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Conserved domains on  [gi|45594312|ref|NP_115647|]
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E3 ubiquitin-protein ligase TRAF7 [Homo sapiens]

Protein Classification

E3 ubiquitin-protein ligase TRAF7( domain architecture ID 11616045)

E3 ubiquitin-protein ligase TRAF7 (TNF receptor-associated factor 7) acts as an E3 ubiquitin-protein ligase that potentiates MAP3K3-mediated activation of the NF-kappa-B, JUN/AP1 and DDIT3 transcriptional regulators

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
387-668 1.51e-66

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 224.02  E-value: 1.51e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 387 KCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWDTcTTYKCQKTLEGHDGIVLALCI--QGCKLYSGSADCTIIVW 464
Cdd:COG2319 111 LLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDL-ATGKLLRTLTGHSGAVTSVAFspDGKLLASGSDDGTVRLW 189
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 465 DIQNLQKVNTIRAHDNPVCTLVSSHN--VLFSGSL-KAIKVWDIVGTelKLKKELTGLNHWVRALVAAQ--SYLYSGSY- 538
Cdd:COG2319 190 DLATGKLLRTLTGHTGAVRSVAFSPDgkLLASGSAdGTVRLWDLATG--KLLRTLTGHSGSVRSVAFSPdgRLLASGSAd 267
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 539 QTIKIWDIRTLDCIHVLQTSGGSVYSIAVT--NHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVisTPDQTKV 616
Cdd:COG2319 268 GTVRLWDLATGELLRTLTGHSGGVNSVAFSpdGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAF--SPDGKTL 345
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 45594312 617 FSASYDRSLRVWSMDNMICTQTLLRHQGSVTALAVSR--GRLFSGAVDSTVKVW 668
Cdd:COG2319 346 ASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPdgRTLASGSADGTVRLW 399
mRING-HC-C3HC3D_TRAF7 cd16644
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
124-168 1.09e-20

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins; TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats.


:

Pssm-ID: 438306 [Multi-domain]  Cd Length: 47  Bit Score: 85.48  E-value: 1.09e-20
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 45594312 124 QPSVKLCCQLCCSVFKDPVITTCGHTFCRRCALKS--EKCPVDNVKL 168
Cdd:cd16644   1 PPSVKLYCPLCQRVFKDPVITSCGHTFCRRCALTApgEKCPVDNMKL 47
DD_cGKI super family cl17044
Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I; Cyclic GMP-dependent ...
282-322 2.06e-03

Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I; Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is also expressed at lower concentrations in other tissues. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing their targeting to different subcellular compartments and intracellular substrates.


The actual alignment was detected with superfamily member cd12085:

Pssm-ID: 473057 [Multi-domain]  Cd Length: 48  Bit Score: 36.48  E-value: 2.06e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 45594312 282 CRFEGLKEFLQQTDDRFHEMHVALAQKDQEIAFLRSMLGKL 322
Cdd:cd12085   2 GSVEELQKLLQAKEERIRELEQLLQQRDEEIQELRSQLDKF 42
Sina super family cl47795
Seven in absentia protein family; The seven in absentia (sina) gene was first identified in ...
208-269 2.42e-03

Seven in absentia protein family; The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain pfam00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologs of Sina have also been identified. The human homolog Siah-1 also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in pfam00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologs, whose similarity was noted previously, this family also includes putative homologs from Caenorhabditis elegans, Arabidopsis thaliana.


The actual alignment was detected with superfamily member pfam03145:

Pssm-ID: 460824 [Multi-domain]  Cd Length: 198  Bit Score: 39.51  E-value: 2.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45594312   208 RGCPFTIKLSARKDHEGSCDYRPVRCP-NNPSCP---PLLRmnLEAHLKEcEHiKCPHSKYGCTFI 269
Cdd:pfam03145  22 SGCSETLPYTEKADHEERCEFRPYSCPcPGSSCTwqgSLDA--VMPHLMD-DH-KKVTTLQGEDFV 83
PRK03918 super family cl35229
DNA double-strand break repair ATPase Rad50;
283-373 2.66e-03

DNA double-strand break repair ATPase Rad50;


The actual alignment was detected with superfamily member PRK03918:

Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 41.20  E-value: 2.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312  283 RFEGLKEFLQQT---DDRFHEMHVALAQKDQEIAFLRSMLGKLSEKIDQLEKSLElKFDVLDENQSKLSEDLMEFRRDAS 359
Cdd:PRK03918 177 RIERLEKFIKRTeniEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVK-ELEELKEEIEELEKELESLEGSKR 255
                         90
                 ....*....|....
gi 45594312  360 MLNDELSHINARLN 373
Cdd:PRK03918 256 KLEEKIRELEERIE 269
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
387-668 1.51e-66

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 224.02  E-value: 1.51e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 387 KCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWDTcTTYKCQKTLEGHDGIVLALCI--QGCKLYSGSADCTIIVW 464
Cdd:COG2319 111 LLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDL-ATGKLLRTLTGHSGAVTSVAFspDGKLLASGSDDGTVRLW 189
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 465 DIQNLQKVNTIRAHDNPVCTLVSSHN--VLFSGSL-KAIKVWDIVGTelKLKKELTGLNHWVRALVAAQ--SYLYSGSY- 538
Cdd:COG2319 190 DLATGKLLRTLTGHTGAVRSVAFSPDgkLLASGSAdGTVRLWDLATG--KLLRTLTGHSGSVRSVAFSPdgRLLASGSAd 267
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 539 QTIKIWDIRTLDCIHVLQTSGGSVYSIAVT--NHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVisTPDQTKV 616
Cdd:COG2319 268 GTVRLWDLATGELLRTLTGHSGGVNSVAFSpdGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAF--SPDGKTL 345
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 45594312 617 FSASYDRSLRVWSMDNMICTQTLLRHQGSVTALAVSR--GRLFSGAVDSTVKVW 668
Cdd:COG2319 346 ASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPdgRTLASGSADGTVRLW 399
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
388-668 3.29e-63

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 211.42  E-value: 3.29e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 388 CKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWDTCTTyKCQKTLEGHDGIV--LALCIQGCKLYSGSADCTIIVWD 465
Cdd:cd00200   1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETG-ELLRTLKGHTGPVrdVAASADGTYLASGSSDKTIRLWD 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 466 IQNLQKVNTIRAHDNPV--CTLVSSHNVLFSGSL-KAIKVWDIvgTELKLKKELTGLNHWVRALVAAQS--YLYSGSY-Q 539
Cdd:cd00200  80 LETGECVRTLTGHTSYVssVAFSPDGRILSSSSRdKTIKVWDV--ETGKCLTTLRGHTDWVNSVAFSPDgtFVASSSQdG 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 540 TIKIWDIRTLDCIHVLQTSGGSVYSIAV--TNHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVisTPDQTKVF 617
Cdd:cd00200 158 TIKLWDLRTGKCVATLTGHTGEVNSVAFspDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAF--SPDGYLLA 235
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 45594312 618 SASYDRSLRVWSMDNMICTQTLLRHQGSVTALAVS--RGRLFSGAVDSTVKVW 668
Cdd:cd00200 236 SGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSpdGKRLASGSADGTIRIW 288
mRING-HC-C3HC3D_TRAF7 cd16644
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
124-168 1.09e-20

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins; TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats.


Pssm-ID: 438306 [Multi-domain]  Cd Length: 47  Bit Score: 85.48  E-value: 1.09e-20
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 45594312 124 QPSVKLCCQLCCSVFKDPVITTCGHTFCRRCALKS--EKCPVDNVKL 168
Cdd:cd16644   1 PPSVKLYCPLCQRVFKDPVITSCGHTFCRRCALTApgEKCPVDNMKL 47
WD40 pfam00400
WD domain, G-beta repeat;
386-424 4.15e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 52.35  E-value: 4.15e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 45594312   386 FKCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWD 424
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
386-424 6.17e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 51.93  E-value: 6.17e-09
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 45594312    386 FKCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWD 424
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
129-162 6.61e-06

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.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: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 48.85  E-value: 6.61e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 45594312   129 LCCQLCCSVFKDPVITTCGHTFC----RRCALKSEKCP 162
Cdd:TIGR00599  27 LRCHICKDFFDVPVLTSCSHTFCslciRRCLSNQPKCP 64
COG5152 COG5152
Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function ...
125-157 3.23e-05

Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only];


Pssm-ID: 227481 [Multi-domain]  Cd Length: 259  Bit Score: 46.22  E-value: 3.23e-05
                        10        20        30
                ....*....|....*....|....*....|...
gi 45594312 125 PSVKLCCQLCCSVFKDPVITTCGHTFCRRCALK 157
Cdd:COG5152 193 EKIPFLCGICKKDYESPVVTECGHSFCSLCAIR 225
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
131-162 6.74e-05

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.


Pssm-ID: 463881 [Multi-domain]  Cd Length: 38  Bit Score: 40.46  E-value: 6.74e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 45594312   131 CQLCCSVFKDPViTTCGHTFCRRCALKSE-------KCP 162
Cdd:pfam13445   1 CPICLELFTDPV-LPCGHTFCRECLEEMSqkkggkfKCP 38
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
131-163 1.17e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 39.80  E-value: 1.17e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 45594312    131 CQLCCSVF-KDPVITTCGHTFCRRCALK-----SEKCPV 163
Cdd:smart00184   1 CPICLEEYlKDPVILPCGHTFCRSCIRKwlesgNNTCPI 39
DD_cGKI-alpha cd12085
Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I alpha; Cyclic ...
282-322 2.06e-03

Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I alpha; Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing for their targeting to different subcellular compartments and intracellular substrates. cGKI-alpha specifically binds to myosin light chain phosphatase targeting subunit (MYPT1) and the regulator of G-protein signaling-2 (RGS-2). cGKI-alpha activates the phosphatase activity of MYPT1, resulting in vasorelaxation. It increases the activity of RGS-2 toward G proteins, with implications in the downstream signaling for vasoconstrictive agents.


