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Conserved domains on  [gi|1034561019|ref|XP_016857558|]
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E3 ubiquitin-protein ligase COP1 isoform X19 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN00181 super family cl31831
protein SPA1-RELATED; Provisional
 210-563 9.81e-104

protein SPA1-RELATED; Provisional


The actual alignment was detected with superfamily member PLN00181:

Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 332.05  E-value: 9.81e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 210 ASRRKRLTAHFEDLEQCYFSTRMSRIS----------DDSRTASQLDEFQECLSKFTRYNSVRPLATLSyASDLYNGSSI 279
Cdd:PLN00181  407 AAAEKPLARYYSALSENGRSSEKSSMSnpakppdfyiNDSRQGGWIDPFLEGLCKYLSFSKLRVKADLK-QGDLLNSSNL 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 280 VSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILWDGFTG 359
Cdd:PLN00181  486 VCAIGFDRDGEFFATAGVNKKIKIFECESIIKDGRDIHYPVVELASRSKLSGICWNSYIKSQVASSNFEGVVQVWDVARS 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 360 QRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYY 439
Cdd:PLN00181  566 QLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAFGSADHKVYYY 645

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 440 DLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNVGKPYC------LRSFKGHINEKNFVGLASNGDYIAC 513
Cdd:PLN00181  646 DLRNPKLPLCTMIGHSKTVSYVRFVDSSTLVSSSTDNTLKLWDLSMSISginetpLHSFMGHTNVKNFVGLSVSDGYIAT 725

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034561019 514 GSENNSLYLYYKGLSKTLLTFKFDTVKSVldKDRKEDDTNEFVSAVCWRA 563
Cdd:PLN00181  726 GSETNEVFVYHKAFPMPVLSYKFKTIDPV--SGLEVDDASQFISSVCWRG 773
RING_Ubox super family cl17238
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
 132-155 4.39e-12

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; 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 different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. 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. RING finger/U-box-containing proteins are 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 enable efficient transfer of ubiquitin from E2 to the substrates.


The actual alignment was detected with superfamily member cd16504:

Pssm-ID: 473075 [Multi-domain]  Cd Length: 47  Bit Score: 60.72  E-value: 4.39e-12
                          10        20
                  ....*....|....*....|....
gi 1034561019 132 NDFVCPICFDMIEEAYMTKCGHSF 155
Cdd:cd16504     1 NDFLCPICFDIIKEAFVTKCGHSF 24
 
Name Accession Description Interval E-value
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 210-563 9.81e-104

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 332.05  E-value: 9.81e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 210 ASRRKRLTAHFEDLEQCYFSTRMSRIS----------DDSRTASQLDEFQECLSKFTRYNSVRPLATLSyASDLYNGSSI 279
Cdd:PLN00181  407 AAAEKPLARYYSALSENGRSSEKSSMSnpakppdfyiNDSRQGGWIDPFLEGLCKYLSFSKLRVKADLK-QGDLLNSSNL 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 280 VSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILWDGFTG 359
Cdd:PLN00181  486 VCAIGFDRDGEFFATAGVNKKIKIFECESIIKDGRDIHYPVVELASRSKLSGICWNSYIKSQVASSNFEGVVQVWDVARS 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 360 QRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYY 439
Cdd:PLN00181  566 QLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAFGSADHKVYYY 645

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 440 DLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNVGKPYC------LRSFKGHINEKNFVGLASNGDYIAC 513
Cdd:PLN00181  646 DLRNPKLPLCTMIGHSKTVSYVRFVDSSTLVSSSTDNTLKLWDLSMSISginetpLHSFMGHTNVKNFVGLSVSDGYIAT 725

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034561019 514 GSENNSLYLYYKGLSKTLLTFKFDTVKSVldKDRKEDDTNEFVSAVCWRA 563
Cdd:PLN00181  726 GSETNEVFVYHKAFPMPVLSYKFKTIDPV--SGLEVDDASQFISSVCWRG 773
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 277-523 7.56e-37

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: 139.01  E-value: 7.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 277 SSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVD-IHYpenemtcnSKISCISWSSYHKNLLASSdYEGTVILWD 355
Cdd:cd00200     9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLkGHT--------GPVRDVAASADGTYLASGS-SDKTIRLWD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 356 GFTGQRSKVYQEHEKRCWSVDFNlMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN-VCCVKFSPSSRYhLAFGCADH 434
Cdd:cd00200    80 LETGECVRTLTGHTSYVSSVAFS-PDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDwVNSVAFSPDGTF-VASSSQDG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 435 CVHYYDLRNTKqPIMVFKGHRKAVSYAKFV-SGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIAC 513
Cdd:cd00200   158 TIKLWDLRTGK-CVATLTGHTGEVNSVAFSpDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLAS 236

