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Conserved domains on  [gi|47575774|ref|NP_001001231|]
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guanine nucleotide-exchange factor SEC12 [Xenopus tropicalis]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 1000017)

WD40 repeat domain-containing protein folds into a beta-propeller structure and functions as a scaffold, providing a platform for the interaction and assembly of several proteins into a signalosome; similar to 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

CATH:  2.130.10.10
Gene Ontology:  GO:0005515
PubMed:  10322433|8090199|30069656|29026209
SCOP:  4002744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 164-385 3.24e-10

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.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 60.81  E-value: 3.24e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 164 AVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCCVW--EADQLLMELHWNE 240
Cdd:cd00200  14 CVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASAdGTYLASGSSDKTIRLWdlETGECVRTLTGHT 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 241 NLPSipdkmyryrACRFgkVPDQQDALCLY---TVQIpykrerrpppcyltkWDGLRFLPLVTQPCGNEVISCLAVSDCG 317
Cdd:cd00200  94 SYVS---------SVAF--SPDGRILSSSSrdkTIKV---------------WDVETGKCLTTLRGHTDWVNSVAFSPDG 147

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47575774 318 KFLGLGTVTGSVAIYiSFSLQRLYYVEEAHGIVVTDLAFFPGSRRcrdlqgdhetaLLSVAVDSRCKL 385
Cdd:cd00200 148 TFVASSSQDGTIKLW-DLRTGKCVATLTGHTGEVNSVAFSPDGEK-----------LLSSSSDGTIKL 203
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 164-385 3.24e-10

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: 60.81  E-value: 3.24e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 164 AVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCCVW--EADQLLMELHWNE 240
Cdd:cd00200  14 CVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASAdGTYLASGSSDKTIRLWdlETGECVRTLTGHT 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 241 NLPSipdkmyryrACRFgkVPDQQDALCLY---TVQIpykrerrpppcyltkWDGLRFLPLVTQPCGNEVISCLAVSDCG 317
Cdd:cd00200  94 SYVS---------SVAF--SPDGRILSSSSrdkTIKV---------------WDVETGKCLTTLRGHTDWVNSVAFSPDG 147

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47575774 318 KFLGLGTVTGSVAIYiSFSLQRLYYVEEAHGIVVTDLAFFPGSRRcrdlqgdhetaLLSVAVDSRCKL 385
Cdd:cd00200 148 TFVASSSQDGTIKLW-DLRTGKCVATLTGHTGEVNSVAFSPDGEK-----------LLSSSSDGTIKL 203
WD40 COG2319
WD40 repeat [General function prediction only];
147-362 3.64e-10

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 61.47  E-value: 3.64e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 147 ELLHTVQTDTSADTlqkAVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCC 225
Cdd:COG2319 195 KLLRTLTGHTGAVR---SVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPdGRLLASGSADGTVR 271

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 226 VWEADqllmelhWNENLPSIPDKMYRYRACRFgkVPDQQDALCL---YTVQIpykrerrpppcyltkWDGLRFLPLVTQP 302
Cdd:COG2319 272 LWDLA-------TGELLRTLTGHSGGVNSVAF--SPDGKLLASGsddGTVRL---------------WDLATGKLLRTLT 327

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 303 CGNEVISCLAVSDCGKFLGLGTVTGSVAIYiSFSLQRLYYVEEAHGIVVTDLAFFPGSRR 362
Cdd:COG2319 328 GHTGAVRSVAFSPDGKTLASGSDDGTVRLW-DLATGELLRTLTGHTGAVTSVAFSPDGRT 386
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 164-187 2.54e-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: 35.37  E-value: 2.54e-03
                           10        20
                   ....*....|....*....|....
gi 47575774    164 AVCFNPDCTKLLTGGVDGYLRVWE 187
Cdd:smart00320  17 SVAFSPDGKYLASGSDDGTIKLWD 40
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 164-385 3.24e-10

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: 60.81  E-value: 3.24e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 164 AVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCCVW--EADQLLMELHWNE 240
Cdd:cd00200  14 CVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASAdGTYLASGSSDKTIRLWdlETGECVRTLTGHT 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 241 NLPSipdkmyryrACRFgkVPDQQDALCLY---TVQIpykrerrpppcyltkWDGLRFLPLVTQPCGNEVISCLAVSDCG 317
Cdd:cd00200  94 SYVS---------SVAF--SPDGRILSSSSrdkTIKV---------------WDVETGKCLTTLRGHTDWVNSVAFSPDG 147

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47575774 318 KFLGLGTVTGSVAIYiSFSLQRLYYVEEAHGIVVTDLAFFPGSRRcrdlqgdhetaLLSVAVDSRCKL 385
Cdd:cd00200 148 TFVASSSQDGTIKLW-DLRTGKCVATLTGHTGEVNSVAFSPDGEK-----------LLSSSSDGTIKL 203
WD40 COG2319
WD40 repeat [General function prediction only];
147-362 3.64e-10