Pssm-ID: 213374 [Multi-domain]  Cd Length: 48  Bit Score: 36.48  E-value: 2.06e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 45594312 282 CRFEGLKEFLQQTDDRFHEMHVALAQKDQEIAFLRSMLGKL 322
Cdd:cd12085   2 GSVEELQKLLQAKEERIRELEQLLQQRDEEIQELRSQLDKF 42
Sina pfam03145
Seven in absentia protein family; The seven in absentia (sina) gene was first identified in ...
208-269 2.42e-03

Seven in absentia protein family; The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain pfam00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologs of Sina have also been identified. The human homolog Siah-1 also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in pfam00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologs, whose similarity was noted previously, this family also includes putative homologs from Caenorhabditis elegans, Arabidopsis thaliana.


Pssm-ID: 460824 [Multi-domain]  Cd Length: 198  Bit Score: 39.51  E-value: 2.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45594312   208 RGCPFTIKLSARKDHEGSCDYRPVRCP-NNPSCP---PLLRmnLEAHLKEcEHiKCPHSKYGCTFI 269
Cdd:pfam03145  22 SGCSETLPYTEKADHEERCEFRPYSCPcPGSSCTwqgSLDA--VMPHLMD-DH-KKVTTLQGEDFV 83
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
283-373 2.66e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 41.20  E-value: 2.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312  283 RFEGLKEFLQQT---DDRFHEMHVALAQKDQEIAFLRSMLGKLSEKIDQLEKSLElKFDVLDENQSKLSEDLMEFRRDAS 359
Cdd:PRK03918 177 RIERLEKFIKRTeniEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVK-ELEELKEEIEELEKELESLEGSKR 255
                         90
                 ....*....|....
gi 45594312  360 MLNDELSHINARLN 373
Cdd:PRK03918 256 KLEEKIRELEERIE 269
Atg16_CCD cd22887
Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family ...
315-374 7.10e-03

Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins.


Pssm-ID: 439196 [Multi-domain]  Cd Length: 91  Bit Score: 36.39  E-value: 7.10e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 315 LRSMLGKLSEKIDQLEKSLElkfdVLDENQSKLSEDLMEFRRDASMLNDELSHINARLNM 374
Cdd:cd22887   2 LESELQELEKRLAELEAELA----SLEEEIKDLEEELKEKNKANEILNDELIALQIENNL 57
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
387-668 1.51e-66

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 224.02  E-value: 1.51e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 387 KCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWDTcTTYKCQKTLEGHDGIVLALCI--QGCKLYSGSADCTIIVW 464
Cdd:COG2319 111 LLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDL-ATGKLLRTLTGHSGAVTSVAFspDGKLLASGSDDGTVRLW 189
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 465 DIQNLQKVNTIRAHDNPVCTLVSSHN--VLFSGSL-KAIKVWDIVGTelKLKKELTGLNHWVRALVAAQ--SYLYSGSY- 538
Cdd:COG2319 190 DLATGKLLRTLTGHTGAVRSVAFSPDgkLLASGSAdGTVRLWDLATG--KLLRTLTGHSGSVRSVAFSPdgRLLASGSAd 267
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 539 QTIKIWDIRTLDCIHVLQTSGGSVYSIAVT--NHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVisTPDQTKV 616
Cdd:COG2319 268 GTVRLWDLATGELLRTLTGHSGGVNSVAFSpdGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAF--SPDGKTL 345
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 45594312 617 FSASYDRSLRVWSMDNMICTQTLLRHQGSVTALAVSR--GRLFSGAVDSTVKVW 668
Cdd:COG2319 346 ASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPdgRTLASGSADGTVRLW 399
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
388-668 3.29e-63

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 211.42  E-value: 3.29e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 388 CKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWDTCTTyKCQKTLEGHDGIV--LALCIQGCKLYSGSADCTIIVWD 465
Cdd:cd00200   1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETG-ELLRTLKGHTGPVrdVAASADGTYLASGSSDKTIRLWD 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 466 IQNLQKVNTIRAHDNPV--CTLVSSHNVLFSGSL-KAIKVWDIvgTELKLKKELTGLNHWVRALVAAQS--YLYSGSY-Q 539
Cdd:cd00200  80 LETGECVRTLTGHTSYVssVAFSPDGRILSSSSRdKTIKVWDV--ETGKCLTTLRGHTDWVNSVAFSPDgtFVASSSQdG 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 540 TIKIWDIRTLDCIHVLQTSGGSVYSIAV--TNHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVisTPDQTKVF 617
Cdd:cd00200 158 TIKLWDLRTGKCVATLTGHTGEVNSVAFspDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAF--SPDGYLLA 235
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 45594312 618 SASYDRSLRVWSMDNMICTQTLLRHQGSVTALAVS--RGRLFSGAVDSTVKVW 668
Cdd:cd00200 236 SGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSpdGKRLASGSADGTIRIW 288
WD40 COG2319
WD40 repeat [General function prediction only];
387-668 9.59e-60

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 205.92  E-value: 9.59e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 387 KCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWDTCTTyKCQKTLEGHDGIVLALCI--QGCKLYSGSADCTIIVW 464
Cdd:COG2319  69 ALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATG-LLLRTLTGHTGAVRSVAFspDGKTLASGSADGTVRLW 147
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 465 DIQNLQKVNTIRAHDNPVCTLVSSHN--VLFSGSL-KAIKVWDIvgTELKLKKELTGLNHWVRALV--AAQSYLYSGSY- 538
Cdd:COG2319 148 DLATGKLLRTLTGHSGAVTSVAFSPDgkLLASGSDdGTVRLWDL--ATGKLLRTLTGHTGAVRSVAfsPDGKLLASGSAd 225
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 539 QTIKIWDIRTLDCIHVLQTSGGSVYSIAVT--NHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVisTPDQTKV 616
Cdd:COG2319 226 GTVRLWDLATGKLLRTLTGHSGSVRSVAFSpdGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAF--SPDGKLL 303
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 45594312 617 FSASYDRSLRVWSMDNMICTQTLLRHQGSVTALAVSR--GRLFSGAVDSTVKVW 668
Cdd:COG2319 304 ASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPdgKTLASGSDDGTVRLW 357
WD40 COG2319
WD40 repeat [General function prediction only];
387-632 1.53e-54

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 191.66  E-value: 1.53e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 387 KCKGTFVGHQGPVWCLcVYS-MGDLLFSGSSDKTIKVWDTCTTyKCQKTLEGHDGIVLALCI--QGCKLYSGSADCTIIV 463
Cdd:COG2319 153 KLLRTLTGHSGAVTSV-AFSpDGKLLASGSDDGTVRLWDLATG-KLLRTLTGHTGAVRSVAFspDGKLLASGSADGTVRL 230
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 464 WDIQNLQKVNTIRAHDNPVCTLVSSHN--VLFSGSL-KAIKVWDIVGTELKlkKELTGLNHWVRALVAAQ--SYLYSGSY 538
Cdd:COG2319 231 WDLATGKLLRTLTGHSGSVRSVAFSPDgrLLASGSAdGTVRLWDLATGELL--RTLTGHSGGVNSVAFSPdgKLLASGSD 308
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 539 -QTIKIWDIRTLDCIHVLQTSGGSVYSIAVT--NHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVisTPDQTK 615
Cdd:COG2319 309 dGTVRLWDLATGKLLRTLTGHTGAVRSVAFSpdGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAF--SPDGRT 386
                       250
                ....*....|....*..
gi 45594312 616 VFSASYDRSLRVWSMDN 632
Cdd:COG2319 387 LASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
388-629 5.63e-49

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 173.29  E-value: 5.63e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 388 CKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWDTcTTYKCQKTLEGHDGIVLALCIQGCK--LYSGSADCTIIVWD 465
Cdd:cd00200  43 LLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL-ETGECVRTLTGHTSYVSSVAFSPDGriLSSSSRDKTIKVWD 121
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 466 IQNLQKVNTIRAHDNPVCTLVSSHN--VLFSGSL-KAIKVWDIvgTELKLKKELTGLNHWVRALVA---AQSYLYSGSYQ 539
Cdd:cd00200 122 VETGKCLTTLRGHTDWVNSVAFSPDgtFVASSSQdGTIKLWDL--RTGKCVATLTGHTGEVNSVAFspdGEKLLSSSSDG 199
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 540 TIKIWDIRTLDCIHVLQTSGGSVYSIAVTNHH--IVCGTYENLIHVWDIESKEQVRTLTGHVGTVYALAVisTPDQTKVF 617
Cdd:cd00200 200 TIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGylLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAW--SPDGKRLA 277
                       250
                ....*....|..
gi 45594312 618 SASYDRSLRVWS 629
Cdd:cd00200 278 SGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
386-545 6.81e-33

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 128.22  E-value: 6.81e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 386 FKCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWDTcTTYKCQKTLEGHDGIVLALCI--QGCKLYSGSADCTIIV 463
Cdd:cd00200 125 GKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL-RTGKCVATLTGHTGEVNSVAFspDGEKLLSSSSDGTIKL 203
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 464 WDIQNLQKVNTIRAHDNPVCTLVSSHN--VLFSGSL-KAIKVWDIVGTElkLKKELTGLNHWVRALVAAQS--YLYSGSY 538
Cdd:cd00200 204 WDLSTGKCLGTLRGHENGVNSVAFSPDgyLLASGSEdGTIRVWDLRTGE--CVQTLSGHTNSVTSLAWSPDgkRLASGSA 281

                ....*...
gi 45594312 539 -QTIKIWD 545
Cdd:cd00200 282 dGTIRIWD 289
WD40 COG2319
WD40 repeat [General function prediction only];
452-668 6.52e-30

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 122.33  E-value: 6.52e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 452 LYSGSADCTIIVWDIQNLQKVNTIRAHDNPVCTLVSSHN---VLFSGSLKAIKVWDIVGTELKLkkELTGLNHWVRALVA 528
Cdd:COG2319   9 LAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDgarLAAGAGDLTLLLLDAAAGALLA--TLLGHTAAVLSVAF 86
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 529 AQ--SYLYSGSYQ-TIKIWDIRTLDCIHVLQTSGGSVYSIAVT--NHHIVCGTYENLIHVWDIESKEQVRTLTGHVGTVY 603
Cdd:COG2319  87 SPdgRLLASASADgTVRLWDLATGLLLRTLTGHTGAVRSVAFSpdGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVT 166
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45594312 604 ALAVisTPDQTKVFSASYDRSLRVWSMDNMICTQTLLRHQGSVTALAVSR-GR-LFSGAVDSTVKVW 668
Cdd:COG2319 167 SVAF--SPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPdGKlLASGSADGTVRLW 231
mRING-HC-C3HC3D_TRAF7 cd16644
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
124-168 1.09e-20

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins; TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats.


