEEYIKL-SEFYEE---YLDELREIEKRLSRLEEEINGIEERIKEL----EEKEERLEELKKKLKELEKRL 354

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  294 GSSEILNKLYDTAMDKL---------------EVVKKDYDALRKRYSEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQ 358
Cdd:PRK03918  355 EELEERHELYEEAKAKKeelerlkkrltgltpEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKA 434

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  359 RDTA------IQLQHQCALsLRRFEA----IHHELNKATAQNKDL-----QWEMELL-QSELTELRTT--QVKTAKES-E 419
Cdd:PRK03918  435 KGKCpvcgreLTEEHRKEL-LEEYTAelkrIEKELKEIEEKERKLrkelrELEKVLKkESELIKLKELaeQLKELEEKlK 513

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  420 KYR-EERDAVYSEYKLIMSERDQVISELDKLQTEVE---LAESKLKSSTSEKKAANEEM-EALRQIKDTVTMDAGRANKE 494
Cdd:PRK03918  514 KYNlEELEKKAEEYEKLKEKLIKLKGEIKSLKKELEkleELKKKLAELEKKLDELEEELaELLKELEELGFESVEELEER 593

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  495 VEILRK------QCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDSIRTLCD------------NLRRERDRAVS 556
Cdd:PRK03918  594 LKELEPfyneylELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRKELEelekkyseeeyeELREEYLELSR 673

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 767964249  557 ELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQL 599
Cdd:PRK03918  674 ELAGLRAELEELEKRREEIKKTLEKLKEELEEREKAKKELEKL 716

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 53.37 E-value: 8.11e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  373 LRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRttqvktaKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTE 452
Cdd:COG4372    37 LFELDKLQEELEQLREELEQAREELEQLEEELEQAR-------SELEQLEEELEELNEQLQAAQAELAQAQEELESLQEE 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  453 VELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEAlqEADVAKCRRDWAFQERDK 532
Cdd:COG4372   110 AEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAAL--EQELQALSEAEAEQALDE 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  533 IVAER----DSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMAHSSHDSA 608
Cdd:COG4372   188 LLKEAnrnaEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEVILKEIEELELAI 267

                         250       260
                  ....*....|....*....|....*...
gi 767964249  609 IDTDSMEWETEVVEFERETEDIDLKALG 636
Cdd:COG4372   268 LVEKDTEEEELEIAALELEALEEAALEL 295

PDZ domain 1 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins, and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467209 [Multi-domain] Cd Length: 87 Bit Score: 48.42 E-value: 8.43e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  634 ALGFDMA--EGVNEPCFP-GDCGIFVTKVDKGSIADGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRR 708
Cdd:cd06727    10 GFGFGIAvsGGRDNPHFQsGDTSIVISDVLKGGPAEGKLQENDRVVSVNGVSMENVEHSFAVQILRKCGKTANITVKR 87

PDZ domain 7 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 6 of PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of MUPP1 and PDZ domain 6 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467159 [Multi-domain] Cd Length: 96 Bit Score: 48.86 E-value: 8.98e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1499 EPRVVFIKK-SQLELGVHLCGGN-----------LHGVFVAEVEDDSPAKGPDGLVPGDLILEYGSLDVRNKTVEEVyVE 1566
Cdd:cd06671     1 PPRRVELWRePGKSLGISIVGGRvmgsrlsngeeIRGIFIKHVLEDSPAGRNGTLKTGDRILEVNGVDLRNATHEEA-VE 79

                          90
                  ....*....|....
gi 767964249 1567 MLK-PRDGVRLKVQ 1579
Cdd:cd06671    80 AIRnAGNPVVFLVQ 93

PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of TAX1BP3, and related domains. TAX1BP3 (also known as glutaminase-interacting protein 3, tax interaction protein 1, TIP-1, tax-interacting protein 1) may regulate a number of protein-protein interactions by competing for PDZ domain binding sites. TAX1BP3 binds beta-catenin and may act as an inhibitor of the Wnt signaling pathway. It competes with LIN7A (also known as Lin-7A or LIN-7A) for inward rectifier potassium channel 4 (KCNJ4) binding, and thereby promotes KCNJ4 internalization. It may play a role in the Rho signaling pathway, and in the activation of CDC42 by the viral protein HPV16 E6. Binding partners of the TAX1BP3 PDZ domain include beta-catenin, KCNJ4, glutaminase liver isoform (GLS2), rho guanine nucleotide exchange factor 16 (ARHGEF16), rhotekin, and CDK5 regulatory subunit-associated protein 3 (also known as LAPZ). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This TAX1BP3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467265 [Multi-domain] Cd Length: 94 Bit Score: 48.49 E-value: 1.03e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1350 HVKVQKGSEPLGISIVSG------------EKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQ 1417
Cdd:cd10822     5 HKLRQGENLILGFSIGGGidqdpsknpfsyTDKGIYVTRVSEGGPAEKAGLQVGDKILQVNGWDMTMVTHKQAVKRLTKK 84


                  ....*..
gi 767964249 1418 CDTITIL 1424
Cdd:cd10822    85 KPVLRML 91

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 51.46 E-value: 1.10e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  373 LRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMS--ERDQ-----VIS- 444
Cdd:COG1579     9 LLDLQELDSELDRLEHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEAriKKYEeqlgnVRNn 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  445 -ELDKLQTEVELAESKLKSSTSEKKAANEEMEALRqikdtvtmdagranKEVEILRKQCKALCQELKEALQEADvakcrr 523
Cdd:COG1579    89 kEYEALQKEIESLKRRISDLEDEILELMERIEELE--------------EELAELEAELAELEAELEEKKAELD------ 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767964249  524 dwafQERDKIVAERDSirtlcdnLRRERDRAVSELAEALRSL-DDTRKQKNDV 575
Cdd:COG1579   149 ----EELAELEAELEE-------LEAEREELAAKIPPELLALyERIRKRKNGL 190

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 53.91 E-value: 1.10e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   140 QQVNEKVENLSIQLRLMTRERNELRKRLAFATHGTAFDKRPYHRLNPDYERLKIQCVRAMSDLQSLQNQHTNaLKrcEEV 219
Cdd:TIGR02168  743 EQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTL-LN--EEA 819

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   220 AKETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEdQKEIGDLRAQQQQVLkhngssEIL 299
Cdd:TIGR02168  820 ANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESE-LEALLNERASLEEAL------ALL 892

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   300 NKLYDTAMDKLEVVKKDYDALRKRYSEKVAIHNADLSRLEQLgeeNQRLLKQTEMLT-QQRDTaiqlqhqcalslrrFEA 378
Cdd:TIGR02168  893 RSELEELSEELRELESKRSELRRELEELREKLAQLELRLEGL---EVRIDNLQERLSeEYSLT--------------LEE 955

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249   379 IHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSER---DQVISELDK 448
Cdd:TIGR02168  956 AEALENKIEDDEEEARRRLKRLENKIKELGPVNLAAIEEYEELKERYDFLTAQKEDLTEAKetlEEAIEEIDR 1028

PDZ domain 11 of MUPP1 of multi-PDZ-domain protein 1 (MUPP1), domain 9 of PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 11 of MUPP1, PDZ domain 9 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ11 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467162 [Multi-domain] Cd Length: 87 Bit Score: 48.05 E-value: 1.33e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767964249 1360 LGISIVSGEKG-GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06674    16 LGLSIVGKRNDtGVFVSDIVKGGAADADGrLMQGDQILSVNGEDVRNASQEAA 68

PDZ domain of membrane palmitoylated proteins 3 (MPP3), MPP4, and MPP7, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP3, MPP4, and MPP7, and related domains. MPP3 (also known as MAGUK p55 subfamily member 3, erythrocyte membrane protein p55, or EMP55), MPP4 (also known as MAGUK p55 subfamily member 4 or Discs large homolog 6), and MPP7 (also known as MAGUK p55 subfamily member 7) are membrane-associated guanylate kinase (MAGUK)-like proteins. MPP3 is part of a cell adhesion protein complex including tumor suppressor CADM1 and actin-binding protein 4.1B. Participation in the Crumbs cell polarity complex has also been demonstrated for MPP7 in epithelial cells, and for MPP3 and MPP4 in the retina. MPP4 is needed for proper localization of plasma membrane calcium ATPases and maintenance of calcium homeostasis at the rod photoreceptor synaptic terminals. Binding partners of the MPP3 PDZ domain include nectin-3, serotonin 5-hydroxytryptamine, 5-HT(2C) receptor, and a cell adhesion protein, TSLC1 (tumor suppressor in lung cancer 1); fragments of MPP4 having the PDZ domain bind CRB (PDZ-SH3-GUK) and GABA transporter GAT1 (PDZ-SH3). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467260 [Multi-domain] Cd Length: 81 Bit Score: 47.62 E-value: 1.55e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249 1351 VKVQKGSEPLGISIVSGEKGG-IYVSKVTVGSIAHQAGLEY-GDQLLEFNGINLRSATEQQARLIIGQQCDTIT 1422
Cdd:cd06799     3 VRLVKNNEPLGATIKRDEKTGaIVVARIMRGGAADRSGLIHvGDELREVNGISVEGKDPEEVIQILANSQGPIT 76

PDZ domain 3 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467167 [Multi-domain] Cd Length: 88 Bit Score: 47.63 E-value: 1.59e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1349 RHVKVQKG-SEPLGISIVSGEKGG-----IYVSKV-TVGSIAHQAGLEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06679     1 KTVTIKKEpSESLGISVAGGRGSRrgdlpIYVTNVqPDGCLGRDGRIKKGDVLLSINGISLTNLSHSEA 69

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 53.05 E-value: 1.65e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   380 HHELNKATAQNKDLQwemELLQSELTEL----------RTTQVKTAKESEKYREERDAVYSEYKLIMSER----DQVISE 445
Cdd:pfam02463  108 EYYINGKNVTKKEVA---ELLESQGISPeaynflvqggKIEIIAMMKPERRLEIEEEAAGSRLKRKKKEAlkklIEETEN 184

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   446 LDKLQTEVELAESKLKSstsEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRdw 525
Cdd:pfam02463  185 LAELIIDLEELKLQELK---LKEQAKKALEYYQLKEKLELEEEYLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQE-- 259

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   526 aFQERDKIVAERDSIRTLC----DNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMA 601
Cdd:pfam02463  260 -IEKEEEKLAQVLKENKEEekekKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKEKKKAEKELKKEKEEIE 338

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 767964249   602 HSSHDSAIDTDSMEWETEVVEFERETEDIDLKALGFDMAE 641
Cdd:pfam02463  339 ELEKELKELEIKREAEEEEEEELEKLQEKLEQLEEELLAK 378

PDZ domain 12 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 10 of protein-associated tight junction (PATJ, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 12 of MUPP1, PDZ domain 10 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like PDZ12 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467163 [Multi-domain] Cd Length: 86 Bit Score: 47.74 E-value: 1.70e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  726 GQKDS-GISLENG---------VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:cd06675     8 GPQDSlGISIAGGvgsplgdvpVFIAMIQPNGVAAQTGKLKVGDRIVSINGQSTDGLTHSEAVNLLKNASGTIILQVV 85

PDZ domain 13 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 13 of MUPP1. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ13 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ13 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467164 [Multi-domain] Cd Length: 83 Bit Score: 47.34 E-value: 1.78e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  738 VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:cd06676    28 IYVKTVFEKGAAAEDGRLKRGDQILAVNGESLEGVTHEEAVNILKKTKGTVTLTVL 83

PDZ domain 9 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 9 of MUPP1. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ9 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ9 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467263 [Multi-domain] Cd Length: 79 Bit Score: 46.96 E-value: 2.00e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSL 792
Cdd:cd10817    21 ENGIVIKSLTEGGPAAKDGRLKVGDQILAVDDESVVGCPYEKAISLLKTAKGTVKLTV 78

PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467253 [Multi-domain] Cd Length: 89 Bit Score: 47.23 E-value: 2.06e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  626 ETEDIDL----KALGFDMAEGVNEPCFPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd06791     1 ETFEVELvkdeQGLGITIAGYVGEKASGELSGIFVKSIIPGSAAdqDGRIQVNDQIIAVDGVNLQGFTNQEAVEVLRN 78

PDZ domain 5 of Danio rerio tyrosine-protein phosphatase non-receptor type 13 (Ptpn13) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of Danio rerio Ptpn13, and related domains. Protein-tyrosine phosphatases (PTPs) dephosphorylate phosphotyrosyl residues in proteins that are phosphorylated by protein tyrosine kinases (PTKs). Danio rerio Ptpn13 is a classical non-receptor-like PTP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467273 [Multi-domain] Cd Length: 80 Bit Score: 46.96 E-value: 2.09e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  736 NGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSL 792
Cdd:cd23060    23 SGIFVKSISPGGVADRDGRLQVGDRLLQVNGESVIGLSHSKAVNILRKAKGTVQLTV 79

Synaptonemal complex protein 1 (SCP-1); Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase.

Pssm-ID: 114219 [Multi-domain] Cd Length: 787 Bit Score: 52.80 E-value: 2.16e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   292 HNGSSEILNKLYDTAMDKLEVVKKDYDALrkrYSEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQCal 371
Cdd:pfam05483   55 NSGDCHYQEGLKDSDFENSEGLSRLYSKL---YKEAEKIKKWKVSIEAELKQKENKLQENRKIIEAQRKAIQELQFEN-- 129

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   372 slrrfEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQT 451
Cdd:pfam05483  130 -----EKVSLKLEEEIQENKDLIKENNATRHLCNLLKETCARSAEKTKKYEYEREETRQVYMDLNNNIEKMILAFEELRV 204

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   452 EVELA--ESKLKSSTSEKKAANEEMEALRQIKDTvtmdagraNKEVEILRKQCKALCQELKE---ALQEAdvakcrRDWA 526
Cdd:pfam05483  205 QAENArlEMHFKLKEDHEKIQHLEEEYKKEINDK--------EKQVSLLLIQITEKENKMKDltfLLEES------RDKA 270

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   527 FQERDKIVAERDSIRTLCDnlrrERDRAVSELAEALRSLDDTRKQKNDVSRELK-------ELKEQMESQLEKEARFRQl 599
Cdd:pfam05483  271 NQLEEKTKLQDENLKELIE----KKDHLTKELEDIKMSLQRSMSTQKALEEDLQiatkticQLTEEKEAQMEELNKAKA- 345


                   ....
gi 767964249   600 mAHS 603
Cdd:pfam05483  346 -AHS 348

PDZ domain of sorting nexin-27 (SNX27), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SNX27, and related domains. SNX27 is involved in retrograde transport from endosome to plasma membrane. The PDZ domain of SNX27 links cargo identification to retromer-mediated transport. SNX27 binds to the retromer complex (vacuolar protein sorting 26(VPS26)-VPS29-VPS35), via its PDZ domain binding to VPS26. The SNX27 PDZ domain also binds to cargo including the G-protein-coupled receptors (GPCRs): beta2-adrenergic receptor (beta2AR), beta1AR, parathyroid hormone receptor (PTHR), alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), NMDA receptors, 5-hydroxytryptamine 4a receptors, frizzled receptors, and somatostatin receptor subtype 5 (SSTR5). Additional binding partners of the SNX27 PDZ domain include G protein-gated inwardly rectifying potassium (Kir3) channels, angiotensin-converting enzyme 2 (ACE2), and PTEN (phosphatase and tensin homolog deleted on chromosome 10); PTEN binding to SNX27 prevents SNX27's association with the retromer complex. SNX27 has been reported to be a host factor needed for efficient entry of an engineered SARS-CoV-2 variant, the spike protein of which contains a deletion at the S1/S2 subunit cleavage site; the PDZ domain of SNX27 binds angiotensin-converting enzyme 2 (ACE2), and may be involved in recycling ACE2 to the plasma membrane, thereby promoting viral entry. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SNX27-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467283 [Multi-domain] Cd Length: 93 Bit Score: 47.40 E-value: 2.29e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  710 KSLGGKVVTPLHinlsgqkdsgislengvYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLT 789
Cdd:cd23070    27 RSINGELYAPLQ-----------------HVSAVLEGGAADKAG-VRKGDRILEVNGVNVEGATHKQVVDLIKSGGDELT 88


                  ....
gi 767964249  790 LSLL 793
Cdd:cd23070    89 LTVI 92

Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction.

Pssm-ID: 212690 [Multi-domain] Cd Length: 51 Bit Score: 45.92 E-value: 2.39e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1597 YIRALYDRLADVEQELSFKKDDILYVDDTLPQGtfgsWMAWQLDENaqkiQRGQIPSKY 1655
Cdd:cd00174     1 YARALYDYEAQDDDELSFKKGDIITVLEKDDDG----WWEGELNGG----REGLFPANY 51

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467281 [Multi-domain] Cd Length: 82 Bit Score: 46.75 E-value: 2.86e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249 1356 GSEPLGISIVSGEKGG--IYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITILAQ 1426
Cdd:cd23068     9 SNTPWGFRLQGGADFGqpLSIQKVNPGSPADKAGLRRGDVILRINGTDTSNLTHKQAQDLIKRAGNDLQLTVQ 81

PDZ domain 2 of PDZ domain containing 2 (PDZD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains, and is expressed at exceptionally high levels in the pancreas and certain cancer tissues such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467239 [Multi-domain] Cd Length: 88 Bit Score: 46.96 E-value: 3.04e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  720 LHINLSGQKDSGISlENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRS 783
Cdd:cd06758    14 LGIQITGGKGSKRG-DIGIFVAGVEEGGSADRDGRLKKGDELLMINGQSLIGLSHQEAVAILRS 76

PDZ domain 2 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Dlg1, human Dlg1,2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197 or SAP-97), Dlg2 (also known as channel-associated protein of synapse-110, postsynaptic density protein 93, or PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95, synapse-associated protein 90, or SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling. It regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord, and it also interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467207 [Multi-domain] Cd Length: 85 Bit Score: 46.49 E-value: 3.55e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06724    27 DNGIYVTKIIEGGAAQKDGRLQVGDKLLAVNDVSLEEVTHEEAVAALKNTSDVVYL 82

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 51.89 E-value: 3.78e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   141 QVNEKVENLSIQLRLMTRERNELRKRLAFATHgtafdkrpyHRLNPDYERLKIQCVRAMSDLqsLQNQHTNALKRCEEVA 220
Cdd:TIGR00618  304 QIEQQAQRIHTELQSKMRSRAKLLMKRAAHVK---------QQSSIEEQRRLLQTLHSQEIH--IRDAHEVATSIREISC 372

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   221 KETDFYHTLHSrLLSDQTRLKD-------DVDMLRRENGQ---LLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQVL 290
Cdd:TIGR00618  373 QQHTLTQHIHT-LQQQKTTLTQklqslckELDILQREQATidtRTSAFRDLQGQLAHAKKQQELQQRYAELCAAAITCTA 451

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   291 KHNGSSEILNKLYDTAMDKLEVVKKDYDALRKRYSEKVAIHNADLSRLEqlgeENQRLLKQTEMLTQQRDTAI------- 363
Cdd:TIGR00618  452 QCEKLEKIHLQESAQSLKEREQQLQTKEQIHLQETRKKAVVLARLLELQ----EEPCPLCGSCIHPNPARQDIdnpgplt 527

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   364 ----QLQHQCALSLRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSER 439
Cdd:TIGR00618  528 rrmqRGEQTYAQLETSEEDVYHQLTSERKQRASLKEQMQEIQQSFSILTQCDNRSKEDIPNLQNITVRLQDLTEKLSEAE 607

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   440 DQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVA 519
Cdd:TIGR00618  608 DMLACEQHALLRKLQPEQDLQDVRLHLQQCSQELALKLTALHALQLTLTQERVREHALSIRVLPKELLASRQLALQKMQS 687

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249   520 KCRRDWAFQErdkIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRE-LKELKEQMESQLEKEA 594
Cdd:TIGR00618  688 EKEQLTYWKE---MLAQCQTLLRELETHIEEYDREFNEIENASSSLGSDLAAREDALNQsLKELMHQARTVLKART 760

PDZ domain 2 of PDZ domain containing 2 (PDZD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains, and is expressed at exceptionally high levels in the pancreas and certain cancer tissues such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467239 [Multi-domain] Cd Length: 88 Bit Score: 46.58 E-value: 3.95e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249 1351 VKVQKGSEPLGISIvSGEKG------GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIG 1415
Cdd:cd06758     5 MHLLKEKGGLGIQI-TGGKGskrgdiGIFVAGVEEGGSADRDGrLKKGDELLMINGQSLIGLSHQEAVAILR 75

PDZ domain of neurabin-1 and neurabin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of neurabin-1 (also known as protein phosphatase 1 regulatory subunit 9A) and neurabin-2 (also known as spinophilin, and protein phosphatase 1 regulatory subunit 9B), and related domains. Neurabin-1 and neurabin-2 are neuronal scaffolding proteins that play important roles in the regulation of synaptic transmission through their ability to interact with and target protein phosphatase 1 (PP1) to dendritic spines where PP1 dephosphorylates and inactivates glutamate receptors. Neurabin-2 interacts with multiple other synaptic proteins, including synaptic signaling and scaffolding proteins (e.g., GluN1 and SAPAP3) and cytoskeletal proteins (e.g., neurofilament medium polypeptide, NF-M). Neurabin-1 and neurabin-2 also binds F-actin. Other binding partners of neurabin-1 include adenosine A1 receptor (A1R), SAD-1 kinase and 70 kDa ribosomal protein S6 kinase (p70-S6K). This PDZ domain is immediately C-terminal to the PP1 binding domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This neurabin-like PDZ domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467252 [Multi-domain] Cd Length: 90 Bit Score: 46.64 E-value: 4.09e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1351 VKVQKGSEPLGISIV-------SG-EKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06790     5 VELEKGSEGLGISIIgmgvgadAGlEKLGIFVKTVTEGGAAQRDGrIQVNDQIVEVDGISLVGVTQAFA 73

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440035 [Multi-domain] Cd Length: 274 Bit Score: 50.15 E-value: 4.26e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  702 INMVVRRRKSL--GGKV------VTPLHINLSGQKDSGISLENGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDN 771
Cdd:COG0265   159 INLAKRVVEQLieTGRVrrgwlgVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAG-LRPGDVILAVDGKPVTS 235

PDZ1 domain of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, and related domains. Gallus gallus STXBP4 isoform X1 contains 2 PDZ domains (PDZ1 and PDZ2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This STXBP4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467179 [Multi-domain] Cd Length: 88 Bit Score: 46.45 E-value: 4.28e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:cd06692    25 EFGIFIKRILPGGLAATDGRLKEGDLILEVNGESLQGVTNERAVSILRSASASNHMSLL 83

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 51.84 E-value: 4.38e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  333 ADLSRLEQLGEenqRLLKQTEMLTQQRDTAIQLQHQcALSLRRFEAIHHELNKATAQNKDLQWEMEL--LQSELTELRTT 410
Cdd:COG4913   235 DDLERAHEALE---DAREQIELLEPIRELAERYAAA-RERLAELEYLRAALRLWFAQRRLELLEAELeeLRAELARLEAE 310

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  411 QVKTAKESEKYREERDAVYSEYklimseRDQVISELDKLQTEVELAESKLKSStseKKAANEEMEALRQIKDTVTMDAgr 490
Cdd:COG4913   311 LERLEARLDALREELDELEAQI------RGNGGDRLEQLEREIERLERELEER---ERRRARLEALLAALGLPLPASA-- 379

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  491 anKEVEILRKQCKALCQELKEALQEADV----AKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEAL 562
Cdd:COG4913   380 --EEFAALRAEAAALLEALEEELEALEEalaeAEAALRDLRRELRELEAEIASLERRKSNIPARLLALRDALAEAL 453

PDZ domain 5 of inactivation no after potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ45 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467279 [Multi-domain] Cd Length: 80 Bit Score: 46.34 E-value: 4.40e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249  728 KDSGISL----ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLK 794
Cdd:cd23066    10 KELGLSLspneGIGCTIADLLPGGYAEIDGKLQKGDIITKFNGDALSGLPFQVCYALFKGANGKISLEVTR 80

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467249 [Multi-domain] Cd Length: 80 Bit Score: 46.28 E-value: 4.53e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  723 NLSGQKDsgislENGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06768    15 NLHAEKG-----RPGHFIREVDPGSPAERAG-LKDGDRLVEVNGENVEGESHEQVVEKIKASGNQVTL 76

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 51.84 E-value: 4.64e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  425 RDAVYSEYKLIMSERDQV---ISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTM--DAGRANKEVEILR 499
Cdd:COG4913   595 RRRIRSRYVLGFDNRAKLaalEAELAELEEELAEAEERLEALEAELDALQERREALQRLAEYSWDeiDVASAEREIAELE 674

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  500 KQ----------CKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTR 569
Cdd:COG4913   675 AElerldassddLAALEEQLEELEAELEELEEELDELKGEIGRLEKELEQAEEELDELQDRLEAAEDLARLELRALLEER 754

                         170       180
                  ....*....|....*....|....*.
gi 767964249  570 KQKNDVSRELKELKEQMESQLEKEAR 595
Cdd:COG4913   755 FAAALGDAVERELRENLEERIDALRA 780

PDZ domain 4 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467185 [Multi-domain] Cd Length: 98 Bit Score: 46.45 E-value: 5.45e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1349 RHVKVQKG-SEPLGISIVSGEKG-----------GIYVSKVT-VGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIG 1415
Cdd:cd06701     5 QELTIVKEpGEKLGISIRGGAKGhagnpldptdeGIFISKINpDGAAARDGRLKVGQRILEVNGQSLLGATHQEAVRILR 84


                  ....*....
gi 767964249 1416 QQCDTITIL 1424
Cdd:cd06701    85 SVGDTLTLL 93

PDZ domain 4 of PDZ domain containing 2 (PDZD2), PDZ domain 2 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the second PDZ domain (PDZ2) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467241 [Multi-domain] Cd Length: 90 Bit Score: 46.11 E-value: 5.62e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249 1350 HVKVQKgsEP---LGISIVS----GEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQ 1416
Cdd:cd06760     6 EVTLNK--EPgvgLGIGLCClpleNDIPGIFIHHLSPGSVAHMDGrLRRGDQILEINGTSLRNVTLNEAYAILSQ 78

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

Pssm-ID: 129694 [Multi-domain] Cd Length: 1311 Bit Score: 51.59 E-value: 5.64e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   196 VRAMSDLQSLQNQHTNALKRCEEVAK--ETDFYHTLHSR--LLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRL 271
Cdd:TIGR00606  185 IKALETLRQVRQTQGQKVQEHQMELKylKQYKEKACEIRdqITSKEAQLESSREIVKSYENELDPLKNRLKEIEHNLSKI 264

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   272 HEEDQkEIGDLRAQQQQVLKHNGS-SEILNKLYDTAMDKLEVVKKDYDALRKRYSEKVAihnaDLSR-LEQLGEENQRL- 348
Cdd:TIGR00606  265 MKLDN-EIKALKSRKKQMEKDNSElELKMEKVFQGTDEQLNDLYHNHQRTVREKERELV----DCQReLEKLNKERRLLn 339

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   349 LKQTEMLTQQRDTAIQLQ-HQCAL----SLRRFEAIHHELN---------------------------KATAQN-KDLQW 395
Cdd:TIGR00606  340 QEKTELLVEQGRLQLQADrHQEHIrardSLIQSLATRLELDgfergpfserqiknfhtlvierqedeaKTAAQLcADLQS 419

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   396 EMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDK-LQTEVELAESKLKSSTSEKKAANE-- 472
Cdd:TIGR00606  420 KERLKQEQADEIRDEKKGLGRTIELKKEILEKKQEELKFVIKELQQLEGSSDRiLELDQELRKAERELSKAEKNSLTEtl 499

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   473 --EMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDWAFQERDKIVAE------RDSIRTLC 544
Cdd:TIGR00606  500 kkEVKSLQNEKADLDRKLRKLDQEMEQLNHHTTTRTQMEMLTKDKMDKDEQIRKIKSRHSDELTSLlgyfpnKKQLEDWL 579

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*...
gi 767964249   545 DNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEK 592
Cdd:TIGR00606  580 HSKSKEINQTRDRLAKLNKELASLEQNKNHINNELESKEEQLSSYEDK 627

PDZ domain 4 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)] and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467182 [Multi-domain] Cd Length: 85 Bit Score: 46.15 E-value: 5.69e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249  733 SLENGVYAAAVLPgSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLKV 795
Cdd:cd06696    24 KDDNGCYIHDIVQ-DPAKSDGRLRPGDRLIMVNGVDVTNMSHTEAVSLLRAAPKEVTLVLGRA 85

PDZ domain 13 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 13 of MUPP1. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ13 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ13 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467164 [Multi-domain] Cd Length: 83 Bit Score: 45.79 E-value: 5.71e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1351 VKVQKGSEPLGISIVSGEKGG-----IYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITI 1423
Cdd:cd06676     2 ITLERGSDGLGFSIVGGFGSPhgdlpIYVKTVFEKGAAAEDGrLKRGDQILAVNGESLEGVTHEEAVNILKKTKGTVTL 80

PDZ domain; PDZ domains are found in diverse signaling proteins.

