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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

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 4.57e-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: 421866 [Multi-domain]  Cd Length: 289  Bit Score: 56.96  E-value: 4.57e-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 4.57e-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: 4.57e-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];
52-301 2.09e-06

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 49.70  E-value: 2.09e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       52 GKLIATLmENEPNSITSSAVSPGETPYLITGSDQGVIKIWNLKEiivGEVYSSSLTYDCSSTVTQITmiPNFDAFAVSSK 131
Cdd:COG2319 188 GKPLSTL-AGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLST---GKLLRSTLSGHSDSVVSSFS--PDGSLLASGSS 261
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      132 DGQIIVLKVNHYQQESEVKFLNCECIRKINLknfgkneyavrmrafvNEEKSLLVALTNLSRVIIFDIRTLERLQIIENS 211
Cdd:COG2319 262 DGTIRLWDLRSSSSLLRTLSGHSSSVLSVAF----------------SPDGKLLASGSSDGTVRLWDLETGKLLSSLTLK 325
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      212 PRHGAVSSICIDEECCVLILG-TTRGIIDIWDIRFNVLIRSWSFGDhaPITHVEVCqfygKNSVIVVGGSSKTFLTIWNF 290
Cdd:COG2319 326 GHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGHS--NVLSVSFS----PDGRVVSSGSTDGTVRLWDL 399
                       250
                ....*....|.
3GRE_A      291 VKGHCQYAFIN 301
Cdd:COG2319 400 STGSLLRNLDG 410
 
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 4.57e-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: 4.57e-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];
52-301 2.09e-06

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 49.70  E-value: 2.09e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       52 GKLIATLmENEPNSITSSAVSPGETPYLITGSDQGVIKIWNLKEiivGEVYSSSLTYDCSSTVTQITmiPNFDAFAVSSK 131
Cdd:COG2319 188 GKPLSTL-AGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLST---GKLLRSTLSGHSDSVVSSFS--PDGSLLASGSS 261
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      132 DGQIIVLKVNHYQQESEVKFLNCECIRKINLknfgkneyavrmrafvNEEKSLLVALTNLSRVIIFDIRTLERLQIIENS 211
Cdd:COG2319 262 DGTIRLWDLRSSSSLLRTLSGHSSSVLSVAF----------------SPDGKLLASGSSDGTVRLWDLETGKLLSSLTLK 325
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      212 PRHGAVSSICIDEECCVLILG-TTRGIIDIWDIRFNVLIRSWSFGDhaPITHVEVCqfygKNSVIVVGGSSKTFLTIWNF 290
Cdd:COG2319 326 GHEGPVSSLSFSPDGSLLVSGgSDDGTIRLWDLRTGKPLKTLEGHS--NVLSVSFS----PDGRVVSSGSTDGTVRLWDL 399
                       250
                ....*....|.
3GRE_A      291 VKGHCQYAFIN 301
Cdd:COG2319 400 STGSLLRNLDG 410
WD40 COG2319
WD40 repeat [General function prediction only];
52-309 2.42e-06

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 49.32  E-value: 2.42e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       52 GKLIATLmENEPNSITSSAVSPGETPYLITGSDQGVIKIWNLKEIIVGEVYSSSltydcSSTVTQITMIPNFDAFAVS-S 130
Cdd:COG2319 145 GKLIRTL-EGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGH-----TDPVSSLAFSPDGGLLIASgS 218
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      131 KDGQIIVLKVNhyqqESEVKFLNCECIRKINLKNFGKNeyavrmrafvneeKSLLVALTNLSRVIIFDIRTLERLqIIEN 210
Cdd:COG2319 219 SDGTIRLWDLS----TGKLLRSTLSGHSDSVVSSFSPD-------------GSLLASGSSDGTIRLWDLRSSSSL-LRTL 280
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      211 SPRHGAVSSICIDEECCVLILGTTRGIIDIWDIRFNVLIRSWSFGDHAPIthVEVCQFYGKNSVIVVGGSSKTFLTIWNF 290
Cdd:COG2319 281 SGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGP--VSSLSFSPDGSLLVSGGSDDGTIRLWDL 358
                       250
                ....*....|....*....
3GRE_A      291 VKGHCQYAFINSDEQPSME 309
Cdd:COG2319 359 RTGKPLKTLEGHSNVLSVS 377
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
52-137 2.12e-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: 2.12e-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 2.82e-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: 2.82e-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
WD40 COG2319
WD40 repeat [General function prediction only];
17-436 8.09e-04

WD40 repeat [General function prediction only];


Pssm-ID: 225201 [Multi-domain]  Cd Length: 466  Bit Score: 41.61  E-value: 8.09e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       17 EKFLSTFKILPPLRDYKEFGPIQEIVRSPNMGNLRGKLIATLMENEPNSITSSAVSPGEtPYLITGSDQGVIKIWNLKEi 96
Cdd:COG2319  19 SELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDG-ELLLSGSSDGTIKLWDLDN- 96
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A       97 ivGEVYSSSLTYDCSSTVTQITMI-PNFDAFAV--SSKDGQIIVLKVNHyqqesevkflNCECIRKINLKNfgKNEYAVr 173
Cdd:COG2319  97 --GEKLIKSLEGLHDSSVSKLALSsPDGNSILLasSSLDGTVKLWDLST----------PGKLIRTLEGHS--ESVTSL- 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      174 mrAFVNEEKSLLVALTNLSRVIIFDIRTLERLQIIENSPRHgaVSSICIDEECCVLILGTTR-GIIDIWDIRFNVLIRSW 252
Cdd:COG2319 162 --AFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDP--VSSLAFSPDGGLLIASGSSdGTIRLWDLSTGKLLRST 237
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      253 SFGDHAPithveVCQFYGKNSVIVVGGSSKTFLTIWNFVKGHCQYAFINSDEQPSME-HFLPIEKGLEELNFCGIRSLNA 331
Cdd:COG2319 238 LSGHSDS-----VVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSvAFSPDGKLLASGSSDGTVRLWD 312
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GRE_A      332 LSTISVSNDKILLTDEATSSIVMFSLNelsSSKAVISPSRFSDVFIPTqvtanlTMLLRKMKRTSTHSVDDSLYHHDIIN 411
Cdd:COG2319 313 LETGKLLSSLTLKGHEGPVSSLSFSPD---GSLLVSGGSDDGTIRLWD------LRTGKPLKTLEGHSNVLSVSFSPDGR 383
                       410       420
                ....*....|....*....|....*
3GRE_A      412 SISTCEVDETPLLVACDNSGLIGIF 436
Cdd:COG2319 384 VVSSGSTDGTVRLWDLSTGSLLRNL 408
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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