Pssm-ID: 438306 [Multi-domain]  Cd Length: 47  Bit Score: 85.48  E-value: 1.09e-20
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 45594312 124 QPSVKLCCQLCCSVFKDPVITTCGHTFCRRCALKS--EKCPVDNVKL 168
Cdd:cd16644   1 PPSVKLYCPLCQRVFKDPVITSCGHTFCRRCALTApgEKCPVDNMKL 47
WD40 pfam00400
WD domain, G-beta repeat;
386-424 4.15e-09

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 52.35  E-value: 4.15e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 45594312   386 FKCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWD 424
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
386-424 6.17e-09

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 51.93  E-value: 6.17e-09
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 45594312    386 FKCKGTFVGHQGPVWCLCVYSMGDLLFSGSSDKTIKVWD 424
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
mRING-HC-C3HC3D_TRAF6 cd16643
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
128-170 1.60e-08

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and similar proteins; TRAF6, also known as interleukin-1 signal transducer or RING finger protein 85 (RNF85), is a cytoplasmic adapter protein that mediates signals induced by the tumor necrosis factor receptor (TNFR) superfamily and Toll-like receptor (TLR)/interleukin-1 receptor (IL-1R) family. It functions as a mediator involved in the activation of mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and interferon regulatory factor pathways, as well as in IL-1R-mediated activation of NF-kappaB. TRAF6 is also an oncogene that plays a vital role in K-RAS-mediated oncogenesis. TRAF6 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain.


Pssm-ID: 438305 [Multi-domain]  Cd Length: 58  Bit Score: 51.23  E-value: 1.60e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRCALKS-----EKCPVDNVKLTV 170
Cdd:cd16643   1 KYECPICLMALREPVQTPCGHRFCKACILKSireagHKCPVDNEPLLE 48
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
129-164 2.76e-07

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 47.10  E-value: 2.76e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCALK-----SEKCPVD 164
Cdd:cd16449   1 LECPICLERLKDPVLLPCGHVFCRECIRRllesgSIKCPIC 41
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
130-163 4.29e-07

RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; RNF113A, also known as zinc finger protein 183 (ZNF183), is an E3 ubiquitin-protein ligase that physically interacts with the E2 protein, UBE2U. A nonsense mutation in RNF113A is associated with an X-linked trichothiodystrophy (TTD). Its yeast ortholog Cwc24p is predicted to have a spliceosome function and acts in a complex with Cef1p to participate in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing. It is also important for the U2 snRNP binding to primary transcripts and co-migrates with spliceosomes. Moreover, the ortholog of RNF113A in fruit flies may also act as a spliceosome and is hypothesized to be involved in splicing, namely within the central nervous system. The ortholog in Caenorhabditis elegans is involved in DNA repair of inter-strand crosslinks. RNF113B, also known as zinc finger protein 183-like 1, shows high sequence similarity with RNF113A. Both RNF113A and RNF113B contain a CCCH-type zinc finger, which is commonly found in RNA-binding proteins involved in splicing, and a C3HC4-type RING-HC finger, which is frequently found in E3 ubiquitin ligases.


Pssm-ID: 438201 [Multi-domain]  Cd Length: 54  Bit Score: 47.20  E-value: 4.29e-07
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 45594312 130 CCQLCCSVFKDPVITTCGHTFCRRCAL----KSEKCPV 163
Cdd:cd16539   7 ACFICRKPFKNPVVTKCGHYFCEKCALkhyrKSKKCFV 44
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
129-154 6.14e-07

RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins; TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438273 [Multi-domain]  Cd Length: 59  Bit Score: 46.68  E-value: 6.14e-07
                        10        20
                ....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16611   5 LHCPLCLDFFRDPVMLSCGHNFCQSC 30
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
128-163 2.67e-06

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis.


Pssm-ID: 438243 [Multi-domain]  Cd Length: 50  Bit Score: 44.81  E-value: 2.67e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRC-----------ALKSEKCPV 163
Cdd:cd16581   2 ELTCSICYNIFDDPKILPCSHTFCKNClekllaasgyyLLASLKCPT 48
RING-HC_TRIM17_C-IV cd16595
RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ...
131-158 3.02e-06

RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar proteins; TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (Terf), is a crucial E3 ubiquitin ligase that is necessary and sufficient for neuronal apoptosis and contributes to Mcl-1 ubiquitination in cerebellar granule neurons (CGNs). It interacts in a SUMO-dependent manner with nuclear factor of activated T cell NFATc3 transcription factor, and thus inhibits the activity of NFATc3 by preventing its nuclear localization. In contrast, it binds to and inhibits NFATc4 transcription factor in a SUMO-independent manner. Moreover, TRIM17 stimulates degradation of kinetochore protein ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for the mitotic spindle checkpoint, and negatively regulates cell proliferation. TRIM17 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438257 [Multi-domain]  Cd Length: 70  Bit Score: 45.37  E-value: 3.02e-06
                        10        20
                ....*....|....*....|....*...
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCALKS 158
Cdd:cd16595   8 CSICLDYFTDPVMTTCGHNFCRACIQLS 35
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
129-162 6.61e-06

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.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: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 48.85  E-value: 6.61e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 45594312   129 LCCQLCCSVFKDPVITTCGHTFC----RRCALKSEKCP 162
Cdd:TIGR00599  27 LRCHICKDFFDVPVLTSCSHTFCslciRRCLSNQPKCP 64
RING-HC_TRIM62_C-IV cd16608
RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar ...
129-154 9.55e-06

RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar proteins; TRIM62, also known as Ductal Epithelium Associated Ring Chromosome 1 (DEAR1), is a cytoplasmic E3 ubiquitin-protein ligase that was identified as a dominant regulator of acinar morphogenesis in the mammary gland. It is implicated in the inflammatory response of immune cells by regulating the Toll-like receptor 4 (TLR4) signaling pathway, leading to increased activity of the activator protein 1 (AP-1) transcription factor in primary macrophages. It is also involved in muscular protein homeostasis, especially during inflammation-induced atrophy, and may play a role in the pathogenesis of ICU-acquired weakness (ICUAW) by activating and maintaining inflammation in myocytes. Moreover, TRIM62 facilitates K27-linked poly-ubiquitination of CARD9 and also regulates CARD9-mediated anti-fungal immunity and intestinal inflammation. It also functions as a chromosome 1p35 tumor suppressor and negatively regulates transforming growth factor beta (TGFbeta)-driven epithelial-mesenchymal transition (EMT) by binding to and promoting the ubiquitination of SMAD3, a major effector of TGFbeta-mediated EMT. TRIM62 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438270 [Multi-domain]  Cd Length: 52  Bit Score: 43.26  E-value: 9.55e-06
                        10        20
                ....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16608   7 LLCSICLSIYQDPVSLGCEHYFCRQC 32
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
131-163 9.97e-06

second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger.


Pssm-ID: 438177 [Multi-domain]  Cd Length: 45  Bit Score: 43.02  E-value: 9.97e-06
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCALK----SEKCPV 163
Cdd:cd16514   4 CSLCLRLLYEPVTTPCGHTFCRACLERcldhSPKCPL 40
RING-HC_RNF39 cd16592
RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ...
131-154 1.05e-05

RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, also called protein HZFw, may play a role in prolonged long term-potentiation (LTP) maintenance. It is involved in the etiology of Behcet's disease (BD). It may also be involved in HIV-1 replication. RNF39 acts as an E3 ubiquitin ligase that inhibits retinoic acid-inducible gene-I (RIG-I)-like receptor (RLR) pathways by mediating K48-linked ubiquitination and proteasomal degradation of DDX3X (DEAD-box RNA helicase 3, X-linked). RNF39 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438254 [Multi-domain]  Cd Length: 58  Bit Score: 43.21  E-value: 1.05e-05
                        10        20
                ....*....|....*....|....
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16592   7 CPICLGYFKDPVILDCEHSFCRAC 30
RING-HC_TRIM72_C-IV cd16612
RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ...
129-162 1.10e-05

RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar proteins; TRIM72, also known as Mitsugumin-53 (MG53), is a muscle-specific protein that plays a central role in cell membrane repair by nucleating the assembly of the repair machinery at muscle injury sites. It is required in repair of alveolar epithelial cells under plasma membrane stress failure. It interacts with dysferlin to regulate sarcolemmal repair. Upregulation of TRIM72 develops obesity, systemic insulin resistance, dyslipidemia, and hyperglycemia, as well as induces diabetic cardiomyopathy through transcriptional activation of the peroxisome proliferation-activated receptor alpha (PPAR-alpha) signaling pathway. Compensation for the absence of AKT signaling by ERK signaling during TRIM72 overexpression leads to pathological hypertrophy. Moreover, TRIM72 functions as a novel negative feedback regulator of myogenesis by targeting insulin receptor substrate-1 (IRS-1). It is transcriptionally activated by the synergism of myogenin (MyoD) and myocyte enhancer factor 2 (MEF2). TRIM72 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438274 [Multi-domain]  Cd Length: 60  Bit Score: 43.19  E-value: 1.10e-05
                        10        20        30
                ....*....|....*....|....*....|....
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCALKSEKCP 162
Cdd:cd16612   5 LSCPLCLKLFQSPVTTECGHTFCQDCLSRVPKEE 38
RING-HC_TRIM7-like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ...
129-157 1.28e-05

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins; TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells.


Pssm-ID: 438256 [Multi-domain]  Cd Length: 61  Bit Score: 43.06  E-value: 1.28e-05
                        10        20
                ....*....|....*....|....*....
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCALK 157
Cdd:cd16594   6 LTCPICLDYFTDPVTLDCGHSFCRACIAR 34
RING-HC_TRIM77_C-IV cd16543
RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ...
128-154 1.68e-05

RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar proteins; TRIM77 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including two consecutive zinc-binding domains, a C3HC4-type RING-HC finger and Bbox2, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438205 [Multi-domain]  Cd Length: 54  Bit Score: 42.76  E-value: 1.68e-05
                        10        20
                ....*....|....*....|....*..
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16543   3 QLTCSICLDLLKDPVTIPCGHSFCMNC 29
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
131-154 2.22e-05

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438263 [Multi-domain]  Cd Length: 44  Bit Score: 42.09  E-value: 2.22e-05
                        10        20
                ....*....|....*....|....
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16601   4 CSLCKEYLKDPVIIECGHNFCRAC 27
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
428-465 2.26e-05

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 41.91  E-value: 2.26e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 45594312    428 TYKCQKTLEGHDGIVLALCI--QGCKLYSGSADCTIIVWD 465
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFspDGKYLASGSDDGTIKLWD 40
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
131-163 2.54e-05

RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins; HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA.