Pssm-ID: 395476 [Multi-domain] Cd Length: 81 Bit Score: 45.73 E-value: 5.99e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  1501 RVVFIKKSQLELGVHLCGGN---LHGVFVAEVEDDSPAKGpDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRDGVRLK 1577
Cdd:pfam00595    1 QVTLEKDGRGGLGFSLKGGSdqgDPGIFVSEVLPGGAAEA-GGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLT 79


                   ..
gi 767964249  1578 VQ 1579
Cdd:pfam00595   80 IL 81

PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F (RhoGAP100F), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Par6 (also known as PAR6 or Par-6), RhoGAP100F, and related domains. Par6 is part of a conserved machinery that directs metazoan cell polarity, a process necessary for the function of diverse cell types. Par6 forms a cell polarity-regulatory complex with atypical protein kinase C (aPKC) and Par3. Par6 can also directly associate with PALS1 (proteins associated with Lin7, also known as Stardust) providing a link between the Par3/aPKC/Par6 complex and the PALS1-PATJ (protein-associated TJ) complex. Binding partners of the Par6-PDZ domain include Par3, PALS1/Stardust; leucine-rich repeat-containing protein netrin-G ligand-2 (NGL-2), human crumbs (CRB3) involve in the morphogenesis of the tight junctions in mammalian epithelial cells, and PAR-6 co-operates with the Par6 semi-CRIB domain to bind CDC42. CDC42 regulates the Par6 PDZ domain through an allosteric CRIB-PDZ transition. Drosophila RhoGAP100F, also known as synapse defective protein 1 homolog (syd-1 homolog), is a GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound form. The RhoGAP100F-PDZ domain binds the neurexin C terminus to control synapse formation at the Drosophila neuromuscular junction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par6-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467202 [Multi-domain] Cd Length: 84 Bit Score: 46.02 E-value: 6.04e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1349 RHVKVQK-GSEPLGISIVSG---EKG-GIYVSKVTVGSIAHQAGLEY-GDQLLEFNGI 1400
Cdd:cd06718     1 RRVELIKpPGKPLGFYIRDGngvERVpGIFISRLVLGSLADSTGLLAvGDEILEVNGV 58

PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila Dlg1, human Dlg1, 2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197; SAP-97), Dlg2 (also known as channel-associated protein of synapse-110; postsynaptic density protein 93, PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95; synapse-associated protein 90, SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling, regulating surface expression of NMDA receptors in dorsal horn neurons of the spinal cord; it interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. The Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development; postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467257 [Multi-domain] Cd Length: 91 Bit Score: 46.19 E-value: 6.05e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  635 LGFDMAEGVNEPcfpgdcGIFVTKVDKGSIAD--GRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRRR 709
Cdd:cd06795    14 LGFNIVGGEDGE------GIFISFILAGGPADlsGELRRGDQILSVNGVDLRNATHEQAAAALKNAGQTVTIIAQYK 84

PDZ domain of caspase recruitment domain-containing protein 11 (CARD11), CARD14, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CARD11, CARD14, and related domains. CARD11 (also known as CARD-containing MAGUK protein 1, CARMA1, Bimp3) and CARD14 (also known as CARD-containing MAGUK protein 2, CARMA2, Bimp2) belong to the CARD-containing membrane-associated guanylate kinase (MAGUK) protein family. They play several crucial biological functions, including regulation of immune response and inflammation. The CARD11-Bcl10-MALT1 (CBM) complex bridges T cell receptor signaling to the canonical IkappaB kinase (IKK)/NF-kappaB pathway. CARD14 can form an analogous biochemical complex to activate NF-kappaB during specialized immunity. The CBM complex of CARD14/CARMA2 may bind with TRAF6 and get involved in IL-17 pathways in keratinocytes. The preponderance of protein interactions occurs through the N-terminal half of CARD11 that includes the CARD, LATCH, and coiled-coil domains; the C-terminal PDZ-SH3-MAGUK region binds the adhesion and degranulation-promoting adapter protein (ADAP) and aryl hydrocarbon receptor interacting protein (AIP). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This CARD11 and CARD14-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467218 [Multi-domain] Cd Length: 75 Bit Score: 45.33 E-value: 6.74e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249 1361 GISIVSGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNG--------INLRSATEQQARLIIGQ 1416
Cdd:cd06736    12 QITIIGGNRTGIFIHSVQPGSAAEKAGLREGTQLLLLEGcirgerqsVSLEDCTKEEAHWTLQR 75

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 50.29 E-value: 7.32e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  437 SERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEalrqikdtvtmdagRANKEVEILRKQCKALCQELKEALQEA 516
Cdd:COG4372    31 EQLRKALFELDKLQEELEQLREELEQAREELEQLEEELE--------------QARSELEQLEEELEELNEQLQAAQAEL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  517 DVAKcrrdwafQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARF 596
Cdd:COG4372    97 AQAQ-------EELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAAL 169


                  ..
gi 767964249  597 RQ 598
Cdd:COG4372   170 EQ 171

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 50.54 E-value: 8.62e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  140 QQVNEKVENLSIQLRLMTRERNELRKRLAFATHGTAFD--KRPYHRLNPDYERLKIQC---VRAMSDLQSLQNQHTNALK 214
Cdd:COG4717    98 EELEEELEELEAELEELREELEKLEKLLQLLPLYQELEalEAELAELPERLEELEERLeelRELEEELEELEAELAELQE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  215 RCEEVAKETDFyhtlhsRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRlhEEDQKEIGDLRAQQQQVLKHNG 294
Cdd:COG4717   178 ELEELLEQLSL------ATEEELQDLAEELEELQQRLAELEEELEEAQEELEELEE--ELEQLENELEAAALEERLKEAR 249

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  295 SSEIlnklydtAMDKLEVVKKDYDALrkrYSEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQCALSLR 374
Cdd:COG4717   250 LLLL-------IAAALLALLGLGGSL---LSLILTIAGVLFLVLGLLALLFLLLAREKASLGKEAEELQALPALEELEEE 319

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  375 RFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKES--EKYREERDAVYSEYKliMSERDQVISELDKLQTE 452
Cdd:COG4717   320 ELEELLAALGLPPDLSPEELLELLDRIEELQELLREAEELEEELqlEELEQEIAALLAEAG--VEDEEELRAALEQAEEY 397

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  453 VELAEsKLKSSTSEKKAANEEMEALRQI--KDTVTMDAGRANKEVEILRKQCKALCQELK----------------EALQ 514
Cdd:COG4717   398 QELKE-ELEELEEQLEELLGELEELLEAldEEELEEELEELEEELEELEEELEELREELAeleaeleqleedgelaELLQ 476

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*...
gi 767964249  515 EADVAKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEAL 562
Cdd:COG4717   477 ELEELKAELRELAEEWAALKLALELLEEAREEYREERLPPVLERASEY 524

PDZ domain 12 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 10 of protein-associated tight junction (PATJ, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 12 of MUPP1, PDZ domain 10 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like PDZ12 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467163 [Multi-domain] Cd Length: 86 Bit Score: 45.43 E-value: 8.62e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  620 VVEFERETEDidlkALGFDMAEGVNEPCfpGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd06675     2 TVEIKRGPQD----SLGISIAGGVGSPL--GDVPVFIAMIQPNGVAaqTGKLKVGDRIVSINGQSTDGLTHSEAVNLLKN 75


                  ....*....
gi 767964249  698 GEGAINMVV 706
Cdd:cd06675    76 ASGTIILQV 84

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 49.90 E-value: 8.64e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  336 SRLEQLGEENQRLLKQTEMLTQQRDTAiqlqhqcalsLRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTA 415
Cdd:COG4372    31 EQLRKALFELDKLQEELEQLREELEQA----------REELEQLEEELEQARSELEQLEEELEELNEQLQAAQAELAQAQ 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  416 KESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQikdtvTMDAGRANKEV 495
Cdd:COG4372   101 EELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQE-----ELAALEQELQA 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  496 EILRKQCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDV 575
Cdd:COG4372   176 LSEAEAEQALDELLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEV 255

                         250
                  ....*....|.
gi 767964249  576 SRELKELKEQM 586
Cdd:COG4372   256 ILKEIEELELA 266

PDZ domain 1 of inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ4,5 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467276 [Multi-domain] Cd Length: 87 Bit Score: 45.58 E-value: 8.80e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 767964249  728 KDSGISLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKS 773
Cdd:cd23063    22 KVSPNTKTTGIFIKGIIPDSPAHKCGRLKVGDRILSVNGNDVRNST 67

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 49.52 E-value: 9.02e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  389 QNKDLQWEMELLQSELTELRttqvktaKESEKYREERDAVYSEYKLIMSERDQVISELDKLQtevelaeSKLKSSTSEKK 468
Cdd:COG1340     2 KTDELSSSLEELEEKIEELR-------EEIEELKEKRDELNEELKELAEKRDELNAQVKELR-------EEAQELREKRD 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  469 AANEEMEALRQIKDTVtmdagraNKEVEILRKQCKALCQELKEA-LQEADVAKCRRD-----WAFQERDkivaerdsirt 542
Cdd:COG1340    68 ELNEKVKELKEERDEL-------NEKLNELREELDELRKELAELnKAGGSIDKLRKEierleWRQQTEV----------- 129

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249  543 lcdnLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMA 601
Cdd:COG1340   130 ----LSPEEEKELVEKIKELEKELEKAKKALEKNEKLKELRAELKELRKEAEEIHKKIK 184

PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467186 [Multi-domain] Cd Length: 89 Bit Score: 45.33 E-value: 9.93e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1502 VVFIKKSQLELGVHLCGGNLH----------GVFVAEVEDDSPAkGPDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPR 1571
Cdd:cd06702     2 EIHLVKAGGPLGLSIVGGSDHsshpfgvdepGIFISKVIPDGAA-AKSGLRIGDRILSVNGKDLRHATHQEAVSALLSPG 80


                  ....*...
gi 767964249 1572 DGVRLKVQ 1579
Cdd:cd06702    81 QEIKLLVR 88

PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange factor 6, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Rap guanine nucleotide exchange factor 2 (RapGEF2, also named RA-GEF-1, PDZ-GEF1, CNrasGEF and nRapGEP) and Rap guanine nucleotide exchange factor 6 (RapGEF6, also named RA-GEF-2 and PDZ-GEF2). RapGEF2 and RapGEF6 constitute a subfamily of guanine nucleotide exchange factors (GEFs) for RAP small GTPases that is characterized by the possession of the PDZ and Ras/Rap-associating domains. They activate Rap small GTPases, by catalyzing the release of GDP from the inactive GDP-bound forms, thereby accelerating GTP loading to yield the active GTP-bound forms. The PDZ domain of RapGEF6 (also known as PDZ-GEF2) binds junctional adhesion molecule A (JAM-A). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RapGEF2 and RapGEF6 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467237 [Multi-domain] Cd Length: 83 Bit Score: 45.33 E-value: 1.02e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  717 VTPLHINLSGQKDSGIslenGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRS 783
Cdd:cd06755    11 ESPLHFSLLGGSEKGF----GIFVSKVEKGSKAAEAG-LKRGDQILEVNGQNFENITLKKALEILRN 72

PDZ domain of membrane palmitoylated protein 5 (MPP5), Drosophila Stardust, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP5, Drosophila Stardust, and related domains. MPP5 (also known as MAGUK p55 subfamily member 1, protein associated with Lin-7 1 or PALS1) and Drosophila Stardust are membrane-associated guanylate kinase (MAGUK)-like proteins that serve as signaling and scaffolding proteins, linking different proteins critical to the formation and maintenance of tight junctions (TJ) and apical-basal polarity. Apical-basal polarity determinants cluster in complexes; in particular, the Crumbs complex (Crb, MPP5, and PATJ) and the PAR/aPKC-complex (PAR-3, PAR-6, aPKC) determine the apical plasma membrane domain. Within the Crumbs complex, Crb is stabilized in the plasma membrane by MPP5, which in turn recruits PATJ and Lin-7 to the complex. MPP5 also links the Crumbs complex with the PAR/aPKC-complex. The Drosophila homolog of the Crumbs complex is the (CRB)-Stardust (Sdt)-Discs Lost (Dlt) complex. MPP5 also acts as an interaction partner for SARS-CoV envelope protein E, which results in delayed formation of TJs and dysregulation of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP5-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467259 [Multi-domain] Cd Length: 79 Bit Score: 45.03 E-value: 1.12e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1349 RHVKVQKGSEPLGiSIVSGEKGGIYVSKVTVGSIAHQAGLEY-GDQLLEFNGINLRSATEQQARLIIGQQCDTITIL 1424
Cdd:cd06798     1 KIVRIEKTREPLG-ATVRNEGDSVIISRIVKGGAAEKSGLLHeGDEILEINGIEIRGKDVNEVCDLLADMHGTLTFL 76

PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467220 [Multi-domain] Cd Length: 82 Bit Score: 45.00 E-value: 1.16e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  722 INLSGQKDSGISLEN------GVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQdSLTLSLL 793
Cdd:cd06738     7 ISLVGTRGLGCSISSgptqkpGIFISNVKPGSLAEEVG-LEVGDQIVEVNGTSFTNVDHKEAVMALKSSR-HLTITVR 82

PDZ domain 2 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467166 [Multi-domain] Cd Length: 82 Bit Score: 44.93 E-value: 1.18e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  719 PLHINLSGQKDsgislENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQD 786
Cdd:cd06678    12 QLGIKLVRKKD-----EPGVFILDLLEGGLAARDGRLKSDDRVLAINGQDLRHGTPEQAAQIIQASGE 74

PDZ domain 2 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP, Drosophila Bazooka) and related domains. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par3 and the Par complex include Par3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467271 [Multi-domain] Cd Length: 93 Bit Score: 45.33 E-value: 1.22e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1349 RHVKVQKGSEPLGISIVS-----GEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd23058     6 LHIQLKKGPEGLGFSITSrdnptGGSGPIYIKNILPKGAAIQDGrLKAGDRLLEVNGVDVTGKTQEEV 73

PDZ domain 4 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467185 [Multi-domain] Cd Length: 98 Bit Score: 45.29 E-value: 1.31e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767964249  737 GVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06701    39 GIFISKINPDGAAARDGRLKVGQRILEVNGQSLLGATHQEAVRILRSVGDTLTL 92

PDZ domain;

Pssm-ID: 433015 [Multi-domain] Cd Length: 74 Bit Score: 44.57 E-value: 1.40e-05

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249   732 ISLENGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALdnKSLNECESLLRSC--QDSLTLSLL 793
Cdd:pfam13180    2 VDLEGGVVVVSVKSSGPAAKAG-LKAGDVILSIDGRKI--NDLTDLESALYGHkpGDTVTLQVY 62

PDZ domain 1 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This delphilin-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467225 [Multi-domain] Cd Length: 76 Bit Score: 44.58 E-value: 1.47e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249 1358 EPLGISIvsGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRS-ATEQQARLiiGQQCDTI 1421
Cdd:cd06743     9 EAFGFSI--GGSGPCYILSVEEGSSAHAAGLQPGDQILELDGQDVSSlSCEAIIAL--ARRCPSV 69

DNA double-strand break repair ATPase Rad50;

Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 50.06 E-value: 1.47e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  391 KDLQWEMELLQSELTelRTTQVKTA-KESEKYREErdaVYSEYKLIMSERDQVISELDKLQTEV--------ELAESKLK 461
Cdd:PRK03918  172 KEIKRRIERLEKFIK--RTENIEELiKEKEKELEE---VLREINEISSELPELREELEKLEKEVkeleelkeEIEELEKE 246

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  462 SSTSEKKAANEEmEALRQIKDTVTmdagRANKEVEILRKQCKALcQELKEALQEADVAKcrrdwafQERDKIVAERDSIR 541
Cdd:PRK03918  247 LESLEGSKRKLE-EKIRELEERIE----ELKKEIEELEEKVKEL-KELKEKAEEYIKLS-------EFYEEYLDELREIE 313

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  542 TLCDNLRRER---DRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMAHSSHDSAIDTDSMEWET 618
Cdd:PRK03918  314 KRLSRLEEEIngiEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTPEKLEKEL 393

                         250
                  ....*....|....*
gi 767964249  619 EVVEFERE--TEDID 631
Cdd:PRK03918  394 EELEKAKEeiEEEIS 408

PDZ domain 3 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467172 [Multi-domain] Cd Length: 87 Bit Score: 44.94 E-value: 1.61e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  731 GISL-------ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRS 783
Cdd:cd06684    16 GITLststhrnKQVIVIDSIKPASIADRCGALHVGDHILSIDGTSVEHCSLAEATQLLAS 75

PDZ domain 3 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467248 [Multi-domain] Cd Length: 82 Bit Score: 44.62 E-value: 1.62e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249  726 GQKDSGISLE----NGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06767    11 GSEPLGISIVsgenGGIFVSSVTEGSLAHQAG-LEYGDQLLEVNGINLRNATEQQAALILRQCGDTITM 78

PDZ domain 4 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467185 [Multi-domain] Cd Length: 98 Bit Score: 44.91 E-value: 1.74e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  635 LGFDMAEGVNE----PCFPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVV 706
Cdd:cd06701    17 LGISIRGGAKGhagnPLDPTDEGIFISKINPDGAAarDGRLKVGQRILEVNGQSLLGATHQEAVRILRSVGDTLTLLV 94

PDZ domain 6 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467171 [Multi-domain] Cd Length: 85 Bit Score: 44.60 E-value: 1.83e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249 1351 VKVQKGSEPLGISIVSGEKGG--IYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITI 1423
Cdd:cd06683     6 VELKRYGGPLGITISGTEEPFdpIVISGLTEGGLAERTGaIHVGDRILAINGESLRGKPLSEAIHLLQNAGDTVTL 81

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 49.53 E-value: 1.86e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  221 KETDFYHTLHSRLLSDQTRLK-DDVDMLRRENGQLLRERnLLQQSwedmKRLHEEDqkeiGDLRAQQQQVLkhnGSSeil 299
Cdd:COG4913   543 KPHPFRAWLEAELGRRFDYVCvDSPEELRRHPRAITRAG-QVKGN----GTRHEKD----DRRRIRSRYVL---GFD--- 607

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  300 nklydtAMDKLEVVKKDYDALRkrysEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQhQCALSLRRFEAi 379
Cdd:COG4913   608 ------NRAKLAALEAELAELE----EELAEAEERLEALEAELDALQERREALQRLAEYSWDEIDVA-SAEREIAELEA- 675

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  380 hhELNKATAQNKDLqwemELLQSELTELRttqvktaKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESK 459
Cdd:COG4913   676 --ELERLDASSDDL----AALEEQLEELE-------AELEELEEELDELKGEIGRLEKELEQAEEELDELQDRLEAAEDL 742

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  460 LKSSTS---EKKAANEEMEAL-----RQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDWAFQERD 531
Cdd:COG4913   743 ARLELRallEERFAAALGDAVerelrENLEERIDALRARLNRAEEELERAMRAFNREWPAETADLDADLESLPEYLALLD 822

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  532 KIVAER-----------------DSIRTLCDNLRRERDRAVSELAE---ALRSLD---DTRKQ---KNDVSRELKELKEQ 585
Cdd:COG4913   823 RLEEDGlpeyeerfkellnensiEFVADLLSKLRRAIREIKERIDPlndSLKRIPfgpGRYLRleaRPRPDPEVREFRQE 902

                         410       420
                  ....*....|....*....|....*
gi 767964249  586 M---------ESQLEKEARFRQLMA 601
Cdd:COG4913   903 LravtsgaslFDEELSEARFAALKR 927

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 49.75 E-value: 1.93e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  266 EDMKRLHEEDQKEIGDLRAQQQQVLKhngSSEILNKLYDTAMDKLEVVKKDYDALRKRYSEkvAIHNADlsRLEQLGEEN 345
Cdd:PTZ00121 1318 DEAKKKAEEAKKKADAAKKKAEEAKK---AAEAAKAEAEAAADEAEAAEEKAEAAEKKKEE--AKKKAD--AAKKKAEEK 1390

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  346 QRLLKQTEMLTQQRDTAIQLQHQCALSLRRFEAIH--HELNKATAQNKDLQwemELLQSELTELRTTQVKTAKESEKYRE 423
Cdd:PTZ00121 1391 KKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKkaEEKKKADEAKKKAE---EAKKADEAKKKAEEAKKAEEAKKKAE 1467

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  424 E-RDAVYSEYKlimSERDQVISELDKLQTEVELAESKLKSSTSEKKAANE--------EMEALRQIKDTVTMDAGRANKE 494
Cdd:PTZ00121 1468 EaKKADEAKKK---AEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEakkaeeakKADEAKKAEEAKKADEAKKAEE 1544

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  495 VEILRKQCKAlcQELKEALQEADVAKCRRDwafQERDKIVAERDSIRTLCDNLRRERDRAVSEL-----AEALRSLDDTR 569
Cdd:PTZ00121 1545 KKKADELKKA--EELKKAEEKKKAEEAKKA---EEDKNMALRKAEEAKKAEEARIEEVMKLYEEekkmkAEEAKKAEEAK 1619

                         330       340
                  ....*....|....*....|....*...
gi 767964249  570 KQKNDVSRELKELK--EQMESQLEKEAR 595
Cdd:PTZ00121 1620 IKAEELKKAEEEKKkvEQLKKKEAEEKK 1647

septation ring formation regulator EzrA; Provisional

Pssm-ID: 179877 [Multi-domain] Cd Length: 569 Bit Score: 49.45 E-value: 2.00e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  199 MSDLQSLQNQHTNALK-----RCEEVAKE--------TDFYHTL------HSRLLSDQTRLKDDVDMLRRENGQLLRERN 259
Cdd:PRK04778  255 EKEIQDLKEQIDENLAlleelDLDEAEEKneeiqeriDQLYDILerevkaRKYVEKNSDTLPDFLEHAKEQNKELKEEID 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  260 LLQQSWEdmkrLHEED-------QKEIGDLRAQQQQVLK--HNGS---SEILNKLyDTAMDKLEVVKKDYD-------AL 320
Cdd:PRK04778  335 RVKQSYT----LNESElesvrqlEKQLESLEKQYDEITEriAEQEiaySELQEEL-EEILKQLEEIEKEQEklsemlqGL 409

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  321 RKrySEKVAihNADLSRLEQLGEENQRLLKQ----------TEMLTQQRDTAIQLQHQcaLSLRRF--EAIHHELNKATA 388
Cdd:PRK04778  410 RK--DELEA--REKLERYRNKLHEIKRYLEKsnlpglpedyLEMFFEVSDEIEALAEE--LEEKPInmEAVNRLLEEATE 483

                         250       260
                  ....*....|....*....|.
gi 767964249  389 QNKDLQWEMELL--QSELTEL 407
Cdd:PRK04778  484 DVETLEEETEELveNATLTEQ 504

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.

Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 49.40 E-value: 2.08e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   232 RLLSDQTRLKD-DVDMLRRENGQLLRERN--LLQ-----QSWEDMKRLHEEDQKEI-GDLRAQQQQvlkhNGSSEILNKL 302
Cdd:pfam01576  334 KALEEETRSHEaQLQEMRQKHTQALEELTeqLEQakrnkANLEKAKQALESENAELqAELRTLQQA----KQDSEHKRKK 409

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   303 YDTAMDKLEVVKKDYDALRKRYSEKVAIHNADL----SRLEQLGEENQRLLKQTEMLTQQ-RDTAIQLQhqcalslrrfE 377
Cdd:pfam01576  410 LEGQLQELQARLSESERQRAELAEKLSKLQSELesvsSLLNEAEGKNIKLSKDVSSLESQlQDTQELLQ----------E 479

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   378 AIHHELNKATaQNKDLQWEMELLQSELTElrttQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELD----KLQTEV 453
Cdd:pfam01576  480 ETRQKLNLST-RLRQLEDERNSLQEQLEE----EEEAKRNVERQLSTLQAQLSDMKKKLEEDAGTLEALEegkkRLQREL 554

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   454 ELAESKLKsstsEKKAANEEMEA----LRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEalQEADVAKcrrdwAFQE 529
Cdd:pfam01576  555 EALTQQLE----EKAAAYDKLEKtknrLQQELDDLLVDLDHQRQLVSNLEKKQKKFDQMLAE--EKAISAR-----YAEE 623

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   530 RDKivAERDSirtlcdnlrRERDRAVSELAealRSLDDTRKQKNDVSRELKELKEQMES-------------QLEKEARf 596
Cdd:pfam01576  624 RDR--AEAEA---------REKETRALSLA---RALEEALEAKEELERTNKQLRAEMEDlvsskddvgknvhELERSKR- 688

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|
gi 767964249   597 rqlmahsshdsAIDTDSMEWETEVVEFERE---TEDIDLK 633
Cdd:pfam01576  689 -----------ALEQQVEEMKTQLEELEDElqaTEDAKLR 717

PDZ domain of segment polarity protein dishevelled homolog DVL1, DVL2, DVL3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of DVL1-3, and related domains. The dishevelleds (DVL1, 2 and 3 in humans) act downstream of Frizzled (FZD) receptors in both the canonical and non-canonical WNT signaling pathway; they bind the cytoplasmic C-terminus of frizzled family members and transduce the Wnt signal to down-stream effectors. They bind to several proteins known to modulate Wnt signaling. Binding partners of the DVL1 PDZ domain include nucleoredoxin (NXN), Van Gogh-like (VANGL1), Wnt receptor RYK, Dapper 1 (DACT1), Frizzled7 (FZD7), transmembrane protein 88 (TMEM88), Daple (dishevelled-associating protein with a high frequency of leucines), also known as Ccdc88c), and cysteine-rich protein Idax. The DVL2 PDZ domain has been shown to bind the nuclear export signal sequence of the DVL2 protein. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This DVL-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467201 [Multi-domain] Cd Length: 87 Bit Score: 44.28 E-value: 2.26e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1359 PLGISIVS----GEKGGIYVSKVT-VGSIAHQAGLEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06717    11 FLGISIVGqsneRGDGGIYVGSIMkGGAVAADGRIEPGDMILQVNDISFENMSNDDA 67

PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2)and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467168 [Multi-domain] Cd Length: 89 Bit Score: 44.26 E-value: 2.31e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  738 VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLkvfpqssSWSG 804
Cdd:cd06680    30 FFVKSIVPGTPAYNDGRLKCGDIILAVNGVSTVGMSHAALVPLLKEQRGRVTLTVV-------SWPG 89

PDZ domain of Ras-associating and dilute domain-containing protein (Radil) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Radil (also known as protein KIAA1849) and related domains. Radil is required for cell adhesion and migration of neural crest precursors during development. Radil is a component of a Rasip1-Radil-ARHGAP29 complex at endothelial cell-cell junctions. Rap1, via its effectors Radil and Rasip1 and their binding partner ArhGAP29, controls the endothelial barrier by decreasing Rho-mediated radial tension on cell-cell junctions. ArhGAP29 binds the Radil PDZ domain. The Radil PDZ domain also binds kinesin family protein 14 (KIF14); KIF14 negatively regulates Rap1-mediated inside-out integrin activation by tethering Radil on microtubules. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Radil-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467177 [Multi-domain] Cd Length: 88 Bit Score: 44.59 E-value: 2.32e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1351 VKVQKGSEPLGISIVSGEK-----GGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06690     6 VELERGPKGLGLGLIDGLHtplrsPGIYIRTLVPDSPAARDGrLRLGDRILAVNGTSLVGADYQSAMDLI 75

PDZ domain of membrane palmitoylated proteins 3 (MPP3), MPP4, and MPP7, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP3, MPP4, and MPP7, and related domains. MPP3 (also known as MAGUK p55 subfamily member 3, erythrocyte membrane protein p55, or EMP55), MPP4 (also known as MAGUK p55 subfamily member 4 or Discs large homolog 6), and MPP7 (also known as MAGUK p55 subfamily member 7) are membrane-associated guanylate kinase (MAGUK)-like proteins. MPP3 is part of a cell adhesion protein complex including tumor suppressor CADM1 and actin-binding protein 4.1B. Participation in the Crumbs cell polarity complex has also been demonstrated for MPP7 in epithelial cells, and for MPP3 and MPP4 in the retina. MPP4 is needed for proper localization of plasma membrane calcium ATPases and maintenance of calcium homeostasis at the rod photoreceptor synaptic terminals. Binding partners of the MPP3 PDZ domain include nectin-3, serotonin 5-hydroxytryptamine, 5-HT(2C) receptor, and a cell adhesion protein, TSLC1 (tumor suppressor in lung cancer 1); fragments of MPP4 having the PDZ domain bind CRB (PDZ-SH3-GUK) and GABA transporter GAT1 (PDZ-SH3). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467260 [Multi-domain] Cd Length: 81 Bit Score: 44.16 E-value: 2.35e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  738 VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTlslLKVFP 797
Cdd:cd06799    25 IVVARIMRGGAADRSGLIHVGDELREVNGISVEGKDPEEVIQILANSQGPIT---FKLIP 81

PDZ domain 1 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZRN4-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467199 [Multi-domain] Cd Length: 92 Bit Score: 44.31 E-value: 2.54e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1351 VKVQKGSEPLGISIVSG------EKG----GIYVSKVT-VGSIAHQAGLEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06715     5 VVLHRENGSLGFNIIGGrpcennQEGssseGIYVSKIVeNGPAADEGGLQVHDRIIEVNGKDLSKATHEEA 75

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 48.97 E-value: 2.64e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   345 NQRLLKQTEMLTQQRDTaiqLQHQCALSLR----RFEAIHHElnkataqnkDLQWEMELLQSELTELRTTQvktakESEK 420
Cdd:pfam17380  261 NGQTMTENEFLNQLLHI---VQHQKAVSERqqqeKFEKMEQE---------RLRQEKEEKAREVERRRKLE-----EAEK 323

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   421 YR----EERDAVYSEYKLIMSERDQvisELDKLQTEvelaesklksstsEKKaanEEMEALRQIKDTVTMDAGRANKEVE 496
Cdd:pfam17380  324 ARqaemDRQAAIYAEQERMAMERER---ELERIRQE-------------ERK---RELERIRQEEIAMEISRMRELERLQ 384

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   497 ILRKQCKALCQELKEALQEADVAKCRRDWAFQERDKivaERDSIRTLCDNLRRERDRAVSElaEALRSLDDTRKQKNDVS 576
Cdd:pfam17380  385 MERQQKNERVRQELEAARKVKILEEERQRKIQQQKV---EMEQIRAEQEEARQREVRRLEE--ERAREMERVRLEEQERQ 459

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249   577 RELKELKEQMESQ------LEKEARFRQLmAHSSHDSAIDTDSMEWETEVVEFERE 626
Cdd:pfam17380  460 QQVERLRQQEEERkrkkleLEKEKRDRKR-AEEQRRKILEKELEERKQAMIEEERK 514

PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS12, and related domains. RGS12 downregulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. The RGS12 PDZ domain can bind selectively to C-terminal (A/S)-T-X-(L/V) motifs as found within both the CXCR2 IL-8 receptor, and the alternative 3' exon form of RGS12. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS12-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467194 [Multi-domain] Cd Length: 76 Bit Score: 43.78 E-value: 2.87e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249 1349 RHVKVQKGSEPLGISIvSGEKGGIyVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSAT-EQQARLI 1413
Cdd:cd06710     1 RTVEIARGRAGYGFTI-SGQAPCV-LSCVVRGSPADVAGLKAGDQILAVNGINVSKAShEDVVKLI 64

chromosome segregation protein; Provisional

Pssm-ID: 100796 [Multi-domain] Cd Length: 895 Bit Score: 49.13 E-value: 2.93e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  183 RLNPDYERLK--IQCVRA-MSDLQSLQNQHTNALKRCEEVAKETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERN 259
Cdd:PRK01156  163 SLERNYDKLKdvIDMLRAeISNIDYLEEKLKSSNLELENIKKQIADDEKSHSITLKEIERLSIEYNNAMDDYNNLKSALN 242

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  260 LLQqSWEDMKRLHEEDQKEI-GDLRAQQQQVLKHNGSSEILNKLYDTAMDKLEVVKKDYDALRKR---YSEKVAIHNADL 335
Cdd:PRK01156  243 ELS-SLEDMKNRYESEIKTAeSDLSMELEKNNYYKELEERHMKIINDPVYKNRNYINDYFKYKNDienKKQILSNIDAEI 321

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  336 SRLEQlgeenqrLLKQTEMLTQQRDTAIQLQhqcalslRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTA 415
Cdd:PRK01156  322 NKYHA-------IIKKLSVLQKDYNDYIKKK-------SRYDDLNNQILELEGYEMDYNSYLKSIESLKKKIEEYSKNIE 387

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  416 KESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEAL------------------ 477
Cdd:PRK01156  388 RMSAFISEILKIQEIDPDAIKKELNEINVKLQDISSKVSSLNQRIRALRENLDELSRNMEMLngqsvcpvcgttlgeeks 467

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  478 RQIKDTVTMDAGRANKEVEILRKQCKALCQE------LKEALQEADVAKCRRDWAFQE--RDKIVAERDSIRTLCD---- 545
Cdd:PRK01156  468 NHIINHYNEKKSRLEEKIREIEIEVKDIDEKivdlkkRKEYLESEEINKSINEYNKIEsaRADLEDIKIKINELKDkhdk 547

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  546 --------------NLRRERDRAVSELAE-ALRSLDDTRKQKNDVSRELKELKEQME 587
Cdd:PRK01156  548 yeeiknrykslkleDLDSKRTSWLNALAViSLIDIETNRSRSNEIKKQLNDLESRLQ 604

PDZ domain 5 of Danio rerio tyrosine-protein phosphatase non-receptor type 13 (Ptpn13) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of Danio rerio Ptpn13, and related domains. Protein-tyrosine phosphatases (PTPs) dephosphorylate phosphotyrosyl residues in proteins that are phosphorylated by protein tyrosine kinases (PTKs). Danio rerio Ptpn13 is a classical non-receptor-like PTP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467273 [Multi-domain] Cd Length: 80 Bit Score: 43.88 E-value: 2.94e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  635 LGFDMAEGvnepcfPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVV 706
Cdd:cd23060    12 LGFSLVGG------EGGSGIFVKSISPGGVAdrDGRLQVGDRLLQVNGESVIGLSHSKAVNILRKAKGTVQLTV 79

PDZ domain of Rab3-interacting molecule 1 (RIM), RIM2, piccolo and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RIM, RIM2, piccolo and related domains. RIM proteins and Gallus gallus protein piccolo (also called aczonin) are involved in neurotransmitter release at presynaptic active zones, the site of vesicle fusion. A protein complex containing RIM proteins positions synaptic vesicles containing synaptotagmin at the active zone. RIM proteins simultaneously activate docking and priming of synaptic vesicles and recruit Ca2+-channels to active zones, thereby connecting primed synaptic vesicles to Ca2+-channels. RIM binding to vesicular Rab proteins (Rab3 and Rab27 isoforms) mediates vesicle docking; RIM binding to Munc13 activates vesicle priming; RIM binding to the Ca2+-channel, both directly and indirectly via RIM-BP, recruits the Ca2+-channels. The RIM PDZ domain interacts with the C-termini of N- and P/Q-type voltage-gated Ca2+-channels. RIM1, RIM2 and piccolo also participate in regulated exocytosis through binding cAMP-GEFII (cAMP-binding protein-guanidine nucleotide exchange factor II). The piccolo PDZ domain binds cAMP-GEFII. RIM2 also plays a role in dendrite formation by melanocytes. Caenorhabditis elegans RIM (also known as unc-10) may be involved in the regulation of defecation and daumone response. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467198 [Multi-domain] Cd Length: 95 Bit Score: 44.47 E-value: 3.02e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 767964249  737 GVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNE-CESLLRSC 784
Cdd:cd06714    39 GAYVTKVKPGSVADTVGHLREGDEVLEWNGISLQGKTFEEvQDIISQSK 87

PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467285 [Multi-domain] Cd Length: 92 Bit Score: 44.40 E-value: 3.06e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249  726 GQKDSGiSLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd23072    21 GGEKSG-RLDLGIFISSITPGGPADLDGRLKPGDRLISVNDVSLEGLSHDAAVEILQNAPEDVTL 84

PDZ domain 1 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467176 [Multi-domain] Cd Length: 102 Bit Score: 44.54 E-value: 3.07e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1350 HVKVQKG-SEPLGISIV---SGEKG--GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSA-TEQQARLIIGQQCDTI 1421
Cdd:cd06689    17 YIELEKPeSGGLGFSVVglkSENRGelGIFVQEIQPGSVAARDGrLKENDQILAINGQPLDQSiSHQQAIAILQQAKGSV 96


                  ..
gi 767964249 1422 TI 1423
Cdd:cd06689    97 EL 98

PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F (RhoGAP100F), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Par6 (also known as PAR6 or Par-6), RhoGAP100F, and related domains. Par6 is part of a conserved machinery that directs metazoan cell polarity, a process necessary for the function of diverse cell types. Par6 forms a cell polarity-regulatory complex with atypical protein kinase C (aPKC) and Par3. Par6 can also directly associate with PALS1 (proteins associated with Lin7, also known as Stardust) providing a link between the Par3/aPKC/Par6 complex and the PALS1-PATJ (protein-associated TJ) complex. Binding partners of the Par6-PDZ domain include Par3, PALS1/Stardust; leucine-rich repeat-containing protein netrin-G ligand-2 (NGL-2), human crumbs (CRB3) involve in the morphogenesis of the tight junctions in mammalian epithelial cells, and PAR-6 co-operates with the Par6 semi-CRIB domain to bind CDC42. CDC42 regulates the Par6 PDZ domain through an allosteric CRIB-PDZ transition. Drosophila RhoGAP100F, also known as synapse defective protein 1 homolog (syd-1 homolog), is a GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound form. The RhoGAP100F-PDZ domain binds the neurexin C terminus to control synapse formation at the Drosophila neuromuscular junction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par6-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467202 [Multi-domain] Cd Length: 84 Bit Score: 43.71 E-value: 3.48e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767964249  731 GISLEN--GVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNE 776
Cdd:cd06718    20 GNGVERvpGIFISRLVLGSLADSTGLLAVGDEILEVNGVEVTGKSLDD 67

PDZ domain 6 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 6 of multi-PDZ-domain protein 1 (MUPP1). MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ6 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467158 [Multi-domain] Cd Length: 87 Bit Score: 43.78 E-value: 3.75e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1349 RHVKVQKGSEPLGISIVSGEKG-GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06670     5 RTITIVKGNSSLGITVSADKDGnGCIVKSIIHGGAVSRDGrISVGDFIVSINNESLRNVTNAQARAIL 72

PDZ domain 2 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which it is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This delphilin-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467226 [Multi-domain] Cd Length: 75 Bit Score: 43.42 E-value: 3.86e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  726 GQKDSGISL--ENGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06744     7 GNGSFGFTLrgHAPVYIESVDPGSAAERAG-LKPGDRILFLNGLDVRNCSHDKVVSLLQGSGSMPTL 72

PDZ domain 1 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467176 [Multi-domain] Cd Length: 102 Bit Score: 44.16 E-value: 4.03e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALD-NKSLNECESLLRSCQDSLTL 790
Cdd:cd06689    42 ELGIFVQEIQPGSVAARDGRLKENDQILAINGQPLDqSISHQQAIAILQQAKGSVEL 98

PDZ domain of sorting nexin-27 (SNX27), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SNX27, and related domains. SNX27 is involved in retrograde transport from endosome to plasma membrane. The PDZ domain of SNX27 links cargo identification to retromer-mediated transport. SNX27 binds to the retromer complex (vacuolar protein sorting 26(VPS26)-VPS29-VPS35), via its PDZ domain binding to VPS26. The SNX27 PDZ domain also binds to cargo including the G-protein-coupled receptors (GPCRs): beta2-adrenergic receptor (beta2AR), beta1AR, parathyroid hormone receptor (PTHR), alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), NMDA receptors, 5-hydroxytryptamine 4a receptors, frizzled receptors, and somatostatin receptor subtype 5 (SSTR5). Additional binding partners of the SNX27 PDZ domain include G protein-gated inwardly rectifying potassium (Kir3) channels, angiotensin-converting enzyme 2 (ACE2), and PTEN (phosphatase and tensin homolog deleted on chromosome 10); PTEN binding to SNX27 prevents SNX27's association with the retromer complex. SNX27 has been reported to be a host factor needed for efficient entry of an engineered SARS-CoV-2 variant, the spike protein of which contains a deletion at the S1/S2 subunit cleavage site; the PDZ domain of SNX27 binds angiotensin-converting enzyme 2 (ACE2), and may be involved in recycling ACE2 to the plasma membrane, thereby promoting viral entry. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SNX27-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467283 [Multi-domain] Cd Length: 93 Bit Score: 43.94 E-value: 4.04e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767964249 1373 YVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLII--GQQCDTITIL 1424
Cdd:cd23070    39 HVSAVLEGGAADKAGVRKGDRILEVNGVNVEGATHKQVVDLIksGGDELTLTVI 92

PDZ domain 2 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZRN4-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467200 [Multi-domain] Cd Length: 88 Bit Score: 43.80 E-value: 4.11e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIalDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06716    30 DTGIYVSEVDPNSIAAKDGRIREGDQILQINGV--DVQNREEAIALLSEEEKSITL 83

PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13),FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467180 [Multi-domain] Cd Length: 92 Bit Score: 43.92 E-value: 4.21e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  620 VVEFERETEdidlKALGFDMAEGVNEPCFpgDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd06694     4 IVTLKKDPQ----KGLGFTIVGGENSGSL--DLGIFVKSIIPGGPAdkDGRIKPGDRIIAINGQSLEGKTHHAAVEIIQN 77

                          90
                  ....*....|....
gi 767964249  698 GEGAINMVVRRRKS 711
Cdd:cd06694    78 APDKVELIISQPKS 91

PDZ domain; PDZ domains are found in diverse signaling proteins.

Pssm-ID: 395476 [Multi-domain] Cd Length: 81 Bit Score: 43.42 E-value: 4.24e-05

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249   635 LGFDMAEGVNEpcfpGDCGIFVTKVDKGSIAD-GRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVR 707
Cdd:pfam00595   12 LGFSLKGGSDQ----GDPGIFVSEVLPGGAAEaGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLTIL 81

PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467269 [Multi-domain] Cd Length: 84 Bit Score: 43.58 E-value: 4.41e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  653 GIFVTKVDKGSIAD-GRLRVNDWLLRINDVDLINKDKKQAIKaLLNGEGAINMVVRR 708
Cdd:cd10833    27 GIFVSKVEEGSAAErAGLCVGDKITEVNGVSLENITMSSAVK-VLTGSNRLRMVVRR 82

circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of HtrA family serine proteases including human HtrA1, HtrA2 (mitochondrial), HtrA3, and HtrA4, and related domains. These proteases are key enzymes associated with pregnancy. Their diverse biological functions include cell growth proliferation, migration and apoptosis. They are also implicated in disorders including Alzheimer's, Parkinson's, arthritis and cancer. HtrA1 (also known as high-temperature requirement A serine peptidase 1, L56, and serine protease 11) substrates include extracellular matrix proteins, proteoglycans, and insulin-like growth factor (IGF)-binding proteins. HtrA1 also inhibits signaling by members of the transforming growth factor beta (TGF-beta) family. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This HtrA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467624 [Multi-domain] Cd Length: 98 Bit Score: 44.03 E-value: 4.43e-05

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 767964249 1370 GGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATE 1407
Cdd:cd06785    31 SGVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKSSSD 68

PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467211 [Multi-domain] Cd Length: 82 Bit Score: 43.33 E-value: 4.48e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249  722 INLSGQKDSGIslengvYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:cd06729    15 LRLAGGNDVGI------FVAGVQEGSPAEKQG-LQEGDQILKVNGVDFRNLTREEAVLFLLDLPKGEEVTIL 79

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 47.45 E-value: 4.92e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  437 SERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEAL--------RQIKDT------VTMDAGRANKEVEILRKQC 502
Cdd:COG4942    20 DAAAEAEAELEQLQQEIAELEKELAALKKEEKALLKQLAALerriaalaRRIRALeqelaaLEAELAELEKEIAELRAEL 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  503 KALCQELKEALQEADVAKCRRDWAF-------------------------QERDKIVAERDSIRTLCDNLRRERDR---A 554
Cdd:COG4942   100 EAQKEELAELLRALYRLGRQPPLALllspedfldavrrlqylkylaparrEQAEELRADLAELAALRAELEAERAEleaL 179

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767964249  555 VSELAEALRSLDDTRKQKNDV----SRELKELKEQMESQLEKEARFRQLMA 601
Cdd:COG4942   180 LAELEEERAALEALKAERQKLlarlEKELAELAAELAELQQEAEELEALIA 230

Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 48.41 E-value: 5.13e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  152 QLRLMTRERNELRKRLAFAthgtAFDKRPYHRL----------------NPDYERLKIQCVRAMSDLQSLQNQHTNALKR 215
Cdd:COG3096   786 RLEELRAERDELAEQYAKA----SFDVQKLQRLhqafsqfvgghlavafAPDPEAELAALRQRRSELERELAQHRAQEQQ 861

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  216 CEEVAKETDFYHTLHSRLLSDQTRLKDD-----VDMLRRENGQLLRERNLLQQSWEDMKRLheEDQKEIgdLRAQQQQVl 290
Cdd:COG3096   862 LRQQLDQLKEQLQLLNKLLPQANLLADEtladrLEELREELDAAQEAQAFIQQHGKALAQL--EPLVAV--LQSDPEQF- 936

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  291 khngssEILNKLYDTAMDKLEVVKKDYDAL---RKR-----YSEKVAIHNADLSRLEQLgeeNQRLLKQTEMLTQQRDTA 362
Cdd:COG3096   937 ------EQLQADYLQAKEQQRRLKQQIFALsevVQRrphfsYEDAVGLLGENSDLNEKL---RARLEQAEEARREAREQL 1007

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  363 IQLQHQCALSLRRFEAIhhelnKATAQNKdlqweMELLQSELTELRTTQVKTAKESE-KYREERDAVYSEYKLIMSERDQ 441
Cdd:COG3096  1008 RQAQAQYSQYNQVLASL-----KSSRDAK-----QQTLQELEQELEELGVQADAEAEeRARIRRDELHEELSQNRSRRSQ 1077

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 767964249  442 VISELDKLQTEVELAESKLKSSTSEKKAANEEMEA 476
Cdd:COG3096  1078 LEKQLTRCEAEMDSLQKRLRKAERDYKQEREQVVQ 1112

Intermediate filament protein;

Pssm-ID: 459643 [Multi-domain] Cd Length: 313 Bit Score: 47.22 E-value: 5.24e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   388 AQNKDLQWEMELLQsELTELRTTQVKTAKESEkYREERDAVYSeyklIMSERDQVISELDKLQTEVELAESKLKSSTSEK 467
Cdd:pfam00038   25 QQNKLLETKISELR-QKKGAEPSRLYSLYEKE-IEDLRRQLDT----LTVERARLQLELDNLRLAAEDFRQKYEDELNLR 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   468 KAANEEMEALRQIKDTVTMdagraNKeVEiLRKQCKALCQELK--EALQEADVAKCRRDWAFQERdkiVAERDSIRTLcd 545
Cdd:pfam00038   99 TSAENDLVGLRKDLDEATL-----AR-VD-LEAKIESLKEELAflKKNHEEEVRELQAQVSDTQV---NVEMDAARKL-- 166

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 767964249   546 nlrrerdravsELAEALRsldDTRKQKND-VSRELKELKEQMESQLEK 592
Cdd:pfam00038  167 -----------DLTSALA---EIRAQYEEiAAKNREEAEEWYQSKLEE 200

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]

Pssm-ID: 273938 [Multi-domain] Cd Length: 428 Bit Score: 47.60 E-value: 5.44e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  1352 KVQKGSepLGISI--VSGEK---------GGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARliigqqcdt 1420
Cdd:TIGR02037  230 KVKRGW--LGVTIqeVTSDLakslglekqRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRA--------- 298

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  1421 itilaqynphVHQLsshsrssshldPAGTHSTLQgsgtttpehpsvidplMEQDEGPSTPPAK-QSSSRIAGDANKKTLE 1499
Cdd:TIGR02037  299 ----------IGTL-----------KPGKKVTLG----------------ILRKGKEKTITVTlGASPEEQASSSNPFLG 341

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  1500 PRVVFIKKSQLELGVHlcGGNLHGVFVAEVEDDSPAKGPdGLVPGDLILEYGSLDVRNktVEEVY--VEMLKPRDGVRLK 1577
Cdd:TIGR02037  342 LTVANLSPEIRKELRL--KGDVKGVVVTKVVSGSPAARA-GLQPGDVILSVNQQPVSS--VAELRkvLARAKKGGRVALL 416


                   ..
gi 767964249  1578 VQ 1579
Cdd:TIGR02037  417 IL 418

PDZ domain 1 of inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ4,5 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467276 [Multi-domain] Cd Length: 87 Bit Score: 43.27 E-value: 5.80e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249 1356 GSEPLGISIVSGE--------KGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd23063     8 EKKSFGICIVRGEvkvspntkTTGIFIKGIIPDSPAHKCGrLKVGDRILSVNGNDVRNSTEQAA 71

PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of TAX1BP3, and related domains. TAX1BP3 (also known as glutaminase-interacting protein 3, tax interaction protein 1, TIP-1, tax-interacting protein 1) may regulate a number of protein-protein interactions by competing for PDZ domain binding sites. TAX1BP3 binds beta-catenin and may act as an inhibitor of the Wnt signaling pathway. It competes with LIN7A (also known as Lin-7A or LIN-7A) for inward rectifier potassium channel 4 (KCNJ4) binding, and thereby promotes KCNJ4 internalization. It may play a role in the Rho signaling pathway, and in the activation of CDC42 by the viral protein HPV16 E6. Binding partners of the TAX1BP3 PDZ domain include beta-catenin, KCNJ4, glutaminase liver isoform (GLS2), rho guanine nucleotide exchange factor 16 (ARHGEF16), rhotekin, and CDK5 regulatory subunit-associated protein 3 (also known as LAPZ). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This TAX1BP3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467265 [Multi-domain] Cd Length: 94 Bit Score: 43.48 E-value: 5.82e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  635 LGFDMAEGVNE-----PCFPGDCGIFVTKVDKGSIAD-GRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRR 708
Cdd:cd10822    15 LGFSIGGGIDQdpsknPFSYTDKGIYVTRVSEGGPAEkAGLQVGDKILQVNGWDMTMVTHKQAVKRLTKKKPVLRMLVTR 94

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 48.04 E-value: 6.05e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   222 ETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQvlkhngSSEILNK 301
Cdd:TIGR00618  174 PLDQYTQLALMEFAKKKSLHGKAELLTLRSQLLTLCTPCMPDTYHERKQVLEKELKHLREALQQTQQ------SHAYLTQ 247

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   302 LYDTAMDKlevvkkdyDALRKRYSEKVAihnadlsRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQcalslrrfEAIHH 381
Cdd:TIGR00618  248 KREAQEEQ--------LKKQQLLKQLRA-------RIEELRAQEAVLEETQERINRARKAAPLAAHI--------KAVTQ 304

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   382 ELNKATAQNKDLQWEMELLQSELTElRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELaESKLK 461
Cdd:TIGR00618  305 IEQQAQRIHTELQSKMRSRAKLLMK-RAAHVKQQSSIEEQRRLLQTLHSQEIHIRDAHEVATSIREISCQQHTL-TQHIH 382

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   462 SSTSEKKAANEEMEALRQIKDTVTmdagrankeveilRKQCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDSIR 541
Cdd:TIGR00618  383 TLQQQKTTLTQKLQSLCKELDILQ-------------REQATIDTRTSAFRDLQGQLAHAKKQQELQQRYAELCAAAITC 449

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249   542 TLCDNLRRERdravsELAEALRSLddtrkqkndvsRELKELKEQMESQLEKEARFRQLMAH 602
Cdd:TIGR00618  450 TAQCEKLEKI-----HLQESAQSL-----------KEREQQLQTKEQIHLQETRKKAVVLA 494

PDZ domain of segment polarity protein dishevelled homolog DVL1, DVL2, DVL3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of DVL1-3, and related domains. The dishevelleds (DVL1, 2 and 3 in humans) act downstream of Frizzled (FZD) receptors in both the canonical and non-canonical WNT signaling pathway; they bind the cytoplasmic C-terminus of frizzled family members and transduce the Wnt signal to down-stream effectors. They bind to several proteins known to modulate Wnt signaling. Binding partners of the DVL1 PDZ domain include nucleoredoxin (NXN), Van Gogh-like (VANGL1), Wnt receptor RYK, Dapper 1 (DACT1), Frizzled7 (FZD7), transmembrane protein 88 (TMEM88), Daple (dishevelled-associating protein with a high frequency of leucines), also known as Ccdc88c), and cysteine-rich protein Idax. The DVL2 PDZ domain has been shown to bind the nuclear export signal sequence of the DVL2 protein. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This DVL-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467201 [Multi-domain] Cd Length: 87 Bit Score: 43.12 E-value: 6.07e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  717 VTPLHINLSGQKDSGisLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSC 784
Cdd:cd06717     9 VNFLGISIVGQSNER--GDGGIYVGSIMKGGAVAADGRIEPGDMILQVNDISFENMSNDDAVRVLREA 74

PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GOPC-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467261 [Multi-domain] Cd Length: 83 Bit Score: 43.13 E-value: 6.08e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1501 RVVFIKKSQLE-LGVHLCGGNLHGV--FVAEVEDDSPAKGPDGLVPGDLILEYGSLDVRNKTVEEVyVEMLKPRDG-VRL 1576
Cdd:cd06800     1 RKVLLSKEPHEgLGISITGGKEHGVpiLISEIHEGQPADRCGGLYVGDAILSVNGIDLRDAKHKEA-VTILSQQRGeITL 79


                  ....
gi 767964249 1577 KVQY 1580
Cdd:cd06800    80 EVVY 83

PDZ domain 2 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which it is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This delphilin-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467226 [Multi-domain] Cd Length: 75 Bit Score: 42.65 E-value: 6.13e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1502 VVFIKKSQLELGVHLCGgnlHG-VFVAEVEDDSPAKGPdGLVPGDLILEYGSLDVRNKTVEEVyVEMLK 1569
Cdd:cd06744     1 TVRVYRGNGSFGFTLRG---HApVYIESVDPGSAAERA-GLKPGDRILFLNGLDVRNCSHDKV-VSLLQ 64

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467249 [Multi-domain] Cd Length: 80 Bit Score: 42.81 E-value: 6.18e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249 1349 RHVKVQKGSEPLGISiVSGEKG--GIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQ 1409
Cdd:cd06768     1 RLCHLVKGPEGYGFN-LHAEKGrpGHFIREVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQ 62

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467281 [Multi-domain] Cd Length: 82 Bit Score: 42.90 E-value: 6.61e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  654 IFVTKVDKGSIADGR-LRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRR 708
Cdd:cd23068    27 LSIQKVNPGSPADKAgLRRGDVILRINGTDTSNLTHKQAQDLIKRAGNDLQLTVQR 82

PDZ domain of protein Lin-7 and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Lin-7 (also known as LIN-7 or LIN7), and related domains. Lin-7 targets and organize protein complexes to epithelial and synaptic plasma membranes. There are three mammalian Lin-7 homologs: Lin-7A (protein lin-7 homolog A, also known as mammalian lin-seven protein 1 (MALS-1), vertebrate lin-7 homolog 1 (Veli-1), tax interaction protein 33); Lin-7B (also known as MALS-2, Veli-2); and Lin-7C (also known as MALS-3, Veli-3). Lin-7 is involved in localization of the Let-23 growth factor receptor to the basolateral membrane of epithelial cells, in tight junction localization of insulin receptor substrate p53 (IRSp53), in retaining gamma-aminobutyric (GABA) transporter (BGT-1) at the basolateral surface of epithelial cells, and in regulating recruitment of neurotransmitter receptors to the postsynaptic density (PSD). The Lin7 PDZ domain binds Let-23, BGT and beta-catenin, and NMDA (N-methyl-D-aspartate) receptor NR2B. Lin-7 also binds to the PDZ binding motif located in the C-terminal tail of Rhotekin, an effector protein for small GTPase Rho. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Lin-7-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467258 [Multi-domain] Cd Length: 86 Bit Score: 43.20 E-value: 6.71e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  620 VVEFERETEdidlkALGFDMAEGVNEpcfpgDCGIFVTKVDKGSIAD--GRLRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd06796     4 VVELPKTEE-----GLGFNVMGGKEQ-----NSPIYISRIIPGGVADrhGGLKRGDQLLSVNGVSVEGEHHEKAVELLKA 73

                          90
                  ....*....|
gi 767964249  698 GEGAINMVVR 707
Cdd:cd06796    74 AQGSVKLVVR 83

PDZ domain of segment polarity protein dishevelled homolog DVL1, DVL2, DVL3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of DVL1-3, and related domains. The dishevelleds (DVL1, 2 and 3 in humans) act downstream of Frizzled (FZD) receptors in both the canonical and non-canonical WNT signaling pathway; they bind the cytoplasmic C-terminus of frizzled family members and transduce the Wnt signal to down-stream effectors. They bind to several proteins known to modulate Wnt signaling. Binding partners of the DVL1 PDZ domain include nucleoredoxin (NXN), Van Gogh-like (VANGL1), Wnt receptor RYK, Dapper 1 (DACT1), Frizzled7 (FZD7), transmembrane protein 88 (TMEM88), Daple (dishevelled-associating protein with a high frequency of leucines), also known as Ccdc88c), and cysteine-rich protein Idax. The DVL2 PDZ domain has been shown to bind the nuclear export signal sequence of the DVL2 protein. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This DVL-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467201 [Multi-domain] Cd Length: 87 Bit Score: 42.74 E-value: 7.60e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767964249  650 GDCGIFVTKVDKGSI--ADGRLRVNDWLLRINDVDLINKDKKQAIKAL 695
Cdd:cd06717    24 GDGGIYVGSIMKGGAvaADGRIEPGDMILQVNDISFENMSNDDAVRVL 71

PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.

Pssm-ID: 436067 [Multi-domain] Cd Length: 54 Bit Score: 41.74 E-value: 8.20e-05

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 767964249   741 AAVLPGSPAAKEGsLAVGDRIVAINGIALdnKSLNECESLLRSCQDSLTL 790
Cdd:pfam17820    3 TAVVPGSPAERAG-LRVGDVILAVNGKPV--RSLEDVARLLQGSAGESVT 49

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467621 [Multi-domain] Cd Length: 91 Bit Score: 43.05 E-value: 8.32e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  728 KDSGISLENGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKslNECESLLRSCQ--DSLTLSLL 793
Cdd:cd06779    17 KELGLPVNRGVLVAEVIPGSPAAKAG-LKEGDVILSVNGKPVTSF--NDLRAALDTKKpgDSLNLTIL 81

Src Homology 3 domain of Sdc25/Cdc25 guanine nucleotide exchange factors; This subfamily is composed of the Saccharomyces cerevisiae guanine nucleotide exchange factors (GEFs) Sdc25 and Cdc25, and similar proteins. These GEFs regulate Ras by stimulating the GDP/GTP exchange on Ras. Cdc25 is involved in the Ras/PKA pathway that plays an important role in the regulation of metabolism, stress responses, and proliferation, depending on available nutrients and conditions. Proteins in this subfamily contain an N-terminal SH3 domain as well as REM (Ras exchanger motif) and RasGEF domains at the C-terminus. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.

Pssm-ID: 212816 Cd Length: 55 Bit Score: 41.88 E-value: 8.35e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1597 YIRALYDRLADVEQELSFKKDDILYVDDTLPQGtfgsWmaWQ--LDENAQKIQRGQIPSKY 1655
Cdd:cd11883     1 VVVALYDFTPKSKNQLSFKAGDIIYVLNKDPSG----W--WDgvIISSSGKVKRGWFPSNY 55

PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS3, and related domains. RGS3 down-regulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. It downregulates G-protein-mediated release of inositol phosphates and activation of MAP kinases. In Eph/ephrin signaling, RGS3 binds via its PDZ domain to the cytoplasmic C terminus of Eph receptor tyrosine kinase EphB. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467195 [Multi-domain] Cd Length: 77 Bit Score: 42.38 E-value: 8.40e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249 1351 VKVQKGSEPLGISIVSGEKggIYVSKVTVGSIAHQAGLEYGDQLLEFNGINL-RSATEQQARLI 1413
Cdd:cd06711     3 ITIQRGKDGFGFTICDDSP--VRVQAVDPGGPAEQAGLQQGDTVLQINGQPVeRSKCVELAHAI 64

RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.