                         250
                  ....*....|
gi 1034561019 514 GSENNSLYLY 523
Cdd:cd00200   237 GSEDGTIRVW 246
WD40 COG2319
WD40 repeat [General function prediction only];
264-542 3.88e-33

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 131.57  E-value: 3.88e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 264 LATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDT--VIQdAVDIHypenemtcNSKISCISWSSyHKNL 341
Cdd:COG2319   107 LATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATgkLLR-TLTGH--------SGAVTSVAFSP-DGKL 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 342 LASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN-VCCVKFS 420
Cdd:COG2319   177 LASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSP-DGKLLASGSADGTVRLWDLATGKLLRTLTGHSGsVRSVAFS 255

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 421 PSSRYhLAFGCADHCVHYYDLrNTKQPIMVFKGHRKAVSYAKFV-SGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEK 499
Cdd:COG2319   256 PDGRL-LASGSADGTVRLWDL-ATGELLRTLTGHSGGVNSVAFSpDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAV 333

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1034561019 500 NFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFK--FDTVKSV 542
Cdd:COG2319   334 RSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTghTGAVTSV 378
RING-HC_COP1 cd16504
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...
 132-155 4.39e-12

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: 60.72  E-value: 4.39e-12
                          10        20
                  ....*....|....*....|....
gi 1034561019 132 NDFVCPICFDMIEEAYMTKCGHSF 155
Cdd:cd16504     1 NDFLCPICFDIIKEAFVTKCGHSF 24
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 358-398 1.55e-04

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: 39.22  E-value: 1.55e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1034561019  358 TGQRSKVYQEHEKRCWSVDFNlMDPKLLASGSDDAKVKLWS 398
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFS-PDGKYLASGSDDGTIKLWD 40
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
135-155 2.69e-04

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 38.57  E-value: 2.69e-04
                          10        20
                  ....*....|....*....|..
gi 1034561019 135 VCPICFDMIEEA-YMTKCGHSF 155
Cdd:pfam13923   1 MCPICMDMLKDPsTTTPCGHVF 22
WD40 pfam00400
WD domain, G-beta repeat;
359-398 1.03e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 36.94  E-value: 1.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1034561019 359 GQRSKVYQEHEKRCWSVDFNlMDPKLLASGSDDAKVKLWS 398
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFS-PDGKLLASGSDDGTVKVWD 39
 
Name Accession Description Interval E-value
PLN00181 PLN00181
protein SPA1-RELATED; Provisional
 210-563 9.81e-104

protein SPA1-RELATED; Provisional


Pssm-ID: 177776 [Multi-domain]  Cd Length: 793  Bit Score: 332.05  E-value: 9.81e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 210 ASRRKRLTAHFEDLEQCYFSTRMSRIS----------DDSRTASQLDEFQECLSKFTRYNSVRPLATLSyASDLYNGSSI 279
Cdd:PLN00181  407 AAAEKPLARYYSALSENGRSSEKSSMSnpakppdfyiNDSRQGGWIDPFLEGLCKYLSFSKLRVKADLK-QGDLLNSSNL 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 280 VSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLASSDYEGTVILWDGFTG 359
Cdd:PLN00181  486 VCAIGFDRDGEFFATAGVNKKIKIFECESIIKDGRDIHYPVVELASRSKLSGICWNSYIKSQVASSNFEGVVQVWDVARS 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 360 QRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYY 439
Cdd:PLN00181  566 QLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAFGSADHKVYYY 645

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 440 DLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNVGKPYC------LRSFKGHINEKNFVGLASNGDYIAC 513
Cdd:PLN00181  646 DLRNPKLPLCTMIGHSKTVSYVRFVDSSTLVSSSTDNTLKLWDLSMSISginetpLHSFMGHTNVKNFVGLSVSDGYIAT 725

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034561019 514 GSENNSLYLYYKGLSKTLLTFKFDTVKSVldKDRKEDDTNEFVSAVCWRA 563
Cdd:PLN00181  726 GSETNEVFVYHKAFPMPVLSYKFKTIDPV--SGLEVDDASQFISSVCWRG 773
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 277-523 7.56e-37

