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Conserved domains on  [gi|57164111|ref|NP_001009416|]
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intraflagellar transport protein 122 homolog isoform 2 [Rattus norvegicus]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 11455410)

WD40 repeat domain-containing protein similar to 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
PubMed:  10322433|8090199
SCOP:  4002744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
15-291 1.14e-40

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 153.91  E-value: 1.14e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  15 IYDLAFKPDGTQLILAAGNR-LLVYDTSDGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW---TSKLEGILKy 90
Cdd:COG2319 123 VRSVAFSPDGKTLASGSADGtVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWdlaTGKLLRTLT- 201

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  91 THNDSIQCVSYNPVTHQLASCSSSDF-GLW---SPEQKSVSKHKSNSkITCCSWTNDGQYLALGMSNGIISIRNKNGEEK 166
Cdd:COG2319 202 GHTGAVRSVAFSPDGKLLASGSADGTvRLWdlaTGKLLRTLTGHSGS-VRSVAFSPDGRLLASGSADGTVRLWDLATGEL 280

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 167 VKieRPGGSLSPIWSICWNPSreehNDILAVADWGQKLSFYQL-SGKQIGKDRPLNFDPCCISYFTKGEYILVGGSDKQV 245
Cdd:COG2319 281 LR--TLTGHSGGVNSVAFSPD----GKLLASGSDDGTVRLWDLaTGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTV 354

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*..
gi 57164111 246 SLF-TKDGVRLGTVGEQNSWVWTCRVKPDSNYVVVGCQDGTISFYQL 291
Cdd:COG2319 355 RLWdLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
Coatomer_WDAD super family cl24022
Coatomer WD associated region; The coatomer, which is a cytosolic protein complex that binds ...
 572-658 2.45e-03

Coatomer WD associated region; The coatomer, which is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunit. It is a heptameric complex that can polymerize into a cage to deform the membrane into a bud. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. This model corresponds to the WD-associated region (WDAD) found in coatomer subunits alpha, beta, and beta' and is composed of a beta-propeller and an alpha-solenoid. The WD40 domain is 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. It 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 the GH and WD lies a conserved core. It forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet. 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. The residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands allowing them to bind either stably or reversibly.


The actual alignment was detected with superfamily member cd22938:

Pssm-ID: 451663  Cd Length: 474  Bit Score: 41.14  E-value: 2.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 572 KEAYQIACLGVTDTDWRELAMEALEGLEFETAKKAFTRVQDLRYL----------ELISTIEERKKRGESNNDLFladvF 641
Cdd:cd22938 353 KIAYQLAHFVKDEKKWFSLALECGSKCNFELALEAAKAANDWEKLgllallqgnhQIVEMLAQRAENFGKNNKAF----F 428

                        90
                ....*....|....*....
gi 57164111 642 SY--QGKFHEAAKLYKRSG 658
Cdd:cd22938 429 LYliTGKLRKMMKLLIIRK 447
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
15-291 1.14e-40

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 153.91  E-value: 1.14e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  15 IYDLAFKPDGTQLILAAGNR-LLVYDTSDGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW---TSKLEGILKy 90
Cdd:COG2319 123 VRSVAFSPDGKTLASGSADGtVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWdlaTGKLLRTLT- 201

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  91 THNDSIQCVSYNPVTHQLASCSSSDF-GLW---SPEQKSVSKHKSNSkITCCSWTNDGQYLALGMSNGIISIRNKNGEEK 166
Cdd:COG2319 202 GHTGAVRSVAFSPDGKLLASGSADGTvRLWdlaTGKLLRTLTGHSGS-VRSVAFSPDGRLLASGSADGTVRLWDLATGEL 280

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 167 VKieRPGGSLSPIWSICWNPSreehNDILAVADWGQKLSFYQL-SGKQIGKDRPLNFDPCCISYFTKGEYILVGGSDKQV 245
Cdd:COG2319 281 LR--TLTGHSGGVNSVAFSPD----GKLLASGSDDGTVRLWDLaTGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTV 354

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*..
gi 57164111 246 SLF-TKDGVRLGTVGEQNSWVWTCRVKPDSNYVVVGCQDGTISFYQL 291
Cdd:COG2319 355 RLWdLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 49-291 2.04e-27