Pssm-ID: 431111 [Multi-domain] Cd Length: 766 Bit Score: 47.51 E-value: 8.81e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   142 VNEKVENLSIQLRLMTRERNELRKRLAFATHGTAFDKRPYHRLNPDYERLKIQCVRAMSDLQSLQNQ------HTNALKr 215
Cdd:pfam10174  252 LEDEVQMLKTNGLLHTEDREEEIKQMEVYKSHSKFMKNKIDQLKQELSKKESELLALQTKLETLTNQnsdckqHIEVLK- 330

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   216 cEEVAKETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQLLR---ERNLLQQSWEDMKRLHEEDQKEIGDLRAQ---QQQV 289
Cdd:pfam10174  331 -ESLTAKEQRAAILQTEVDALRLRLEEKESFLNKKTKQLQDlteEKSTLAGEIRDLKDMLDVKERKINVLQKKienLQEQ 409

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   290 LKH-----NGSSEILNKLY------DTAMDKLEVVKKDYDALRKRYSEKVAIHN-ADLSRLEQLGEENQRLLKQTEML-- 355
Cdd:pfam10174  410 LRDkdkqlAGLKERVKSLQtdssntDTALTTLEEALSEKERIIERLKEQREREDrERLEELESLKKENKDLKEKVSALqp 489

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   356 --TQQRDTAIQLQHQcALSLRRfeaihhELNKATAQNKDLQWEMELLQSELTELRTtQVKTAKESEKYREERDAVYSEYK 433
Cdd:pfam10174  490 elTEKESSLIDLKEH-ASSLAS------SGLKKDSKLKSLEIAVEQKKEECSKLEN-QLKKAHNAEEAVRTNPEINDRIR 561

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   434 LIMSERDQVISELDKLQTEVE-----LAESKLKSSTSEKKAANEEMEALRQIKDTVT-----------MDAGRANKEVEI 497
Cdd:pfam10174  562 LLEQEVARYKEESGKAQAEVErllgiLREVENEKNDKDKKIAELESLTLRQMKEQNKkvanikhgqqeMKKKGAQLLEEA 641

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   498 LR-----------KQCKALCQELKEALQEADVAKCRrdwaFQERDKIVAERDSIRTlcdNLRRERDRAVSELAE------ 560
Cdd:pfam10174  642 RRrednladnsqqLQLEELMGALEKTRQELDATKAR----LSSTQQSLAEKDGHLT---NLRAERRKQLEEILEmkqeal 714

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|
gi 767964249   561 -----------ALRSLDDTRKQKND-----VSRE----LKELKEQMESQL 590
Cdd:pfam10174  715 laaisekdaniALLELSSSKKKKTQeevmaLKREkdrlVHQLKQQTQNRM 764

Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];

Pssm-ID: 443174 [Multi-domain] Cd Length: 591 Bit Score: 47.12 E-value: 9.10e-05

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 767964249  741 AAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNE 776
Cdd:COG3975   499 TSVLWGSPAYKAG-LSAGDELLAIDGLRVTADNLDD 533

PDZ domain 2 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP, Drosophila Bazooka) and related domains. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par3 and the Par complex include Par3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467271 [Multi-domain] Cd Length: 93 Bit Score: 43.01 E-value: 9.14e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  649 PGDCGIFVTKV-DKG-SIADGRLRVNDWLLRINDVDLINKDKKQAIKALLNGE--GAINMVVRR 708
Cdd:cd23058    29 GGSGPIYIKNIlPKGaAIQDGRLKAGDRLLEVNGVDVTGKTQEEVVSLLRSTKlgGTVSLVVSR 92

PDZ domain of membrane palmitoylated protein1 (MPP1), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP1, and related domains. MPP1 (also known as MAGUK p55 subfamily member 1, erythrocyte membrane protein p55, EMP55) is a membrane-associated guanylate kinase (MAGUK)-like protein which forms a complex with protein 4.1 and glycophorin C (GPC) at the cytoplasmic face of the plasma membrane; this complex is essential for cytoskeleton-membrane linkage in erythrocytes and many non-erythroid cells, and participates in the determination of membrane stability and cell shape. MPP1, by interacting with various scaffold proteins and cytoskeletal proteins in the postsynaptic density, also plays an important role in organizing synaptic and non-synaptic structures. MPP1 is also a component of the Crumbs protein complex in the mammalian retina and may link the Usher protein network and the Crumbs protein complex. The MPP1 PDZ domain binding partners include GPC, ABCC4, and CADM1/Necl-2/SynCAM1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467266 [Multi-domain] Cd Length: 81 Bit Score: 42.54 E-value: 9.15e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1349 RHVKVQKGS-EPLGISIVSGEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITI 1423
Cdd:cd10830     1 RLVQFEKNTeEPMGITLKLNEKQSCIVARILHGGMIHRQGsLHVGDEILEINGKSVTNHSVDQLQKMLKETKGMVSL 77

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 47.44 E-value: 9.55e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  266 EDMKRLHE----EDQKEIGDLRAQQQQVLKHNGSSEILNKLYDTamdKLEVVKKDYDALRKRYSEKVAIHNADLSRLEQL 341
Cdd:PTZ00121 1549 DELKKAEElkkaEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEA---RIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEEL 1625

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  342 GEENQrllkqtemltqQRDTAIQLQHQCALSLRRFEAIH--HELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESE 419
Cdd:PTZ00121 1626 KKAEE-----------EKKKVEQLKKKEAEEKKKAEELKkaEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEAL 1694

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  420 KYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILR 499
Cdd:PTZ00121 1695 KKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIR 1774

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  500 KQCKALcqeLKEALQEADvAKCRRDWAFQERD-----KIVAERDSIRTLCDNLRRERDraVSELAEALrsldDTRKQKND 574
Cdd:PTZ00121 1775 KEKEAV---IEEELDEED-EKRRMEVDKKIKDifdnfANIIEGGKEGNLVINDSKEME--DSAIKEVA----DSKNMQLE 1844

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  575 VSRELKELKEQMESQLEKEarfrqlmAHSSHDSAIDTDSMEWETEVVEFERETEDID 631
Cdd:PTZ00121 1845 EADAFEKHKFNKNNENGED-------GNKEADFNKEKDLKEDDEEEIEEADEIEKID 1894

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 47.27 E-value: 1.03e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   168 AFATHGTAFDKRPYHRLNPDYERLKIQCvRAMSDLQSLQNQhTNALKRCEEVAKETDFYHTLHSRLLSDQtrlkDDVDML 247
Cdd:TIGR00618  185 EFAKKKSLHGKAELLTLRSQLLTLCTPC-MPDTYHERKQVL-EKELKHLREALQQTQQSHAYLTQKREAQ----EEQLKK 258

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   248 RRENGQLLRErnllQQSWEDMKRLHEEDQKEIgDLRAQQQQVLKHNGSSEILNKLYDTAMDKLEVvkkdydalRKRYSEK 327
Cdd:TIGR00618  259 QQLLKQLRAR----IEELRAQEAVLEETQERI-NRARKAAPLAAHIKAVTQIEQQAQRIHTELQS--------KMRSRAK 325

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   328 VAIHNADLSRLEQLGEENQRLLKQTemltQQRDTAIQLQHQCALSLR-RFEAIHHELNKATAQNKDLQWEMELLQSELTE 406
Cdd:TIGR00618  326 LLMKRAAHVKQQSSIEEQRRLLQTL----HSQEIHIRDAHEVATSIReISCQQHTLTQHIHTLQQQKTTLTQKLQSLCKE 401

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   407 LRTTQVKTAKESEKYREERDAvysEYKLIMSERDQVISELDKLQTEVELAEsKLKSSTSEKKAANEEMEALRQIKDTVtm 486
Cdd:TIGR00618  402 LDILQREQATIDTRTSAFRDL---QGQLAHAKKQQELQQRYAELCAAAITC-TAQCEKLEKIHLQESAQSLKEREQQL-- 475

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   487 dagrANKEVEILR-KQCKALCQELKEALQEADVAKCRrdwafQERDKIVAERDSIRTLCDNLRRERdrAVSELAEALRSL 565
Cdd:TIGR00618  476 ----QTKEQIHLQeTRKKAVVLARLLELQEEPCPLCG-----SCIHPNPARQDIDNPGPLTRRMQR--GEQTYAQLETSE 544

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|.
gi 767964249   566 DDTRKQKNDVSRELKELKEQMESQLEKEARFRQLMAHSSHD 606
Cdd:TIGR00618  545 EDVYHQLTSERKQRASLKEQMQEIQQSFSILTQCDNRSKED 585

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.

Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 47.09 E-value: 1.04e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   237 QTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQVlkhngsSEILNKLyDTAMDKLEVVKKD 316
Cdd:pfam01576   21 QQKAESELKELEKKHQQLCEEKNALQEQLQAETELCAEAEEMRARLAARKQEL------EEILHEL-ESRLEEEEERSQQ 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   317 YDALRKRYSEkvaiHNADLSrlEQLGEEN---QRLlkQTEMLTqqrdtaiqlqhqCALSLRRFEAihhELNKATAQNKDL 393
Cdd:pfam01576   94 LQNEKKKMQQ----HIQDLE--EQLDEEEaarQKL--QLEKVT------------TEAKIKKLEE---DILLLEDQNSKL 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   394 QWEMELLQSELTELRTT---QVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAA 470
Cdd:pfam01576  151 SKERKLLEERISEFTSNlaeEEEKAKSLSKLKNKHEAMISDLEERLKKEEKGRQELEKAKRKLEGESTDLQEQIAELQAQ 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   471 NEEMEALRQIKDTVTMDA-GRANKEV---EILRKQCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDSIRT-LCD 545
Cdd:pfam01576  231 IAELRAQLAKKEEELQAAlARLEEETaqkNNALKKIRELEAQISELQEDLESERAARNKAEKQRRDLGEELEALKTeLED 310

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   546 N---------LRRERDRAVSELAEALRslDDTRK---QKNDVSRELKELKEQMESQLEKEARFRQLMAHSSHdsAIDTDS 613
Cdd:pfam01576  311 TldttaaqqeLRSKREQEVTELKKALE--EETRSheaQLQEMRQKHTQALEELTEQLEQAKRNKANLEKAKQ--ALESEN 386


                   ....*..
gi 767964249   614 MEWETEV 620
Cdd:pfam01576  387 AELQAEL 393

PDZ domain 5 of multi-PDZ-domain protein 1 (MUPP1), PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467157 [Multi-domain] Cd Length: 98 Bit Score: 42.60 E-value: 1.16e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1347 EPRHVKVQKGSEPLGISI------VSGEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06669     7 EVTVIELEKGDRGLGFSIldyqdpLDPSETVIVIRSLVPGGVAEQDGrLLPGDRLVFVNDVSLENASLDEA 77

PDZ domain 3 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467248 [Multi-domain] Cd Length: 82 Bit Score: 42.31 E-value: 1.23e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  617 ETEVVEFERETEdidlkALGFDMAEGvnepcfpGDCGIFVTKVDKGSIAD-GRLRVNDWLLRINDVDLINKDKKQAIKAL 695
Cdd:cd06767     2 EPRHVSIEKGSE-----PLGISIVSG-------ENGGIFVSSVTEGSLAHqAGLEYGDQLLEVNGINLRNATEQQAALIL 69

                          90
                  ....*....|.
gi 767964249  696 LNGEGAINMVV 706
Cdd:cd06767    70 RQCGDTITMLV 80

PDZ domain of membrane palmitoylated protein 6 (MPP6), MPP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP6, MPP2, and related domains. MPP6 (also known as MAGUK p55 subfamily member, Protein associated with Lin-7, 2 (PALS2), Veli-associated MAGUK 1, and VAM-1) is a membrane-associated guanylate kinase (MAGUK)-like protein. MPP6 is a regulator of Lin-7 expression and localization. MPP6 is also known to bind cell-adhesion protein, nectin-like molecule-2 (Necl-2), and localize to the basolateral plasma membrane in mammalian epithelial cells. MPP2 (also known as MAGUK p55 subfamily member 2) is a postsynaptic protein that links SynCAM1 cell adhesion molecules to core components of the postsynaptic density. Other members of this family include the Drosophila Vari protein, an essential basolateral septate junction protein which interacts with the cell-adhesion protein neurexin IV. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP6-MPP2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467268 [Multi-domain] Cd Length: 78 Bit Score: 42.21 E-value: 1.23e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249 1349 RHVKVQK-GSEPLGIsIVSGEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARL 1412
Cdd:cd10832     1 RMVGIRKnPGEPLGV-TVRLEEGELVIARILHGGMIDRQGlLHVGDIIKEVNGVPVGSPEQLQEML 65

PDZ domain 3 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467181 [Multi-domain] Cd Length: 90 Bit Score: 42.25 E-value: 1.37e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  706 VRRRKSLGGkvvtpLHINLSGQKDSGISLENG--VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRS 783
Cdd:cd06695     4 VKLTKGSSG-----LGFSFLGGENNSPEDPFSglVRIKKLFPGQPAAESGLIQEGDVILAVNGEPLKGLSYQEVLSLLRG 78


                  ....*....
gi 767964249  784 CQDSLTLSL 792
Cdd:cd06695    79 APPEVTLLL 87

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467281 [Multi-domain] Cd Length: 82 Bit Score: 42.13 E-value: 1.39e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767964249  743 VLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLK 794
Cdd:cd23068    32 VNPGSPADKAG-LRRGDVILRINGTDTSNLTHKQAQDLIKRAGNDLQLTVQR 82

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

Pssm-ID: 275316 [Multi-domain] Cd Length: 745 Bit Score: 46.55 E-value: 1.42e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   183 RLNPDYERLKIQCVRAMSDLQSLQNQHTNALKRCEEVAKETDFYHTLHSRLLSDQTRLKDDVDMLRRENGQL-------L 255
Cdd:TIGR04523  339 QLNEQISQLKKELTNSESENSEKQRELEEKQNEIEKLKKENQSYKQEIKNLESQINDLESKIQNQEKLNQQKdeqikklQ 418

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   256 RERNLLQQSWEDMKRLHEEDQKEIGDLRAQ----QQQVLKHNGSSEILNKLYDTAMDKLEVVKKDYDALRKRYSEKVaih 331
Cdd:TIGR04523  419 QEKELLEKEIERLKETIIKNNSEIKDLTNQdsvkELIIKNLDNTRESLETQLKVLSRSINKIKQNLEQKQKELKSKE--- 495

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   332 nadlSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHQcaLSLR------------------------------------R 375
Cdd:TIGR04523  496 ----KELKKLNEEKKELEEKVKDLTKKISSLKEKIEK--LESEkkekeskisdledelnkddfelkkenlekeideknkE 569

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   376 FEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVEL 455
Cdd:TIGR04523  570 IEELKQTQKSLKKKQEEKQELIDQKEKEKKDLIKEIEEKEKKISSLEKELEKAKKENEKLSSIIKNIKSKKNKLKQEVKQ 649

                          330       340       350
                   ....*....|....*....|....*....|
gi 767964249   456 AESKLksstseKKAANEEMEALRQIKDTVT 485
Cdd:TIGR04523  650 IKETI------KEIRNKWPEIIKKIKESKT 673

PDZ domain 7 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467173 [Multi-domain] Cd Length: 85 Bit Score: 42.24 E-value: 1.43e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1350 HVKVQK--GSEPLGISIVSG--EKGgIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITILA 1425
Cdd:cd06685     5 KVTLYKdsDTEDFGFSVSDGlyEKG-VYVNAIRPGGPADLSGLQPYDRILQVNHVRTRDFDCCLVVPLIAESGDKLELVV 83


                  .
gi 767964249 1426 Q 1426
Cdd:cd06685    84 S 84

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 45.98 E-value: 1.46e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  382 ELNKATAQNKDLQWEMELLQSELTELRttqvktaKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLK 461
Cdd:COG3883    17 QIQAKQKELSELQAELEAAQAELDALQ-------AELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERREELG 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  462 ---SSTSEKKAANEEMEALRQIKDTVTMdAGRANKeVEILRKQCKALCQELKEALQEADvakcrrdwafQERDKIVAERD 538
Cdd:COG3883    90 eraRALYRSGGSVSYLDVLLGSESFSDF-LDRLSA-LSKIADADADLLEELKADKAELE----------AKKAELEAKLA 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  539 SIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEAR 595
Cdd:COG3883   158 ELEALKAELEAAKAELEAQQAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAA 214

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNJ2BP-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467193 [Multi-domain] Cd Length: 86 Bit Score: 41.89 E-value: 1.50e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1351 VKVQKGSEPLGISIVSG-------EKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06709     3 ITLKRGPSGLGFNIVGGtdqpyipNDSGIYVAKIKEDGAAAIDGrLQEGDKILEINGQSLENLTHQDA 70

Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding proteins; CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of integrins at focal adhesions where they localize, and thus, regulate cell invasion and survival. Over-expression of these proteins is implicated in poor prognosis, increased metastasis, and resistance to chemotherapeutics in many cancers such as breast, lung, melanoma, and glioblastoma. CAS proteins have also been linked to the pathogenesis of inflammatory disorders, Alzheimer's, Parkinson's, and developmental defects. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. Vertebrates contain four CAS proteins: BCAR1 (or p130Cas), NEDD9 (or HEF1), EFS (or SIN), and CASS4 (or HEPL). The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212778 Cd Length: 56 Bit Score: 41.18 E-value: 1.52e-04

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 767964249 1599 RALYDRLADVEQELSFKKDDILYVDDTLPQGTFGSWM 1635
Cdd:cd11844     3 RALYDNVAESPDELAFRRGDILTVLEQNTAGLEGWWL 39

PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GOPC-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467261 [Multi-domain] Cd Length: 83 Bit Score: 41.97 E-value: 1.54e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249  720 LHINLSGQKDSGISlengVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06800    13 LGISITGGKEHGVP----ILISEIHEGQPADRCGGLYVGDAILSVNGIDLRDAKHKEAVTILSQQRGEITL 79

PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila Dlg1, human Dlg1, 2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197; SAP-97), Dlg2 (also known as channel-associated protein of synapse-110; postsynaptic density protein 93, PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95; synapse-associated protein 90, SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling, regulating surface expression of NMDA receptors in dorsal horn neurons of the spinal cord; it interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. The Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development; postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467257 [Multi-domain] Cd Length: 91 Bit Score: 41.96 E-value: 1.58e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249  718 TPLHINLSGQKDsgislENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06795    12 TGLGFNIVGGED-----GEGIFISFILAGGPADLSGELRRGDQILSVNGVDLRNATHEQAAAALKNAGQTVTI 79

PDZ domain of syntrophins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of syntrophins (including alpha-1-syntrophin, beta-1-syntrophin, beta-2-syntrophin, gamma-1-syntrophin, and gamma-2-syntrophin), and related domains. Syntrophins play a role in recruiting various signaling molecules into signaling complexes and help provide appropriate spatiotemporal regulation of signaling pathways. They function in cytoskeletal organization and maintenance; as components of the dystrophin-glycoprotein complex (DGC), they help maintain structural integrity of skeletal muscle fibers. They link voltage-gated sodium channels to the actin cytoskeleton and the extracellular matrix, and control the localization and activity of the actin reorganizing proteins such as PI3K, PI(3,4)P2 and TAPP1. Through association with various cytoskeletal proteins within the cells, they are involved in processes such as regulation of focal adhesions, myogenesis, calcium homeostasis, and cell migration. They also have roles in synapse formation and in the organization of utrophin, acetylcholine receptor, and acetylcholinesterase at the neuromuscular synapse. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This syntrophin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467262 [Multi-domain] Cd Length: 83 Bit Score: 41.79 E-value: 1.63e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767964249  743 VLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06801    32 IFKGQAADQTGQLFVGDAILSVNGENLEDATHDEAVQALKNAGDEVTL 79

PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467220 [Multi-domain] Cd Length: 82 Bit Score: 41.92 E-value: 1.67e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  653 GIFVTKVDKGSIAD--GrLRVNDWLLRINDVDLINKDKKQAIKALLnGEGAINMVVR 707
Cdd:cd06738    28 GIFISNVKPGSLAEevG-LEVGDQIVEVNGTSFTNVDHKEAVMALK-SSRHLTITVR 82

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 46.45 E-value: 1.71e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  472 EEMEALRQIKDTVT--MDAGRANKEVEILRKQCKAL------CQELKEALQEADVAKCRRDW-----AFQERDKIVAERD 538
Cdd:COG4913   219 EEPDTFEAADALVEhfDDLERAHEALEDAREQIELLepirelAERYAAARERLAELEYLRAAlrlwfAQRRLELLEAELE 298

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249  539 SIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVS--------RELKELKEQMESQLEKEARFRQLMA 601
Cdd:COG4913   299 ELRAELARLEAELERLEARLDALREELDELEAQIRGNGgdrleqleREIERLERELEERERRRARLEALLA 369

Centrosomal colon cancer autoantigen protein family; CCCAP is a family of proteins found in eukaryotes. CCCAP is also known as SDCCAG8, serologically defined colon cancer antigen 8. It is associated with the centrosome.

Pssm-ID: 435040 [Multi-domain] Cd Length: 703 Bit Score: 46.44 E-value: 1.81e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   332 NADLSRLEQLGEENQRL------LKQTEMLTQQRDTAIQLQHQCALSLRrfEAIHHELNKATAQNKDLQWEMELLQSELT 405
Cdd:pfam15964  296 NVHMQTIERLTKERDDLmsalvsVRSSLAEAQQRESSAYEQVKQAVQMT--EEANFEKTKALIQCEQLKSELERQKERLE 373

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   406 ElrttqvKTAKESEKYREERDAVYSEYKlimSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVT 485
Cdd:pfam15964  374 K------ELASQQEKRAQEKEALRKEMK---KEREELGATMLALSQNVAQLEAQVEKVTREKNSLVSQLEEAQKQLASQE 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   486 MDAGRANKEVEILRKQCKALCQELKEALQEADvAKCRRDWAF--QERDKIVAERDSIRTLCDNLRRERDRAVSE------ 557
Cdd:pfam15964  445 MDVTKVCGEMRYQLNQTKMKKDEAEKEHREYR-TKTGRQLEIkdQEIEKLGLELSESKQRLEQAQQDAARAREEclklte 523

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249   558 -LAEALRSLDDTRKQKNDVSR------------------ELKELKEQMESQLEKEARFRQLMAHS 603
Cdd:pfam15964  524 lLGESEHQLHLTRLEKESIQQsfsneakaqalqaqqreqELTQKMQQMEAQHDKTVNEQYSLLTS 588

Src homology 3 domain of Src kinase-like Protein Tyrosine Kinases; Src subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr, Fyn, Yrk, Yes, and Brk. Src (or c-Src) proteins are cytoplasmic (or non-receptor) PTKs which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). However, Brk lacks the N-terminal myristoylation sites. Src proteins are involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. They were identified as the first proto-oncogene products, and they regulate cell adhesion, invasion, and motility in cancer cells, and tumor vasculature, contributing to cancer progression and metastasis. Src kinases are overexpressed in a variety of human cancers, making them attractive targets for therapy. They are also implicated in acute inflammatory responses and osteoclast function. Src, Fyn, Yes, and Yrk are widely expressed, while Blk, Lck, Hck, Fgr, Lyn, and Brk show a limited expression pattern. This subfamily also includes Drosophila Src42A, Src oncogene at 42A (also known as Dsrc41) which accumulates at sites of cell-cell or cell-matrix adhesion, and participates in Drosphila development and wound healing. It has been shown to promote tube elongation in the tracheal system, is essential for proper cell-cell matching during dorsal closure, and regulates cell-cell contacts in developing Drosophila eyes. The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212779 [Multi-domain] Cd Length: 52 Bit Score: 40.64 E-value: 1.95e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1599 RALYDRLADVEQELSFKKDDILYVDDTlpqgTFGSWmaWqLDENAQKIQRGQIPSKY 1655
Cdd:cd11845     3 VALYDYEARTDDDLSFKKGDRLQILDD----SDGDW--W-LARHLSTGKEGYIPSNY 52

PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467222 [Multi-domain] Cd Length: 82 Bit Score: 41.58 E-value: 1.97e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  737 GVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQdSLTLSL 792
Cdd:cd06740    28 GIYVSLVEPGSLAEKEG-LRVGDQILRVNDVSFEKVTHAEAVKILRVSK-KLVLSV 81

PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467186 [Multi-domain] Cd Length: 89 Bit Score: 41.86 E-value: 2.08e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  705 VVRRRKSLGgkvvtPLHINLSGQKDS-----GISlENGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECES 779
Cdd:cd06702     2 EIHLVKAGG-----PLGLSIVGGSDHsshpfGVD-EPGIFISKVIPDGAAAKSG-LRIGDRILSVNGKDLRHATHQEAVS 74

                          90
                  ....*....|.
gi 767964249  780 LLRSCQDSLTL 790
Cdd:cd06702    75 ALLSPGQEIKL 85

flagellar biosynthesis chaperone FliJ;

Pssm-ID: 181091 [Multi-domain] Cd Length: 146 Bit Score: 43.14 E-value: 2.21e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  310 LEVVKKDYDALRKRYSEKVaihnadlSRLEQLGEENQRLLKQTEMLTQQRDTAIQ-------LQHQCALSLRRFEAIHHe 382
Cdd:PRK07720   11 LELKENEKEKALGEYEEAV-------SRFEQVAEKLYELLKQKEDLEQAKEEKLQsglsiqeIRHYQQFVTNLERTIDH- 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  383 LNKATAQNKDlqwEMELLQSELTELRTtqvktakESEKYREERDAVYSEYKLIMSERDQviSELDKL 449
Cdd:PRK07720   83 YQLLVMQARE---QMNRKQQDLTEKNI-------EVKKYEKMKEKKQEMFALEEKAAEM--KEMDEI 137

PDZ domain 8 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 7 of protein-associated tight junction (PATJ), PDZ domain 2 of Drosophila melanogaster inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 8 of MUPP1, PDZ domain 7 of PATJ, and PDZ domain 2 of Drosophila melanogaster INAD, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ8 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467160 [Multi-domain] Cd Length: 84 Bit Score: 41.51 E-value: 2.21e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  718 TPLHINLSGQKD-SGISlengVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKS 773
Cdd:cd06672    11 SGLGLSLAGNKDrSRMS----VFVVGIDPDGAAGKDGRIQVGDELLEINGQVLYGRS 63

PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F (RhoGAP100F), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Par6 (also known as PAR6 or Par-6), RhoGAP100F, and related domains. Par6 is part of a conserved machinery that directs metazoan cell polarity, a process necessary for the function of diverse cell types. Par6 forms a cell polarity-regulatory complex with atypical protein kinase C (aPKC) and Par3. Par6 can also directly associate with PALS1 (proteins associated with Lin7, also known as Stardust) providing a link between the Par3/aPKC/Par6 complex and the PALS1-PATJ (protein-associated TJ) complex. Binding partners of the Par6-PDZ domain include Par3, PALS1/Stardust; leucine-rich repeat-containing protein netrin-G ligand-2 (NGL-2), human crumbs (CRB3) involve in the morphogenesis of the tight junctions in mammalian epithelial cells, and PAR-6 co-operates with the Par6 semi-CRIB domain to bind CDC42. CDC42 regulates the Par6 PDZ domain through an allosteric CRIB-PDZ transition. Drosophila RhoGAP100F, also known as synapse defective protein 1 homolog (syd-1 homolog), is a GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound form. The RhoGAP100F-PDZ domain binds the neurexin C terminus to control synapse formation at the Drosophila neuromuscular junction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par6-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467202 [Multi-domain] Cd Length: 84 Bit Score: 41.40 E-value: 2.25e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249 1501 RVVFIKKSQLELGVHLCGGN----LHGVFVAEVEDDSPAKGPDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRD 1572
Cdd:cd06718     2 RVELIKPPGKPLGFYIRDGNgverVPGIFISRLVLGSLADSTGLLAVGDEILEVNGVEVTGKSLDDVTDMMVAPTR 77

PDZ domain 8 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 7 of protein-associated tight junction (PATJ), PDZ domain 2 of Drosophila melanogaster inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 8 of MUPP1, PDZ domain 7 of PATJ, and PDZ domain 2 of Drosophila melanogaster INAD, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ8 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467160 [Multi-domain] Cd Length: 84 Bit Score: 41.51 E-value: 2.25e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1351 VKVQKGSEPLGISIvSGEKGG----IYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06672     4 IELEKGSSGLGLSL-AGNKDRsrmsVFVVGIDPDGAAGKDGrIQVGDELLEINGQVLYGRSHLNASAII 71

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 45.53 E-value: 2.29e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  339 EQLGEENQRLLKQTEMLTQQRDTAIQLQHQCALSLRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKES 418
Cdd:COG4942    20 DAAAEAEAELEQLQQEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRAEL 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  419 EKYREE-RDAVYSEYKLIMSERDQVISEldklQTEVELAESKLKSSTSEKKAANEEMEALRQIKdtvtmdagranKEVEI 497
Cdd:COG4942   100 EAQKEElAELLRALYRLGRQPPLALLLS----PEDFLDAVRRLQYLKYLAPARREQAEELRADL-----------AELAA 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  498 LRKQCKALCQELKEALQEADvakcrrdwafQERDKIVAERDsirtlcdnlrrERDRAVSELAEALRSLDDTRKQKNDVSR 577
Cdd:COG4942   165 LRAELEAERAELEALLAELE----------EERAALEALKA-----------ERQKLLARLEKELAELAAELAELQQEAE 223

                         250
                  ....*....|....*...
gi 767964249  578 ELKELKEQMESQLEKEAR 595
Cdd:COG4942   224 ELEALIARLEAEAAAAAE 241

PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467223 [Multi-domain] Cd Length: 84 Bit Score: 41.48 E-value: 2.31e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  653 GIFVTKVDKGSIADGR-LRVNDWLLRINDVDLINKDKKQAIKaLLNGEGAINMVVRR 708
Cdd:cd06741    27 GIYVTGVDPGSVAENAgLKVGDQILEVNGRSFLDITHDEAVK-ILKSSKHLIMTVKD 82

RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.