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: 139.01  E-value: 7.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 277 SSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVD-IHYpenemtcnSKISCISWSSYHKNLLASSdYEGTVILWD 355
Cdd:cd00200     9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLkGHT--------GPVRDVAASADGTYLASGS-SDKTIRLWD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 356 GFTGQRSKVYQEHEKRCWSVDFNlMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN-VCCVKFSPSSRYhLAFGCADH 434
Cdd:cd00200    80 LETGECVRTLTGHTSYVSSVAFS-PDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDwVNSVAFSPDGTF-VASSSQDG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 435 CVHYYDLRNTKqPIMVFKGHRKAVSYAKFV-SGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIAC 513
Cdd:cd00200   158 TIKLWDLRTGK-CVATLTGHTGEVNSVAFSpDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLAS 236

                         250
                  ....*....|
gi 1034561019 514 GSENNSLYLY 523
Cdd:cd00200   237 GSEDGTIRVW 246
WD40 COG2319
WD40 repeat [General function prediction only];
264-542 3.88e-33

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 131.57  E-value: 3.88e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 264 LATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDT--VIQdAVDIHypenemtcNSKISCISWSSyHKNL 341
Cdd:COG2319   107 LATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATgkLLR-TLTGH--------SGAVTSVAFSP-DGKL 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 342 LASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN-VCCVKFS 420
Cdd:COG2319   177 LASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSP-DGKLLASGSADGTVRLWDLATGKLLRTLTGHSGsVRSVAFS 255

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 421 PSSRYhLAFGCADHCVHYYDLrNTKQPIMVFKGHRKAVSYAKFV-SGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEK 499
Cdd:COG2319   256 PDGRL-LASGSADGTVRLWDL-ATGELLRTLTGHSGGVNSVAFSpDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAV 333

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1034561019 500 NFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFK--FDTVKSV 542
Cdd:COG2319   334 RSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTghTGAVTSV 378
WD40 COG2319
WD40 repeat [General function prediction only];
262-523 1.72e-31

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 126.56  E-value: 1.72e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 262 RPLATLSyasdlyNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDT-VIQDAVDIHypenemtcNSKISCISWSSyHKN 340
Cdd:COG2319   153 KLLRTLT------GHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATgKLLRTLTGH--------TGAVRSVAFSP-DGK 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 341 LLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN-VCCVKF 419
Cdd:COG2319   218 LLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSP-DGRLLASGSADGTVRLWDLATGELLRTLTGHSGgVNSVAF 296

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 420 SPSSRYhLAFGCADHCVHYYDLrNTKQPIMVFKGHRKAVSYAKFVS-GEEIVSASTDSQLKLWNVGKPYCLRSFKGHINE 498
Cdd:COG2319   297 SPDGKL-LASGSDDGTVRLWDL-ATGKLLRTLTGHTGAVRSVAFSPdGKTLASGSDDGTVRLWDLATGELLRTLTGHTGA 374

                         250       260
                  ....*....|....*....|....*
gi 1034561019 499 KNFVGLASNGDYIACGSENNSLYLY 523
Cdd:COG2319   375 VTSVAFSPDGRTLASGSADGTVRLW 399
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 264-523 8.86e-31

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: 122.06  E-value: 8.86e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 264 LATLSYASDLYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTViqdavdihYPENEMTC-NSKISCISWSSyHKNLL 342
Cdd:cd00200    38 LETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETG--------ECVRTLTGhTSYVSSVAFSP-DGRIL 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 343 ASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTNLDNSVASIEA-KANVCCVKFSP 421
Cdd:cd00200   109 SSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSP-DGTFVASSSQDGTIKLWDLRTGKCVATLTGhTGEVNSVAFSP 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 422 SSRyHLAFGCADHCVHYYDLRnTKQPIMVFKGHRKAVSYAKF-VSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKN 500
Cdd:cd00200   188 DGE-KLLSSSSDGTIKLWDLS-TGKCLGTLRGHENGVNSVAFsPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVT 265

                         250       260
                  ....*....|....*....|...
gi 1034561019 501 FVGLASNGDYIACGSENNSLYLY 523
Cdd:cd00200   266 SLAWSPDGKRLASGSADGTIRIW 288
WD40 COG2319
WD40 repeat [General function prediction only];
341-542 1.24e-26

