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Conserved domains on  [gi|149388305|gb|EAZ63306|]
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SVP1-like protein 2, partial [Scheffersomyces stipitis CBS 6054]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 1903264)

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:  30069656|29026209
SCOP:  4002744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WD40 super family cl43672
WD40 repeat [General function prediction only];
179-277 1.18e-06

WD40 repeat [General function prediction only];


The actual alignment was detected with superfamily member COG2319:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 50.29  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 179 GQIQLVDVsphgQEKNLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFRRglDRAIITSMKFSH 258
Cdd:COG2319  184 GTVRLWDL----ATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGT-VRLWDLATGKLLRTLTG--HSGSVRSVAFSP 256

                         90
                 ....*....|....*....
gi 149388305 259 NDLKLAVLSDKNTLHIFNI 277
Cdd:COG2319  257 DGRLLASGSADGTVRLWDL 275
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
179-277 1.18e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 50.29  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 179 GQIQLVDVsphgQEKNLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFRRglDRAIITSMKFSH 258
Cdd:COG2319  184 GTVRLWDL----ATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGT-VRLWDLATGKLLRTLTG--HSGSVRSVAFSP 256

                         90
                 ....*....|....*....
gi 149388305 259 NDLKLAVLSDKNTLHIFNI 277
Cdd:COG2319  257 DGRLLASGSADGTVRLWDL 275
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 193-227 1.16e-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: 36.52  E-value: 1.16e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 149388305   193 KNLVSIIKAHKSKIRCLALNRTGTLIASASETGTI 227
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTI 36
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 179-277 1.86e-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: 40.01  E-value: 1.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 179 GQIQLVDVsphgQEKNLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFRRGLDRaiITSMKFSH 258
Cdd:cd00200   73 KTIRLWDL----ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKT-IKVWDVETGKCLTTLRGHTDW--VNSVAFSP 145

                         90
                 ....*....|....*....
gi 149388305 259 NDLKLAVLSDKNTLHIFNI 277
Cdd:cd00200  146 DGTFVASSSQDGTIKLWDL 164
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
179-277 1.18e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 50.29  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 179 GQIQLVDVsphgQEKNLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFRRglDRAIITSMKFSH 258
Cdd:COG2319  184 GTVRLWDL----ATGKLLRTLTGHTGAVRSVAFSPDGKLLASGSADGT-VRLWDLATGKLLRTLTG--HSGSVRSVAFSP 256

                         90
                 ....*....|....*....
gi 149388305 259 NDLKLAVLSDKNTLHIFNI 277
Cdd:COG2319  257 DGRLLASGSADGTVRLWDL 275
WD40 COG2319
WD40 repeat [General function prediction only];
164-277 3.08e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 49.14  E-value: 3.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 164 DGakyQTLAFpGRSVGQIQLVDVSphgqEKNLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFR 243
Cdd:COG2319  299 DG---KLLAS-GSDDGTVRLWDLA----TGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGT-VRLWDLATGELLRTLT 369

                         90       100       110
                 ....*....|....*....|....*....|....
gi 149388305 244 RGLDRaiITSMKFSHNDLKLAVLSDKNTLHIFNI 277
Cdd:COG2319  370 GHTGA--VTSVAFSPDGRTLASGSADGTVRLWDL 401
WD40 COG2319
WD40 repeat [General function prediction only];
175-277 3.39e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 48.75  E-value: 3.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 175 GRSVGQIQLVDVSPHGqeknLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFRRGLDRaiITSM 254
Cdd:COG2319   96 ASADGTVRLWDLATGL----LLRTLTGHTGAVRSVAFSPDGKTLASGSADGT-VRLWDLATGKLLRTLTGHSGA--VTSV 168

                         90       100
                 ....*....|....*....|...
gi 149388305 255 KFSHNDLKLAVLSDKNTLHIFNI 277
Cdd:COG2319  169 AFSPDGKLLASGSDDGTVRLWDL 191
WD40 COG2319
WD40 repeat [General function prediction only];
179-277 7.57e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 47.98  E-value: 7.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 179 GQIQLVDVsphgQEKNLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFRRGLDRaiITSMKFSH 258
Cdd:COG2319  142 GTVRLWDL----ATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGT-VRLWDLATGKLLRTLTGHTGA--VRSVAFSP 214

                         90
                 ....*....|....*....
gi 149388305 259 NDLKLAVLSDKNTLHIFNI 277
Cdd:COG2319  215 DGKLLASGSADGTVRLWDL 233
WD40 COG2319
WD40 repeat [General function prediction only];
164-277 9.43e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 47.60  E-value: 9.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 164 DGakyQTLAFpGRSVGQIQLVDVsphgQEKNLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFR 243
Cdd:COG2319  257 DG---RLLAS-GSADGTVRLWDL----ATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGT-VRLWDLATGKLLRTLT 327

                         90       100       110
                 ....*....|....*....|....*....|....
gi 149388305 244 RGLDRaiITSMKFSHNDLKLAVLSDKNTLHIFNI 277
Cdd:COG2319  328 GHTGA--VRSVAFSPDGKTLASGSDDGTVRLWDL 359
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 193-227 1.16e-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: 36.52  E-value: 1.16e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 149388305   193 KNLVSIIKAHKSKIRCLALNRTGTLIASASETGTI 227
Cdd:smart00320   2 GELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTI 36
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 179-277 1.86e-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: 40.01  E-value: 1.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149388305 179 GQIQLVDVsphgQEKNLVSIIKAHKSKIRCLALNRTGTLIASASETGTiIRVHSTHNTALLYEFRRGLDRaiITSMKFSH 258
Cdd:cd00200   73 KTIRLWDL----ETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKT-IKVWDVETGKCLTTLRGHTDW--VNSVAFSP 145

                         90
                 ....*....|....*....
gi 149388305 259 NDLKLAVLSDKNTLHIFNI 277
Cdd:cd00200  146 DGTFVASSSQDGTIKLWDL 164
 
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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