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: 112.81  E-value: 2.04e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  49 LKGHKDTVYCVAYAKDGKRFASGSADKSIIIWTSKlEGILKYT---HNDSIQCVSYNPVTHQLASCSSSDFG-LWSPEQK 124
Cdd:cd00200   5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLE-TGELLRTlkgHTGPVRDVAASADGTYLASGSSDKTIrLWDLETG 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 125 SVSK----HKSNskITCCSWTNDGQYLALGMSNGiiSIRNKNGEEKVKIERPGGSLSPIWSICWNPSreehNDILAVADW 200
Cdd:cd00200  84 ECVRtltgHTSY--VSSVAFSPDGRILSSSSRDK--TIKVWDVETGKCLTTLRGHTDWVNSVAFSPD----GTFVASSSQ 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 201 GQKLSFYQLSGKQI-----GKDRPLNfdpcCISYFTKGEYILVGGSDKQVSLF-TKDGVRLGTVGEQNSWVWTCRVKPDS 274
Cdd:cd00200 156 DGTIKLWDLRTGKCvatltGHTGEVN----SVAFSPDGEKLLSSSSDGTIKLWdLSTGKCLGTLRGHENGVNSVAFSPDG 231

                       250
                ....*....|....*..
gi 57164111 275 NYVVVGCQDGTISFYQL 291
Cdd:cd00200 232 YLLASGSEDGTIRVWDL 248
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 42-80 1.07e-08

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: 51.16  E-value: 1.07e-08
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 57164111     42 DGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW 80
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
43-80 4.52e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 49.65  E-value: 4.52e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 57164111    43 GTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW 80
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
Coatomer_WDAD cd22938
Coatomer WD associated region; The coatomer, which is a cytosolic protein complex that binds ...
 572-658 2.45e-03

Coatomer WD associated region; The coatomer, which is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunit. It is a heptameric complex that can polymerize into a cage to deform the membrane into a bud. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. This model corresponds to the WD-associated region (WDAD) found in coatomer subunits alpha, beta, and beta' and is composed of a beta-propeller and an alpha-solenoid. The WD40 domain is 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. It 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 the GH and WD lies a conserved core. It forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet. 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. The residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands allowing them to bind either stably or reversibly.


Pssm-ID: 438571  Cd Length: 474  Bit Score: 41.14  E-value: 2.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 572 KEAYQIACLGVTDTDWRELAMEALEGLEFETAKKAFTRVQDLRYL----------ELISTIEERKKRGESNNDLFladvF 641
Cdd:cd22938 353 KIAYQLAHFVKDEKKWFSLALECGSKCNFELALEAAKAANDWEKLgllallqgnhQIVEMLAQRAENFGKNNKAF----F 428

                        90
                ....*....|....*....
gi 57164111 642 SY--QGKFHEAAKLYKRSG 658
Cdd:cd22938 429 LYliTGKLRKMMKLLIIRK 447
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
15-291 1.14e-40

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 153.91  E-value: 1.14e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  15 IYDLAFKPDGTQLILAAGNR-LLVYDTSDGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW---TSKLEGILKy 90
Cdd:COG2319 123 VRSVAFSPDGKTLASGSADGtVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWdlaTGKLLRTLT- 201

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  91 THNDSIQCVSYNPVTHQLASCSSSDF-GLW---SPEQKSVSKHKSNSkITCCSWTNDGQYLALGMSNGIISIRNKNGEEK 166
Cdd:COG2319 202 GHTGAVRSVAFSPDGKLLASGSADGTvRLWdlaTGKLLRTLTGHSGS-VRSVAFSPDGRLLASGSADGTVRLWDLATGEL 280

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 167 VKieRPGGSLSPIWSICWNPSreehNDILAVADWGQKLSFYQL-SGKQIGKDRPLNFDPCCISYFTKGEYILVGGSDKQV 245
Cdd:COG2319 281 LR--TLTGHSGGVNSVAFSPD----GKLLASGSDDGTVRLWDLaTGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTV 354

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*..
gi 57164111 246 SLF-TKDGVRLGTVGEQNSWVWTCRVKPDSNYVVVGCQDGTISFYQL 291
Cdd:COG2319 355 RLWdLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 COG2319
WD40 repeat [General function prediction only];
15-291 7.94e-34

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 134.27  E-value: 7.94e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  15 IYDLAFKPDGTQLILAAG-NRLLVYDTSDGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW---TSKLEGILKy 90
Cdd:COG2319  81 VLSVAFSPDGRLLASASAdGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWdlaTGKLLRTLT- 159

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  91 THNDSIQCVSYNPVTHQLASCSSSD-FGLWSP----EQKSVSKHKSNskITCCSWTNDGQYLALGMSNGIISIRN-KNGE 164
Cdd:COG2319 160 GHSGAVTSVAFSPDGKLLASGSDDGtVRLWDLatgkLLRTLTGHTGA--VRSVAFSPDGKLLASGSADGTVRLWDlATGK 237

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 165 EkvkIERPGGSLSPIWSICWNPSreehNDILAVADWGQKLSFYQLSGKQIGKDRPLNFDP-CCISYFTKGEYILVGGSDK 243
Cdd:COG2319 238 L---LRTLTGHSGSVRSVAFSPD----GRLLASGSADGTVRLWDLATGELLRTLTGHSGGvNSVAFSPDGKLLASGSDDG 310

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 57164111 244 QVSLF-TKDGVRLGTVGEQNSWVWTCRVKPDSNYVVVGCQDGTISFYQL 291
Cdd:COG2319 311 TVRLWdLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDL 359
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 49-291 2.04e-27

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: 112.81  E-value: 2.04e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  49 LKGHKDTVYCVAYAKDGKRFASGSADKSIIIWTSKlEGILKYT---HNDSIQCVSYNPVTHQLASCSSSDFG-LWSPEQK 124
Cdd:cd00200   5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLE-TGELLRTlkgHTGPVRDVAASADGTYLASGSSDKTIrLWDLETG 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 125 SVSK----HKSNskITCCSWTNDGQYLALGMSNGiiSIRNKNGEEKVKIERPGGSLSPIWSICWNPSreehNDILAVADW 200
Cdd:cd00200  84 ECVRtltgHTSY--VSSVAFSPDGRILSSSSRDK--TIKVWDVETGKCLTTLRGHTDWVNSVAFSPD----GTFVASSSQ 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 201 GQKLSFYQLSGKQI-----GKDRPLNfdpcCISYFTKGEYILVGGSDKQVSLF-TKDGVRLGTVGEQNSWVWTCRVKPDS 274
Cdd:cd00200 156 DGTIKLWDLRTGKCvatltGHTGEVN----SVAFSPDGEKLLSSSSDGTIKLWdLSTGKCLGTLRGHENGVNSVAFSPDG 231

                       250
                ....*....|....*..
gi 57164111 275 NYVVVGCQDGTISFYQL 291
Cdd:cd00200 232 YLLASGSEDGTIRVWDL 248
WD40 COG2319
WD40 repeat [General function prediction only];
2-291 3.16e-27

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 114.62  E-value: 3.16e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111   2 RAVLTWRDKAEQCIYDLAFKPDGTQLILAAGNRL-LVYDTSDGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW 80
Cdd:COG2319  26 GALLLLLLGLAAAVASLAASPDGARLAAGAGDLTlLLLDAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLW 105

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  81 --TSKLEGILKYTHNDSIQCVSYNPVTHQLAScSSSDFG--LWSPEQ----KSVSKHksNSKITCCSWTNDGQYLALGMS 152
Cdd:COG2319 106 dlATGLLLRTLTGHTGAVRSVAFSPDGKTLAS-GSADGTvrLWDLATgkllRTLTGH--SGAVTSVAFSPDGKLLASGSD 182

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 153 NGIISIRN-KNGEEkvkIERPGGSLSPIWSICWNPSreehNDILAVADWGQKLSFYQL-SGKQIGKDRPLNFDPCCISYF 230
Cdd:COG2319 183 DGTVRLWDlATGKL---LRTLTGHTGAVRSVAFSPD----GKLLASGSADGTVRLWDLaTGKLLRTLTGHSGSVRSVAFS 255

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57164111 231 TKGEYILVGGSDKQVSLF-TKDGVRLGTVGEQNSWVWTCRVKPDSNYVVVGCQDGTISFYQL 291
Cdd:COG2319 256 PDGRLLASGSADGTVRLWdLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDL 317
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 15-290 2.84e-26

