NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|6319912|ref|NP_009993|]
View 

GTPase-activating protein SED4 [Saccharomyces cerevisiae S288C]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
142-335 1.27e-12

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 71.10  E-value: 1.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   142 IASSEVPTVIRIIDPRNLTENYEIET-GREVNDLHFAPNG-ILLSYITSNSLEVASVRDGNFVARKTDfDKNLVLSnIRF 219
Cdd:COG2319  219 LASGSADGTVRLWDLATGKLLRTLTGhSGSVRSVAFSPDGrLLASGSADGTVRLWDLATGELLRTLTG-HSGGVNS-VAF 296

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   220 LNDNTLLVAASLSNSdgvsllklgvsskgVKI--LKTASFMFDLNG----ITSMDVSPNKKFVALSSNDNLVAIVSVEKL 293
Cdd:COG2319  297 SPDGKLLASGSDDGT--------------VRLwdLATGKLLRTLTGhtgaVRSVAFSPDGKTLASGSDDGTVRLWDLATG 362

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 6319912   294 KLVQlVPRVHESTITKVTFSPDSRYLASTSMGNTINVLKLSG 335
Cdd:COG2319  363 ELLR-TLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
142-335 1.27e-12

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 71.10  E-value: 1.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   142 IASSEVPTVIRIIDPRNLTENYEIET-GREVNDLHFAPNG-ILLSYITSNSLEVASVRDGNFVARKTDfDKNLVLSnIRF 219
Cdd:COG2319  219 LASGSADGTVRLWDLATGKLLRTLTGhSGSVRSVAFSPDGrLLASGSADGTVRLWDLATGELLRTLTG-HSGGVNS-VAF 296

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   220 LNDNTLLVAASLSNSdgvsllklgvsskgVKI--LKTASFMFDLNG----ITSMDVSPNKKFVALSSNDNLVAIVSVEKL 293
Cdd:COG2319  297 SPDGKLLASGSDDGT--------------VRLwdLATGKLLRTLTGhtgaVRSVAFSPDGKTLASGSDDGTVRLWDLATG 362

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 6319912   294 KLVQlVPRVHESTITKVTFSPDSRYLASTSMGNTINVLKLSG 335
Cdd:COG2319  363 ELLR-TLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 171-330 2.14e-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: 60.04  E-value: 2.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   171 VNDLHFAPNGILLSYITSN-SLEVASVRDGNFVARKTDFDKNlVLSnIRFLNDNTLLVAASLSNSdgvslLKLGVSSKGV 249
Cdd:cd00200  138 VNSVAFSPDGTFVASSSQDgTIKLWDLRTGKCVATLTGHTGE-VNS-VAFSPDGEKLLSSSSDGT-----IKLWDLSTGK 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   250 KIlktASFMFDLNGITSMDVSPNKKFVALSSNDNLVAIVSVEKLKLVQLVPRvHESTITKVTFSPDSRYLASTSMGNTIN 329
Cdd:cd00200  211 CL---GTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSG-HTNSVTSLAWSPDGKRLASGSADGTIR 286


                 .
gi 6319912   330 V 330
Cdd:cd00200  287 I 287
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 303-330 6.34e-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: 35.37  E-value: 6.34e-03
                            10        20
                    ....*....|....*....|....*...
gi 6319912      303 HESTITKVTFSPDSRYLASTSMGNTINV 330
Cdd:smart00320   11 HTGPVTSVAFSPDGKYLASGSDDGTIKL 38
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
142-335 1.27e-12

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 71.10  E-value: 1.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   142 IASSEVPTVIRIIDPRNLTENYEIET-GREVNDLHFAPNG-ILLSYITSNSLEVASVRDGNFVARKTDfDKNLVLSnIRF 219
Cdd:COG2319  219 LASGSADGTVRLWDLATGKLLRTLTGhSGSVRSVAFSPDGrLLASGSADGTVRLWDLATGELLRTLTG-HSGGVNS-VAF 296