Pssm-ID: 431111 [Multi-domain] Cd Length: 766 Bit Score: 45.97 E-value: 2.48e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   247 LRRENGQLLRERNLLQQSWEDMKrLHEEDQKEIgdLRAQQQQVLKhngsseILNKLYDTAMDKleVVKKDYDALRKRyse 326
Cdd:pfam10174  121 LQSEHERQAKELFLLRKTLEEME-LRIETQKQT--LGARDESIKK------LLEMLQSKGLPK--KSGEEDWERTRR--- 186

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   327 kVAIHNADLSRLEQLgeenqrlLKQTEMLTQQRDTAIQLQHQCALSLRRFEAIHHELNKATAQNKDLQWEMELLQSELTE 406
Cdd:pfam10174  187 -IAEAEMQLGHLEVL-------LDQKEKENIHLREELHRRNQLQPDPAKTKALQTVIEMKDTKISSLERNIRDLEDEVQM 258

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   407 LRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALrqiKDTVTM 486
Cdd:pfam10174  259 LKTNGLLHTEDREEEIKQMEVYKSHSKFMKNKIDQLKQELSKKESELLALQTKLETLTNQNSDCKQHIEVL---KESLTA 335

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   487 DAGRAN---KEVEILR-----------KQCKALcQELKE--ALQEADVAKCRRDWAFQERdKIVAERDSIRTLCDNLrRE 550
Cdd:pfam10174  336 KEQRAAilqTEVDALRlrleekesflnKKTKQL-QDLTEekSTLAGEIRDLKDMLDVKER-KINVLQKKIENLQEQL-RD 412

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   551 RDRAVSELAEALRSLD------DT-------------------RKQKN-----------DVSRELKELKEQMESQ----L 590
Cdd:pfam10174  413 KDKQLAGLKERVKSLQtdssntDTalttleealsekeriierlKEQREredrerleeleSLKKENKDLKEKVSALqpelT 492

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249   591 EKEARFRQLMAHSS--------HDSAIDTDSMEWETEVVEFEReTEDIDLKALGFDMAEGVNE 645
Cdd:pfam10174  493 EKESSLIDLKEHASslassglkKDSKLKSLEIAVEQKKEECSK-LENQLKKAHNAEEAVRTNP 554

Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication.

Pssm-ID: 432349 [Multi-domain] Cd Length: 1191 Bit Score: 45.98 E-value: 2.54e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   309 KLEVVKKDYDALR---KRYSEKVAIHNADLSRLeQLGEENQRllkqtEMLTQQRDTAIQL--QHQcALSLRRFEAIHHEL 383
Cdd:pfam12128  605 RLDKAEEALQSARekqAAAEEQLVQANGELEKA-SREETFAR-----TALKNARLDLRRLfdEKQ-SEKDKKNKALAERK 677

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   384 NKATAQNKDLQWEMELLQSELtelrttQVKTAKESEKYREERDAVYSEYKLIMSERDqviSELDKLQTEVELAESKLKSs 463
Cdd:pfam12128  678 DSANERLNSLEAQLKQLDKKH------QAWLEEQKEQKREARTEKQAYWQVVEGALD---AQLALLKAAIAARRSGAKA- 747

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   464 tsekkaaneEMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDWA----FQERDKIVAE--- 536
Cdd:pfam12128  748 ---------ELKALETWYKRDLASLGVDPDVIAKLKREIRTLERKIERIAVRRQEVLRYFDWYqetwLQRRPRLATQlsn 818

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 767964249   537 -RDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQME 587
Cdd:pfam12128  819 iERAISELQQQLARLIADTKLRRAKLEMERKASEKQQVRLSENLRGLRCEMS 870

PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.

Pssm-ID: 436067 [Multi-domain] Cd Length: 54 Bit Score: 40.20 E-value: 2.59e-04

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 767964249  1373 YVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSaTEQQARLIIGQQCDTITIL 1424
Cdd:pfam17820    1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRS-LEDVARLLQGSAGESVTLT 51

PDZ domain 1 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP) and related domains; Drosophila bazooka PDZ1 belongs to a different PDZ family. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par3 and the Par complex include: Par-3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467178 [Multi-domain] Cd Length: 98 Bit Score: 41.83 E-value: 2.76e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  718 TPLHINLSGQKDSGISLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLsLLKVFP 797
Cdd:cd06691    15 GPLGIHVVPFSSSLSGRTLGLLIRGIEEGSRAERDGRFQENDCIVEINGVDLIDKSFEQAQDIFRQAMRSPEV-KLHVVP 93


                  .
gi 767964249  798 Q 798
Cdd:cd06691    94 A 94

PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the second PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467270 [Multi-domain] Cd Length: 85 Bit Score: 41.22 E-value: 2.80e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  720 LHINLSGQKDSGIslenGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRS 783
Cdd:cd10834    15 LGFNIRGGSEYGL----GIYVSKVDPGGLAEQNG-IKVGDQILAVNGVSFEDITHSKAVEVLKS 73

PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the first PDZ domain (PDZ1) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467240 [Multi-domain] Cd Length: 87 Bit Score: 41.11 E-value: 2.83e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249  708 RRKSLGGKVVtplhinlsGQKDSgISLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIAL 769
Cdd:cd06759    10 GGKGLGFSIV--------GGRDS-PRGPMGIYVKTIFPGGAAAEDGRLKEGDEILEVNGESL 62

Src Homology 3 domain of metazoan osteoclast stimulating factor 1; OSTF1, also named OSF or SH3P2, is a signaling protein containing SH3 and ankyrin-repeat domains. It acts through a Src-related pathway to enhance the formation of osteoclasts and bone resorption. It also acts as a negative regulator of cell motility. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212706 [Multi-domain] Cd Length: 53 Bit Score: 40.36 E-value: 2.87e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1599 RALYDRLADVEQELSFKKDDILYVDDTLPQGtfgsWmaWQLDENAQKiqrGQIPSKYV 1656
Cdd:cd11772     3 RALYDYEAQHPDELSFEEGDLLYISDKSDPN----W--WKATCGGKT---GLIPSNYV 51

Src homology 3 domain of Type I fungal Myosins; Type I myosins (myosin-I) are actin-dependent motors in endocytic actin structures and actin patches. They play roles in membrane traffic in endocytic and secretory pathways, cell motility, and mechanosensing. Saccharomyces cerevisiae has two myosins-I, Myo3 and Myo5, which are involved in endocytosis and the polarization of the actin cytoskeleton. Myosin-I contains an N-terminal actin-activated ATPase, a phospholipid-binding TH1 (tail homology 1) domain, and a C-terminal extension which includes an F-actin-binding TH2 domain, an SH3 domain, and an acidic peptide that participates in activating the Arp2/3complex. The SH3 domain of myosin-I is required for myosin-I-induced actin polymerization. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212792 [Multi-domain] Cd Length: 55 Bit Score: 40.45 E-value: 2.93e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1599 RALYDRLADVEQELSFKKDDILYVDDTLPQGTfgsWMAWQLDENAQkiqrGQIPSKYVKR 1658
Cdd:cd11858     3 KALYDFAGSVANELSLKKDDIVYIVQKEDNGW---WLAKKLDESKE----GWVPAAYLEE 55

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription];

Pssm-ID: 440513 [Multi-domain] Cd Length: 349 Bit Score: 45.08 E-value: 3.06e-04

                          10        20        30
                  ....*....|....*....|....*....|.
gi 767964249  741 AAVLPGSPAAKEGsLAVGDRIVAINGIALDN 771
Cdd:COG0750   133 GEVVPGSPAAKAG-LQPGDRIVAINGQPVTS 162

circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and YyxA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis HtrA/YkdA, HtrB/YvtA and YyxA/YycK, and related domains. HtrA-type serine proteases participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. HtrA, HtrB, and YyxA have a single transmembrane domain at the N-terminus and a PDZ domain at the C-terminus. Expression of htrA and htrB genes is induced both by heat shock and by secretion stress (by a common) mechanism; yyxA is neither heat shock nor secretion stress inducible. HtrA and HtrB may have overlapping cellular functions; YyxA may have a cellular function distinct from the other two proteases or have the same function but under different conditions. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This BsHtrA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467622 [Multi-domain] Cd Length: 98 Bit Score: 41.47 E-value: 3.06e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 767964249 1369 KGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITI 1423
Cdd:cd06781    29 NKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSHKVGDTVKV 83

PDZ domain 6 of PDZ domain containing 2 (PDZD2), PDZ domain 3 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 6 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the third PDZ domain (PDZ3) of human pro-interleukin-16 (isoform 1, also known as nPro-IL-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467243 [Multi-domain] Cd Length: 86 Bit Score: 41.09 E-value: 3.07e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767964249  731 GISLEN-GVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRS 783
Cdd:cd06762    21 GSDLENkSITVHRVFPSGLAAQEGTIQKGDRILSINGKSLKGVTHGDALSVLKQ 74

PDZ domain 4 of PDZ domain containing 2 (PDZD2), PDZ domain 2 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the second PDZ domain (PDZ2) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467241 [Multi-domain] Cd Length: 90 Bit Score: 41.10 E-value: 3.08e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  646 PCFPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLN-GEGAINMVVRR 708
Cdd:cd06760    25 PLENDIPGIFIHHLSPGSVAhmDGRLRRGDQILEINGTSLRNVTLNEAYAILSQcKPGPVTLIISR 90

PDZ domain 6 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 6 of multi-PDZ-domain protein 1 (MUPP1). MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ6 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467158 [Multi-domain] Cd Length: 87 Bit Score: 41.09 E-value: 3.42e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  719 PLHINLSGQKDSgisleNGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQ 785
Cdd:cd06670    15 SLGITVSADKDG-----NGCIVKSIIHGGAVSRDGRISVGDFIVSINNESLRNVTNAQARAILRRAS 76

Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.

Pssm-ID: 461677 [Multi-domain] Cd Length: 660 Bit Score: 45.50 E-value: 3.45e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   189 ERLKIQCVRAMSDLQSLQNQHTNALKRCEEVAKETDFYHTLHSRLLSDQTRLKDdvdmlrrengqlLRERNLLQQSWEDM 268
Cdd:pfam05557  121 QRAELELQSTNSELEELQERLDLLKAKASEAEQLRQNLEKQQSSLAEAEQRIKE------------LEFEIQSQEQDSEI 188

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   269 KRLHEEDQKEIGDLRAQQQQVLKHN-------GSSEILN--------KLY--DTAMDKLEVVKKDYDALRKRYSEKVAI- 330
Cdd:pfam05557  189 VKNSKSELARIPELEKELERLREHNkhlneniENKLLLKeevedlkrKLEreEKYREEAATLELEKEKLEQELQSWVKLa 268

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   331 --HNADL-------SRLEQLGEENQRLLKQTEMLTQQ----RDTAIQLQHQCALSLRRFEAIHHELNKATAQNKDLQWEM 397
Cdd:pfam05557  269 qdTGLNLrspedlsRRIEQLQQREIVLKEENSSLTSSarqlEKARRELEQELAQYLKKIEDLNKKLKRHKALVRRLQRRV 348

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   398 ELL--------------QSELTELRTTQVKTA--KESEKYREERDAVYSEYKLIMSE-RDQVISELDKLQT-EVELAESK 459
Cdd:pfam05557  349 LLLtkerdgyrailesyDKELTMSNYSPQLLEriEEAEDMTQKMQAHNEEMEAQLSVaEEELGGYKQQAQTlERELQALR 428

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   460 LKSSTSEKKAANEEMEALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDWAFQERDKIVAERDS 539
Cdd:pfam05557  429 QQESLADPSYSKEEVDSLRRKLETLELERQRLREQKNELEMELERRCLQGDYDPKKTKVLHLSMNPAAEAYQQRKNQLEK 508

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   540 IRTLCDNLRReRDRAVSELAEALRSLDDTRKQKNDvsRELKELKEQMESqleKEARFRQL 599
Cdd:pfam05557  509 LQAEIERLKR-LLKKLEDDLEQVLRLPETTSTMNF--KEVLDLRKELES---AELKNQRL 562

PDZ domain 2 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467166 [Multi-domain] Cd Length: 82 Bit Score: 40.69 E-value: 3.48e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  633 KALGFDMAEGVNEPcfpgdcGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRR 708
Cdd:cd06678    11 EQLGIKLVRKKDEP------GVFILDLLEGGLAarDGRLKSDDRVLAINGQDLRHGTPEQAAQIIQASGERVHFVVSR 82

PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZD11, and related domains. PDZD11 (also known as ATPase-interacting PDZ protein, plasma membrane calcium ATPase-interacting single-PDZ protein, PMCA-interacting single-PDZ protein, PISP) is involved in the dynamic assembly of apical junctions (AJs). It is recruited by PLEKHA7 to AJs to promote the efficient junctional recruitment and stabilization of nectins, and the efficient early phases of assembly of AJs in epithelial cells. The PDZD11 PDZ domain binds nectin-1 and nectin-3. PDZD11 also binds to a PDZ binding motif located in the C-terminal tail of the human sodium-dependent multivitamin transporter, to the cytoplasmic tail of the Menkes copper ATPase ATP7A, and to the cytoplasmic tail of all plasma membrane Ca2+-ATPase b-splice variants. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD11-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467234 [Multi-domain] Cd Length: 83 Bit Score: 40.76 E-value: 3.58e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  703 NMVVRRRKSlggkvVTPLHINLSGQKDSGIslenGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLR 782
Cdd:cd06752     1 RTVVLKRPP-----GEQLGFNIRGGKASGL----GIFISKVIPDSDAHRLG-LKEGDQILSVNGVDFEDIEHSEAVKVLK 70

                          90
                  ....*....|....*.
gi 767964249  783 ScqdSLTLSL-LKVFP 797
Cdd:cd06752    71 T---AREIQMrVRYFP 83

PDZ domain 2 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which it is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This delphilin-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467226 [Multi-domain] Cd Length: 75 Bit Score: 40.34 E-value: 4.03e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249 1351 VKVQKGSEPLGISIVSgeKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSAT 1406
Cdd:cd06744     2 VRVYRGNGSFGFTLRG--HAPVYIESVDPGSAAERAGLKPGDRILFLNGLDVRNCS 55

PDZ domain 2 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467155 [Multi-domain] Cd Length: 80 Bit Score: 40.73 E-value: 4.21e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  628 EDIDL----KALGFDMAEGVNEpcfpgdcGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGA 701
Cdd:cd06667     1 EVIELvndgSGLGFGIVGGKST-------GVVVKTILPGGVAdrDGRLRSGDHILQIGDTNLRGMGSEQVAQVLRQCGSH 73


                  ....*..
gi 767964249  702 INMVVRR 708
Cdd:cd06667    74 VRLVVAR 80

PDZ domain of afadin (AFDN), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of afadin (AFDN, also known as ALL1-fused gene from chromosome 6 protein (AF6) and MLLT4), and related domains. AFDN belongs to the adhesion system, probably together with the E-cadherin-catenin system, that plays a role in the organization of homotypic, interneuronal, and heterotypic cell-cell adherens junctions. The AFDN PDZ domain interaction partners include poliovirus receptor-related protein PRR2/nectin, the junctional adhesion molecule (JAM), the breakpoint-cluster-region protein (BCR), connexin36 (Cx36), and a subset of Eph-related receptor tyrosine kinases; it can also bind low molecular weight ligands, in competition with a natural peptide ligand. Other AFDN-binding proteins have been identified. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This AFDN family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467251 [Multi-domain] Cd Length: 89 Bit Score: 40.73 E-value: 4.27e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767964249  725 SGQKDSGIslengvYAAAVLPGSPAAKEGSLAVGDRIVAINGIAL 769
Cdd:cd06789    25 AGQDKLGI------YIKSVVKGGAADLDGRLQAGDQLLSVDGHSL 63

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467196 [Multi-domain] Cd Length: 78 Bit Score: 40.26 E-value: 4.63e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  719 PLHINLS-GQKDSGISLENG--VYAAAVLPGSPAAKEGsLAVGDRIVAINGiaLDNK--SLNECESLLRSC-QDSLTLSL 792
Cdd:cd06712     1 PRTVHLTkEEGGFGFTLRGDspVQVASVDPGSCAAEAG-LKEGDYIVSVGG--VDCKwsKHSEVVKLLKSAgEEGLELQV 77

PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNPO2, SYNPO2L, and related domains. SYNPO2 (also known as genethonin-2, myopodin) is a cytoskeleton adaptor protein. It participates in chaperone-assisted selective autophagy (CASA), a mechanism for the disposal of misfolded and damaged proteins and provides a link between the CASA chaperone complex and a membrane-tethering and fusion machinery that generates autophagosome membranes. The SYNPO2 PPxY motif binds CASA cochaperone BCL2-associated athanogene 3 (BAG3) and the SYNPO2 PDZ domain binds vacuolar protein sorting 18 homolog (VPS18). There are three isoforms of SYNPO2, which possess an amino-terminal PDZ domain (SYNPO2a, b, c); the short isoform SYNPO2d, lacks the PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNPO2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467264 [Multi-domain] Cd Length: 78 Bit Score: 40.37 E-value: 4.64e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1366 SGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITILAQ 1426
Cdd:cd10820    18 SEQKKPLQVAKIRKKSKAALAGLCEGDELLSINGKPCADLSHSEAMDLIDSSGDTLQLLIK 78

Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];

Pssm-ID: 443174 [Multi-domain] Cd Length: 591 Bit Score: 44.81 E-value: 4.76e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1360 LGISiVSGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSAT--EQQARLIIGqqcDTITILA 1425
Cdd:COG3975   485 LGLR-VSADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTADNldDALAAYKPG---DPIELLV 548

PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467253 [Multi-domain] Cd Length: 89 Bit Score: 40.68 E-value: 4.89e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  706 VRRRKSLGgkvvtplhINLSGQKDSGISLE-NGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSC 784
Cdd:cd06791     8 VKDEQGLG--------ITIAGYVGEKASGElSGIFVKSIIPGSAADQDGRIQVNDQIIAVDGVNLQGFTNQEAVEVLRNT 79

                          90
                  ....*....|
gi 767964249  785 QDSLTLSLLK 794
Cdd:cd06791    80 GQVVHLTLAR 89

PDZ domain 3 of harmonin isoforms a and b, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of harmonin isoforms a and b, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467221 [Multi-domain] Cd Length: 94 Bit Score: 40.76 E-value: 5.03e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249  719 PLHINLSGQKDSgiSLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDS 787
Cdd:cd06739    13 PLDLALEGGIDS--PLGGKIVVSAVYEGGAADKHGGIVKGDQIMMVNGKSLTDVTLAEAEAALQRAMNS 79

PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZD11, and related domains. PDZD11 (also known as ATPase-interacting PDZ protein, plasma membrane calcium ATPase-interacting single-PDZ protein, PMCA-interacting single-PDZ protein, PISP) is involved in the dynamic assembly of apical junctions (AJs). It is recruited by PLEKHA7 to AJs to promote the efficient junctional recruitment and stabilization of nectins, and the efficient early phases of assembly of AJs in epithelial cells. The PDZD11 PDZ domain binds nectin-1 and nectin-3. PDZD11 also binds to a PDZ binding motif located in the C-terminal tail of the human sodium-dependent multivitamin transporter, to the cytoplasmic tail of the Menkes copper ATPase ATP7A, and to the cytoplasmic tail of all plasma membrane Ca2+-ATPase b-splice variants. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD11-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467234 [Multi-domain] Cd Length: 83 Bit Score: 40.37 E-value: 5.24e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  652 CGIFVTKVDKGSIADGR-LRVNDWLLRINDVDLINKDKKQAIKALLNGEgAINMVVR 707
Cdd:cd06752    25 LGIFISKVIPDSDAHRLgLKEGDQILSVNGVDFEDIEHSEAVKVLKTAR-EIQMRVR 80

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440035 [Multi-domain] Cd Length: 274 Bit Score: 43.60 E-value: 5.57e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1522 HGVFVAEVEDDSPA-KGpdGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRDGVRLKV 1578
Cdd:COG0265   201 EGVLVARVEPGSPAaKA--GLRPGDVILAVDGKPVTSARDLQRLLASLKPGDTVTLTV 256

PDZ domain of shroom2, shroom3, shroom4, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of shroom2, shroom3, shroom4, and related domains. Shroom family proteins shroom2 (also known as apical-like protein; protein APXL), shroom3 (also known as shroom-related protein), and shroom4 (also known as second homolog of apical protein) are essential regulators of cell morphology during animal development; they regulate cell architecture by directing the subcellular distribution and activation of Rho kinase (ROCK), which results in the localized activation of non-muscle myosin. The interaction between shroom and ROCK is mediated by the shroom domain 2 (SD2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This shroom2,3,4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467232 [Multi-domain] Cd Length: 82 Bit Score: 40.40 E-value: 5.66e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249  720 LHINLSGQKDSGISLENG------VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALdNKSLNECESLLRSCQDSLTLSL 792
Cdd:cd06750     3 IEVQLQGGAPWGFTLKGGlehgepLVISKIEEGGKAASVGKLQVGDEVVNINGVPL-SGSRQEAIQLVKGSHKTLKLVV 80

PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467188 [Multi-domain] Cd Length: 87 Bit Score: 40.34 E-value: 5.82e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  713 GGKVVTPLHINlsgqkDSGIslengvYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSL 792
Cdd:cd06704    18 GGKGSTPYKGD-----DEGI------FISRVTEGGPAAKAG-VRVGDKLLEVNGVDLVDADHHEAVEALKNSGNTVTMVV 85


                  ..
gi 767964249  793 LK 794
Cdd:cd06704    86 LR 87

PDZ domain 2 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467155 [Multi-domain] Cd Length: 80 Bit Score: 40.34 E-value: 5.99e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1360 LGISIVSGEKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIgQQC 1418
Cdd:cd06667    12 LGFGIVGGKSTGVVVKTILPGGVADRDGrLRSGDHILQIGDTNLRGMGSEQVAQVL-RQC 70

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440035 [Multi-domain] Cd Length: 274 Bit Score: 43.60 E-value: 6.09e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249 1360 LGISIVS-----------GEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARL 1412
Cdd:COG0265   180 LGVTIQPvtpelaealglPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRLL 243

PDZ domain 1 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP) and related domains; Drosophila bazooka PDZ1 belongs to a different PDZ family. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par3 and the Par complex include: Par-3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467178 [Multi-domain] Cd Length: 98 Bit Score: 40.68 E-value: 6.19e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 767964249  653 GIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQA 691
Cdd:cd06691    34 GLLIRGIEEGSRAerDGRFQENDCIVEINGVDLIDKSFEQA 74

PDZ domain of peripheral plasma membrane protein CASK, Caenorhabditis Lin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CASK, Caenorhabditis elegans Lin-2, and related domains. CASK and Lin-2 are membrane-associated guanylate kinase (MAGUK)-like proteins. CASK (also known as Calcium/calmodulin-dependent protein kinase, CAKI, and Camguk) has a role in synaptic transmembrane protein anchoring and ion channel trafficking. CASK may regulate transmembrane proteins that bind calcium, calmodulin, or nucleotides; it regulates the Drosophila ether a go-go (eag) potassium channel, and also regulates autophosphorylation of CaMKII. CASK binding partners include the transcription factor TBR1, and cell-surface proteins, including amyloid precursor protein, neurexins, and syndecans. Lin-2, as a component of the CLin-10-Lin-2-Lin-7 complex, plays a role in controlling the basolateral localization of the EGF receptor Let-23; this complex also associates with the neuron-specific motor protein KIF17 to transport vesicles containing N-methyl-D-aspartate (NMDA) receptor 2B along microtubules. CASK may also function in targeting or scaffolding of the protein parkin which is selectively truncated by a Parkinson's disease-causing mutation; the C-terminus of parkin functions as a class II PDZ-binding motif that binds CASK. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP6-MPP2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467267 [Multi-domain] Cd Length: 81 Bit Score: 40.16 E-value: 6.30e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249  727 QKDS----GISL----ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTlslLKVFP 797
Cdd:cd10831     6 QKNTdepmGITLkmneDGRCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREARGSIT---FKIVP 81

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CPP (also known as tail-specific protease, PRC protein, Protease Re, and Photosystem II D1 protein processing peptidase), and related domains. CPP belongs to the peptidase S41A family. It cleaves a C-terminal 11 residue peptide from the precursor form of penicillin-binding protein 3, and may have a role in protecting bacterium from thermal and osmotic stresses. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This CPP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467623 [Multi-domain] Cd Length: 88 Bit Score: 40.16 E-value: 6.50e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1512 LGVHLCGGNLHGVFVAEVEDDSPA-KGpdGLVPGDLILEYGSLDVRNKTVEEVyVEMLKPRDG--VRLKVQ 1579
Cdd:cd06782     4 IGIEIGKDDDGYLVVVSPIPGGPAeKA--GIKPGDVIVAVDGESVRGMSLDEV-VKLLRGPKGtkVKLTIR 71

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 44.34 E-value: 6.82e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   256 RERNLLQQSWEDMKRLHEedqkeigdlRAQQQQVLKHNGSSEILNKLYDTAMDKLEVVKKDYDALRKrysekvaihnadl 335
Cdd:pfam17380  346 RERELERIRQEERKRELE---------RIRQEEIAMEISRMRELERLQMERQQKNERVRQELEAARK------------- 403

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   336 srLEQLGEENQRLLKQ----TEMLTQQRDTAIQLQhqcalsLRRFEAIH-HELNKATAQNKDLQWEMELLQSELTELRTT 410
Cdd:pfam17380  404 --VKILEEERQRKIQQqkveMEQIRAEQEEARQRE------VRRLEEERaREMERVRLEEQERQQQVERLRQQEEERKRK 475

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   411 QVKTAKESEKYRE---------ERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIK 481
Cdd:pfam17380  476 KLELEKEKRDRKRaeeqrrkilEKELEERKQAMIEEERKRKLLEKEMEERQKAIYEEERRREAEEERRKQQEMEERRRIQ 555

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 767964249   482 DTVtMDAGRANKEVEILRKQCKALCQ--ELKEALQEADVA 519
Cdd:pfam17380  556 EQM-RKATEERSRLEAMEREREMMRQivESEKARAEYEAT 594

PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467187 [Multi-domain] Cd Length: 92 Bit Score: 40.32 E-value: 7.05e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06703    31 DEGIFISRITEGGAADRDGKLQVGDRVLSINGVDVTEARHDQAVALLTSSSPTITL 86

circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine endoprotease DegP and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do) and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for combining with other DegP monomers to form a stable oligomer structure. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegP family PDZ domain 1 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467630 [Multi-domain] Cd Length: 91 Bit Score: 40.16 E-value: 7.06e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249 1523 GVFVAEVEDDSPAKgPDGLVPGDLILEY------GSLDVRNKtveevyVEMLKPRDGVRLKV 1578
Cdd:cd10839    26 GALVAQVLPDSPAA-KAGLKAGDVILSLngkpitSSADLRNR------VATTKPGTKVELKI 80

PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F (RhoGAP100F), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Par6 (also known as PAR6 or Par-6), RhoGAP100F, and related domains. Par6 is part of a conserved machinery that directs metazoan cell polarity, a process necessary for the function of diverse cell types. Par6 forms a cell polarity-regulatory complex with atypical protein kinase C (aPKC) and Par3. Par6 can also directly associate with PALS1 (proteins associated with Lin7, also known as Stardust) providing a link between the Par3/aPKC/Par6 complex and the PALS1-PATJ (protein-associated TJ) complex. Binding partners of the Par6-PDZ domain include Par3, PALS1/Stardust; leucine-rich repeat-containing protein netrin-G ligand-2 (NGL-2), human crumbs (CRB3) involve in the morphogenesis of the tight junctions in mammalian epithelial cells, and PAR-6 co-operates with the Par6 semi-CRIB domain to bind CDC42. CDC42 regulates the Par6 PDZ domain through an allosteric CRIB-PDZ transition. Drosophila RhoGAP100F, also known as synapse defective protein 1 homolog (syd-1 homolog), is a GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound form. The RhoGAP100F-PDZ domain binds the neurexin C terminus to control synapse formation at the Drosophila neuromuscular junction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par6-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467202 [Multi-domain] Cd Length: 84 Bit Score: 39.86 E-value: 7.66e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  633 KALGFDMAEGVNEPCFPGdcgIFVTKVDKGSIAD--GRLRVNDWLLRINDVDLINKD 687
Cdd:cd06718    11 KPLGFYIRDGNGVERVPG---IFISRLVLGSLADstGLLAVGDEILEVNGVEVTGKS 64

PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS12, and related domains. RGS12 downregulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. The RGS12 PDZ domain can bind selectively to C-terminal (A/S)-T-X-(L/V) motifs as found within both the CXCR2 IL-8 receptor, and the alternative 3' exon form of RGS12. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS12-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467194 [Multi-domain] Cd Length: 76 Bit Score: 39.54 E-value: 7.81e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  705 VVRRRKSLGgkvvtplhINLSGQKDSGISlengvyaaAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSC 784
Cdd:cd06710     5 IARGRAGYG--------FTISGQAPCVLS--------CVVRGSPADVAG-LKAGDQILAVNGINVSKASHEDVVKLIGKC 67


                  ....*...
gi 767964249  785 QDSLTLSL 792
Cdd:cd06710    68 TGVLRLVI 75

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 42.99 E-value: 8.05e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  438 ERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQ-I-KDTVTMDAGRANKEVEILRKQCkalcqelkealqe 515
Cdd:COG1579    32 ELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEArIkKYEEQLGNVRNNKEYEALQKEI------------- 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  516 advakcrrdwAFQERDKIVAErDSIRTL---CDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEK 592
Cdd:COG1579    99 ----------ESLKRRISDLE-DEILELmerIEELEEELAELEAELAELEAELEEKKAELDEELAELEAELEELEAEREE 167

PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467223 [Multi-domain] Cd Length: 84 Bit Score: 39.94 E-value: 8.40e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  702 INMVVRRRKSLGgkvvtplhINLSGQKDSGIslenGVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLL 781
Cdd:cd06741     4 VNLVVEDGQSLG--------LMIRGGAEYGL----GIYVTGVDPGSVAENAG-LKVGDQILEVNGRSFLDITHDEAVKIL 70