Pssm-ID: 438172 [Multi-domain]  Cd Length: 53  Bit Score: 41.91  E-value: 2.54e-05
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCALKS-----EKCPV 163
Cdd:cd16509   6 CAICLDSLTNPVITPCAHVFCRRCICEViqrekAKCPM 43
COG5152 COG5152
Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function ...
125-157 3.23e-05

Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only];


Pssm-ID: 227481 [Multi-domain]  Cd Length: 259  Bit Score: 46.22  E-value: 3.23e-05
                        10        20        30
                ....*....|....*....|....*....|...
gi 45594312 125 PSVKLCCQLCCSVFKDPVITTCGHTFCRRCALK 157
Cdd:COG5152 193 EKIPFLCGICKKDYESPVVTECGHSFCSLCAIR 225
RING-HC_COP1 cd16504
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...
131-169 3.56e-05

RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and similar proteins; COP1, also known as RING finger and WD repeat domain protein 2 (RFWD2) or RING finger protein 200 (RNF200), is a central regulator of photomorphogenic development in plants, which targets key transcription factors for proteasome-dependent degradation. It is localized predominantly in the nucleus, but may also be present in the cytosol. Mammalian COP1 functions as an E3 ubiquitin-protein ligase that interacts with Jun transcription factors and modulates their transcriptional activity. It also interacts with and negatively regulates the tumor-suppressor protein p53. Moreover, COP1 associates with COP9 signalosome subunit 6 (CSN6), and is involved in 14-3-3sigma ubiquitin-mediated degradation. The CSN6-COP1 link enhances ubiquitin-mediated degradation of p27(Kip1), a critical CDK inhibitor involved in cell cycle regulation, to promote cancer cell growth. Furthermore, COP1 functions as the negative regulator of ETV1 and influences prognosis in triple-negative breast cancer. COP1 contains an N-terminal extension, a C3HC4-type RING-HC finger, a coiled coil domain, and seven WD40 repeats. In human COP1, a classic leucine-rich NES, and a novel bipartite NLS is bridged by the RING-HC finger.


Pssm-ID: 438167 [Multi-domain]  Cd Length: 47  Bit Score: 41.46  E-value: 3.56e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCALKS----EKCPVDNVKLT 169
Cdd:cd16504   5 CPICFDIIKEAFVTKCGHSFCYKCIVKHleqkNRCPKCNFYLT 47
mRING-HC-C3HC3D_LNX1-like cd16637
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, ...
129-165 3.71e-05

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4 or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for substrate-binding. LNX1/LNX2-like proteins contain a modified C3HC3D-type RING-HC finger and four PDZ domains. This model corresponds to the RING finger.


Pssm-ID: 438299 [Multi-domain]  Cd Length: 42  Bit Score: 41.23  E-value: 3.71e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCA---LKSEK-CPVDN 165
Cdd:cd16637   2 LTCHICLQPLVEPLDTPCGHTFCYKCLtnyLKIQQcCPLDR 42
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
128-154 4.71e-05

RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438271 [Multi-domain]  Cd Length: 58  Bit Score: 41.59  E-value: 4.71e-05
                        10        20
                ....*....|....*....|....*..
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16609   3 ELTCSICLGLYQDPVTLPCQHSFCRAC 29
RING-HC_TRIM59_C-V cd16763
RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar ...
129-154 5.38e-05

RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins; TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis. It is upregulated in gastric cancer and promotes gastric carcinogenesis by interacting with and targeting the P53 tumor suppressor for its ubiquitination and degradation. It also acts as a novel accessory molecule involved in cytotoxicity of BCG-activated macrophages (BAM). Moreover, TRIM59 may serve as a multifunctional regulator for innate immune signaling pathways. It interacts with ECSIT and negatively regulates nuclear factor-kappaB (NF- kappa B) and interferon regulatory factor (IRF)-3/7-mediated signal pathways. TRIM59 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM59 contains a C-terminal transmembrane domain.


Pssm-ID: 438419 [Multi-domain]  Cd Length: 56  Bit Score: 41.44  E-value: 5.38e-05
                        10        20
                ....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16763   4 LTCSVCYSLFEDPRVLPCSHTFCRNC 29
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
131-162 6.74e-05

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.


Pssm-ID: 463881 [Multi-domain]  Cd Length: 38  Bit Score: 40.46  E-value: 6.74e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 45594312   131 CQLCCSVFKDPViTTCGHTFCRRCALKSE-------KCP 162
Cdd:pfam13445   1 CPICLELFTDPV-LPCGHTFCRECLEEMSqkkggkfKCP 38
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
129-154 8.07e-05

RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins; TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438259 [Multi-domain]  Cd Length: 71  Bit Score: 41.14  E-value: 8.07e-05
                        10        20
                ....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16597   6 LTCSICLELFKDPVTLPCGHNFCGVC 31
WD40 pfam00400
WD domain, G-beta repeat;
430-465 8.80e-05

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 40.02  E-value: 8.80e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 45594312   430 KCQKTLEGHDGIVLALCIQ--GCKLYSGSADCTIIVWD 465
Cdd:pfam00400   2 KLLKTLEGHTGSVTSLAFSpdGKLLASGSDDGTVKVWD 39
RING-HC_TRIM13_C-V cd16762
RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ...
129-154 8.93e-05

RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins; TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates melanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain.


Pssm-ID: 438418 [Multi-domain]  Cd Length: 56  Bit Score: 40.67  E-value: 8.93e-05
                        10        20
                ....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16762   4 LTCPICCCLFDDPRVLPCSHNFCKKC 29
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
588-629 8.94e-05

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 39.99  E-value: 8.94e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 45594312    588 SKEQVRTLTGHVGTVYALAVisTPDQTKVFSASYDRSLRVWS 629
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAF--SPDGKYLASGSDDGTIKLWD 40
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
131-163 1.17e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 39.80  E-value: 1.17e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 45594312    131 CQLCCSVF-KDPVITTCGHTFCRRCALK-----SEKCPV 163
Cdd:smart00184   1 CPICLEEYlKDPVILPCGHTFCRSCIRKwlesgNNTCPI 39
RING-HC_LNX3 cd16718
RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ ...
129-163 1.67e-04

RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ domain-containing RING finger protein 3 (PDZRN3), or Semaphorin cytoplasmic domain-associated protein 3 (SEMACAP3), is an E3 ubiquitin-protein ligase that was first identified as a Semaphorin-binding partner. It is also responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX3 acts as a negative regulator of osteoblast differentiation by inhibiting Wnt-beta-catenin signaling. LNX3 also plays an important role in neuromuscular junction formation. It interacts with and ubiquitinates the muscle specific tyrosine kinase (MuSK), thus promoting its endocytosis and negatively regulating the cell surface expression of this key regulator of postsynaptic assembly. LNX3 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 438378 [Multi-domain]  Cd Length: 47  Bit Score: 39.58  E-value: 1.67e-04
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCAL----KSEKCPV 163
Cdd:cd16718   5 FKCNLCNKVLEDPLTTPCGHVFCAGCVLpwvvQQGSCPV 43
RING-HC_LNX4 cd16719
RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ ...
129-163 1.82e-04

RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ domain-containing RING finger protein 4 (PDZRN4), or SEMACAP3-like protein (SEMCAP3L), is an E3 ubiquitin-protein ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX4 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 438379 [Multi-domain]  Cd Length: 53  Bit Score: 39.53  E-value: 1.82e-04
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC----ALKSEKCPV 163
Cdd:cd16719   5 LKCKLCGKVLEEPLSTPCGHVFCAGCllpwAVQRRLCPL 43
RING-HC_TRIM4_C-IV cd16590
RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar ...
128-154 1.99e-04

RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar proteins; TRIM4 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM4, also known as RING finger protein 87 (RNF87), is a cytoplasmic E3 ubiquitin-protein ligase that has recently evolved and is present only in higher mammals. It transiently interacts with mitochondria, induces mitochondrial aggregation and sensitizes the cells to hydrogen peroxide (H2O2) induced death. Its interaction with peroxiredoxin 1 (PRX1) is critical for the regulation of H2O2 induced cell death. Moreover, TRIM4 functions as a positive regulator of RIG-I-mediated type I interferon induction. It regulates the K63-linked ubiquitination of RIG-1 and assembly of antiviral signaling complex at the mitochondria.


Pssm-ID: 438252 [Multi-domain]  Cd Length: 61  Bit Score: 40.02  E-value: 1.99e-04
                        10        20
                ....*....|....*....|....*..
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16590   6 ELTCPICLDYFQDPVSIECGHNFCRGC 32
WD40 pfam00400
WD domain, G-beta repeat;
589-629 2.11e-04

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 38.87  E-value: 2.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 45594312   589 KEQVRTLTGHVGTVYALAVisTPDQTKVFSASYDRSLRVWS 629
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAF--SPDGKLLASGSDDGTVKVWD 39
RING-HC_Bre1-like cd16499
RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ...
128-162 2.92e-04

RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ubiquitin-protein ligase that catalyzes monoubiquitination of histone H2B in concert with the E2 ubiquitin-conjugating enzyme, Rad6. The Rad6-Bre1-mediated histone H2B ubiquitylation modulates the formation of double-strand breaks (DSBs) during meiosis in yeast. it is also required, indirectly, for the methylation of histone 3 on lysine 4 (H3K4) and 79. RNF20, also known as BRE1A and RNF40, also known as BRE1B, are the mammalian homologs of Bre1. They work together to form a heterodimeric Bre1 complex that facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. Moreover, the Bre1 complex acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. Deficiency in the mammalian histone H2B ubiquitin ligase Bre1 leads to replication stress and chromosomal instability. All subfamily members contain a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438162 [Multi-domain]  Cd Length: 59  Bit Score: 39.08  E-value: 2.92e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRC-----ALKSEKCP 162
Cdd:cd16499   6 LLKCSVCNDRFKDVIITKCGHVFCNECvqkrlETRQRKCP 45
Ubox smart00504
Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2 ...
129-183 3.45e-04

Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.