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 112.31  E-value: 1.24e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 341 LLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN-VCCVKF 419
Cdd:COG2319    92 LLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSP-DGKTLASGSADGTVRLWDLATGKLLRTLTGHSGaVTSVAF 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 420 SPSSRYhLAFGCADHCVHYYDLRnTKQPIMVFKGHRKAVSYAKFvS--GEEIVSASTDSQLKLWNVGKPYCLRSFKGHIN 497
Cdd:COG2319   171 SPDGKL-LASGSDDGTVRLWDLA-TGKLLRTLTGHTGAVRSVAF-SpdGKLLASGSADGTVRLWDLATGKLLRTLTGHSG 247

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1034561019 498 EKNFVGLASNGDYIACGSENNSLYLY--YKGLSKTLLTFKFDTVKSV 542
Cdd:COG2319   248 SVRSVAFSPDGRLLASGSADGTVRLWdlATGELLRTLTGHSGGVNSV 294
WD40 COG2319
WD40 repeat [General function prediction only];
277-483 8.75e-26

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 110.00  E-value: 8.75e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 277 SSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDT-VIQDAVDIHypenemtcNSKISCISWSSYHKnLLASSDYEGTVILWD 355
Cdd:COG2319   204 TGAVRSVAFSPDGKLLASGSADGTVRLWDLATgKLLRTLTGH--------SGSVRSVAFSPDGR-LLASGSADGTVRLWD 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 356 GFTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN-VCCVKFSPSSRYhLAFGCADH 434
Cdd:COG2319   275 LATGELLRTLTGHSGGVNSVAFSP-DGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGaVRSVAFSPDGKT-LASGSDDG 352

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1034561019 435 CVHYYDLrNTKQPIMVFKGHRKAVSYAKFVS-GEEIVSASTDSQLKLWNV 483
Cdd:COG2319   353 TVRLWDL-ATGELLRTLTGHTGAVTSVAFSPdGRTLASGSADGTVRLWDL 401
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 280-482 1.46e-22

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: 98.18  E-value: 1.46e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 280 VSSIEFDRDCDYFAIAGVTKKIKVYeydtviqdavDIHYPENEMTCNSK---ISCISWSSYHKnLLASSDYEGTVILWDG 356
Cdd:cd00200    96 VSSVAFSPDGRILSSSSRDKTIKVW----------DVETGKCLTTLRGHtdwVNSVAFSPDGT-FVASSSQDGTIKLWDL 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 357 FTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN-VCCVKFSPSSRYhLAFGCADHC 435
Cdd:cd00200   165 RTGKCVATLTGHTGEVNSVAFSP-DGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENgVNSVAFSPDGYL-LASGSEDGT 242

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1034561019 436 VHYYDLRnTKQPIMVFKGHRKAVSYAKFV-SGEEIVSASTDSQLKLWN 482
Cdd:cd00200   243 IRVWDLR-TGECVQTLSGHTNSVTSLAWSpDGKRLASGSADGTIRIWD 289
WD40 COG2319
WD40 repeat [General function prediction only];
341-523 6.98e-22

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 98.44  E-value: 6.98e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 341 LLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTNLDNSVASIEA-KANVCCVKF 419
Cdd:COG2319    50 RLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSP-DGRLLASASADGTVRLWDLATGLLLRTLTGhTGAVRSVAF 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 420 SPSSRYhLAFGCADHCVHYYDLRnTKQPIMVFKGHRKAVSYAKFVS-GEEIVSASTDSQLKLWNVGKPYCLRSFKGHINE 498
Cdd:COG2319   129 SPDGKT-LASGSADGTVRLWDLA-TGKLLRTLTGHSGAVTSVAFSPdGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGA 206

                         170       180
                  ....*....|....*....|....*
gi 1034561019 499 KNFVGLASNGDYIACGSENNSLYLY 523
Cdd:COG2319   207 VRSVAFSPDGKLLASGSADGTVRLW 231
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 362-523 1.72e-21

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: 95.09  E-value: 1.72e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 362 SKVYQEHEKRCWSVDFNlMDPKLLASGSDDAKVKLWSTNLDNSVASIE-AKANVCCVKFSPSSRYhLAFGCADHCVHYYD 440
Cdd:cd00200     2 RRTLKGHTGGVTCVAFS-PDGKLLATGSGDGTIKVWDLETGELLRTLKgHTGPVRDVAASADGTY-LASGSSDKTIRLWD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 441 LrNTKQPIMVFKGHRKAVSYAKFVSGEEIV-SASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNS 519
Cdd:cd00200    80 L-ETGECVRTLTGHTSYVSSVAFSPDGRILsSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGT 158


