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Conserved domains on  [gi|998614199|ref|NP_956534|]
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WD repeat domain phosphoinositide-interacting protein 3 [Danio rerio]

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 ...
 34-257 3.96e-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: 60.04  E-value: 3.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199  34 RVYNTDPLKEKEKQEFLEGGVGHVemLFRC--NYLALVGGGKKpkyppnkVMIWDDLKKKTVIEIE-FSTEVKAVKLRRD 110
Cdd:cd00200   34 KVWDLETGELLRTLKGHTGPVRDV--AASAdgTYLASGSSDKT-------IRLWDLETGECVRTLTgHTSYVSSVAFSPD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 111 RIVVV---LDSMIKVFTFTHNPhQLHVFETCynPKGLCVLCPNSNNSLLAFpATHSGHVQIVDLaNTEKPPVDIPAHEGV 187
Cdd:cd00200  105 GRILSsssRDKTIKVWDVETGK-CLTTLRGH--TDWVNSVAFSPDGTFVAS-SSQDGTIKLWDL-RTGKCVATLTGHTGE 179

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 188 LCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELRrgSQTANIYCINFNQDASLICVSSDHGTVHIF 257
Cdd:cd00200  180 VNSVAFSPDGEKLLSSSSDGT-IKLWDLSTGKCLGTLR--GHENGVNSVAFSPDGYLLASGSEDGTIRVW 246
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 34-257 3.96e-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: 60.04  E-value: 3.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199  34 RVYNTDPLKEKEKQEFLEGGVGHVemLFRC--NYLALVGGGKKpkyppnkVMIWDDLKKKTVIEIE-FSTEVKAVKLRRD 110
Cdd:cd00200   34 KVWDLETGELLRTLKGHTGPVRDV--AASAdgTYLASGSSDKT-------IRLWDLETGECVRTLTgHTSYVSSVAFSPD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 111 RIVVV---LDSMIKVFTFTHNPhQLHVFETCynPKGLCVLCPNSNNSLLAFpATHSGHVQIVDLaNTEKPPVDIPAHEGV 187
Cdd:cd00200  105 GRILSsssRDKTIKVWDVETGK-CLTTLRGH--TDWVNSVAFSPDGTFVAS-SSQDGTIKLWDL-RTGKCVATLTGHTGE 179

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 188 LCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELRrgSQTANIYCINFNQDASLICVSSDHGTVHIF 257
Cdd:cd00200  180 VNSVAFSPDGEKLLSSSSDGT-IKLWDLSTGKCLGTLR--GHENGVNSVAFSPDGYLLASGSEDGTIRVW 246
WD40 COG2319
WD40 repeat [General function prediction only];
152-264 7.75e-09

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 56.46  E-value: 7.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 152 NNSLLAFpATHSGHVQIVDLAnTEKPPVDIPAHEGVLCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELrrGSQTA 231
Cdd:COG2319  215 DGKLLAS-GSADGTVRLWDLA-TGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGT-VRLWDLATGELLRTL--TGHSG 289

                         90       100       110
                 ....*....|....*....|....*....|...
gi 998614199 232 NIYCINFNQDASLICVSSDHGTVHIFAAEDPKR 264
Cdd:COG2319  290 GVNSVAFSPDGKLLASGSDDGTVRLWDLATGKL 322
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 34-257 3.96e-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: 60.04  E-value: 3.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199  34 RVYNTDPLKEKEKQEFLEGGVGHVemLFRC--NYLALVGGGKKpkyppnkVMIWDDLKKKTVIEIE-FSTEVKAVKLRRD 110
Cdd:cd00200   34 KVWDLETGELLRTLKGHTGPVRDV--AASAdgTYLASGSSDKT-------IRLWDLETGECVRTLTgHTSYVSSVAFSPD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 111 RIVVV---LDSMIKVFTFTHNPhQLHVFETCynPKGLCVLCPNSNNSLLAFpATHSGHVQIVDLaNTEKPPVDIPAHEGV 187
Cdd:cd00200  105 GRILSsssRDKTIKVWDVETGK-CLTTLRGH--TDWVNSVAFSPDGTFVAS-SSQDGTIKLWDL-RTGKCVATLTGHTGE 179

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 188 LCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELRrgSQTANIYCINFNQDASLICVSSDHGTVHIF 257
Cdd:cd00200  180 VNSVAFSPDGEKLLSSSSDGT-IKLWDLSTGKCLGTLR--GHENGVNSVAFSPDGYLLASGSEDGTIRVW 246
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 25-258 6.23e-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: 59.27  E-value: 6.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199  25 FACGMENGFRVYNTDplKEKEKQEFleggVGHVEMLFRCNYLA----LVGGGKKpkyppNKVMIWDDLKKKTVIEIEFST 100
Cdd:cd00200   67 ASGSSDKTIRLWDLE--TGECVRTL----TGHTSYVSSVAFSPdgriLSSSSRD-----KTIKVWDVETGKCLTTLRGHT 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 101 E-VKAVKLRRDRIVVV---LDSMIKVF---------TFTHnpHQLHVFETCYNPKGlcvlcpnsnNSLLAfpATHSGHVQ 167
Cdd:cd00200  136 DwVNSVAFSPDGTFVAsssQDGTIKLWdlrtgkcvaTLTG--HTGEVNSVAFSPDG---------EKLLS--SSSDGTIK 202