Pssm-ID: 128780 [Multi-domain]  Cd Length: 63  Bit Score: 39.14  E-value: 3.45e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45594312    129 LCCQLCCSVFKDPVITTCGHTFCRRC----ALKSEKCPVDNVKLT--VVVNNIAVAEQIGE 183
Cdd:smart00504   2 FLCPISLEVMKDPVILPSGQTYERSAiekwLLSHGTDPVTGQPLTheDLIPNLALKSAIQE 62
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
129-154 3.50e-04

RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins; TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle.


Pssm-ID: 438266 [Multi-domain]  Cd Length: 49  Bit Score: 38.56  E-value: 3.50e-04
                        10        20
                ....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16604   1 LSCPICLDLLKDPVTLPCGHSFCMGC 26
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
131-168 4.60e-04

RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as T-cell RING activation protein 1 (TRAC-1), is an E3 ubiquitin-protein ligase that is predominantly expressed in lymphoid cells, and functions as a positive regulator of T cell activation. It also down-modulates HIV replication and inhibits pathogen-induced cytokine production. It negatively regulates type I interferon signaling, which conjugates Lys(48)-linked ubiquitination to retinoic acid-inducible gene-I (RIG-I) and subsequently leads to the proteasome-dependent degradation of RIG-I. Further, RNF125 conjugates ubiquitin to melanoma differentiation-associated gene 5 (MDA5), a family protein of RIG-I. It thus acts as a negative regulator of RIG-I signaling, and is a direct target of miR-15b in the context of Japanese encephalitis virus (JEV) infection. Moreover, RNF125 binds to and ubiquitinates JAK1, prompting its degradation and inhibition of receptor tyrosine kinase (RTK) expression. It also negatively regulates p53 function through physical interaction and ubiquitin-mediated proteasome degradation. Mutations in RNF125 may lead to overgrowth syndromes (OGS). RNF125, together with three closely related proteins: RNF114, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). The UIM of RNF125 binds K48-linked poly-ubiquitin chains and is, together with the RING domain, required for auto-ubiquitination.


Pssm-ID: 438204 [Multi-domain]  Cd Length: 50  Bit Score: 38.32  E-value: 4.60e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRC---ALKSEK--CPVDNVKL 168
Cdd:cd16542   4 CAVCLEVLHQPVRTRCGHVFCRPCiatSLRNNTwtCPYCRAYL 46
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
131-163 4.63e-04

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 38.19  E-value: 4.63e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 45594312   131 CQLCCSVFKDPVITT-CGHTFCRRCALK----SEKCPV 163
Cdd:pfam13923   2 CPICMDMLKDPSTTTpCGHVFCQDCILRalraGNECPL 39
mRING-HC-C3HC3D_Roquin cd16638
Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar ...
129-164 4.80e-04

Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar proteins; The ROQUIN family includes Roquin-1, Roquin-2, and similar proteins, which localize to the cytoplasm and upon stress, are concentrated in stress granules. They may play essential roles in preventing T-cell-mediated autoimmune disease and in microRNA-mediated repression of inducible costimulator (Icos) mRNA. They function as E3 ubiquitin ligases consisting of an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 activity, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger involved in RNA recognition.


Pssm-ID: 438300 [Multi-domain]  Cd Length: 44  Bit Score: 38.10  E-value: 4.80e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 45594312 129 LCCQLCCSVFKD----PVITTCGHTFCRRC--ALKSEKCPVD 164
Cdd:cd16638   2 LSCPVCTNEFDGtqrkPISLGCGHTVCKTClsKLHRKQCPFD 43
RING-HC_RNF166 cd16549
RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...
128-163 5.35e-04

RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; RNF166 is encoded by the gene RNF166 targeted by thyroid hormone receptor alpha1 (TRalpha1), which is important in brain development. It plays an important role in RNA virus-induced interferon-beta production by enhancing the ubiquitination of TRAF3 and TRAF6. RNF166, together with three closely related proteins: RNF114, RNF125 and RNF138, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438211 [Multi-domain]  Cd Length: 47  Bit Score: 38.25  E-value: 5.35e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 45594312 128 KLCCQLCCSVFKDPV-ITTCGHTFCRRC-----ALKSEKCPV 163
Cdd:cd16549   1 QFSCPICLEVYHKPVvITSCGHTFCGEClqpclQVASPLCPL 42
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
131-163 5.79e-04

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 37.72  E-value: 5.79e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 45594312   131 CQLCCSVFKDPV-ITTCGHTFCRRCALK-----SEKCPV 163
Cdd:pfam00097   1 CPICLEEPKDPVtLLPCGHLFCSKCIRSwlesgNVTCPL 39
RING-HC_GEFO-like cd16507
RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange ...
120-162 5.87e-04

RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange factor O (RasGEFO) and similar proteins; RasGEFO, also known as RasGEF domain-containing protein O, functions as a Ras guanine-nucleotide exchange factor (RasGEFs), activating Ras by catalyzing the replacement of GDP with GTP. RasGEFs are particularly important for signaling in development and chemotaxis in many organisms, including Dictyostelium. RasGEFO contains a C3HC4-type RING-HC finger that may be responsible for E3 ubiquitin ligase activity.


Pssm-ID: 438170 [Multi-domain]  Cd Length: 58  Bit Score: 38.48  E-value: 5.87e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 45594312 120 VFAEQPSVKLCCQLCCSVFKDP-VITTCGHTFCRRC---ALKSEKCP 162
Cdd:cd16507   1 SKSLNLLQSLTCGICQNLFKDPnTLIPCGHAFCLDClttNASIKNCI 47
RING-HC_RNF138 cd16544
RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ...
131-163 6.08e-04

RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; RNF138, also known as Nemo-like kinase-associated RING finger protein (NARF) or NLK-associated RING finger protein, is an E3 ubiquitin-protein ligase that plays an important role in glioma cell proliferation, apoptosis, and cell cycle. It specifically cooperates with the E2 conjugating enzyme E2-25K (Hip-2/UbcH1), regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF), and further suppresses Wnt-beta-catenin signaling. RNF138, together with three closely related proteins: RNF114, RNF125 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438206 [Multi-domain]  Cd Length: 53  Bit Score: 38.15  E-value: 6.08e-04
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 45594312 131 CQLCCSVFKDPV-ITTCGHTFCRRCAL-----KSEKCPV 163
Cdd:cd16544   5 CPVCQEVLKDPVeLPPCRHIFCKACILlalrsSGARCPL 43
RING-HC_LONFs_rpt1 cd16513
first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
131-154 6.51e-04

first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the first RING-HC finger.


Pssm-ID: 438176 [Multi-domain]  Cd Length: 47  Bit Score: 38.06  E-value: 6.51e-04
                        10        20
                ....*....|....*....|....
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16513   5 CPLCRGLLFEPVTLPCGHTFCKRC 28
RING-HC_MmTRIM43-like cd23133
RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) ...
129-160 7.93e-04

RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) and similar propteins; This subfamily includes TRIM43A, TRIM43B and TRIM43C, which are expressed specifically in mouse preimplantation embryos. They contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438495 [Multi-domain]  Cd Length: 57  Bit Score: 37.97  E-value: 7.93e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCALKSEK 160
Cdd:cd23133   4 LTCSICQGIFMNPVYLRCGHKFCEACLLLFQE 35
RING-HC_TRIM43-like_C-IV cd16603
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, ...
129-154 8.38e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, TRIM51, TRIM64 and similar proteins; The family includes a group of closely related uncharacterized tripartite motif-containing proteins, TRIM43, TRIM43B, TRIM48/RNF101, TRIM49/RNF18, TRIM49B, TRIM49C/TRIM49L2, TRIM49D/TRIM49L, TRIM51/SPRYD5, TRIM64, TRIM64B, and TRIM64C, whose biological function remain unclear. TRIM49, also known as testis-specific RING-finger protein, has moderate similarity with SS-A/Ro52 antigen, suggesting it may be one of the target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. In RBCC region, they all have a C3HC4-type RING-HC finger.


Pssm-ID: 438265 [Multi-domain]  Cd Length: 59  Bit Score: 37.85  E-value: 8.38e-04
                        10        20
                ....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16603   5 LTCPICMNYFIDPVTIDCGHSFCRPC 30
RING-HC_TRIM41-like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
131-162 9.00e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins; TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain.


Pssm-ID: 438264 [Multi-domain]  Cd Length: 53  Bit Score: 37.60  E-value: 9.00e-04
                        10        20        30
                ....*....|....*....|....*....|....
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCA--LKSEKCP 162
Cdd:cd16602   6 CAICLDYFKDPVSIGCGHNFCRVCVtqLWGFTCP 39
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
125-154 1.11e-03

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 42.00  E-value: 1.11e-03
                        10        20        30
                ....*....|....*....|....*....|....*
gi 45594312 125 PSVK-----LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:COG5432  17 PSLKgldsmLRCRICDCRISIPCETTCGHTFCSLC 51
RING-HC_AtBRCA1-like cd23147
RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 ...
129-163 1.25e-03

RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 homolog (AtBRCA1) and similar proteins; AtBRCA1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBRCA1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438509 [Multi-domain]  Cd Length: 54  Bit Score: 37.45  E-value: 1.25e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCALKSEK----CPV 163
Cdd:cd23147   5 LKCPICLSLFKSAANLSCNHCFCAGCIGESLKlsaiCPV 43
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
129-157 1.28e-03

RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and similar proteins; BRCA1, also known as RING finger protein 53 (RNF53), is a RING finger protein encoded by the tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus.


Pssm-ID: 438161 [Multi-domain]  Cd Length: 94  Bit Score: 38.43  E-value: 1.28e-03
                        10        20
                ....*....|....*....|....*....
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCALK 157
Cdd:cd16498  17 LECPICLELLKEPVSTKCDHQFCRFCILK 45
mRING-HC-C3HC3D_TRAF4 cd16641
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
128-164 1.38e-03

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4) and similar proteins; TRAF4, also known as cysteine-rich domain associated with RING and Traf domains protein 1, metastatic lymph node gene 62 protein (MLN 62), or RING finger protein 83 (RNF83), is a member of the TRAF protein family, which mainly function in the immune system, where they mediate signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a critical role in nervous system, as well as in carcinogenesis. TRAF4 promotes the growth and invasion of colon cancer through the Wnt/beta-catenin pathway. It contributes to the TNFalpha-induced activation of the 70 kDa ribosomal protein S6 kinase (p70s6k) signaling pathway, and activation of transforming growth factor beta (TGF-beta)-induced SMAD-dependent signaling and non-SMAD signaling in breast cancer. It also enhances osteosarcoma cell proliferation and invasion by the Akt signaling pathway. Moreover, TRAF4 is a novel phosphoinositide-binding protein modulating tight junctions and favoring cell migration. TRAF4 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain.


