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Conserved domains on  [gi|254839349|pdb|3GRE|A]
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Chain A, Serine/threonine-protein kinase VPS15

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 ...
 63-295 5.02e-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.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 56.96  E-value: 5.02e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       63 PNSITSSAVSPgETPYLITGSDQGVIKIWNLKeiivGEVYSSSLTyDCSSTVTQITMIPNFDAFAVSSKDGQIIVLKVNh 142
Cdd:cd00200   9 TGGVTCVAFSP-DGKLLATGSGDGTIKVWDLE----TGELLRTLK-GHTGPVRDVAASADGTYLASGSSDKTIRLWDLE- 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      143 yqqesevkflNCECIRKinLKNFGKNEYAVrmrAFVNeEKSLLVALTNLSRVIIFDIRTLERLQIIENsprH-GAVSSIC 221
Cdd:cd00200  82 ----------TGECVRT--LTGHTSYVSSV---AFSP-DGRILSSSSRDKTIKVWDVETGKCLTTLRG---HtDWVNSVA 142

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
3GRE_A      222 IDEECCVLILGTTRGIIDIWDIRFNVLIRswSFGDH-APITHVevcQFYGKNSVIVVGGSSKTfLTIWNFVKGHC 295
Cdd:cd00200 143 FSPDGTFVASSSQDGTIKLWDLRTGKCVA--TLTGHtGEVNSV---AFSPDGEKLLSSSSDGT-IKLWDLSTGKC 211
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 63-295 5.02e-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: 5.02e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       63 PNSITSSAVSPgETPYLITGSDQGVIKIWNLKeiivGEVYSSSLTyDCSSTVTQITMIPNFDAFAVSSKDGQIIVLKVNh 142
Cdd:cd00200   9 TGGVTCVAFSP-DGKLLATGSGDGTIKVWDLE----TGELLRTLK-GHTGPVRDVAASADGTYLASGSSDKTIRLWDLE- 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      143 yqqesevkflNCECIRKinLKNFGKNEYAVrmrAFVNeEKSLLVALTNLSRVIIFDIRTLERLQIIENsprH-GAVSSIC 221
Cdd:cd00200  82 ----------TGECVRT--LTGHTSYVSSV---AFSP-DGRILSSSSRDKTIKVWDVETGKCLTTLRG---HtDWVNSVA 142

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
3GRE_A      222 IDEECCVLILGTTRGIIDIWDIRFNVLIRswSFGDH-APITHVevcQFYGKNSVIVVGGSSKTfLTIWNFVKGHC 295
Cdd:cd00200 143 FSPDGTFVASSSQDGTIKLWDLRTGKCVA--TLTGHtGEVNSV---AFSPDGEKLLSSSSDGT-IKLWDLSTGKC 211
WD40 COG2319
WD40 repeat [General function prediction only];
52-289 3.49e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 49.14  E-value: 3.49e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       52 GKLIATLmENEPNSITSSAVSPGETpYLITGSDQGVIKIWNLKEIIVGEVYSSSltydcSSTVTQITMIPNFDAFAVSSK 131
Cdd:COG2319 194 GKLLRTL-TGHTGAVRSVAFSPDGK-LLASGSADGTVRLWDLATGKLLRTLTGH-----SGSVRSVAFSPDGRLLASGSA 266

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      132 DGQIIVLKVNHYQQesevkflncecirkinLKNFGKNEYAVR-MrAFVNEEKSLLVAlTNLSRVIIFDIRTLERLQIIen 210
Cdd:COG2319 267 DGTVRLWDLATGEL----------------LRTLTGHSGGVNsV-AFSPDGKLLASG-SDDGTVRLWDLATGKLLRTL-- 326

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
3GRE_A      211 SPRHGAVSSICIDEECCVLILGTTRGIIDIWDIRFNVLIRSWSfGDHAPITHVEvcqFYGKNSVIVVGGSSKTfLTIWN 289
Cdd:COG2319 327 TGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLT-GHTGAVTSVA---FSPDGRTLASGSADGT-VRLWD 400
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 63-295 5.02e-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: 5.02e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       63 PNSITSSAVSPgETPYLITGSDQGVIKIWNLKeiivGEVYSSSLTyDCSSTVTQITMIPNFDAFAVSSKDGQIIVLKVNh 142
Cdd:cd00200   9 TGGVTCVAFSP-DGKLLATGSGDGTIKVWDLE----TGELLRTLK-GHTGPVRDVAASADGTYLASGSSDKTIRLWDLE- 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      143 yqqesevkflNCECIRKinLKNFGKNEYAVrmrAFVNeEKSLLVALTNLSRVIIFDIRTLERLQIIENsprH-GAVSSIC 221
Cdd:cd00200  82 ----------TGECVRT--LTGHTSYVSSV---AFSP-DGRILSSSSRDKTIKVWDVETGKCLTTLRG---HtDWVNSVA 142