                  ..
gi 767964249  782 RS 783
Cdd:cd06741    71 KS 72

PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467269 [Multi-domain] Cd Length: 84 Bit Score: 39.72 E-value: 8.48e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1502 VVFIKKSQLE-LGVHLCGGNLHG--VFVAEVEDDSPAKgPDGLVPGDLILEYGSLDVRNKTVEEVyVEMLKPRDGVRLKV 1578
Cdd:cd10833     3 TVTVEKSPDGsLGFSVRGGSEHGlgIFVSKVEEGSAAE-RAGLCVGDKITEVNGVSLENITMSSA-VKVLTGSNRLRMVV 80


                  .
gi 767964249 1579 Q 1579
Cdd:cd10833    81 R 81

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 43.67 E-value: 8.72e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  437 SERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALR-QIKDTVTmDAGRANKEVEILRKQCKALCQELKEALQE 515
Cdd:COG3883    16 PQIQAKQKELSELQAELEAAQAELDALQAELEELNEEYNELQaELEALQA-EIDKLQAEIAEAEAEIEERREELGERARA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  516 ADVAKCRRDW-----------AFQER----DKIV-AERDSIRTLcdnlrrERDRAvsELAEALRSLDDTRKQKNDVSREL 579
Cdd:COG3883    95 LYRSGGSVSYldvllgsesfsDFLDRlsalSKIAdADADLLEEL------KADKA--ELEAKKAELEAKLAELEALKAEL 166

                         170       180
                  ....*....|....*....|...
gi 767964249  580 KELKEQMESQL-EKEARFRQLMA 601
Cdd:COG3883   167 EAAKAELEAQQaEQEALLAQLSA 189

PDZ domain 3 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467215 [Multi-domain] Cd Length: 85 Bit Score: 39.90 E-value: 9.00e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  738 VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLL----RSCQDSLTL 790
Cdd:cd06733    27 VSIGAIVPGGAADLDGRLRTGDELLSVDGVNVVGASHHKVVDLMgnaaRNGQVNLTV 83

PDZ domain of afadin (AFDN), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of afadin (AFDN, also known as ALL1-fused gene from chromosome 6 protein (AF6) and MLLT4), and related domains. AFDN belongs to the adhesion system, probably together with the E-cadherin-catenin system, that plays a role in the organization of homotypic, interneuronal, and heterotypic cell-cell adherens junctions. The AFDN PDZ domain interaction partners include poliovirus receptor-related protein PRR2/nectin, the junctional adhesion molecule (JAM), the breakpoint-cluster-region protein (BCR), connexin36 (Cx36), and a subset of Eph-related receptor tyrosine kinases; it can also bind low molecular weight ligands, in competition with a natural peptide ligand. Other AFDN-binding proteins have been identified. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This AFDN family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467251 [Multi-domain] Cd Length: 89 Bit Score: 39.96 E-value: 9.16e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249  640 AEGVNEPcfpgDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRRR 709
Cdd:cd06789    22 AKGAGQD----KLGIYIKSVVKGGAAdlDGRLQAGDQLLSVDGHSLVGLSQERAAELMTKTGSVVTLEVAKQ 89

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]

Pssm-ID: 273938 [Multi-domain] Cd Length: 428 Bit Score: 43.75 E-value: 9.67e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   627 TEDIdLKALGFDMAEGVnepcfpgdcgiFVTKVDKGSIAD-GRLRVNDWLLRINDVDLIN-KDKKQAIKALLNGEGAINM 704
Cdd:TIGR02037  244 TSDL-AKSLGLEKQRGA-----------LVAQVLPGSPAEkAGLKAGDVITSVNGKPISSfADLRRAIGTLKPGKKVTLG 311

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   705 VVRRRKSLGGKVV--TPLHINLSGQKDS-GISLEN----------------GVYAAAVLPGSPAAKEGsLAVGDRIVAIN 765
Cdd:TIGR02037  312 ILRKGKEKTITVTlgASPEEQASSSNPFlGLTVANlspeirkelrlkgdvkGVVVTKVVSGSPAARAG-LQPGDVILSVN 390

                          170       180
                   ....*....|....*....|....*...
gi 767964249   766 GIALdnKSLNECESLLRSCQDSLTLSLL 793
Cdd:TIGR02037  391 QQPV--SSVAELRKVLARAKKGGRVALL 416

PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SHANK1, SHANK2, SHANK3, and related domains. SHANK family proteins, SHANK1 (also known as somatostatin receptor-interacting protein, SSTR-interacting protein, SSTRIP), SHANK2 (also known as cortactin-binding protein 1, proline-rich synapse-associated protein 1), and SHANK3 (proline-rich synapse-associated protein 2) are synaptic scaffolding proteins which are highly enriched in the post-synaptic densities of excitatory synapses. They have been implicated in synaptic transmission, synapse formation, synaptic plasticity, and cytoskeletal remodeling, and are regulators of Cav1 calcium current and CREB target expression. Many protein ligands have been identified for the Shank PDZ domain, such as GKAP (also known as SAPAP), betaPIX (a guanine nucleotide exchange factor used by Rho GTPase family members Rac1 and Cdc42), alpha-latrotoxin, neuroligin, group I metabotropic glutamate receptors (mGluRs), and L-type calcium channels. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SHANK-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F.

Pssm-ID: 467228 [Multi-domain] Cd Length: 101 Bit Score: 40.27 E-value: 9.76e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  739 YAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLLKV 795
Cdd:cd06746    45 YLESVDPGGVADKAG-LKKGDFLLEINGEDVVKASHEQVVNLIRQSGNTLVLKVVTV 100

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNJ2BP-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467193 [Multi-domain] Cd Length: 86 Bit Score: 39.58 E-value: 1.00e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  718 TPLHINLSGQKDSG-ISLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06709    10 SGLGFNIVGGTDQPyIPNDSGIYVAKIKEDGAAAIDGRLQEGDKILEINGQSLENLTHQDAVELFRNAGEDVKL 83

PDZ domain of membrane palmitoylated protein1 (MPP1), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP1, and related domains. MPP1 (also known as MAGUK p55 subfamily member 1, erythrocyte membrane protein p55, EMP55) is a membrane-associated guanylate kinase (MAGUK)-like protein which forms a complex with protein 4.1 and glycophorin C (GPC) at the cytoplasmic face of the plasma membrane; this complex is essential for cytoskeleton-membrane linkage in erythrocytes and many non-erythroid cells, and participates in the determination of membrane stability and cell shape. MPP1, by interacting with various scaffold proteins and cytoskeletal proteins in the postsynaptic density, also plays an important role in organizing synaptic and non-synaptic structures. MPP1 is also a component of the Crumbs protein complex in the mammalian retina and may link the Usher protein network and the Crumbs protein complex. The MPP1 PDZ domain binding partners include GPC, ABCC4, and CADM1/Necl-2/SynCAM1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467266 [Multi-domain] Cd Length: 81 Bit Score: 39.46 E-value: 1.02e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  741 AAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTlslLKVFP 797
Cdd:cd10830    28 ARILHGGMIHRQGSLHVGDEILEINGKSVTNHSVDQLQKMLKETKGMVS---LKVIP 81

PDZ domain 5 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5, and belongs to this MAGI1,2,3-like family. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467217 [Multi-domain] Cd Length: 84 Bit Score: 39.48 E-value: 1.09e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1350 HVKVQKGSEPLGISIVSGE---KGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITILA 1425
Cdd:cd06735     3 SVELERGPKGFGFSIRGGReynNMPLYVLRLAEDGPAQRDGrLRVGDQILEINGESTQGMTHAQAIELIRSGGSVVRLLL 82


                  .
gi 767964249 1426 Q 1426
Cdd:cd06735    83 R 83

PDZ domain of Rab3-interacting molecule 1 (RIM), RIM2, piccolo and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RIM, RIM2, piccolo and related domains. RIM proteins and Gallus gallus protein piccolo (also called aczonin) are involved in neurotransmitter release at presynaptic active zones, the site of vesicle fusion. A protein complex containing RIM proteins positions synaptic vesicles containing synaptotagmin at the active zone. RIM proteins simultaneously activate docking and priming of synaptic vesicles and recruit Ca2+-channels to active zones, thereby connecting primed synaptic vesicles to Ca2+-channels. RIM binding to vesicular Rab proteins (Rab3 and Rab27 isoforms) mediates vesicle docking; RIM binding to Munc13 activates vesicle priming; RIM binding to the Ca2+-channel, both directly and indirectly via RIM-BP, recruits the Ca2+-channels. The RIM PDZ domain interacts with the C-termini of N- and P/Q-type voltage-gated Ca2+-channels. RIM1, RIM2 and piccolo also participate in regulated exocytosis through binding cAMP-GEFII (cAMP-binding protein-guanidine nucleotide exchange factor II). The piccolo PDZ domain binds cAMP-GEFII. RIM2 also plays a role in dendrite formation by melanocytes. Caenorhabditis elegans RIM (also known as unc-10) may be involved in the regulation of defecation and daumone response. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467198 [Multi-domain] Cd Length: 95 Bit Score: 39.84 E-value: 1.11e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1523 GVFVAEVEDDSPAKGPDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRDGVRLKVQ 1579
Cdd:cd06714    39 GAYVTKVKPGSVADTVGHLREGDEVLEWNGISLQGKTFEEVQDIISQSKGEVELVVS 95

PDZ domain of membrane palmitoylated protein 5 (MPP5), Drosophila Stardust, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP5, Drosophila Stardust, and related domains. MPP5 (also known as MAGUK p55 subfamily member 1, protein associated with Lin-7 1 or PALS1) and Drosophila Stardust are membrane-associated guanylate kinase (MAGUK)-like proteins that serve as signaling and scaffolding proteins, linking different proteins critical to the formation and maintenance of tight junctions (TJ) and apical-basal polarity. Apical-basal polarity determinants cluster in complexes; in particular, the Crumbs complex (Crb, MPP5, and PATJ) and the PAR/aPKC-complex (PAR-3, PAR-6, aPKC) determine the apical plasma membrane domain. Within the Crumbs complex, Crb is stabilized in the plasma membrane by MPP5, which in turn recruits PATJ and Lin-7 to the complex. MPP5 also links the Crumbs complex with the PAR/aPKC-complex. The Drosophila homolog of the Crumbs complex is the (CRB)-Stardust (Sdt)-Discs Lost (Dlt) complex. MPP5 also acts as an interaction partner for SARS-CoV envelope protein E, which results in delayed formation of TJs and dysregulation of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP5-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467259 [Multi-domain] Cd Length: 79 Bit Score: 39.25 E-value: 1.14e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  736 NGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSLL 793
Cdd:cd06798    21 DSVIISRIVKGGAAEKSGLLHEGDEILEINGIEIRGKDVNEVCDLLADMHGTLTFLLI 78

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 43.35 E-value: 1.15e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  240 LKDDVDMLRRENGQLLRERNL----LQQSWEDMKRLHEEDQKEIGDLRAQQQQVLKHNGSSEILNKLYDTAMDKLEVVKK 315
Cdd:COG4372    29 LSEQLRKALFELDKLQEELEQlreeLEQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQE 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  316 DYDALRKRYSEkvaiHNADLSRLEQLGEENQRLLKQTEMLTQQRDTAI-QLQHQCALSLRRFEAIHHELNKATAQNKDLQ 394
Cdd:COG4372   109 EAEELQEELEE----LQKERQDLEQQRKQLEAQIAELQSEIAEREEELkELEEQLESLQEELAALEQELQALSEAEAEQA 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  395 WEMELLQSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEM 474
Cdd:COG4372   185 LDELLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEVILKEIEELE 264

                         250       260
                  ....*....|....*....|....*..
gi 767964249  475 EALRQIKDTVTMDAGRANKEVEILRKQ 501
Cdd:COG4372   265 LAILVEKDTEEEELEIAALELEALEEA 291

SWI5-dependent HO expression protein 3; SWI5-dependent HO expression protein 3 (She3) is an RNA-binding protein that binds specific mRNAs, including the mRNA of Ash1, which is invalid in cell-fate determination. She3 acts as an adapter protein that docks the myosin motor Myo4p onto an Ash1-She2p ribonucleoprotein complex. She3 seems to bind to Myo4p and Shep2p via different domains.

Pssm-ID: 293683 [Multi-domain] Cd Length: 228 Bit Score: 42.42 E-value: 1.16e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   240 LKDDVDMLRRENGQLLrernllQQSWEDMKRLHEEDQKEigDLRAQQQQVLKHngSSEILNKLYDTAMDKLEVVKKDYDA 319
Cdd:pfam17078    8 LHDQIDALTKTNLQLT------VQSQNLLSKLEIAQQKE--SKFLENLASLKH--ENDNLSSMLNRKERRLKDLEDQLSE 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   320 LRKRYSEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDTAIQLQHqcalslRRFEAIHHELNKATAQNKDLQWEMEl 399
Cdd:pfam17078   78 LKNSYEELTESNKQLKKRLENSSASETTLEAELERLQIQYDALVDSQN------EYKDHYQQEINTLQESLEDLKLENE- 150

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249   400 lqSELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQ-VISELDKLQTEVELAESKLKSSTSEKKA 469
Cdd:pfam17078  151 --KQLENYQQRISSNDKDIDTKLDSYNNKFKNLDNIYVNKNNkLLTKLDSLAQLLDLPSWLNLYPESRNKI 219

PDZ domain 7 of PDZ domain containing 2 (PDZD2), PDZ domain 4 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of PDZD2, also known as KIAA0300, PIN-1, PAPIN, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family include the PDZ domain of the secreted mature form of human interleukin-16 (IL-16); this is the fourth PDZ domain (PDZ4) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467244 [Multi-domain] Cd Length: 86 Bit Score: 39.52 E-value: 1.18e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  618 TEVVEFERetediDLKALGFDMAEGVNEPCfpGDCGIFVTKVDKGSIAD--GRLRVNDWLLRINDVDLINKDKKQA---I 692
Cdd:cd06763     1 AVTVELEK-----GSAGLGFSLEGGKGSPL--GDRPLTIKRIFKGGAAEqsGVLQVGDEILQINGTSLQGLTRFEAwniI 73

                          90
                  ....*....|....*
gi 767964249  693 KALlnGEGAINMVVR 707
Cdd:cd06763    74 KSL--PEGPVTLLIR 86

chromosome partition protein MukB;

Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 43.79 E-value: 1.25e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  147 ENLSIQLRlmtRERNELRKRLAFAthgtAFDKRPYHRLNPDYERLKIQCVR---------AMSDLQSLQNQHTNALKRCE 217
Cdd:PRK04863  785 EKRIEQLR---AEREELAERYATL----SFDVQKLQRLHQAFSRFIGSHLAvafeadpeaELRQLNRRRVELERALADHE 857

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  218 EvaketdfyHTLHSRLLSDQtrLKDDVDMLRRENGQL-LRERNLLQQswedmkRLhEEDQKEIGDLRAQQQQVLKHNGSS 296
Cdd:PRK04863  858 S--------QEQQQRSQLEQ--AKEGLSALNRLLPRLnLLADETLAD------RV-EEIREQLDEAEEAKRFVQQHGNAL 920

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  297 EILNKLYDTAM---DKLEVVKKDYDALRKR----------------------YSEKVAIHNADLSRLEQLgeeNQRLLKQ 351
Cdd:PRK04863  921 AQLEPIVSVLQsdpEQFEQLKQDYQQAQQTqrdakqqafaltevvqrrahfsYEDAAEMLAKNSDLNEKL---RQRLEQA 997

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  352 TEMLTQQRDTAIQLQHQcalsLRRFEAIHHELNKA-TAQNKDLQwemELLQsELTELrTTQVkTAKESEKYREERDAVYS 430
Cdd:PRK04863  998 EQERTRAREQLRQAQAQ----LAQYNQVLASLKSSyDAKRQMLQ---ELKQ-ELQDL-GVPA-DSGAEERARARRDELHA 1067

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  431 EYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVtMDAGRANKEVEILRKqckalcQELk 510
Cdd:PRK04863 1068 RLSANRSRRNQLEKQLTFCEAEMDNLTKKLRKLERDYHEMREQVVNAKAGWCAV-LRLVKDNGVERRLHR------REL- 1139

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  511 eALQEADVAKCRRDWAFQERDKIVAE----RDSIRTLCDNLRRERD-----RAVSELAEALRslddtrkqkNDVSR--EL 579
Cdd:PRK04863 1140 -AYLSADELRSMSDKALGALRLAVADnehlRDVLRLSEDPKRPERKvqfyiAVYQHLRERIR---------QDIIRtdDP 1209

                         490       500       510
                  ....*....|....*....|....*....|....
gi 767964249  580 KELKEQMESQL-----EKEARFRQLmAHSSHDSA 608
Cdd:PRK04863 1210 VEAIEQMEIELsrlteELTSREQKL-AISSESVA 1242

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467196 [Multi-domain] Cd Length: 78 Bit Score: 39.10 E-value: 1.27e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1500 PRVVFIKKSQLELGVHLCGGNlhGVFVAEVEDDSPAKGpDGLVPGDLILEYGSLDVRNKTVEEVyVEMLK--PRDGVRLK 1577
Cdd:cd06712     1 PRTVHLTKEEGGFGFTLRGDS--PVQVASVDPGSCAAE-AGLKEGDYIVSVGGVDCKWSKHSEV-VKLLKsaGEEGLELQ 76


                  .
gi 767964249 1578 V 1578
Cdd:cd06712    77 V 77

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467235 [Multi-domain] Cd Length: 79 Bit Score: 39.05 E-value: 1.31e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249 1356 GSEPLGISIVsgekGG------IYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06753     6 GPAPWGFRLQ----GGkdfnqpLTISRVTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQNKI 66

PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467219 [Multi-domain] Cd Length: 85 Bit Score: 39.16 E-value: 1.36e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767964249  737 GVYAAAVLPGSPAAKEGsLAVGDRIVAINGIALDNKSLNECESLLRScQDSLTL 790
Cdd:cd06737    28 GLFVSHVSPGSQADNKG-LRVGDEIVRINGYSISQCTHEEVINLIKT-KKTVSL 79

transferase, transferring glycosyl groups

Pssm-ID: 215507 [Multi-domain] Cd Length: 977 Bit Score: 43.35 E-value: 1.40e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  168 AFATHGTAFDKRPYHRLNPDYERLKIQCV---RAMSDLQSLQNQHTNALKRCEEVAK---ETDFYHTLHSRLL------- 234
Cdd:PLN02939    8 ALLSHGCGPIRSRAPFYLPSRRRLAVSCRarrRGFSSQQKKKRGKNIAPKQRSSNSKlqsNTDENGQLENTSLrtvmelp 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  235 SDQTRLKDDVDMLRRENGQLLRERNLLQQswEDMKRLHEEDQKEIGDLRAQQQQVLKhngSSEILNKLYDTAMDKLEVVK 314
Cdd:PLN02939   88 QKSTSSDDDHNRASMQRDEAIAAIDNEQQ--TNSKDGEQLSDFQLEDLVGMIQNAEK---NILLLNQARLQALEDLEKIL 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  315 KDYDALRKryseKVAIHNADLS----RLEQLGEENQRLLKQTEMLTQQRDtaiQLQHQCALSLRRFEAIHHELNKATAQN 390
Cdd:PLN02939  163 TEKEALQG----KINILEMRLSetdaRIKLAAQEKIHVEILEEQLEKLRN---ELLIRGATEGLCVHSLSKELDVLKEEN 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  391 KDLQWEMELLQSELTELRTTQVKTAKeSEKYREERDAVYS--EYKLIMSERDqvISELDKLQTE-----VELAESKLKSS 463
Cdd:PLN02939  236 MLLKDDIQFLKAELIEVAETEERVFK-LEKERSLLDASLRelESKFIVAQED--VSKLSPLQYDcwwekVENLQDLLDRA 312

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  464 TSEKKAANEEMEALRQIKDTVtmdagrankeveilrkqckalcQELKEALQEADVAK--CRRDWAFQERDKIVAER 537
Cdd:PLN02939  313 TNQVEKAALVLDQNQDLRDKV----------------------DKLEASLKEANVSKfsSYKVELLQQKLKLLEER 366

PDZ1 domain of human syntaxin-binding protein 4 (STXBP4), PDZ2 domain of Gallus gallus uncharacterized STXBP4 isoform X1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of human syntaxin-binding protein 4 (STXBP4), PDZ2 domain of Gallus gallus uncharacterized STXBP4 isoform X1, and related domains. Human STXBP4 (also known as Synip) includes a single PDZ domain, a coiled-coil domain, and a WW domain (named for its two conserved tryptophans); Gallus gallus STXBP4 isoform X1 contains 2 PDZ domains (PDZ1 and PDZ2). Human STXBP4 plays a role in the translocation of transport vesicles from the cytoplasm to the plasma membrane: insulin induces the dissociation of the STXBP4 and STX4 complex liberating STX4 to interact with Vamp2, and to form the SNARE complex thereby promoting vesicle fusion. It may also play a role in the regulation of insulin release by pancreatic beta cells after stimulation by glucose. Human STXBP4 is also known to physically associate with a prominent isoform of TP63 (deltaNp63alpha 9) whose overexpression promotes squamous cell carcinoma development, and in doing so prevents degradation of this isoform by the Cdc20-APC/C complex, Itch, and RACK1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This STXBP4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467184 [Multi-domain] Cd Length: 89 Bit Score: 39.21 E-value: 1.40e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1349 RHVKVQKGSEpLGISIVSG----EKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLII 1414
Cdd:cd06698     3 QLITVAKSTG-LGLSIVGGinrpEGPMVFIQEVIPGGDCYKDGrLRPGDQLVSINKESLIGVTLEEAKSIL 72

PDZ domain of peripheral plasma membrane protein CASK, Caenorhabditis Lin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CASK, Caenorhabditis elegans Lin-2, and related domains. CASK and Lin-2 are membrane-associated guanylate kinase (MAGUK)-like proteins. CASK (also known as Calcium/calmodulin-dependent protein kinase, CAKI, and Camguk) has a role in synaptic transmembrane protein anchoring and ion channel trafficking. CASK may regulate transmembrane proteins that bind calcium, calmodulin, or nucleotides; it regulates the Drosophila ether a go-go (eag) potassium channel, and also regulates autophosphorylation of CaMKII. CASK binding partners include the transcription factor TBR1, and cell-surface proteins, including amyloid precursor protein, neurexins, and syndecans. Lin-2, as a component of the CLin-10-Lin-2-Lin-7 complex, plays a role in controlling the basolateral localization of the EGF receptor Let-23; this complex also associates with the neuron-specific motor protein KIF17 to transport vesicles containing N-methyl-D-aspartate (NMDA) receptor 2B along microtubules. CASK may also function in targeting or scaffolding of the protein parkin which is selectively truncated by a Parkinson's disease-causing mutation; the C-terminus of parkin functions as a class II PDZ-binding motif that binds CASK. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP6-MPP2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467267 [Multi-domain] Cd Length: 81 Bit Score: 39.00 E-value: 1.41e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1349 RHVKVQKGS-EPLGISIVSGEKGGIYVSKVTVGSIAH-QAGLEYGDQLLEFNGINLRSAT 1406
Cdd:cd10831     1 RLVQFQKNTdEPMGITLKMNEDGRCIVARIMHGGMIHrQGTLHVGDEIREINGISVANQT 60

DNA repair ATPase RecN [Replication, recombination and repair];

Pssm-ID: 440263 [Multi-domain] Cd Length: 555 Bit Score: 43.14 E-value: 1.45e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  335 LSRLEQLGE---------ENQRLLK---QTEMLtqqrDT---AIQLQHQCALSLRRFEAIHHELNKATAQNKDLQWEMEL 399
Cdd:COG0497   115 LSQLRELGEllvdihgqhEHQSLLDpdaQRELL----DAfagLEELLEEYREAYRAWRALKKELEELRADEAERARELDL 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  400 LQSELTELRTTQVKtAKESEKYREER----------DAVYSEYKLIMSERDQVISELDKLQTEVE-LAE--SKLKSSTSE 466
Cdd:COG0497   191 LRFQLEELEAAALQ-PGEEEELEEERrrlsnaeklrEALQEALEALSGGEGGALDLLGQALRALErLAEydPSLAELAER 269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  467 KKAANEEME----ALRQIKDTVTMDAGRANkEVE----ILRKQCK----------ALCQELKEALQEADvakcRRDWAFQ 528
Cdd:COG0497   270 LESALIELEeaasELRRYLDSLEFDPERLE-EVEerlaLLRRLARkygvtveellAYAEELRAELAELE----NSDERLE 344

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  529 ERDKIVAE-RDSIRTLCDNLRRERDRAVSELAEAlrslddtrkqkndVSRELKELKeqMESqlekeARFR 597
Cdd:COG0497   345 ELEAELAEaEAELLEAAEKLSAARKKAAKKLEKA-------------VTAELADLG--MPN-----ARFE 394

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

Pssm-ID: 129694 [Multi-domain] Cd Length: 1311 Bit Score: 43.50 E-value: 1.53e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   197 RAMSDLQSLQNQHTNALKRCEEVAKE-TDFYHTLH---SRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLh 272
Cdd:TIGR00606  518 RKLDQEMEQLNHHTTTRTQMEMLTKDkMDKDEQIRkikSRHSDELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKL- 596

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   273 eedQKEIGDLRAQQQQVLKHNGS-SEILNKLYDTAMD---------KLEVVKKDYDALRKRYSEKVAIHNADLSRLEQLG 342
Cdd:TIGR00606  597 ---NKELASLEQNKNHINNELESkEEQLSSYEDKLFDvcgsqdeesDLERLKEEIEKSSKQRAMLAGATAVYSQFITQLT 673

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   343 EENQRLlkqtemltqqrdtaiqlqhqCALSLRRFEAihhelnkataqNKDLQWEMELLQSELTELRTTQVKTAKESEKYR 422
Cdd:TIGR00606  674 DENQSC--------------------CPVCQRVFQT-----------EAELQEFISDLQSKLRLAPDKLKSTESELKKKE 722

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   423 EERDAVY-------SEYKLIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTMdagrankeV 495
Cdd:TIGR00606  723 KRRDEMLglapgrqSIIDLKEKEIPELRNKLQKVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTI--------M 794

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   496 EILRKQCKALcqELKEALQEADVAKCRRDWAFQERDKIVAERDsirtlcdnlrRERDRAVSELAEALRSLDDTRKQKNDV 575
Cdd:TIGR00606  795 ERFQMELKDV--ERKIAQQAAKLQGSDLDRTVQQVNQEKQEKQ----------HELDTVVSKIELNRKLIQDQQEQIQHL 862

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 767964249   576 SRELKELKEQmESQLEKEARFRQLMAHSshdsaidtdSMEWETEVVEFERETED 629
Cdd:TIGR00606  863 KSKTNELKSE-KLQIGTNLQRRQQFEEQ---------LVELSTEVQSLIREIKD 906

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.

Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 39.90 E-value: 1.58e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   373 LRRFEAIHHELNKataQNKDLQWEMELLQS-------ELTELRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISE 445
Cdd:pfam20492   29 LEESEETAEELEE---ERRQAEEEAERLEQkrqeaeeEKERLEESAEMEAEEKEQLEAELAEAQEEIARLEEEVERKEEE 105

                           90
                   ....*....|....*
gi 767964249   446 LDKLQTEVELAESKL 460
Cdd:pfam20492  106 ARRLQEELEEAREEE 120

PDZ domain 3 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467167 [Multi-domain] Cd Length: 88 Bit Score: 39.16 E-value: 1.61e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  719 PLHINLSGQKDSGiSLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTLSL 792
Cdd:cd06679    12 SLGISVAGGRGSR-RGDLPIYVTNVQPDGCLGRDGRIKKGDVLLSINGISLTNLSHSEAVAVLKASAASSSIVL 84

Src Homology 3 domain of Disks large homolog proteins; The DLG-like proteins are scaffolding proteins that cluster at synapses and are also called PSD (postsynaptic density)-95 proteins or SAPs (synapse-associated proteins). They play important roles in synaptic development and plasticity, cell polarity, migration and proliferation. They are members of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. DLG-like proteins contain three PDZ domains and varying N-terminal regions. All DLG proteins exist as alternatively-spliced isoforms. Vertebrates contain four DLG proteins from different genes, called DLG1-4. DLG4 and DLG2 are found predominantly at postsynaptic sites and they mediate surface ion channel and receptor clustering. DLG3 is found axons and some presynaptic terminals. DLG1 interacts with AMPA-type glutamate receptors and is critical in their maturation and delivery to synapses. The SH3 domain of DLG4 binds and clusters the kainate subgroup of glutamate receptors via two proline-rich sequences in their C-terminal tail. It also binds AKAP79/150 (A-kinase anchoring protein). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212795 [Multi-domain] Cd Length: 61 Bit Score: 38.46 E-value: 1.62e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1597 YIRALYDRLADVE-----QELSFKKDDILYV----DDTLpqgtfgsWMAWQLDENAQKIQRGQIPSK 1654
Cdd:cd11861     1 YVRALFDYDPSRDsglpsQGLSFKFGDILHVtnasDDEW-------WQARRVTPNGEEEEVGVIPSK 60

endonuclease subunit; Provisional

Pssm-ID: 222878 [Multi-domain] Cd Length: 562 Bit Score: 43.08 E-value: 1.66e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  265 WEDMKRLHEEdqKEIGDLRAQQQQVLKHN----------GSS--------------EILNKLYD----TAMDKLEVVK-- 314
Cdd:PHA02562  100 YCNGKLLDES--ASSKDFQKYFEQMLGMNyksfkqivvlGTAgyvpfmqlsaparrKLVEDLLDisvlSEMDKLNKDKir 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  315 ------KDYDALRKRYSEKVAIHNADLSRLEQLGEENQRLLKqtEMLTQQRDTAiqlqhqcalslrrfEAIHHELNKATA 388
Cdd:PHA02562  178 elnqqiQTLDMKIDHIQQQIKTYNKNIEEQRKKNGENIARKQ--NKYDELVEEA--------------KTIKAEIEELTD 241

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  389 QNKDLQWEMELLQSELTELRTTQVKTAKESEKYreERDAVYSEYKLIMSERDQVISELDKLQTEVElaeSKLKSSTSEKK 468
Cdd:PHA02562  242 ELLNLVMDIEDPSAALNKLNTAAAKIKSKIEQF--QKVIKMYEKGGVCPTCTQQISEGPDRITKIK---DKLKELQHSLE 316

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  469 AANEEMEALRQIKDtvtmdagrankevEILRKQCKAlcQELKealqeADVAKCRRDWAfqerdKIVAERDSIRTLCDNLR 548
Cdd:PHA02562  317 KLDTAIDELEEIMD-------------EFNEQSKKL--LELK-----NKISTNKQSLI-----TLVDKAKKVKAAIEELQ 371

                         330       340       350
                  ....*....|....*....|....*....|....
gi 767964249  549 RERDRAVSELAEALRSLDDTRKQKNDVSRELKEL 582
Cdd:PHA02562  372 AEFVDNAEELAKLQDELDKIVKTKSELVKEKYHR 405

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 42.21 E-value: 1.74e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  482 DTVTMDAGRANKEVEILRKQCKALCQELKEALQEAdvakcrRDWAfQERDKIVAERDSIRTLCDNLRRERDRAVSELAEA 561
Cdd:COG1340     4 DELSSSLEELEEKIEELREEIEELKEKRDELNEEL------KELA-EKRDELNAQVKELREEAQELREKRDELNEKVKEL 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249  562 lrslddtRKQKNDVSRELKELKEQMESQLEKEARFRQlmahsshdSAIDTDSMEWETEVVEFERETEDIDLK 633
Cdd:COG1340    77 -------KEERDELNEKLNELREELDELRKELAELNK--------AGGSIDKLRKEIERLEWRQQTEVLSPE 133

PDZ domain of LIM Kinase (LIMK) family, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the LIMK protein family, and related domains. The LIMK family is composed of LIMK1 and LIMK2, which are common downstream effectors of several signalization pathways and function as signaling nodes that control cytoskeleton dynamics through the phosphorylation of cofilin family proteins. They also control microtubule dynamics. The LIMK1 PDZ domain binds tubulin and nischarin. LIMK1 also binds a carboxy-terminal motif of membrane type 1-matrix metalloproteinase (MT1-MMP, also known as MMP14) having features of a PDZ domain-binding site; MT1-MMP is a major protease involved in dissemination of carcinoma cells during cancer progression. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LIMK-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467236 [Multi-domain] Cd Length: 92 Bit Score: 39.18 E-value: 1.75e-03

                          10        20        30
                  ....*....|....*....|....*....|
gi 767964249  754 SLAVGDRIVAINGIALDNKSLNECESLLRS 783
Cdd:cd06754    50 SLHVGDRILEVNGTPVRDLSLEEIDDLIQS 79

PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2)and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467168 [Multi-domain] Cd Length: 89 Bit Score: 39.25 E-value: 1.77e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  635 LGFDMAEGVNEpcFPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVV 706
Cdd:cd06680    13 LGFSIVGGYEE--SHGNQPFFVKSIVPGTPAynDGRLKCGDIILAVNGVSTVGMSHAALVPLLKEQRGRVTLTV 84

PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467285 [Multi-domain] Cd Length: 92 Bit Score: 39.01 E-value: 1.79e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1347 EPRHVKVQKGSEP-LGISIVSGEKG-----GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQQCD 1419
Cdd:cd23072     1 EITLVNLKKDAKYgLGFQIVGGEKSgrldlGIFISSITPGGPADLDGrLKPGDRLISVNDVSLEGLSHDAAVEILQNAPE 80


                  ....*
gi 767964249 1420 TITIL 1424
Cdd:cd23072    81 DVTLV 85

PDZ domain 7 of PDZ domain containing 2 (PDZD2), PDZ domain 4 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of PDZD2, also known as KIAA0300, PIN-1, PAPIN, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family include the PDZ domain of the secreted mature form of human interleukin-16 (IL-16); this is the fourth PDZ domain (PDZ4) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467244 [Multi-domain] Cd Length: 86 Bit Score: 39.13 E-value: 1.81e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249 1351 VKVQKGSEPLGISIvSGEKGG------IYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06763     4 VELEKGSAGLGFSL-EGGKGSplgdrpLTIKRIFKGGAAEQSGvLQVGDEILQINGTSLQGLTRFEA 69

PDZ domain of ARHGAP21 and ARHGAP23, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ARHGAP21, ARHGAP23, and related domains. This subfamily includes the GAPs (GTPase activating proteins): ARHGAP21 (Rho GTPase-activating protein 21; also known as Rho GTPase-activating protein 10, Rho-type GTPase-activating protein 21) and ARHGAP23 (Rho GTPase-activating protein 23; also known as Rho-type GTPase-activating protein 23). GAPs deactivate Rho GTPases by accelerating GTP hydrolysis. ARHGAP21/23 interact with a planar cell polarity (PCP) protein Pk1 to regulate a lateral signaling pathway in migrating cells. The ARHGAP21 PDZ domain binds claudin-2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ARHGAP21-23-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467238 [Multi-domain] Cd Length: 109 Bit Score: 39.75 E-value: 1.84e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767964249 1372 IYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIgQQCDTITILA 1425
Cdd:cd06756    55 IFVKQVKEGGPAHQAGLCTGDRIVKVNGESVIGKTYSQVIALI-QNSDSTLELS 107

circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine endoprotease DegP and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do) and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for combining with other DegP monomers to form a stable oligomer structure. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegP family PDZ domain 1 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467630 [Multi-domain] Cd Length: 91 Bit Score: 39.00 E-value: 1.91e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 767964249  731 GISLENGVYAAAVLPGSPAAKEGsLAVGDRIVAING 766
Cdd:cd10839    20 GLKEPKGALVAQVLPDSPAAKAG-LKAGDVILSLNG 54

PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the first PDZ domain (PDZ1) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467240 [Multi-domain] Cd Length: 87 Bit Score: 38.79 E-value: 2.06e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249 1355 KGSEPLGISIVSGE---KG--GIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06759     9 AGGKGLGFSIVGGRdspRGpmGIYVKTIFPGGAAAEDGrLKEGDEILEVNGESLQGLTHQEA 70

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 42.21 E-value: 2.10e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   393 LQWEMELLQSELTE-LRTTQVKTAKESEKYREERDAVYSEYKLIMSERDQVISELDKLQTEV--ELAESKLKSSTSEKKA 469
Cdd:pfam13868   67 RKEERKRYRQELEEqIEEREQKRQEEYEEKLQEREQMDEIVERIQEEDQAEAEEKLEKQRQLreEIDEFNEEQAEWKELE 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   470 ANEEMEALRQIKDTVTMDAGR-ANKEVEILRKQCK--ALCQELKEALQEADVAKcrrdwafQERDKIVAERdsirTLCDN 546
Cdd:pfam13868  147 KEEEREEDERILEYLKEKAEReEEREAEREEIEEEkeREIARLRAQQEKAQDEK-------AERDELRAKL----YQEEQ 215

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 767964249   547 LRRERDRAVSELAEALRSLDDTRKQkNDVSRELKELKEQMESQLEKEARFRQL 599
Cdd:pfam13868  216 ERKERQKEREEAEKKARQRQELQQA-REEQIELKERRLAEEAEREEEEFERML 267

PDZ domain 1 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467213 [Multi-domain] Cd Length: 85 Bit Score: 38.73 E-value: 2.18e-03

                          10        20
                  ....*....|....*....|....*
gi 767964249  743 VLPGSPAAKEGSLAVGDRIVAINGI 767
Cdd:cd06731    32 VVPDGPAALDGKLRTGDVLVSVNDT 56

PDZ domain 5 of multi-PDZ-domain protein 1 (MUPP1), PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467157 [Multi-domain] Cd Length: 98 Bit Score: 39.13 E-value: 2.24e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  616 WETEVVEFERETEDidlKALGFDMAEgVNEPCFPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIK 693
Cdd:cd06669     4 WSDEVTVIELEKGD---RGLGFSILD-YQDPLDPSETVIVIRSLVPGGVAeqDGRLLPGDRLVFVNDVSLENASLDEAVQ 79


                  ..
gi 767964249  694 AL 695
Cdd:cd06669    80 AL 81

PDZ domain 0 of Gallus gallus interleukin-16, and related domains; N-terminal PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1) of Gallus gallus IL16, and related domains. This IL16-PDZ0 domain is not found in the human pro-interleukin-16 (isoform 1, 1332 AA, pro-IL-16) which has 4 PDZ domains (PDZ1-4). Gallus gallus IL-16 has 5 PDZ domains: this N-terminal PDZ0, followed by 4 PDZ domains (PDZ1-4) which are homologous to human pro-IL-16 PDZ1-4. Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers, including Gallus gallus IL-16 in the development of ovarian tumor and tumor-associated neoangiogenesis (TAN) in laying hens, an animal model of spontaneous ovarian cancer. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This IL16-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467275 [Multi-domain] Cd Length: 83 Bit Score: 38.72 E-value: 2.26e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  720 LHINLSGQKDSGiSLENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRS 783
Cdd:cd23062    11 SGIKLSRNPNCA-SLWKGFTGCHVPAGGTANRDGCLSPRDELLTLNGQSLKDLSSKEAESLIQS 73

Ciliary protein causing Leber congenital amaurosis disease; Lebercilin is a family of eukaryotic ciliary proteins. Mutations in the gene, LCA5, are implicated in the disease Leber congenital amaurosis. In photoreceptors, lebercilin is uniquely localized at the cilium that bridges the inner and outer segments. Lebercilin functions as an integral element of selective protein transport through photoreceptor cilia. Lebercilin specifically interacts with the intraflagellar transport (IFT), and disruption of IFT can lead to Leber congenital amaurosis.

Pssm-ID: 464776 [Multi-domain] Cd Length: 193 Bit Score: 41.04 E-value: 2.29e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   238 TRLKDDVDMLRRENGQLLRERNLLQQswedMKRLHEEDQKEIGDLRAQQQQVL-KHNGSSEILNKLYDTAMDKLEVVKKd 316
Cdd:pfam15619   14 KELQNELAELQSKLEELRKENRLLKR----LQKRQEKALGKYEGTESELPQLIaRHNEEVRVLRERLRRLQEKERDLER- 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   317 ydALRKRYSEkvaIH--NADLSRLEQLG--------EENQRLLKQTEMLTQQRDTAIQ-LQHQCALSLRRFeaiHHELNK 385
Cdd:pfam15619   89 --KLKEKEAE---LLrlRDQLKRLEKLSedknlaerEELQKKLEQLEAKLEDKDEKIQdLERKLELENKSF---RRQLAA 160

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 767964249   386 ATAQNKDLQWEMELLQSELTELRTtqvktaKESEKYRE 423
Cdd:pfam15619  161 EKKKHKEAQEEVKILQEEIERLQQ------KLKEKERE 192

PDZ domain 11 of MUPP1 of multi-PDZ-domain protein 1 (MUPP1), domain 9 of PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 11 of MUPP1, PDZ domain 9 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ11 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467162 [Multi-domain] Cd Length: 87 Bit Score: 38.80 E-value: 2.35e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249  727 QKDSGISL---------ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06674     9 QKKPGRGLglsivgkrnDTGVFVSDIVKGGAADADGRLMQGDQILSVNGEDVRNASQEAAAALLKCAQGKVRL 81

reticulocyte binding protein 2-like protein; Provisional

Pssm-ID: 240419 [Multi-domain] Cd Length: 2722 Bit Score: 42.90 E-value: 2.39e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  296 SEILNKLYDTAMDKLEVVKKDYD----ALRKRYSEKVAIHNADLSRLEQLGEENQRLLKQTEMLTQQRDTA-----IQLQ 366
Cdd:PTZ00440 1086 VEALLKKIDENKNKLIEIKNKSHehvvNADKEKNKQTEHYNKKKKSLEKIYKQMEKTLKELENMNLEDITLnevneIEIE 1165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  367 HQCALslrrfeaIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESE------KYREERDAVYSEYKLIM---- 436
Cdd:PTZ00440 1166 YERIL-------IDHIVEQINNEAKKSKTIMEEIESYKKDIDQVKKNMSKERNdhlttfEYNAYYDKATASYENIEeltt 1238

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  437 --------SERDQVISELDKLQTEVelaESKLKSSTSEkkaaNEEME-ALRQIKDT----VTMDAGRANKEVEILRKQCK 503
Cdd:PTZ00440 1239 eakglkgeANRSTNVDELKEIKLQV---FSYLQQVIKE----NNKMEnALHEIKNMyeflISIDSEKILKEILNSTKKAE 1311

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  504 ALCQELKEALQEADvakcrrDWAFQERDKIVAERDSIRTLCDNLRRER-DRAVSELAEALRSLDDTRKQKNDVSRELKEL 582
Cdd:PTZ00440 1312 EFSNDAKKELEKTD------NLIKQVEAKIEQAKEHKNKIYGSLEDKQiDDEIKKIEQIKEEISNKRKEINKYLSNIKSN 1385

                         330
                  ....*....|...
gi 767964249  583 KEQMESQLEKEAR 595
Cdd:PTZ00440 1386 KEKCDLHVRNASR 1398

Borrelia P83/100 protein; This family consists of several Borrelia P83/P100 antigen proteins.

Pssm-ID: 114011 [Multi-domain] Cd Length: 489 Bit Score: 42.30 E-value: 2.47e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   404 LTELRTTQVKTAKESEKYREERDavyseyklimserdqviSELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDT 483
Cdd:pfam05262  169 VSDVDTDSISDKKVVEALREDNE-----------------KGVNFRRDMTDLKERESQEDAKRAQQLKEELDKKQIDADK 231

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   484 VTMDAGRANKEVEILRKqckalcqELKEALQE-------ADVAKCRRDWAFQERDKIVAERDSIRT--LCDNLRRERDRA 554
Cdd:pfam05262  232 AQQKADFAQDNADKQRD-------EVRQKQQEaknlpkpADTSSPKEDKQVAENQKREIEKAQIEIkkNDEEALKAKDHK 304

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   555 VSELAEALRSLDDTRKQKN-DVSRELKELKEQMESQL-EKEARfrqlmAHSSHDSAIDTDSMEWETEVVE 622
Cdd:pfam05262  305 AFDLKQESKASEKEAEDKElEAQKKREPVAEDLQKTKpQVEAQ-----PTSLNEDAIDSSNPVYGLKVVD 369

PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of tamalin, cytohesin-1-interacting protein, and related domains. Tamalin (trafficking regulator and scaffold protein tamalin, also known as general receptor for phosphoinositides 1-associated scaffold protein, GRASP) functions to link receptors, including group 1 metabotropic glutamate receptors (mGluRs), to neuronal proteins. The tamalin PDZ domain binds the C-terminal domains of group I mGluRs; it also binds potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2), neurotrophin-3 (NT3) TrkCT1-truncated receptor, SAP90/PSD-95-associated protein, and tamalin itself. CYTIP (cytohesin-1-interacting protein, also known as Pleckstrin homology Sec7 and coiled-coil domain-binding protein) sequesters cytohesin-1 in the cytoplasm, limiting its interaction with beta2 integrins; cytohesin-1 binds the CYTIP coiled coil domain. The CYTIP PDZ domain can bind the C-terminal peptide of protocadherin alpha-1 (PCDHA1), indicating a possible interaction between the two. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This tamalin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467197 [Multi-domain] Cd Length: 91 Bit Score: 38.76 E-value: 2.51e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767964249 1373 YVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARLIIGQQCDTITIL 1424
Cdd:cd06713    38 YVCRVHEDSPAYLAGLTAGDVILSVNGVSVEGASHQEIVELIRSSGNTLRLE 89

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467621 [Multi-domain] Cd Length: 91 Bit Score: 38.81 E-value: 2.62e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249 1357 SEPLGISIVSGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQARL 1412
Cdd:cd06779    12 SPLLAKELGLPVNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAAL 67

N-terminal Src Homology 3 domain of Ct10 Regulator of Kinase adaptor proteins; CRK adaptor proteins consists of SH2 and SH3 domains, which bind tyrosine-phosphorylated peptides and proline-rich motifs, respectively. They function downstream of protein tyrosine kinases in many signaling pathways started by various extracellular signals, including growth and differentiation factors. Cellular CRK (c-CRK) contains a single SH2 domain, followed by N-terminal and C-terminal SH3 domains. It is involved in the regulation of many cellular processes including cell growth, motility, adhesion, and apoptosis. CRK has been implicated in the malignancy of various human cancers. The N-terminal SH3 domain of CRK binds a number of target proteins including DOCK180, C3G, SOS, and cABL. The CRK family includes two alternatively spliced protein forms, CRKI and CRKII, that are expressed by the CRK gene, and the CRK-like (CRKL) protein, which is expressed by a distinct gene (CRKL). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212692 [Multi-domain] Cd Length: 55 Bit Score: 37.34 E-value: 2.81e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249 1597 YIRALYDRLADVEQELSFKKDDILYVDDTlPQGTFgsWMAwqldENAQKiQRGQIPSKYVKR 1658
Cdd:cd11758     2 YVRALFDFPGNDDEDLPFKKGEILTVIRK-PEEQW--WNA----RNSEG-KTGMIPVPYVEK 55

PDZ domain 2 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467155 [Multi-domain] Cd Length: 80 Bit Score: 38.03 E-value: 2.90e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767964249  737 GVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06667    23 GVVVKTILPGGVADRDGRLRSGDHILQIGDTNLRGMGSEQVAQVLRQCGSHVRL 76

circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB, and HtrA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the cyanobacterial Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB and HtrA, and related domains. These three proteases are functionally overlapping, and are involved in a number of key physiological responses, ranging from protection against light and heat stresses to phototaxis. HhoA assembles into trimers, mediated by its protease domain and further into a hexamer by a novel interaction between the PDZ domains of opposing trimers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This HhoA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467629 [Multi-domain] Cd Length: 104 Bit Score: 38.84 E-value: 2.93e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767964249 1368 EKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQAR 1411
Cdd:cd10838    31 EVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRI 74

circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Escherichia coli DegS and related domains. DegS (also known as Site-1 protease DegS, S1P protease DegS, and Site-1-type intramembrane protease) participates in the activation of the sigma(E) extracytoplasmic stress response. Initially, there is an accumulation of misfolded membrane proteins (OMPs) in the periplasm which bind by their YXF motif to the DegS PDZ domain, activating DegS-catalyzed cleavage of the RseA periplasmic domain and making RseA a substrate for cleavage by another membrane protease RseP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegS family PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467620 [Multi-domain] Cd Length: 93 Bit Score: 38.53 E-value: 2.93e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 767964249 1370 GGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATE 1407
Cdd:cd06777    25 QGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLE 62

PDZ domain 1 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZRN4-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467199 [Multi-domain] Cd Length: 92 Bit Score: 38.53 E-value: 2.95e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249  635 LGFDMAEG---VNEPCFPGDCGIFVTKV-DKGSIAD-GRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRR 708
Cdd:cd06715    14 LGFNIIGGrpcENNQEGSSSEGIYVSKIvENGPAADeGGLQVHDRIIEVNGKDLSKATHEEAVEAFRTAKEPIVVQVLR 92

Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding protein family member, Neural precursor cell Expressed, Developmentally Down-regulated 9; NEDD9 is also called human enhancer of filamentation 1 (HEF1) or CAS-L (Crk-associated substrate in lymphocyte). It was first described as a gene predominantly expressed in early embryonic brain, and was also isolated from a screen of human proteins that regulate filamentous budding in yeast, and as a tyrosine phosphorylated protein in lymphocytes. It promotes metastasis in different solid tumors. NEDD9 localizes in focal adhesions and associates with FAK and Abl kinase. It also interacts with SMAD3 and the proteasomal machinery which allows its rapid turnover; these interactions are not shared by other CAS proteins. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212935 Cd Length: 57 Bit Score: 37.27 E-value: 3.35e-03

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 767964249 1599 RALYDRLADVEQELSFKKDDILYVDDTLPQGTFGSWM 1635
Cdd:cd12002     3 RALYDNVPECAEELAFRKGDILTVIEQNTGGLEGWWL 39

PDZ domain 2 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZRN4-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467200 [Multi-domain] Cd Length: 88 Bit Score: 38.02 E-value: 3.58e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249 1357 SEPLGISIVSG----EKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSatEQQARLIIGQQCDTITIL 1424
Cdd:cd06716    14 QEKLGLTLCYRtddeEDTGIYVSEVDPNSIAAKDGrIREGDQILQINGVDVQN--REEAIALLSEEEKSITLL 84

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467249 [Multi-domain] Cd Length: 80 Bit Score: 37.80 E-value: 3.61e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249  653 GIFVTKVDKGSIAD-GRLRVNDWLLRINDVDLINKDKKQaikallngegainmVVRRRKSLGGKVV 717
Cdd:cd06768    24 GHFIREVDPGSPAErAGLKDGDRLVEVNGENVEGESHEQ--------------VVEKIKASGNQVT 75

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467621 [Multi-domain] Cd Length: 91 Bit Score: 38.43 E-value: 3.68e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249 1522 HGVFVAEVEDDSPAKGPdGLVPGDLILEYGSLDVRNKT-VEEVYVEMlKPRDGVRLKVQYRPEEFT 1586
Cdd:cd06779    25 RGVLVAEVIPGSPAAKA-GLKEGDVILSVNGKPVTSFNdLRAALDTK-KPGDSLNLTILRDGKTLT 88

Src Homology 3 domain of Nephrocystin (or Nephrocystin-1); Nephrocystin contains an SH3 domain involved in signaling pathways that regulate cell adhesion and cytoskeletal organization. It is a protein that in humans is associated with juvenile nephronophthisis, an inherited kidney disease characterized by renal fibrosis that lead to chronic renal failure in children. It is localized in cell-cell junctions in renal duct cells, and is known to interact with Ack1, an activated Cdc42-associated kinase. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212704 [Multi-domain] Cd Length: 54 Bit Score: 37.29 E-value: 3.70e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1597 YIRALYDRLADVEQELSFKKDDILYVDDTLPQGtfgswmaWQLDENAqKIQRGQIPSKYVK 1657
Cdd:cd11770     1 LYEALSDFQAEQEGDLSFKKGEVLRIISKRADG-------WWLAENS-KGNRGLVPKTYLK 53

PDZ domain 4 of inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ4,5 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467278 [Multi-domain] Cd Length: 82 Bit Score: 37.88 E-value: 3.99e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767964249  719 PLHINLSGQKDSgisLENGVYAAAVLPGSPAAKEGSLAVGDRIVAING 766
Cdd:cd23065    10 PLGVSVVGGKNH---VTTGCIITHIYPNSIVAADKRLKVFDQILDING 54

Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. The structure contains 5 spectrin like alpha helical repeats.

Pssm-ID: 428797 [Multi-domain] Cd Length: 542 Bit Score: 41.76 E-value: 4.02e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   250 ENGQLLRERNLLQQSWEDMKRLhEEDQKEIGDLRAQQQQVLK------HNGSSEILNKLYDTAMDKLEVVKKDYDALRKR 323
Cdd:pfam06160  170 ESGDYLEAREVLEKLEEETDAL-EELMEDIPPLYEELKTELPdqleelKEGYREMEEEGYALEHLNVDKEIQQLEEQLEE 248

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   324 YSEkvAIHNADLSRLEqlgEENQRLLKQTEMLTQQRDTAIQLQHQCALSLRRFEAihhELNKATAQNKDLQWEMELLQ-- 401
Cdd:pfam06160  249 NLA--LLENLELDEAE---EALEEIEERIDQLYDLLEKEVDAKKYVEKNLPEIED---YLEHAEEQNKELKEELERVQqs 320

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   402 -----SELTELR--TTQVKTAK----ESEKYREERDAVYSEyklIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAA 470
Cdd:pfam06160  321 ytlneNELERVRglEKQLEELEkrydEIVERLEEKEVAYSE---LQEELEEILEQLEEIEEEQEEFKESLQSLRKDELEA 397

                          250
                   ....*....|
gi 767964249   471 NEEMEALRQI 480
Cdd:pfam06160  398 REKLDEFKLE 407

PDZ domain 1 of inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ4,5 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467276 [Multi-domain] Cd Length: 87 Bit Score: 37.88 E-value: 4.05e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  653 GIFVTKVDKGSIAD--GRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVR 707
Cdd:cd23063    31 GIFIKGIIPDSPAHkcGRLKVGDRILSVNGNDVRNSTEQAAIDLIKEADFKIVLEIQ 87

PDZ domain 2 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PSZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467246 [Multi-domain] Cd Length: 77 Bit Score: 37.71 E-value: 4.21e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767964249 1361 GISIvsgeKGGIYVSKVTVGS-IAHQAGLEYGDQLLEFNGINL--RSATEQQARLIIGQQCDTITILAQ 1426
Cdd:cd06765    11 GISL----ENGVFISRIVPGSpAAKEGSLTVGDRIIAINGIALdnKSLSECEALLRSCRDSLSLSLMKV 75

PDZ domain 3 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of the Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa and can also form homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the third PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467233 [Multi-domain] Cd Length: 89 Bit Score: 38.19 E-value: 4.27e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1351 VKVQKGSEPLGISIVSGEKGG----IYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQARLIIGQ 1416
Cdd:cd06751     4 VELSKMKQSLGISISGGIESKvqpvVKIEKIFPGGAAALSGnLKAGYELVSVDGESLQQVTHQQAVDIIRR 74

circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis YlbL and related domains. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. Deletion of both proteases leads to accumulation of the cell division inhibitor YneA. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This YlbL family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

Pssm-ID: 467637 [Multi-domain] Cd Length: 83 Bit Score: 37.86 E-value: 4.32e-03

                          10        20        30
                  ....*....|....*....|....*....|
gi 767964249  737 GVYAAAVLPGSPAAkeGSLAVGDRIVAING 766
Cdd:cd23080     1 GVYVLSVVENMPAK--GILEAGDKITAIDG 28

PDZ domain 9 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 9 of MUPP1. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ9 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ9 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467263 [Multi-domain] Cd Length: 79 Bit Score: 37.71 E-value: 4.33e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767964249 1350 HVKVQKGSEPLGISIVSGEK-GGIYVSKVTVGSIAHQAG-LEYGDQLLEFN 1398
Cdd:cd10817     1 HVELPKDQGGLGIAISEEDTeNGIVIKSLTEGGPAAKDGrLKVGDQILAVD 51

PDZ domain 1 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZRN4-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467199 [Multi-domain] Cd Length: 92 Bit Score: 38.14 E-value: 4.41e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  707 RRRKSLGGKVVTPlhiNLSGQKDSGISLEnGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQD 786
Cdd:cd06715     9 RENGSLGFNIIGG---RPCENNQEGSSSE-GIYVSKIVENGPAADEGGLQVHDRIIEVNGKDLSKATHEEAVEAFRTAKE 84


                  ....*...
gi 767964249  787 SLTLSLLK 794
Cdd:cd06715    85 PIVVQVLR 92

PDZ domain 1 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467213 [Multi-domain] Cd Length: 85 Bit Score: 37.96 E-value: 4.58e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249 1350 HVKVQKGSEPLGISIVSGEKGG--IYVSKVTVGSIAHQAG-LEYGDQLLEFNGINLRSATEQQA 1410
Cdd:cd06731     3 RTSLKKSARGFGFTIIGGDEPDefLQIKSVVPDGPAALDGkLRTGDVLVSVNDTCVLGYTHADV 66

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440556 [Multi-domain] Cd Length: 341 Bit Score: 41.01 E-value: 4.63e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1346 EEPRHVKVQKGSEPLGISI-VSGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLRSATEQQA-RLIIGQQCDTITI 1423
Cdd:COG0793    46 EEYEDFQESTSGEFGGLGAeLGEEDGKVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAvKLLRGKAGTKVTL 125

PDZ domain of Rab3-interacting molecule 1 (RIM), RIM2, piccolo and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RIM, RIM2, piccolo and related domains. RIM proteins and Gallus gallus protein piccolo (also called aczonin) are involved in neurotransmitter release at presynaptic active zones, the site of vesicle fusion. A protein complex containing RIM proteins positions synaptic vesicles containing synaptotagmin at the active zone. RIM proteins simultaneously activate docking and priming of synaptic vesicles and recruit Ca2+-channels to active zones, thereby connecting primed synaptic vesicles to Ca2+-channels. RIM binding to vesicular Rab proteins (Rab3 and Rab27 isoforms) mediates vesicle docking; RIM binding to Munc13 activates vesicle priming; RIM binding to the Ca2+-channel, both directly and indirectly via RIM-BP, recruits the Ca2+-channels. The RIM PDZ domain interacts with the C-termini of N- and P/Q-type voltage-gated Ca2+-channels. RIM1, RIM2 and piccolo also participate in regulated exocytosis through binding cAMP-GEFII (cAMP-binding protein-guanidine nucleotide exchange factor II). The piccolo PDZ domain binds cAMP-GEFII. RIM2 also plays a role in dendrite formation by melanocytes. Caenorhabditis elegans RIM (also known as unc-10) may be involved in the regulation of defecation and daumone response. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467198 [Multi-domain] Cd Length: 95 Bit Score: 37.92 E-value: 4.68e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 767964249  650 GDCGIFVTKVDKGSIAD--GRLRVNDWLLRINDVDLINK 686
Cdd:cd06714    36 GRLGAYVTKVKPGSVADtvGHLREGDEVLEWNGISLQGK 74

PDZ domain of protein Lin-7 and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Lin-7 (also known as LIN-7 or LIN7), and related domains. Lin-7 targets and organize protein complexes to epithelial and synaptic plasma membranes. There are three mammalian Lin-7 homologs: Lin-7A (protein lin-7 homolog A, also known as mammalian lin-seven protein 1 (MALS-1), vertebrate lin-7 homolog 1 (Veli-1), tax interaction protein 33); Lin-7B (also known as MALS-2, Veli-2); and Lin-7C (also known as MALS-3, Veli-3). Lin-7 is involved in localization of the Let-23 growth factor receptor to the basolateral membrane of epithelial cells, in tight junction localization of insulin receptor substrate p53 (IRSp53), in retaining gamma-aminobutyric (GABA) transporter (BGT-1) at the basolateral surface of epithelial cells, and in regulating recruitment of neurotransmitter receptors to the postsynaptic density (PSD). The Lin7 PDZ domain binds Let-23, BGT and beta-catenin, and NMDA (N-methyl-D-aspartate) receptor NR2B. Lin-7 also binds to the PDZ binding motif located in the C-terminal tail of Rhotekin, an effector protein for small GTPase Rho. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Lin-7-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467258 [Multi-domain] Cd Length: 86 Bit Score: 37.80 E-value: 4.69e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767964249  738 VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLLRSCQDSLTL 790
Cdd:cd06796    28 IYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAAQGSVKL 80