Pssm-ID: 438303 [Multi-domain]  Cd Length: 45  Bit Score: 37.05  E-value: 1.38e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45594312 128 KLCCQLCCSVFKDPV-ITTCGHTFCRRCALK--SE---KCPVD 164
Cdd:cd16641   1 RLLCPLCRLPMREPVqISTCGHRFCDTCLQEflSEgvfKCPED 43
RING-HC_TRIM9-like_C-I cd16576
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and ...
129-163 1.39e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and similar proteins; Tripartite motif-containing proteins TRIM9 and TRIM67 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. TRIM67, also known as TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H, also known as glucosidase II beta, a protein kinase C substrate.


Pssm-ID: 438238 [Multi-domain]  Cd Length: 42  Bit Score: 37.00  E-value: 1.39e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCALKSE-KCPV 163
Cdd:cd16576   4 LKCPVCGSLFTEPVILPCSHNLCLGCALNIQlTCPI 39
RING-HC_AtRMA-like cd16745
RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ...
131-163 1.47e-03

RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) and similar proteins; AtRMAs, including AtRma1, AtRma2, and AtRma3, are endoplasmic reticulum (ER)-localized Arabidopsis homologs of human outer membrane of the ER-anchor E3 ubiquitin-protein ligase, RING finger protein 5 (RNF5). AtRMAs possess E3 ubiquitin ligase activity, and may play a role in the growth and development of Arabidopsis. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot-root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. AtRma1 probably functions with the Ubc4/5 subfamily of E2. AtRma2 is likely involved in the cellular regulation of ABP1 expression levels through interacting with auxin binding protein 1 (ABP1). AtRMA proteins contain an N-terminal C3HC4-type RING-HC finger and a trans-membrane-anchoring domain in their extreme C-terminal region.


Pssm-ID: 438403 [Multi-domain]  Cd Length: 45  Bit Score: 36.69  E-value: 1.47e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRC-------ALKSEKCPV 163
Cdd:cd16745   3 CNICLDLAQDPVVTLCGHLFCWPClhkwlrrQSSQPECPV 42
vRING-HC-C4C4_RBBP6 cd16620
Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ...
128-163 1.52e-03

Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) and similar proteins; RBBP6, also known as proliferation potential-related protein, protein P2P-R, retinoblastoma-binding Q protein 1 (RBQ-1), or p53-associated cellular protein of testis (PACT), is a nuclear E3 ubiquitin-protein ligase involved in multiple processes, such as the control of gene expression, mitosis, cell differentiation, and cell apoptosis. It plays a role in both promoting and inhibiting apoptosis in many human cancers, including esophageal, lung, hepatocellular, and colon cancers, familial myeloproliferative neoplasms, as well as in human immunodeficiency virus-associated nephropathy (HIVAN). It functions as an Rb- and p53-binding protein that plays an important role in chaperone-mediated ubiquitination and possibly in protein quality control. It acts as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in an increase of MDM2-mediated ubiquitination and degradation of p53/TP53, and leading to both apoptosis and cell growth. It is also a double-stranded RNA-binding protein that plays a role in mRNA processing by regulating the human polyadenylation machinery and modulating expression of mRNAs with AU-rich 3' untranslated regions (UTRs). Moreover, RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38 that negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Furthermore, RBBP6 is involved in tunicamycin-induced apoptosis by mediating protein kinase (PKR) activation. RBBP6 contains an N-terminal ubiquitin-like domain and a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger. RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. It promotes the ubiquitination of p53 by Hdm2 in an E4-like manner through its RING finger. It also interacts directly with the pro-proliferative transcription factor Y-box-binding protein-1 (YB-1) via its RING finger.


Pssm-ID: 438282 [Multi-domain]  Cd Length: 55  Bit Score: 37.00  E-value: 1.52e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 45594312 128 KLCCQLCCSVFKDPVITT-CGHTFCRRC---ALKSEK--CPV 163
Cdd:cd16620   3 ELKCPICKDLMKDAVLTPcCGNSFCDECirtALLEEDftCPT 44
RING-HC_RSPRY1 cd16566
RING finger, HC subclass, found in RING finger and SPRY domain-containing protein 1 (RSPRY1) ...
130-162 1.74e-03

RING finger, HC subclass, found in RING finger and SPRY domain-containing protein 1 (RSPRY1) and similar proteins; RSPRY1 is a hypothetical RING and SPRY domain-containing protein of unknown physiological function. Mutations in its corresponding gene RSPRY1 may associate with a distinct skeletal dysplasia syndrome. RSPRY1 contains a B30.2/SPRY domain and a C3HC4-type RING-HC finger.


Pssm-ID: 438228 [Multi-domain]  Cd Length: 43  Bit Score: 36.57  E-value: 1.74e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 45594312 130 CCQLCCSVFKDPVITTCGHT-FCRRCALKSEKCP 162
Cdd:cd16566   4 SCTLCFDKVADTELRPCGHSgFCMECALQLETCP 37
RING-HC_TRIM58_C-IV cd16606
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...
131-161 1.82e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar proteins; TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization. TRIM58 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438268 [Multi-domain]  Cd Length: 53  Bit Score: 36.76  E-value: 1.82e-03
                        10        20        30
                ....*....|....*....|....*....|.
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCAlkSEKC 161
Cdd:cd16606   5 CPVCLDFLQEPVSVDCGHSFCLRCI--SEFC 33
DD_cGKI-alpha cd12085
Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I alpha; Cyclic ...
282-322 2.06e-03

Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I alpha; Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing for their targeting to different subcellular compartments and intracellular substrates. cGKI-alpha specifically binds to myosin light chain phosphatase targeting subunit (MYPT1) and the regulator of G-protein signaling-2 (RGS-2). cGKI-alpha activates the phosphatase activity of MYPT1, resulting in vasorelaxation. It increases the activity of RGS-2 toward G proteins, with implications in the downstream signaling for vasoconstrictive agents.


Pssm-ID: 213374 [Multi-domain]  Cd Length: 48  Bit Score: 36.48  E-value: 2.06e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 45594312 282 CRFEGLKEFLQQTDDRFHEMHVALAQKDQEIAFLRSMLGKL 322
Cdd:cd12085   2 GSVEELQKLLQAKEERIRELEQLLQQRDEEIQELRSQLDKF 42
RING-HC_RAG1 cd16530
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ...
131-163 2.21e-03

RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins; RAG-1, also known as V(D)J recombination-activating protein 1, RING finger protein 74 (RNF74), or endonuclease RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. RAG1 is a lymphoid-specific factor that mediates DNA-binding to conserved recombination signal sequences (RSS) and catalyzes DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. It also functions as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3, which is required for the joining step of V(D)J recombination. RAG-1 contains an N-terminal C3HC4-type RING-HC finger that mediates monoubiquitylation of histone H3, an adjacent C2H2-type zinc finger, and a nonamer binding (NBD) DNA-binding domain.


Pssm-ID: 319444 [Multi-domain]  Cd Length: 46  Bit Score: 36.27  E-value: 2.21e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCALKSEK-----CPV 163
Cdd:cd16530   5 CQVCEHILADPVQTPCKHLFCRTCILKCLKvmgsyCPS 42
WD40 COG2319
WD40 repeat [General function prediction only];
583-670 2.26e-03

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 41.05  E-value: 2.26e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 583 VWDIESKEQVRTLTGHVGTVYALAVIstPDQTKVFSASYDRSLRVWSMDNMICTQTLLRHQGSVTALAVS--RGRLFSGA 660
Cdd:COG2319  20 LLAAALGALLLLLLGLAAAVASLAAS--PDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSpdGRLLASAS 97
                        90
                ....*....|
gi 45594312 661 VDSTVKVWTC 670
Cdd:COG2319  98 ADGTVRLWDL 107
Sina pfam03145
Seven in absentia protein family; The seven in absentia (sina) gene was first identified in ...
208-269 2.42e-03

Seven in absentia protein family; The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain pfam00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologs of Sina have also been identified. The human homolog Siah-1 also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in pfam00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologs, whose similarity was noted previously, this family also includes putative homologs from Caenorhabditis elegans, Arabidopsis thaliana.


Pssm-ID: 460824 [Multi-domain]  Cd Length: 198  Bit Score: 39.51  E-value: 2.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45594312   208 RGCPFTIKLSARKDHEGSCDYRPVRCP-NNPSCP---PLLRmnLEAHLKEcEHiKCPHSKYGCTFI 269
Cdd:pfam03145  22 SGCSETLPYTEKADHEERCEFRPYSCPcPGSSCTwqgSLDA--VMPHLMD-DH-KKVTTLQGEDFV 83
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
283-373 2.66e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 41.20  E-value: 2.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312  283 RFEGLKEFLQQT---DDRFHEMHVALAQKDQEIAFLRSMLGKLSEKIDQLEKSLElKFDVLDENQSKLSEDLMEFRRDAS 359
Cdd:PRK03918 177 RIERLEKFIKRTeniEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVK-ELEELKEEIEELEKELESLEGSKR 255
                         90
                 ....*....|....
gi 45594312  360 MLNDELSHINARLN 373
Cdd:PRK03918 256 KLEEKIRELEERIE 269
RING-HC_RNF114 cd16540
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...
128-154 3.01e-03

RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; RNF114, also known as zinc finger protein 228 (ZNF228) or zinc finger protein 313 (ZNF313), is a p21(WAF1)-targeting ubiquitin E3 ligase that interacts with X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) and may play a role in p53-mediated cell-fate decisions. It is involved in the immune response to double-stranded RNA in disease pathogenesis. Moreover, RNF114 interacts with A20 and modulates its ubiquitylation. It negatively regulates nuclear factor-kappaB (NF-kappaB)-dependent transcription and positively regulates T-cell activation. RNF114 may play a putative role in the regulation of immune responses, since it corresponds to a novel psoriasis susceptibility gene, ZNF313. RNF114, together with three closely related proteins: RNF125, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438202 [Multi-domain]  Cd Length: 46  Bit Score: 35.89  E-value: 3.01e-03
                        10        20
                ....*....|....*....|....*..
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16540   1 RFTCPVCLEIFETPVRVPCGHVFCNAC 27
RING-HC_TRIM9 cd16755
RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar ...
128-155 3.27e-03

RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins; TRIM9, human ortholog of rat Spring, also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in the neurodegenerative disorders through its ligase activity. It interacts with the WD repeat region of beta-transducin repeat-containing protein (beta-TrCP) through its N-terminal degron motif depending on the phosphorylation status, and thus negatively regulates nuclear factor-kappaB (NF-kappaB) activation in the NF-kappaB pro-inflammatory signaling pathway. Moreover, TRIM9 acts as a critical catalytic link between Netrin-1 and the exocytic soluble NSF attachment receptor protein (SNARE) machinery in murine cortical neurons. It promotes SNARE-mediated vesicle fusion and axon branching in a Netrin-dependent manner. TRIM9 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438413 [Multi-domain]  Cd Length: 55  Bit Score: 36.16  E-value: 3.27e-03
                        10        20
                ....*....|....*....|....*...
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRCA 155
Cdd:cd16755   3 ELKCPVCGSFYREPIILPCSHNLCLACA 30
RING-HC_PCGF1 cd16733
RING finger, HC subclass, found in polycomb group RING finger protein 1 (PCGF1) and similar ...
129-168 4.57e-03

RING finger, HC subclass, found in polycomb group RING finger protein 1 (PCGF1) and similar proteins; PCGF1, also known as nervous system Polycomb-1 (NSPc1) or RING finger protein 68 (RNF68), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like BCOR complex that also contains RING1, RNF2, RYBP, SKP1, as well as the BCL6 co-repressor BCOR and the histone demethylase KDM2B, and is required to maintain the transcriptionally repressive state of some genes, such as Hox genes, BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. PCGF1 promotes cell cycle progression and enhances cell proliferation as well. It is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the retinoid acid response element (RARE element). Moreover, PCGF1 functions as an epigenetic regulator involved in hematopoietic cell differentiation. It cooperates with the transcription factor runt-related transcription factor 1 (Runx1) in regulating differentiation and self-renewal of hematopoietic cells. Furthermore, PCGF1 represents a physical and functional link between Polycomb function and pluripotency. PCGF1 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438391 [Multi-domain]  Cd Length: 71  Bit Score: 36.48  E-value: 4.57e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 45594312 129 LCCQLCCSVFKDPV-ITTCGHTFCRRCALK----SEKCPVDNVKL 168
Cdd:cd16733  10 IVCYLCAGYFIDATtITECLHTFCKSCIVKylqtSKYCPMCNIKI 54
RING-Ubox_CHIP cd16654
U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein ...
129-187 4.64e-03

U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein (CHIP) and similar proteins; CHIP, also known as STIP1 homology and U box-containing protein 1 (STUB1), CLL-associated antigen KW-8, or Antigen NY-CO-7, is a multifunctional protein that functions both as a co-chaperone and an E3 ubiquitin-protein ligase. It couples protein folding and proteasome mediated degradation by interacting with heat shock proteins (e.g. HSC70) and ubiquitinating their misfolded client proteins, thereby targeting them for proteasomal degradation. It is also important for cellular differentiation and survival (or apoptosis), as well as susceptibility to stress. It targets a wide range of proteins, such as expanded ataxin-1, ataxin-3, huntingtin, and androgen receptor, which play roles in glucocorticoid response, tau degradation, and both p53 and cAMP signaling. CHIP contains an N-terminal tetratricopeptide repeat (TPR) domain responsible for protein-protein interaction, a highly charged middle coiled-coil (CC), and a C-terminal RING-like U-box domain acting as an ubiquitin ligase.


Pssm-ID: 438316 [Multi-domain]  Cd Length: 71  Bit Score: 36.01  E-value: 4.64e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCAL-----KSEKCPVDNVKLTV--VVNNIAVAEQIgELFIH 187
Cdd:cd16654   5 LCCKISFELMRDPVITPSGITYERKDIEehlqrVGHFDPITREPLTQdqLIPNLALKEAI-EAFLE 69
RING-HC_RAD16-like cd16567
RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, ...
131-155 4.72e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, Schizosaccharomyces pombe rhp16, and similar proteins; Budding yeast RAD16, also known as ATP-dependent helicase RAD16, is encoded by a yeast excision repair gene homologous to the recombinational repair gene RAD54 and to the SNF2 gene involved in transcriptional activation. It is a component of the global genome repair (GGR) complex that promotes global genome nucleotide excision repair (GG-NER) by removing DNA damage from non-transcribing DNA. RAD16 is involved in differential repair of DNA after UV damage, and repairs preferentially the MAT-alpha locus compared with the HML-alpha locus. Fission yeast rhp16, also known as ATP-dependent helicase rhp16, is a RAD16 homolog. It is involved in GGR via nucleotide excision repair (NER), in conjunction with rhp7, after UV irradiation. Both RAD16 and rhp16 contain a C3HC4-type RING-HC finger, as well as a DEAD-like helicase domain and a helicase superfamily C-terminal domain.


Pssm-ID: 438229 [Multi-domain]  Cd Length: 48  Bit Score: 35.39  E-value: 4.72e-03
                        10        20
                ....*....|....*....|....*
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCA 155
Cdd:cd16567   3 CGICHEEAEDPVVARCHHVFCRACV 27
RING-HC_TRIM26_C-IV cd16598
RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ...
128-154 4.81e-03

RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar proteins; TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM26 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438260 [Multi-domain]  Cd Length: 64  Bit Score: 35.91  E-value: 4.81e-03
                        10        20
                ....*....|....*....|....*..
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16598   4 EVTCSICLDYLRDPVTIDCGHNFCRSC 30
zf-RING_5 pfam14634
zinc-RING finger domain;
131-163 5.20e-03

zinc-RING finger domain;


Pssm-ID: 434085 [Multi-domain]  Cd Length: 43  Bit Score: 35.10  E-value: 5.20e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 45594312   131 CQLCCSVFKD---PVITTCGHTFCRRCA---LKSEKCPV 163
Cdd:pfam14634   2 CNKCFKELSKtrpFYLTSCGHIFCEECLtrlLQERQCPI 40
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
131-169 5.31e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 35.42  E-value: 5.31e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCAL------KSEKCPVDNVKLT 169
Cdd:cd16568   7 CIICHEYLYEPMVTTCGHTYCYTCLNtwfksnRSLSCPDCRTKIT 51
RING-HC_RNF151 cd16547
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...
129-162 5.76e-03

RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; RNF151 is a testis-specific RING finger protein that interacts with dysbindin, a synaptic and microtubular protein that binds brain snapin, a SNARE-binding protein that mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain.


Pssm-ID: 438209 [Multi-domain]  Cd Length: 49  Bit Score: 35.13  E-value: 5.76e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRCAL----KSEKCP 162
Cdd:cd16547   4 LICSICHGVLRCPVRLSCSHIFCKKCILqwlkRQETCP 41
RING-HC_TRIM60-like_C-IV cd16607
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 ...
131-163 5.94e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 and similar proteins; TRIM60, also known as RING finger protein 129 (RNF129) or RING finger protein 33 (RNF33), is a cytoplasmic protein expressed in the testis. It may play an important role in the spermatogenesis process, the development of the preimplantation embryo, and in testicular functions. RNF33 interacts with the cytoplasmic kinesin motor proteins KIF3A and KIF3B suggesting possible contribution to cargo movement along the microtubule in the expressed sites. It is also involved in spermatogenesis in Sertoli cells under the regulation of nuclear factor-kappaB (NF-kappaB). TRIM75 mainly localizes within spindles, suggesting it may function in spindle organization and thereby affect meiosis. Both TRIM60 and TRIM75 belong the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B2-box, and two coiled coil domains, as well as a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM61 belongs to the C-V subclass of the TRIM family that contains RBCC domains only. Its biological function remains unclear.


Pssm-ID: 438269 [Multi-domain]  Cd Length: 48  Bit Score: 35.09  E-value: 5.94e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCALKSEK-------CPV 163
Cdd:cd16607   4 CPICLDYLKDPVTINCGHNFCRSCISMSWKdlqdtfpCPV 43
RING-HC_LNX3-like cd16512
RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; ...
131-162 5.98e-03

RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4, or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for the substrate-binding. This family corresponds to LNX3/LNX4-like proteins, which contains a C3HC4-type RING-HC finger and two PDZ domains.


Pssm-ID: 438175 [Multi-domain]  Cd Length: 43  Bit Score: 35.08  E-value: 5.98e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRC----ALKSEKCP 162
Cdd:cd16512   3 CKLCLGVLEEPLATPCGHVFCAGCvlpwVVRNGSCP 38
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
635-668 5.98e-03

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 34.98  E-value: 5.98e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 45594312    635 CTQTLLRHQGSVTALAVS--RGRLFSGAVDSTVKVW 668
Cdd:smart00320   4 LLKTLKGHTGPVTSVAFSpdGKYLASGSDDGTIKLW 39
zf-C3HC4_4 pfam15227
zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like ...
131-154 6.10e-03

zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like (RFPL) zinc-fingers of the C3HC4 type. Ret finger protein-like proteins are primate-specific target genes of Pax6, a key transcription factor for pancreas, eye and neocortex development. This domain is likely to be DNA-binding. This zinc-finger domain together with the RDM domain, pfam11002, forms a large zinc-finger structure of the RING/U-Box superfamily. RING-containing proteins are known to exert an E3 ubiquitin protein ligase activity with the zinc-finger structure being mandatory for binding to the E2 ubiquitin-conjugating enzyme.