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: 109.35  E-value: 2.84e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  15 IYDLAFKPDGtQLILAAG--NRLLVYDTSDGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW---TSKLEGILK 89
Cdd:cd00200  12 VTCVAFSPDG-KLLATGSgdGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWdleTGECVRTLT 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  90 yTHNDSIQCVSYNPvTHQLASCSSSD--FGLW---SPEQKSVSKHKSNSkITCCSWTNDGQYLALGMSNGIISI-RNKNG 163
Cdd:cd00200  91 -GHTSYVSSVAFSP-DGRILSSSSRDktIKVWdveTGKCLTTLRGHTDW-VNSVAFSPDGTFVASSSQDGTIKLwDLRTG 167

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 164 EEKVKIErpgGSLSPIWSICWNPSREEHndILAVAD-----WgqKLSFYQLSGKQIGKDRPLNfdpcCISYFTKGEYILV 238
Cdd:cd00200 168 KCVATLT---GHTGEVNSVAFSPDGEKL--LSSSSDgtiklW--DLSTGKCLGTLRGHENGVN----SVAFSPDGYLLAS 236

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 57164111 239 GGSDKQVSLF-TKDGVRLGTVGEQNSWVWTCRVKPDSNYVVVGCQDGTISFYQ 290
Cdd:cd00200 237 GSEDGTIRVWdLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 12-248 7.55e-26

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: 108.19  E-value: 7.55e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  12 EQCIYDLAFKPDGTQLILAAGNRLL-VYDTSDGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW---TSKLEGI 87
Cdd:cd00200  51 TGPVRDVAASADGTYLASGSSDKTIrLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWdveTGKCLTT 130

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111  88 LKyTHNDSIQCVSYNPvTHQLASCSSSDF--GLWSPEQKSVSK----HKSNskITCCSWTNDGQYLALGMSNGIISIRNK 161
Cdd:cd00200 131 LR-GHTDWVNSVAFSP-DGTFVASSSQDGtiKLWDLRTGKCVAtltgHTGE--VNSVAFSPDGEKLLSSSSDGTIKLWDL 206

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 162 NGEEKVKIERpgGSLSPIWSICWNPSReehnDILAVADWGQKLSFYQLSGKQIGKDRPLNFDPC-CISYFTKGEYILVGG 240
Cdd:cd00200 207 STGKCLGTLR--GHENGVNSVAFSPDG----YLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVtSLAWSPDGKRLASGS 280


                ....*...
gi 57164111 241 SDKQVSLF 248
Cdd:cd00200 281 ADGTIRIW 288
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 42-80 1.07e-08

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: 51.16  E-value: 1.07e-08
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 57164111     42 DGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW 80
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
43-80 4.52e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 49.65  E-value: 4.52e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 57164111    43 GTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW 80
Cdd:pfam00400   1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
NBCH_WD40 pfam20426
Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at ...
 33-80 1.02e-05

Neurobeachin beta propeller domain; This entry represents the beta propeller domain found at the C-terminus of neurobeachin-like proteins.


Pssm-ID: 466575 [Multi-domain]  Cd Length: 350  Bit Score: 48.53  E-value: 1.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 57164111    33 NRLLVYDTSDGTLLQPLKGHKDTVYCVAYAKDGKRFASGSADKSIIIW 80
Cdd:pfam20426 104 NSFQVISLNDGRMVQSIRQHKDVVSCVAVTSDGSILATGSYDTTVMVW 151
Coatomer_WDAD cd22938
Coatomer WD associated region; The coatomer, which is a cytosolic protein complex that binds ...
 572-658 2.45e-03

Coatomer WD associated region; The coatomer, which is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunit. It is a heptameric complex that can polymerize into a cage to deform the membrane into a bud. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. This model corresponds to the WD-associated region (WDAD) found in coatomer subunits alpha, beta, and beta' and is composed of a beta-propeller and an alpha-solenoid. The WD40 domain is 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. It 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 the GH and WD lies a conserved core. It forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet. 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. The residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands allowing them to bind either stably or reversibly.


Pssm-ID: 438571  Cd Length: 474  Bit Score: 41.14  E-value: 2.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57164111 572 KEAYQIACLGVTDTDWRELAMEALEGLEFETAKKAFTRVQDLRYL----------ELISTIEERKKRGESNNDLFladvF 641
Cdd:cd22938 353 KIAYQLAHFVKDEKKWFSLALECGSKCNFELALEAAKAANDWEKLgllallqgnhQIVEMLAQRAENFGKNNKAF----F 428

                        90
                ....*....|....*....
gi 57164111 642 SY--QGKFHEAAKLYKRSG 658
Cdd:cd22938 429 LYliTGKLRKMMKLLIIRK 447
 
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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