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
3GRE_A      222 IDEECCVLILGTTRGIIDIWDIRFNVLIRswSFGDH-APITHVevcQFYGKNSVIVVGGSSKTfLTIWNFVKGHC 295
Cdd:cd00200 143 FSPDGTFVASSSQDGTIKLWDLRTGKCVA--TLTGHtGEVNSV---AFSPDGEKLLSSSSDGT-IKLWDLSTGKC 211
WD40 COG2319
WD40 repeat [General function prediction only];
52-289 3.49e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 49.14  E-value: 3.49e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       52 GKLIATLmENEPNSITSSAVSPGETpYLITGSDQGVIKIWNLKEIIVGEVYSSSltydcSSTVTQITMIPNFDAFAVSSK 131
Cdd:COG2319 194 GKLLRTL-TGHTGAVRSVAFSPDGK-LLASGSADGTVRLWDLATGKLLRTLTGH-----SGSVRSVAFSPDGRLLASGSA 266

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      132 DGQIIVLKVNHYQQesevkflncecirkinLKNFGKNEYAVR-MrAFVNEEKSLLVAlTNLSRVIIFDIRTLERLQIIen 210
Cdd:COG2319 267 DGTVRLWDLATGEL----------------LRTLTGHSGGVNsV-AFSPDGKLLASG-SDDGTVRLWDLATGKLLRTL-- 326

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
3GRE_A      211 SPRHGAVSSICIDEECCVLILGTTRGIIDIWDIRFNVLIRSWSfGDHAPITHVEvcqFYGKNSVIVVGGSSKTfLTIWN 289
Cdd:COG2319 327 TGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLT-GHTGAVTSVA---FSPDGRTLASGSADGT-VRLWD 400
WD40 COG2319
WD40 repeat [General function prediction only];
52-244 2.96e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 46.06  E-value: 2.96e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       52 GKLIATLmENEPNSITSSAVSP-GETpyLITGSDQGVIKIWNLKEiivGEVySSSLTYDcSSTVTQITMIPNFDAFAVSS 130
Cdd:COG2319 236 GKLLRTL-TGHSGSVRSVAFSPdGRL--LASGSADGTVRLWDLAT---GEL-LRTLTGH-SGGVNSVAFSPDGKLLASGS 307

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      131 KDGQIIVLKVNHYQQesevkflncecirkinLKNFGKNEYAVRMRAFVNEEKSLLVALTNlSRVIIFDIRTLERLQIIEN 210
Cdd:COG2319 308 DDGTVRLWDLATGKL----------------LRTLTGHTGAVRSVAFSPDGKTLASGSDD-GTVRLWDLATGELLRTLTG 370

                       170       180       190
                ....*....|....*....|....*....|....*
3GRE_A      211 sprH-GAVSSICIDEECCVLILGTTRGIIDIWDIR 244
Cdd:COG2319 371 ---HtGAVTSVAFSPDGRTLASGSADGTVRLWDLA 402
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 52-137 2.33e-04

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: 42.71  E-value: 2.33e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       52 GKLIATLMENEpNSITSSAVSPGETPYLITGSDqGVIKIWNLKEIIVGEVYSSsltydCSSTVTQITMIPNFDAFAVSSK 131
Cdd:cd00200 167 GKCVATLTGHT-GEVNSVAFSPDGEKLLSSSSD-GTIKLWDLSTGKCLGTLRG-----HENGVNSVAFSPDGYLLASGSE 239


                ....*.
3GRE_A      132 DGQIIV 137
Cdd:cd00200 240 DGTIRV 245
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 64-242 3.10e-04

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: 42.32  E-value: 3.10e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       64 NSITSSAVSPGETpYLITGSDQGVIKIWNLKEIIVGEVYSSSltydcSSTVTQITMIPNFDAFAVSSKDGQIIVlkvnhy 143
Cdd:cd00200 136 DWVNSVAFSPDGT-FVASSSQDGTIKLWDLRTGKCVATLTGH-----TGEVNSVAFSPDGEKLLSSSSDGTIKL------ 203

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      144 qqeSEVKFLNCecirkinLKNFGKNEYAVRMRAFvNEEKSLLVALTNLSRVIIFDIRTLERLQIIENSPrhGAVSSICID 223
Cdd:cd00200 204 ---WDLSTGKC-------LGTLRGHENGVNSVAF-SPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHT--NSVTSLAWS 270

                       170
                ....*....|....*....
3GRE_A      224 EECCVLILGTTRGIIDIWD 242
Cdd:cd00200 271 PDGKRLASGSADGTIRIWD 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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