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 61.47  E-value: 3.64e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 147 ELLHTVQTDTSADTlqkAVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCC 225
Cdd:COG2319 195 KLLRTLTGHTGAVR---SVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPdGRLLASGSADGTVR 271

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 226 VWEADqllmelhWNENLPSIPDKMYRYRACRFgkVPDQQDALCL---YTVQIpykrerrpppcyltkWDGLRFLPLVTQP 302
Cdd:COG2319 272 LWDLA-------TGELLRTLTGHSGGVNSVAF--SPDGKLLASGsddGTVRL---------------WDLATGKLLRTLT 327

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 303 CGNEVISCLAVSDCGKFLGLGTVTGSVAIYiSFSLQRLYYVEEAHGIVVTDLAFFPGSRR 362
Cdd:COG2319 328 GHTGAVRSVAFSPDGKTLASGSDDGTVRLW-DLATGELLRTLTGHTGAVTSVAFSPDGRT 386
WD40 COG2319
WD40 repeat [General function prediction only];
147-230 1.57e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 56.07  E-value: 1.57e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 147 ELLHTVQTDTSADTlqkAVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCC 225
Cdd:COG2319 321 KLLRTLTGHTGAVR---SVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPdGRTLASGSADGTVR 397


                ....*
gi 47575774 226 VWEAD 230
Cdd:COG2319 398 LWDLA 402
WD40 COG2319
WD40 repeat [General function prediction only];
147-362 6.38e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 54.15  E-value: 6.38e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 147 ELLHTVQTDTSADTlqkAVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCC 225
Cdd:COG2319 153 KLLRTLTGHSGAVT---SVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPdGKLLASGSADGTVR 229

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 226 VWEAD--QLLMELHWNENLPsipdkmyryRACRFGkvPDQQ-------DAlclyTVQIpykrerrpppcyltkWDGLRFL 296
Cdd:COG2319 230 LWDLAtgKLLRTLTGHSGSV---------RSVAFS--PDGRllasgsaDG----TVRL---------------WDLATGE 279

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47575774 297 PLVTQPCGNEVISCLAVSDCGKFLGLGTVTGSVAIYiSFSLQRLYYVEEAHGIVVTDLAFFPGSRR 362
Cdd:COG2319 280 LLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLW-DLATGKLLRTLTGHTGAVRSVAFSPDGKT 344
WD40 COG2319
WD40 repeat [General function prediction only];
164-230 6.85e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 54.15  E-value: 6.85e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47575774 164 AVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCCVWEAD 230
Cdd:COG2319 125 SVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPdGKLLASGSDDGTVRLWDLA 192
WD40 COG2319
WD40 repeat [General function prediction only];
125-362 1.07e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 50.68  E-value: 1.07e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 125 SSRVSIDGGIRGTKDETPEVSIELLHTVQTDTSADTlqkAVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEI 204
Cdd:COG2319  47 DGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVL---SVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAV 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 205 EDIASSP-GNKMVSVGQDFRCCVWEAD--QLLMELHWNENlpsipdkmyRYRACRFGkvPDQQ-------DAlclyTVQI 274
Cdd:COG2319 124 RSVAFSPdGKTLASGSADGTVRLWDLAtgKLLRTLTGHSG---------AVTSVAFS--PDGKllasgsdDG----TVRL 188

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47575774 275 pykrerrpppcyltkWDGLRFLPLVTQPCGNEVISCLAVSDCGKFLGLGTVTGSVAIYiSFSLQRLYYVEEAHGIVVTDL 354
Cdd:COG2319 189 ---------------WDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLW-DLATGKLLRTLTGHSGSVRSV 252


                ....*...
gi 47575774 355 AFFPGSRR 362
Cdd:COG2319 253 AFSPDGRL 260
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 163-230 1.76e-06

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: 49.26  E-value: 1.76e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 47575774 163 KAVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCCVWEAD 230
Cdd:cd00200 139 NSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPdGEKLLSSSSDGTIKLWDLS 207
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 164-230 2.19e-06

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: 48.87  E-value: 2.19e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 47575774 164 AVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSPGNKMVSVG-QDFRCCVWEAD 230
Cdd:cd00200 182 SVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGsEDGTIRVWDLR 249
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 164-187 2.54e-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: 35.37  E-value: 2.54e-03
                           10        20
                   ....*....|....*....|....
gi 47575774    164 AVCFNPDCTKLLTGGVDGYLRVWE 187
Cdd:smart00320  17 SVAFSPDGKYLASGSDDGTIKLWD 40
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 164-228 2.86e-03

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: 39.24  E-value: 2.86e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47575774 164 AVCFNPDCTKLLTGGVDGYLRVWEFPGMKKLLDFKAHNGEIEDIASSP-GNKMVSVGQDFRCCVWE 228
Cdd:cd00200 224 SVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPdGKRLASGSADGTIRIWD 289
 
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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