Pssm-ID: 464570 [Multi-domain]  Cd Length: 42  Bit Score: 35.10  E-value: 6.10e-03
                          10        20
                  ....*....|....*....|....
gi 45594312   131 CQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:pfam15227   1 CPICLDYLEKPVSIECGHSFCLSC 24
RING-HC_TRIM8_C-V cd16580
RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar ...
128-154 6.30e-03

RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar proteins; TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53 impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM8 deficit dramatically impairs p53 stabilization and activation in response to chemotherapeutic drugs. TRIM8 also modulates tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta)-triggered nuclear factor-kappaB (NF- kappa B) activation by targeting transforming growth factor beta (TGFbeta) activated kinase 1 (TAK1) for K63-linked polyubiquitination. Moreover, TRIM8 modulates translocation of phosphorylated STAT3 into the nucleus through interaction with Hsp90beta and consequently regulates transcription of Nanog in embryonic stem cells. It also interacts with protein inhibitor of activated STAT3 (PIAS3), which inhibits IL-6-dependent activation of STAT3. TRIM8 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The coiled coil domain is required for homodimerization and the region immediately C-terminal to the RING motif is sufficient to mediate the interaction with SOCS1.


Pssm-ID: 438242 [Multi-domain]  Cd Length: 67  Bit Score: 35.64  E-value: 6.30e-03
                        10        20
                ....*....|....*....|....*..
gi 45594312 128 KLCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16580  11 ELICPICLHVFVEPVQLPCKHNFCRGC 37
RING-Ubox cd16453
U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that ...
129-168 6.89e-03

U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that also includes the HECT family and the RING finger family. The E3 enzyme is ubiquitin-protein ligase that cooperates with a ubiquitin-activating enzyme (E1) and a ubiquitin-conjugating enzyme (E2), and plays a central role in determining the specificity of the ubiquitination system. It removes the ubiquitin molecule from the E2 enzyme and attaches it to the target substrate, forming a covalent bond between ubiquitin and the target. U-box proteins are characterized by the presence of a U-box domain of approximately 70 amino acids. The U-box is a modified form of the RING finger domain that lacks metal chelating cysteines and histidines. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms.


Pssm-ID: 438117 [Multi-domain]  Cd Length: 44  Bit Score: 34.84  E-value: 6.89e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC---ALKSEK-CPVDNVKL 168
Cdd:cd16453   1 FLCPISGELMKDPVITPSGITYDRSAierWLLSDNtDPFTREPL 44
Atg16_CCD cd22887
Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family ...
315-374 7.10e-03

Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins.


Pssm-ID: 439196 [Multi-domain]  Cd Length: 91  Bit Score: 36.39  E-value: 7.10e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 45594312 315 LRSMLGKLSEKIDQLEKSLElkfdVLDENQSKLSEDLMEFRRDASMLNDELSHINARLNM 374
Cdd:cd22887   2 LESELQELEKRLAELEAELA----SLEEEIKDLEEELKEKNKANEILNDELIALQIENNL 57
zf-TRAF pfam02176
TRAF-type zinc finger;
222-266 7.20e-03

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 35.51  E-value: 7.20e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 45594312   222 HEGSCDYRPVRCPNNPSCPPLLRMNLEAHLK----ECEhIKCPHSKYGC 266
Cdd:pfam02176   1 HLETCPFFPIPCPNGCCKKKILREDLPDHLEldcpKAE-VPCPFKVFGC 48
SPL-RING_NSE2 cd16651
SPL-RING finger found in E3 SUMO-protein ligase NSE2 and similar proteins; NSE2, also known as ...
129-163 7.89e-03

SPL-RING finger found in E3 SUMO-protein ligase NSE2 and similar proteins; NSE2, also known as MMS21 homolog (MMS21) or non-structural maintenance of chromosomes element 2 homolog (Non-SMC element 2 homolog, NSMCE2), is an autosumoylating small ubiquitin-like modifier (SUMO) ligase required for the response to DNA damage. It regulates sumoylation and nuclear-to-cytoplasmic translocation of skeletal and heart muscle-specific variant of the alpha subunit of nascent polypeptide associated complex (skNAC)-Smyd1 in myogenesis. It is also required for resisting extrinsically induced genotoxic stress. Moreover, NSE2 together with its partner proteins SMC6 and SMC5 form a tight subcomplex of the structural maintenance of chromosomes SMC5-6 complex, which includes another two subcomplexes, NSE1-NSE3-NSE4 and NSE5-NSE6. SMC6 and NSE3 are sumoylated in an NSE2-dependent manner, but SMC5 and NSE1 are not. NSE2-dependent E3 SUMO ligase activity is required for efficient DNA repair, but not for SMC5-6 complex stability. NSE2 contains a RING variant known as a Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription)-like RING (SPL-RING) finger that is likely shared by the SP-RING type SUMO E3 ligases, such as PIAS family proteins. The SPL-RING finger is a variant of the RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It harbors only one Zn binding site and is required for the sumoylating activity.


Pssm-ID: 438313 [Multi-domain]  Cd Length: 67  Bit Score: 35.32  E-value: 7.89e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45594312 129 LCCQLCCSVFKDPVI-TTCGHTFCR-------RCALKSEKCPV 163
Cdd:cd16651   1 LKCPITQQLMVDPVRnKKCGHTYEKaailqylQSRKKKAKCPV 43
mRING-HC-C3HC3D_PHRF1 cd16635
Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger ...
131-167 8.27e-03

Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger domain-containing protein 1 (PHRF1) and similar proteins; PHRF1, also known as KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase which induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a modified C3HC3D-type RING-HC finger.


Pssm-ID: 438297 [Multi-domain]  Cd Length: 51  Bit Score: 35.09  E-value: 8.27e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 45594312 131 CQLCCSVFKDPVITT---CGHTFCRRCALKSEK----CPVDNVK 167
Cdd:cd16635   7 CPICLNTFRDQAVGTpesCDHIFCLDCILEWSKnantCPVDRIV 50
RING-HC_ScRAD18-like cd23148
RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ...
131-162 8.82e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 (RAD18) and similar proteins; RAD18, also called RING-type E3 ubiquitin transferase RAD18, acts as a postreplication repair E3 ubiquitin-protein ligase that associates with the E2 ubiquitin conjugating enzyme UBC2/RAD6 to form the UBC2-RAD18 ubiquitin ligase complex involved in postreplicative repair (PRR) of damaged DNA. The UBC2-RAD18 complex cooperates with RAD5 and the UBC13-MMS2 dimer to attach mono-ubiquitin chains on 'Lys-164' of POL30, which is necessary for PRR. The UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. RAD18 is an E3 RING-finger protein belonging to the UBC2/RAD6 epistasis group. It contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438510 [Multi-domain]  Cd Length: 52  Bit Score: 34.82  E-value: 8.82e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 45594312 131 CQLCCSVFKDPVITTCGHTFC----RRCALKSEKCP 162
Cdd:cd23148   6 CHICKDLLKAPMRTPCNHTFCsfciRTHLNNDARCP 41
RING-HC_PCGF cd16525
RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and ...
129-163 8.94e-03

RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6), and similar proteins; This subfamily includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which is involved in the maintenance of gene repression and which target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger.


Pssm-ID: 438188 [Multi-domain]  Cd Length: 42  Bit Score: 34.51  E-value: 8.94e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 45594312 129 LCCQLCCSVFKDPV-ITTCGHTFCRRCALK----SEKCPV 163
Cdd:cd16525   1 LTCSLCKGYLIDATtITECLHSFCKSCIVRhletSKNCPV 40
RING-HC_TRIM50_like_C-IV cd16605
RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 ...
129-154 8.98e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 and similar proteins; TRIM50 is a stomach-specific E3 ubiquitin-protein ligase, encoded by the Williams-Beuren syndrome (WBS) TRIM50 gene, which regulates vesicular trafficking for acid secretion in gastric parietal cells. It colocalizes, interacts with, and increases the level of p62/SQSTM1, a multifunctional adaptor protein implicated in various cellular processes including the autophagy clearance of polyubiquitinated protein aggregates. It also promotes the formation and clearance of aggresome-associated polyubiquitinated proteins through the interaction with histone deacetylase 6 (HDAC6), a tubulin specific deacetylase that regulates microtubule-dependent aggresome formation. TRIM50 can be acetylated by PCAF and p300. TRIM50 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. This subfamily also includes two paralogs of TRIM50, tripartite motif-containing protein 73 (TRIM73), also known as tripartite motif-containing protein 50B (TRIM50B), and tripartite motif-containing protein 74 (TRIM74), also known as tripartite motif-containing protein 50C (TRIM50C), both of which are WBS-related genes encoding proteins that may also act as E3 ligases. In contrast with TRIM50, TRIM73 and TRIM74 belong to the C-V subclass of TRIM family of proteins that are defined by N-terminal RBCC domains only.


Pssm-ID: 438267 [Multi-domain]  Cd Length: 45  Bit Score: 34.73  E-value: 8.98e-03
                        10        20
                ....*....|....*....|....*.
gi 45594312 129 LCCQLCCSVFKDPVITTCGHTFCRRC 154
Cdd:cd16605   1 LLCPICLEVFKEPLMLQCGHSYCKSC 26
RING-HC_RNF5-like cd16534
RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 ...
131-163 9.43e-03

RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 and RNF185 are E3 ubiquitin-protein ligases that are anchored to the outer membrane of the endoplasmic reticulum (ER). RNF5 acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis, and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. RNF185 controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical endoplasmic reticulum-associated degradation (ERAD) model substrates. Moreover, both RNF5 and RNF185 play important roles in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) are also included in this family. They possess E3 ubiquitin-protein ligase activity and may play a role in the growth and development of Arabidopsis. All members of this family contain a C3HC4-type RING-HC finger.


Pssm-ID: 438196 [Multi-domain]  Cd Length: 44  Bit Score: 34.58  E-value: 9.43e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRC-------ALKSEKCPV 163
Cdd:cd16534   3 CNICLDTASDPVVTMCGHLFCWPClyqwletRPDRQTCPV 42
WD40 pfam00400
WD domain, G-beta repeat;
635-668 9.83e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 34.24  E-value: 9.83e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 45594312   635 CTQTLLRHQGSVTALAVSRGR--LFSGAVDSTVKVW 668
Cdd:pfam00400   3 LLKTLEGHTGSVTSLAFSPDGklLASGSDDGTVKVW 38
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
131-163 9.89e-03

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 38.34  E-value: 9.89e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 45594312 131 CQLCCSVFKDPVITTCGHTFCRRCAL------KSEKCPV 163
Cdd:COG5574 218 CFLCLEEPEVPSCTPCGHLFCLSCLLiswtkkKYEFCPL 256
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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