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 168 IVDLaNTEKPPVDIPAHEGVLCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELRrGSQTAnIYCINFNQDASLICV 247
Cdd:cd00200  203 LWDL-STGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGT-IRVWDLRTGECVQTLS-GHTNS-VTSLAWSPDGKRLAS 278

                        250
                 ....*....|.
gi 998614199 248 SSDHGTVHIFA 258
Cdd:cd00200  279 GSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 141-263 4.08e-09

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: 56.96  E-value: 4.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 141 PKGLCVLCPNSNNSLLAFpATHSGHVQIVDLaNTEKPPVDIPAHEGVLCCITLNLQGTRIATASEKGTlIRIFDTSAGQL 220
Cdd:cd00200    9 TGGVTCVAFSPDGKLLAT-GSGDGTIKVWDL-ETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKT-IRLWDLETGEC 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 998614199 221 IQELRrgSQTANIYCINFNQDASLICVSSDHGTVHIFAAEDPK 263
Cdd:cd00200   86 VRTLT--GHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGK 126
WD40 COG2319
WD40 repeat [General function prediction only];
152-264 7.75e-09

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 56.46  E-value: 7.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 152 NNSLLAFpATHSGHVQIVDLAnTEKPPVDIPAHEGVLCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELrrGSQTA 231
Cdd:COG2319  215 DGKLLAS-GSADGTVRLWDLA-TGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGT-VRLWDLATGELLRTL--TGHSG 289

                         90       100       110
                 ....*....|....*....|....*....|...
gi 998614199 232 NIYCINFNQDASLICVSSDHGTVHIFAAEDPKR 264
Cdd:COG2319  290 GVNSVAFSPDGKLLASGSDDGTVRLWDLATGKL 322
WD40 COG2319
WD40 repeat [General function prediction only];
160-277 1.14e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 56.07  E-value: 1.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 160 ATHSGHVQIVDLAnTEKPPVDIPAHEGVLCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELRrgSQTANIYCINFN 239
Cdd:COG2319  180 GSDDGTVRLWDLA-TGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGT-VRLWDLATGKLLRTLT--GHSGSVRSVAFS 255

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 998614199 240 QDASLICVSSDHGTVHIFAAEDPKRNK-----QSSLASASFLP 277
Cdd:COG2319  256 PDGRLLASGSADGTVRLWDLATGELLRtltghSGGVNSVAFSP 298
WD40 COG2319
WD40 repeat [General function prediction only];
152-261 6.16e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 53.76  E-value: 6.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 152 NNSLLAFpATHSGHVQIVDLAnTEKPPVDIPAHEGVLCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELRrgSQTA 231
Cdd:COG2319  299 DGKLLAS-GSDDGTVRLWDLA-TGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGT-VRLWDLATGELLRTLT--GHTG 373

                         90       100       110
                 ....*....|....*....|....*....|
gi 998614199 232 NIYCINFNQDASLICVSSDHGTVHIFAAED 261
Cdd:COG2319  374 AVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 117-316 5.79e-07

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: 50.41  E-value: 5.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 117 DSMIKVFTFTHNpHQLHVFETCYNPKGLCVLCPNSNnsLLAfpATHSGH-VQIVDLaNTEKPPVDIPAHEGVLCCITLNL 195
Cdd:cd00200   30 DGTIKVWDLETG-ELLRTLKGHTGPVRDVAASADGT--YLA--SGSSDKtIRLWDL-ETGECVRTLTGHTSYVSSVAFSP 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 196 QGTRIATASEKGTlIRIFDTSAGQLIQELRrgSQTANIYCINFNQDASLICVSSDHGTVHIFAAEDPKRNK-----QSSL 270
Cdd:cd00200  104 DGRILSSSSRDKT-IKVWDVETGKCLTTLR--GHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVAtltghTGEV 180

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 998614199 271 ASASFLP---KYFSS-------KWSFSKFQvpsgspCVCAFGTEPNAVIAICADGS 316
Cdd:cd00200  181 NSVAFSPdgeKLLSSssdgtikLWDLSTGK------CLGTLRGHENGVNSVAFSPD 230
WD40 COG2319
WD40 repeat [General function prediction only];
160-277 1.00e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 49.91  E-value: 1.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998614199 160 ATHSGHVQIVDLAnTEKPPVDIPAHEGVLCCITLNLQGTRIATASEKGTlIRIFDTSAGQLIQELRRGSQTanIYCINFN 239
Cdd:COG2319   96 ASADGTVRLWDLA-TGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGT-VRLWDLATGKLLRTLTGHSGA--VTSVAFS 171

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 998614199 240 QDASLICVSSDHGTVHIFAAEDPK-----RNKQSSLASASFLP 277
Cdd:COG2319  172 PDGKLLASGSDDGTVRLWDLATGKllrtlTGHTGAVRSVAFSP 214
 
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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