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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13994253     3 LGVSAE--QPAGGAE-GFHLHGVQENSPAQQAGLEPYFDFIITIGHSRLNKENDtLKALLKANVEKPVKLEVFNMKTMRV 79
Cdd:pfam04495  28 LGLSLRwcSFAKALEnVWHVLDVHENSPAAKAGLQPYSDYIIGTPKGLLKGEDD-LYTLVEDHEDRPLRLYVYNSETDTV 106

                          90       100
                  ....*....|....*....|.
gi 13994253    80 REVEVVPSNMWGGQGLLGASV 100
Cdd:pfam04495 107 REVTITPNRNWGGEGALGCGL 127

Peripheral Golgi membrane protein [Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13994253  95 LLGASVRFCSFRRASEQVWHVLDVE-PSSPAALAGLRPYTDYVVGSD--QILQESE-DFFTLIESHEGKPLKLMVYNSKS 170
Cdd:COG5233 170 LRGKDIQWSRLKDVVCSDSHILNVSiQDKPPAYALLSPDEDYIDGSSdgQPLEIGElDLEDVNESPVNLPLSLYYYNPID 249

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13994253 171 DSCREVTVTPNAAWGGEGSLGCGIGYGYLHRIPTqPPSYHKKPPGtpppsalplgapppdalppgptpedspSLETGSRQ 250
Cdd:COG5233 250 DQERAKTERDGVHKGIVGILGCQVGHGFLHRLPL-AGVGQKPQLQ---------------------------KLGTTKRT 301

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 13994253 251 SDYMEALLQAPGSSmEDPLPGPGSPSHsAPDPDGLPHFMETPLQP 295
Cdd:COG5233 302 EDPESHQVEQRGVE-ENFLPIPKPDTH-RSEFAAKNFLSSLPLSF 344

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 13994253  15 EGFHLHGVQENSPAQQAGLEPyFDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVF---NMKTMRVR 80
Cdd:cd10838  33 DGVLIMQVLPNSPAARAGLRR-GDVIQAVDGQPVTTADDVQRIVEQAGVGEELELTVLrgdRRQTLAVK 100

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. 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 RseP 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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 13994253 118 VEPSSPAALAGLRPyTDYVV-GSDQILQESEDFFTLIESHEGKPLKLMVynSKSDSCREVTVTP 180
Cdd:cd23081   6 VVANSPAAEAGLKP-GDRILkIDGQKVRTWEDIVRIVRENPGKPLTLKI--ERDGKILTVTVTP 66

Peripheral Golgi membrane protein [Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13994253  95 LLGASVRFCSFRRASEQVWHVLDVE-PSSPAALAGLRPYTDYVVGSD--QILQESE-DFFTLIESHEGKPLKLMVYNSKS 170
Cdd:COG5233 170 LRGKDIQWSRLKDVVCSDSHILNVSiQDKPPAYALLSPDEDYIDGSSdgQPLEIGElDLEDVNESPVNLPLSLYYYNPID 249

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13994253 171 DSCREVTVTPNAAWGGEGSLGCGIGYGYLHRIPTqPPSYHKKPPGtpppsalplgapppdalppgptpedspSLETGSRQ 250
Cdd:COG5233 250 DQERAKTERDGVHKGIVGILGCQVGHGFLHRLPL-AGVGQKPQLQ---------------------------KLGTTKRT 301

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 13994253 251 SDYMEALLQAPGSSmEDPLPGPGSPSHsAPDPDGLPHFMETPLQP 295
Cdd:COG5233 302 EDPESHQVEQRGVE-ENFLPIPKPDTH-RSEFAAKNFLSSLPLSF 344

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 13994253  15 EGFHLHGVQENSPAQQAGLEPyFDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVF---NMKTMRVR 80
Cdd:cd10838  33 DGVLIMQVLPNSPAARAGLRR-GDVIQAVDGQPVTTADDVQRIVEQAGVGEELELTVLrgdRRQTLAVK 100

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13994253 115 VLDVEPSSPAALAGLRPytdyvvGsDQIL-------QESEDFFTLIESHEGKPLKLMVY-NSKSdscREVTVTPNA-AWG 185
Cdd:COG0750 132 VGEVVPGSPAAKAGLQP------G-DRIVaingqpvTSWDDLVDIIRASPGKPLTLTVErDGEE---LTLTVTPRLvEED 201

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 13994253 186 GEGSLgcGIGygylhriPTQPPSYHKKPPGTPPPSAL 222
Cdd:COG0750 202 GVGRI--GVS-------PSGEVVTVRYGPLEALGAGV 229

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. 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 RseP 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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 13994253 118 VEPSSPAALAGLRPyTDYVV-GSDQILQESEDFFTLIESHEGKPLKLMVynSKSDSCREVTVTP 180
Cdd:cd23081   6 VVANSPAAEAGLKP-GDRILkIDGQKVRTWEDIVRIVRENPGKPLTLKI--ERDGKILTVTVTP 66

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. 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 RseP 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13994253  21 GVQENSPAQQAGLEPYfDFIITIGHSRLNKENDTLKAlLKANVEKPVKLEVfnmktMR---VREVEVVPSNM---WGGQG 94
Cdd:cd23081   5 EVVANSPAAEAGLKPG-DRILKIDGQKVRTWEDIVRI-VRENPGKPLTLKI-----ERdgkILTVTVTPELVeveGKGVG 77

                ...
gi 13994253  95 LLG 97
Cdd:cd23081  78 RIG 80

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13994253   3 LGVSAEQ-PAGGAEGFHLH--------GVQENSPAQQAGLEPYfDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVfn 73
Cdd:COG0265 180 LGVTIQPvTPELAEALGLPepegvlvaRVEPGSPAAKAGLRPG-DVILAVDGKPVTSARDLQRLLASLKPGDTVTLTV-- 256

                        90
                ....*....|....*.
gi 13994253  74 mktMR---VREVEVVP 86
Cdd:COG0265 257 ---LRggkELTVTVTL 269

PDZ domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 13994253    22 VQENSPAQQAGLEPYfDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVF 72
Cdd:pfam13180  13 VKSSGPAAKAGLKAG-DVILSIDGRKINDLTDLESALYGHKPGDTVTLQVY 62