                  ....
gi 1034561019 520 LYLY 523
Cdd:cd00200   159 IKLW 162
WD40 COG2319
WD40 repeat [General function prediction only];
277-400 2.50e-12

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 69.17  E-value: 2.50e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 277 SSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTviQDAVDIHYPENEMtcnskISCISWSSYHKnLLASSDYEGTVILWDG 356
Cdd:COG2319   288 SGGVNSVAFSPDGKLLASGSDDGTVRLWDLAT--GKLLRTLTGHTGA-----VRSVAFSPDGK-TLASGSDDGTVRLWDL 359

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1034561019 357 FTGQRSKVYQEHEKRCWSVDFNLmDPKLLASGSDDAKVKLWSTN 400
Cdd:COG2319   360 ATGELLRTLTGHTGAVTSVAFSP-DGRTLASGSADGTVRLWDLA 402
RING-HC_COP1 cd16504
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...
 132-155 4.39e-12

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: 60.72  E-value: 4.39e-12
                          10        20
                  ....*....|....*....|....
gi 1034561019 132 NDFVCPICFDMIEEAYMTKCGHSF 155
Cdd:cd16504     1 NDFLCPICFDIIKEAFVTKCGHSF 24
WD40 COG2319
WD40 repeat [General function prediction only];
381-523 6.48e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 48.75  E-value: 6.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034561019 381 DPKLLASGSDDAKVKLWSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSY 460
Cdd:COG2319     5 DGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSV 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034561019 461 AKFVSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLY 523
Cdd:COG2319    85 AFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLW 147
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 358-398 1.55e-04

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: 39.22  E-value: 1.55e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1034561019  358 TGQRSKVYQEHEKRCWSVDFNlMDPKLLASGSDDAKVKLWS 398
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFS-PDGKYLASGSDDGTIKLWD 40
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
135-155 2.69e-04

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 38.57  E-value: 2.69e-04
                          10        20
                  ....*....|....*....|..
gi 1034561019 135 VCPICFDMIEEA-YMTKCGHSF 155
Cdd:pfam13923   1 MCPICMDMLKDPsTTTPCGHVF 22
WD40 pfam00400
WD domain, G-beta repeat;
359-398 1.03e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 36.94  E-value: 1.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1034561019 359 GQRSKVYQEHEKRCWSVDFNlMDPKLLASGSDDAKVKLWS 398
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFS-PDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 444-482 1.22e-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: 36.91  E-value: 1.22e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1034561019  444 TKQPIMVFKGHRKAVSYAKFV-SGEEIVSASTDSQLKLWN 482
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSpDGKYLASGSDDGTIKLWD 40
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
 136-155 1.90e-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: 38.05  E-value: 1.90e-03
                          10        20
                  ....*....|....*....|
gi 1034561019 136 CPICFDMIEEAYMTKCGHSF 155
Cdd:cd16498    19 CPICLELLKEPVSTKCDHQF 38
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
 129-155 2.79e-03

RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins; TRIM40, also known as probable E3 NEDD8-protein ligase or RING finger protein 35 (RNF35), is highly expressed in the gastrointestinal tract including the stomach, small intestine, and large intestine. It enhances neddylation of inhibitor of nuclear factor kappaB kinase subunit gamma (IKKgamma), inhibits the activity of nuclear factor-kappaB (NF-kappaB)-mediated transcription, and thus prevents inflammation-associated carcinogenesis in the gastrointestinal tract. TRIM40 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, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438245 [Multi-domain]  Cd Length: 63  Bit Score: 36.35  E-value: 2.79e-03
                          10        20
                  ....*....|....*....|....*..
gi 1034561019 129 DKSNDFVCPICFDMIEEAYMTKCGHSF 155
Cdd:cd16583     1 DSDEEGVCPICQEPLKEAVSTDCGHLF 27
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
 134-155 5.01e-03

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: 35.15  E-value: 5.01e-03
                          10        20
                  ....*....|....*....|..
gi 1034561019 134 FVCPICFDMIEEAYMTKCGHSF 155
Cdd:cd16449     1 LECPICLERLKDPVLLPCGHVF 22
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
 135-155 8.85e-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: 34.65  E-value: 8.85e-03
                          10        20
                  ....*....|....*....|.
gi 1034561019 135 VCPICFDMIEEAYMTKCGHSF 155
Cdd:cd16568     6 ECIICHEYLYEPMVTTCGHTY 26
 
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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