PDZ domain 7 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 6 of PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of MUPP1 and PDZ domain 6 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467159 [Multi-domain] Cd Length: 96 Bit Score: 38.07 E-value: 5.18e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  617 ETEVVEFERETEdidlKALGFDMAEGVNEPCFPGD----CGIFVTKVDKGSIAD--GRLRVNDWLLRINDVDLINKDKKQ 690
Cdd:cd06671     1 PPRRVELWREPG----KSLGISIVGGRVMGSRLSNgeeiRGIFIKHVLEDSPAGrnGTLKTGDRILEVNGVDLRNATHEE 76


                  ....*..
gi 767964249  691 AIKALLN 697
Cdd:cd06671    77 AVEAIRN 83

Myosin heavy chain [General function prediction only];

Pssm-ID: 227355 [Multi-domain] Cd Length: 1463 Bit Score: 41.60 E-value: 5.22e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  321 RKRYSEKVAIhNADLsrleQLGEENQRLLKQTEmltqqrdtAIQLQHQCALSLRRFEAIHHELNKATAQNKDL-----QW 395
Cdd:COG5022   809 RKEYRSYLAC-IIKL----QKTIKREKKLRETE--------EVEFSLKAEVLIQKFGRSLKAKKRFSLLKKETiylqsAQ 875

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  396 EMELLQSELTELRTTqvktakesekyREERDAVYseykLIMSERDQVISELDKLQTEVELAESKLKS--STSEKKAANEe 473
Cdd:COG5022   876 RVELAERQLQELKID-----------VKSISSLK----LVNLELESEIIELKKSLSSDLIENLEFKTelIARLKKLLNN- 939

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  474 mealRQIKDTVTMDAGRaNKEVEILRKQCKalcqELKEALQEadvakcrrdwafqerdkivaeRDSIRTLCDNLRRERDR 553
Cdd:COG5022   940 ----IDLEEGPSIEYVK-LPELNKLHEVES----KLKETSEE---------------------YEDLLKKSTILVREGNK 989

                         250       260       270
                  ....*....|....*....|....*....|.
gi 767964249  554 AVSELAEALRSLDDTRKQKNDVSRELKELKE 584
Cdd:COG5022   990 ANSELKNFKKELAELSKQYGALQESTKQLKE 1020

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.70 E-value: 5.37e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  874 GGPLQVCPQACPSASERSLSSFRSDASGDRGFGLVD---VRGRRPLLPFETEVGPCGVGEAsldKADSEGSNSGGTWPka 950
Cdd:PHA03307   17 GGEFFPRPPATPGDAADDLLSGSQGQLVSDSAELAAvtvVAGAAACDRFEPPTGPPPGPGT---EAPANESRSTPTWS-- 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  951 mlSSTAVPEKlsvykkPKQRKSIFDPNTFKRPQTPPKIDYLLPGPGPAHSPQPSKRAGPLTPPKPPRRSDSIKFQHRLET 1030
Cdd:PHA03307   92 --LSTLAPAS------PAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVA 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1031 SSESEATLVGSSPSTSP---------PSALPPDVDPGEPMHASPPRKARVRIASSYYPEGDGDSSHLPAKKSCDEDLTSQ 1101
Cdd:PHA03307  164 SDAASSRQAALPLSSPEetarapsspPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSE 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1102 KVD-ELGQKRRRPKSAPSFRPKLAPVVIPAQFLEEQKCVPASGELSPELQEWAPYSPGHSSRHSNPPLYPSRPSVGTVPR 1180
Cdd:PHA03307  244 SSGcGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRE 323

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1181 SLTPSTTVSSILRNPIYTVRS---HRVGPCSSPPAARDAGPQGLHPSVQHQGRLSldlshrtcsdysemRATHGSNSLPS 1257
Cdd:PHA03307  324 SSSSSTSSSSESSRGAAVSPGpspSRSPSPSRPPPPADPSSPRKRPRPSRAPSSP--------------AASAGRPTRRR 389

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*.
gi 767964249 1258 SARLGSSSNLQfkaeRIKIPSTPRYPRSVVGSERGSVSHSECSTPP 1303
Cdd:PHA03307  390 ARAAVAGRARR----RDATGRFPAGRPRPSPLDAGAASGAFYARYP 431

PDZ domain 11 of MUPP1 of multi-PDZ-domain protein 1 (MUPP1), domain 9 of PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 11 of MUPP1, PDZ domain 9 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ11 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467162 [Multi-domain] Cd Length: 87 Bit Score: 37.65 E-value: 5.40e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249  651 DCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRRRK 710
Cdd:cd06674    26 DTGVFVSDIVKGGAAdaDGRLMQGDQILSVNGEDVRNASQEAAAALLKCAQGKVRLEVGRLK 87

Src homology 3 domain of Signal Transducing Adaptor Molecules; STAMs were discovered as proteins that are highly phosphorylated following cytokine and growth factor stimulation. They function in cytokine signaling and surface receptor degradation, as well as regulate Golgi morphology. They associate with many proteins including Jak2 and Jak3 tyrosine kinases, Hrs, AMSH, and UBPY. STAM adaptor proteins contain VHS (Vps27, Hrs, STAM homology), ubiquitin interacting (UIM), and SH3 domains. There are two vertebrate STAMs, STAM1 and STAM2, which may be functionally redundant; vertebrate STAMs contain ITAM motifs. They are part of the endosomal sorting complex required for transport (ESCRT-0). STAM2 deficiency in mice did not cause any obvious abnormality, while STAM1 deficiency resulted in growth retardation. Loss of both STAM1 and STAM2 in mice proved lethal, indicating that STAMs are important for embryonic development. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212754 [Multi-domain] Cd Length: 54 Bit Score: 36.67 E-value: 5.89e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249 1598 IRALYDRLADVEQELSFKKDDILYV-DDTLPQgtfgswmaWQLDENAQKIqrGQIPSKYVKR 1658
Cdd:cd11820     3 VRALYDFEAAEDNELTFKAGEIITVlDDSDPN--------WWKGSNHRGE--GLFPANFVTA 54

Src homology 3 domain of Cortactin and related proteins; This subfamily includes cortactin, Abp1 (actin-binding protein 1), hematopoietic lineage cell-specific protein 1 (HS1), and similar proteins. These proteins are involved in regulating actin dynamics through direct or indirect interaction with the Arp2/3 complex, which is required to initiate actin polymerization. They all contain at least one C-terminal SH3 domain. Cortactin and HS1 bind Arp2/3 and actin through an N-terminal region that contains an acidic domain and several copies of a repeat domain found in cortactin and HS1. Abp1 binds actin via an N-terminal actin-depolymerizing factor (ADF) homology domain. Yeast Abp1 binds Arp2/3 directly through two acidic domains. Mammalian Abp1 does not directly interact with Arp2/3; instead, it regulates actin dynamics indirectly by interacting with dynamin and WASP family proteins. The C-terminal region of these proteins acts as an adaptor or scaffold that can connect membrane trafficking and signaling proteins that bind the SH3 domain within the actin network. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

Pssm-ID: 212753 [Multi-domain] Cd Length: 54 Bit Score: 36.52 E-value: 5.99e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249 1599 RALYDRLADVEQELSFKKDDILY----VDDtlpqgtfgswmAWQLDENAQKiQRGQIPSKYVK 1657
Cdd:cd11819     3 KALYDYQAAEDNEISFVEGDIITqieqIDE-----------GWWLGVNAKG-QKGLFPANYVE 53

PDZ domain 10 of multi-PDZ-domain protein 1 (MUPP1), domain 8 of PATJ (protein-associated tight junction) and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 10 of MUPP1, PDZ domain 8 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ10 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467161 [Multi-domain] Cd Length: 86 Bit Score: 37.66 E-value: 6.07e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1505 IKKSQLELGVHLCGGN---LHGVFVAEVEDDSPAKGPDGLVPGDLILEYGSLDVRNKTVEEVYVEMLKPRDGVRLKVqYR 1581
Cdd:cd06673     8 INKGKKGLGLSIVGGSdtlLGAIIIHEVYEDGAAAKDGRLWAGDQILEVNGEDLRKATHDEAINVLRQTPQKVRLLV-YR 86

PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.

Pssm-ID: 436067 [Multi-domain] Cd Length: 54 Bit Score: 36.35 E-value: 6.29e-03

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 767964249   655 FVTKVDKGSIAD-GRLRVNDWLLRINDVDLinKDKKQAIKALLNGEGA-INMVVRR 708
Cdd:pfam17820    1 VVTAVVPGSPAErAGLRVGDVILAVNGKPV--RSLEDVARLLQGSAGEsVTLTVRR 54

PDZ domain 4 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)] and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467182 [Multi-domain] Cd Length: 85 Bit Score: 37.29 E-value: 6.53e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767964249  635 LGFDMAEGVNepcfpgDCGIFVTK-VDKGSIADGRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRR 708
Cdd:cd06696    16 LGFTVTKGKD------DNGCYIHDiVQDPAKSDGRLRPGDRLIMVNGVDVTNMSHTEAVSLLRAAPKEVTLVLGR 84

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 41.46 E-value: 6.68e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  975 DPNTFKRPQTPPKIDYLLPGPGPAHSPQPSKRAGPLTPPKPPRRSDSI-----KFQHRLETSSESEATLVGSSPSTSPPS 1049
Cdd:PHA03247 2607 DPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDdpapgRVSRPRRARRLGRAAQASSPPQRPRRR 2686

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1050 ALPPDV---------DPGEPMHASPPRKARVRIASSYYPEGDGDSSHLPAKKSCDEDLTSQKVDELGQKRRRPKSAPSFR 1120
Cdd:PHA03247 2687 AARPTVgsltsladpPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGP 2766

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1121 PKLAPVVIPAQFLEEQKCVPASGELSPELQE----WAPYSPGHSSRHSNPPLYPSRPSVGTVPRSLTPSTTVSSILRNPI 1196
Cdd:PHA03247 2767 PAPAPPAAPAAGPPRRLTRPAVASLSESRESlpspWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPP 2846

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1197 YTVRS-----------HRVGPCSSPPAARDAGPqglHPSVQHQGRLSLDLSHRtcsdysemrathgSNSLPssarlgsss 1265
Cdd:PHA03247 2847 PPSLPlggsvapggdvRRRPPSRSPAAKPAAPA---RPPVRRLARPAVSRSTE-------------SFALP--------- 2901

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1266 nlQFKAERIKIPSTPRYPRSVVGSERGSVSHSECSTP--PQSPLNIDTLSSCSQSQTSASTLPRI-AVNPASLGERR--- 1339
Cdd:PHA03247 2902 --PDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPprPQPPLAPTTDPAGAGEPSGAVPQPWLgALVPGRVAVPRfrv 2979

                         410
                  ....*....|
gi 767964249 1340 -KDRPYVEEP 1348
Cdd:PHA03247 2980 pQPAPSREAP 2989

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 40.97 E-value: 6.71e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  235 SDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQvlkhngsseilnklydtAMDKLEVVK 314
Cdd:COG3883    16 PQIQAKQKELSELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDK-----------------LQAEIAEAE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  315 KDYDALRKRYSEKVA---IHNADLSRLEQL--GEENQRLLKQTEMLTQ--QRDTAIqlqhqcalsLRRFEAIHHELNKAT 387
Cdd:COG3883    79 AEIEERREELGERARalyRSGGSVSYLDVLlgSESFSDFLDRLSALSKiaDADADL---------LEELKADKAELEAKK 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  388 AQNKDLQWEMELLQSELTELRttqvktaKESEKYREERDAVYSEYKlimSERDQVISELDKLQTEVELAESKLKSSTSEK 467
Cdd:COG3883   150 AELEAKLAELEALKAELEAAK-------AELEAQQAEQEALLAQLS---AEEAAAEAQLAELEAELAAAEAAAAAAAAAA 219


                  ....*
gi 767964249  468 KAANE 472
Cdd:COG3883   220 AAAAA 224

PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467222 [Multi-domain] Cd Length: 82 Bit Score: 37.34 E-value: 6.83e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767964249  653 GIFVTKVDKGSIADGR-LRVNDWLLRINDVDLINKDKKQAIKAL 695
Cdd:cd06740    28 GIYVSLVEPGSLAEKEgLRVGDQILRVNDVSFEKVTHAEAVKIL 71

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 40.67 E-value: 6.86e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   373 LRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKESEKYREERDAVY-SEYKLIMSERDQVISELDKLQT 451
Cdd:pfam13868   33 RIKAEEKEEERRLDEMMEEERERALEEEEEKEEERKEERKRYRQELEEQIEEREQKRqEEYEEKLQEREQMDEIVERIQE 112

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   452 EvELAESKLKSStsEKKAANEEM-EALRQIKDTVTMDAGRANKEVEILRKQCKALCQELKEALQEADVAKCRRDWAFQE- 529
Cdd:pfam13868  113 E-DQAEAEEKLE--KQRQLREEIdEFNEEQAEWKELEKEEEREEDERILEYLKEKAEREEEREAEREEIEEEKEREIARl 189

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767964249   530 RDKIVAERDSIRTLcDNLRRERDRAVSELAEALRSLDDTRKQKndvsRELKELKEQMESQLEKEARFRQLMA 601
Cdd:pfam13868  190 RAQQEKAQDEKAER-DELRAKLYQEEQERKERQKEREEAEKKA----RQRQELQQAREEQIELKERRLAEEA 256

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 40.58 E-value: 7.06e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  355 LTQQRDTAIQLQHQCALSLRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRtTQVKTAKESEKYREER--DAVYSEY 432
Cdd:COG3883    18 IQAKQKELSELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQ-AEIAEAEAEIEERREElgERARALY 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  433 K----------------------------LIMSERDQVISELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQikdtv 484
Cdd:COG3883    97 RsggsvsyldvllgsesfsdfldrlsalsKIADADADLLEELKADKAELEAKKAELEAKLAELEALKAELEAAKA----- 171

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 767964249  485 TMDAGRANKEVEI--LRKQCKALCQELKEALQEADVAK 520
Cdd:COG3883   172 ELEAQQAEQEALLaqLSAEEAAAEAQLAELEAELAAAE 209

PDZ domain 3 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467167 [Multi-domain] Cd Length: 88 Bit Score: 37.23 E-value: 7.07e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767964249  634 ALGFDMAEGVNEPcfPGDCGIFVTKVD-KGSIA-DGRLRVNDWLLRINDVDLINKDKKQAIKAL 695
Cdd:cd06679    12 SLGISVAGGRGSR--RGDLPIYVTNVQpDGCLGrDGRIKKGDVLLSINGISLTNLSHSEAVAVL 73

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 39.91 E-value: 7.14e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  245 DMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQqvlKHNGSSEILNKLYDTAMDKLEVVK--KDYDALRK 322
Cdd:COG1579    20 DRLEHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIK---RLELEIEEVEARIKKYEEQLGNVRnnKEYEALQK 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  323 ryseKVAIHNADLSRLEqlgEENQRLLKQTEMLTQQRDtaiQLQHQCALSLRRFEAIHHELNKATAqnkDLQWEMELLQS 402
Cdd:COG1579    97 ----EIESLKRRISDLE---DEILELMERIEELEEELA---ELEAELAELEAELEEKKAELDEELA---ELEAELEELEA 163


                  ....*...
gi 767964249  403 ELTELRTT 410
Cdd:COG1579   164 EREELAAK 171

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CPP (also known as tail-specific protease, PRC protein, Protease Re, and Photosystem II D1 protein processing peptidase), and related domains. CPP belongs to the peptidase S41A family. It cleaves a C-terminal 11 residue peptide from the precursor form of penicillin-binding protein 3, and may have a role in protecting bacterium from thermal and osmotic stresses. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This CPP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467623 [Multi-domain] Cd Length: 88 Bit Score: 37.46 E-value: 7.27e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767964249 1360 LGISIVSGEKGGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINLR 1403
Cdd:cd06782     4 IGIEIGKDDDGYLVVVSPIPGGPAEKAGIKPGDVIVAVDGESVR 47

RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.

Pssm-ID: 431111 [Multi-domain] Cd Length: 766 Bit Score: 40.96 E-value: 7.57e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   139 DQQVN---EKVENLSIQLRLMTRERNELRKRL------------AFATHGTAFDKRpyHRLnpdYERLKIQcvRAMSDLQ 203
Cdd:pfam10174  393 ERKINvlqKKIENLQEQLRDKDKQLAGLKERVkslqtdssntdtALTTLEEALSEK--ERI---IERLKEQ--REREDRE 465

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   204 SLQNQHTnaLKRCEEVAKETdfYHTLHSRLLSDQTRLKDDVDMLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLR 283
Cdd:pfam10174  466 RLEELES--LKKENKDLKEK--VSALQPELTEKESSLIDLKEHASSLASSGLKKDSKLKSLEIAVEQKKEECSKLENQLK 541

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   284 AQQQQVLKHNGSSEILnklydtamDKLEVVKKDYdalrKRYSEKVAIHNADLSRLeqLGeenqrLLKQTEMLTQQRDTAI 363
Cdd:pfam10174  542 KAHNAEEAVRTNPEIN--------DRIRLLEQEV----ARYKEESGKAQAEVERL--LG-----ILREVENEKNDKDKKI 602

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   364 QLQHQCALSLrrfeaiHHELNKATAQNKDLQWEMELLQSELTElrttqvktakesEKYREERDAVYSEYKLIMSErdqVI 443
Cdd:pfam10174  603 AELESLTLRQ------MKEQNKKVANIKHGQQEMKKKGAQLLE------------EARRREDNLADNSQQLQLEE---LM 661

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   444 SELDKlqTEVELAESKLKSSTSEKKAANEE--MEALRQIKdtvtmdagrankeveilRKQCkalcQELKEALQEADVAkc 521
Cdd:pfam10174  662 GALEK--TRQELDATKARLSSTQQSLAEKDghLTNLRAER-----------------RKQL----EEILEMKQEALLA-- 716

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....
gi 767964249   522 rrdwAFQERDKIVA-------ERDSIRTLCDNLRRERDRAVSEL 558
Cdd:pfam10174  717 ----AISEKDANIAllelsssKKKKTQEEVMALKREKDRLVHQL 756

PDZ domain 1 of syntenin-1, syntenin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of syntenin-1, syntenin-2, and related domains. Syntenins are implicated in various cellular processes such as trafficking, signaling, and cancer metastasis. They bind to signaling and adhesion molecules, such as syndecans, neurexins, ephrin B, and phospholipid PIP2. Through its tandem PDZ domains (PDZ1 and PDZ2), syntenin links syndecans to other cell surface receptors and kinases, such as E-cadherin and ephrin-B, establishing signaling crosstalk. During syndecan binding, syntenin PDZ2 serves as a high-affinity domain, and PDZ1, also necessary for binding, acts as a complementary, low-affinity domain; this is also the case for syntenin binding to proto-oncogene c-Src. The syntenin PDZ domain-PIP2 interaction controls Arf6-mediated syndecan recycling through endosomal compartments; both PDZ1 and PDZ2 interact with PIP2. Different binding partners and downstream regulators of syntenin1 PDZ domains, such as to proto-oncogene c-Src, mitogen-activated protein kinase (MAPK), and focal adhesion kinase (FAK), have been identified that promote the progression and invasion of a variety of cancers, such as melanoma, glioblastoma multiforme and breast cancer. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This syntenin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F.

Pssm-ID: 467204 [Multi-domain] Cd Length: 79 Bit Score: 36.83 E-value: 7.58e-03

                          10        20        30
                  ....*....|....*....|....*....|...
gi 767964249 1370 GGIYVSKVTVGSIAHQAGLEYGDQLLEFNGINL 1402
Cdd:cd06721    22 KGVFVQLVQANSPAALAGLRFGDQILQINGENV 54

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 39.91 E-value: 7.61e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767964249  528 QERDKivaERDSIRTLCDNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQMESQLEKEARFRQLM 600
Cdd:COG1579    13 QELDS---ELDRLEHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEARIKKYEEQL 82

PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the first PDZ domain (PDZ1) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467240 [Multi-domain] Cd Length: 87 Bit Score: 37.25 E-value: 7.72e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  633 KALGFDMAEGVNEPcfPGDCGIFVTKVDKGSIA--DGRLRVNDWLLRINDVDLINKDKKQAIKALLN-GEGAINMVVR 707
Cdd:cd06759    12 KGLGFSIVGGRDSP--RGPMGIYVKTIFPGGAAaeDGRLKEGDEILEVNGESLQGLTHQEAIQKFKQiKKGLVVLTVR 87

PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467285 [Multi-domain] Cd Length: 92 Bit Score: 37.47 E-value: 7.77e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249  635 LGFDMAEGvnEPCFPGDCGIFVTKVDKGSIAD--GRLRVNDWLLRINDVDLINKDKKQAIKALLNGEGAINMVVRRRK 710
Cdd:cd23072    15 LGFQIVGG--EKSGRLDLGIFISSITPGGPADldGRLKPGDRLISVNDVSLEGLSHDAAVEILQNAPEDVTLVVSQPK 90

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

Pssm-ID: 129694 [Multi-domain] Cd Length: 1311 Bit Score: 41.19 E-value: 7.91e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   224 DFYHTLHSRLLSDQTRLKDdvdmLRRENGQLLRERNLLQQSWEDMKRLHEEDQKEIGDLRAQQQQV------LKHNGSSE 297
Cdd:TIGR00606  695 EFISDLQSKLRLAPDKLKS----TESELKKKEKRRDEMLGLAPGRQSIIDLKEKEIPELRNKLQKVnrdiqrLKNDIEEQ 770

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   298 ilNKLYDTAMDKLEVVKkdydalrkrysekvaIHNADLSRLEQLGEENQRLLKQTEMLTQQRD------TAIQLQHQCAL 371
Cdd:TIGR00606  771 --ETLLGTIMPEEESAK---------------VCLTDVTIMERFQMELKDVERKIAQQAAKLQgsdldrTVQQVNQEKQE 833

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   372 SLRRFEAIHHELNKATAQNKDLQWEMELLQSELTELRTTQVKTAKE-------SEKYREERDAVYSEYKLIMSERDQVIS 444
Cdd:TIGR00606  834 KQHELDTVVSKIELNRKLIQDQQEQIQHLKSKTNELKSEKLQIGTNlqrrqqfEEQLVELSTEVQSLIREIKDAKEQDSP 913

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   445 ELDKLQTEVELAESKLKSSTSEKKAANEEMEALRQIKDTVTM-------------DAGRANKEVEILRKQCK-ALCQELK 510
Cdd:TIGR00606  914 LETFLEKDQQEKEELISSKETSNKKAQDKVNDIKEKVKNIHGymkdienkiqdgkDDYLKQKETELNTVNAQlEECEKHQ 993

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249   511 EALQEaDVAKCRRDWAFQERDKivaerdsiRTLCDNL-RRERDRAVSELAEALRSLDDTRKQknDVSRELKELKEQMESQ 589
Cdd:TIGR00606  994 EKINE-DMRLMRQDIDTQKIQE--------RWLQDNLtLRKRENELKEVEEELKQHLKEMGQ--MQVLQMKQEHQKLEEN 1062

                          410       420       430
                   ....*....|....*....|....*....|....*..
gi 767964249   590 LEKEARfrqlmahssHDSAIDTDSMEWETEVVEFERE 626
Cdd:TIGR00606 1063 IDLIKR---------NHVLALGRQKGYEKEIKHFKKE 1090

PDZ domain of membrane palmitoylated protein 6 (MPP6), MPP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP6, MPP2, and related domains. MPP6 (also known as MAGUK p55 subfamily member, Protein associated with Lin-7, 2 (PALS2), Veli-associated MAGUK 1, and VAM-1) is a membrane-associated guanylate kinase (MAGUK)-like protein. MPP6 is a regulator of Lin-7 expression and localization. MPP6 is also known to bind cell-adhesion protein, nectin-like molecule-2 (Necl-2), and localize to the basolateral plasma membrane in mammalian epithelial cells. MPP2 (also known as MAGUK p55 subfamily member 2) is a postsynaptic protein that links SynCAM1 cell adhesion molecules to core components of the postsynaptic density. Other members of this family include the Drosophila Vari protein, an essential basolateral septate junction protein which interacts with the cell-adhesion protein neurexin IV. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP6-MPP2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467268 [Multi-domain] Cd Length: 78 Bit Score: 36.82 E-value: 8.21e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  735 ENGVYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDN-KSLNEcesLLRSCQDSLTLSLL 793
Cdd:cd10832    21 EGELVIARILHGGMIDRQGLLHVGDIIKEVNGVPVGSpEQLQE---MLKNASGSVTLKIL 77

PDZ1 domain of human syntaxin-binding protein 4 (STXBP4), PDZ2 domain of Gallus gallus uncharacterized STXBP4 isoform X1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of human syntaxin-binding protein 4 (STXBP4), PDZ2 domain of Gallus gallus uncharacterized STXBP4 isoform X1, and related domains. Human STXBP4 (also known as Synip) includes a single PDZ domain, a coiled-coil domain, and a WW domain (named for its two conserved tryptophans); Gallus gallus STXBP4 isoform X1 contains 2 PDZ domains (PDZ1 and PDZ2). Human STXBP4 plays a role in the translocation of transport vesicles from the cytoplasm to the plasma membrane: insulin induces the dissociation of the STXBP4 and STX4 complex liberating STX4 to interact with Vamp2, and to form the SNARE complex thereby promoting vesicle fusion. It may also play a role in the regulation of insulin release by pancreatic beta cells after stimulation by glucose. Human STXBP4 is also known to physically associate with a prominent isoform of TP63 (deltaNp63alpha 9) whose overexpression promotes squamous cell carcinoma development, and in doing so prevents degradation of this isoform by the Cdc20-APC/C complex, Itch, and RACK1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This STXBP4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467184 [Multi-domain] Cd Length: 89 Bit Score: 36.90 E-value: 9.09e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  717 VTPLHINLSGqkdsGISLENG--VYAAAVLPGSPAAKEGSLAVGDRIVAINGIALDNKSLNECESLL 781
Cdd:cd06698    10 STGLGLSIVG----GINRPEGpmVFIQEVIPGGDCYKDGRLRPGDQLVSINKESLIGVTLEEAKSIL 72

PDZ domain 3 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467172 [Multi-domain] Cd Length: 87 Bit Score: 36.85 E-value: 9.17e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249 1351 VKVQK--GSEpLGISIVSG---EKGGIYVSKVTVGSIAHQAG-LEYGDQLLEFNGIN------------LRSATEQQARL 1412
Cdd:cd06684     5 VEIEKtpGSS-LGITLSTSthrNKQVIVIDSIKPASIADRCGaLHVGDHILSIDGTSvehcslaeatqlLASNSGDQVKL 83


                  ..
gi 767964249 1413 II 1414
Cdd:cd06684    84 EI 85

putative mechanosensitive channel protein; Provisional

Pssm-ID: 236798 [Multi-domain] Cd Length: 1109 Bit Score: 40.81 E-value: 9.22e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  379 IHHELNKATAQNKDLQWE-MELLQSELTELRTTQvKTAKESEKYREerdaVYSEY-KLIMSERDQVISELDKL------Q 450
Cdd:PRK10929   28 ITQELEQAKAAKTPAQAEiVEALQSALNWLEERK-GSLERAKQYQQ----VIDNFpKLSAELRQQLNNERDEPrsvppnM 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767964249  451 TEVELAESKLKSSTS---EKKAANEEMEALRQIKDTVTM------DAGRANKEVE----ILRKQCKALCQELKEALQeAD 517
Cdd:PRK10929  103 STDALEQEILQVSSQlleKSRQAQQEQDRAREISDSLSQlpqqqtEARRQLNEIErrlqTLGTPNTPLAQAQLTALQ-AE 181

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767964249  518 VAkcrrdwafqeRDKIVAERDSIRTLCDNLRRERDRAVSELAEalrslddtrKQKNDVSRELKELKEQMESQLEKEA 594
Cdd:PRK10929  182 SA----------ALKALVDELELAQLSANNRQELARLRSELAK---------KRSQQLDAYLQALRNQLNSQRQREA 239

Centrosome localization domain of PPC89; The N-terminal region of the fission yeast spindle pole body protein PPC89 has low similarity to the human Cep57 protein. The CLD or centrosome localization domain of Cep57 and PPC89 is found at the N-terminus. This region localizes to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component. This N-terminal region can also multimerize with the N-terminus of other Cep57 molecules. The C-terminal part, Family Cep57_MT_bd, pfam06657, is the microtubule-binding region of Cep57 and PPC89.

Pssm-ID: 372959 [Multi-domain] Cd Length: 67 Bit Score: 36.49 E-value: 9.60e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 767964249   545 DNLRRERDRAVSELAEALRSLDDTRKQKNDVSRELKELKEQ 585
Cdd:pfam14197   27 KRLRRERDSAVRQLGVAYLEIQELKAENEALRKELKEQRAQ 67

PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467211 [Multi-domain] Cd Length: 82 Bit Score: 36.78 E-value: 9.60e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 767964249  651 DCGIFVTKVDKGSIADGR-LRVNDWLLRINDVDLINKDKKQAIKALLN 697
Cdd:cd06729    22 DVGIFVAGVQEGSPAEKQgLQEGDQILKVNGVDFRNLTREEAVLFLLD 69

PDZ domain 3 of harmonin isoforms a and b, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of harmonin isoforms a and b, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467221 [Multi-domain] Cd Length: 94 Bit Score: 37.29 E-value: 9.97e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767964249 1349 RHVKVQKgSEPLGISIVSGE----KGGIYVSKVTVGSIAH-QAGLEYGDQLLEFNGINLRSATEQQAR 1411
Cdd:cd06739     4 RLLRIKK-NGPLDLALEGGIdsplGGKIVVSAVYEGGAADkHGGIVKGDQIMMVNGKSLTDVTLAEAE 70