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   220 LNDNTLLVAASLSNSdgvsllklgvsskgVKI--LKTASFMFDLNG----ITSMDVSPNKKFVALSSNDNLVAIVSVEKL 293
Cdd:COG2319  297 SPDGKLLASGSDDGT--------------VRLwdLATGKLLRTLTGhtgaVRSVAFSPDGKTLASGSDDGTVRLWDLATG 362

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 6319912   294 KLVQlVPRVHESTITKVTFSPDSRYLASTSMGNTINVLKLSG 335
Cdd:COG2319  363 ELLR-TLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
WD40 COG2319
WD40 repeat [General function prediction only];
142-334 1.99e-11

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 67.24  E-value: 1.99e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   142 IASSEVPTVIRIIDPRNLTENYEIETGRE-VNDLHFAPNG-ILLSYITSNSLEVASVRDGNFVARKTDfDKNLVLSnIRF 219
Cdd:COG2319  135 LASGSADGTVRLWDLATGKLLRTLTGHSGaVTSVAFSPDGkLLASGSDDGTVRLWDLATGKLLRTLTG-HTGAVRS-VAF 212

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   220 LNDNTLLVAASlsnsdgvsllklgvSSKGVKI--LKTASFMFDLNG----ITSMDVSPNKKFVALSSNDNLVAIVSVEKL 293
Cdd:COG2319  213 SPDGKLLASGS--------------ADGTVRLwdLATGKLLRTLTGhsgsVRSVAFSPDGRLLASGSADGTVRLWDLATG 278

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 6319912   294 KLVQLVPRvHESTITKVTFSPDSRYLASTSMGNTINVLKLS 334
Cdd:COG2319  279 ELLRTLTG-HSGGVNSVAFSPDGKLLASGSDDGTVRLWDLA 318
WD40 COG2319
WD40 repeat [General function prediction only];
136-335 4.60e-10

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 63.01  E-value: 4.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   136 RATVAAIASSEVPTVIRIIDPRNLTENYEIETGREVNDLHFAPNG-ILLSYITSNSLEVASVRDGNFVARKTDFDKNlVL 214
Cdd:COG2319   46 PDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDGrLLASASADGTVRLWDLATGLLLRTLTGHTGA-VR 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   215 SnIRFLNDNTLLVAASlsnsdgvsllklgvSSKGVKI--LKTASFMFDLNG----ITSMDVSPNKKFVALSSNDNLVAIV 288
Cdd:COG2319  125 S-VAFSPDGKTLASGS--------------ADGTVRLwdLATGKLLRTLTGhsgaVTSVAFSPDGKLLASGSDDGTVRLW 189

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 6319912   289 SVEKLKLVQLVpRVHESTITKVTFSPDSRYLASTSMGNTINVLKLSG 335
Cdd:COG2319  190 DLATGKLLRTL-TGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLAT 235
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 171-330 2.14e-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: 60.04  E-value: 2.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   171 VNDLHFAPNGILLSYITSN-SLEVASVRDGNFVARKTDFDKNlVLSnIRFLNDNTLLVAASLSNSdgvslLKLGVSSKGV 249
Cdd:cd00200  138 VNSVAFSPDGTFVASSSQDgTIKLWDLRTGKCVATLTGHTGE-VNS-VAFSPDGEKLLSSSSDGT-----IKLWDLSTGK 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   250 KIlktASFMFDLNGITSMDVSPNKKFVALSSNDNLVAIVSVEKLKLVQLVPRvHESTITKVTFSPDSRYLASTSMGNTIN 329
Cdd:cd00200  211 CL---GTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSG-HTNSVTSLAWSPDGKRLASGSADGTIR 286


                 .
gi 6319912   330 V 330
Cdd:cd00200  287 I 287
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 262-335 3.69e-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: 53.11  E-value: 3.69e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6319912   262 NGITSMDVSPNKKFVALSSNDNLVAIVSVEKLKLvQLVPRVHESTITKVTFSPDSRYLASTSMGNTINVLKLSG 335
Cdd:cd00200   10 GGVTCVAFSPDGKLLATGSGDGTIKVWDLETGEL-LRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLET 82
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 210-330 2.33e-06

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: 2.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   210 KNLVLSnIRFLNDNTLLVAASLSNSdgvsllklgvsskgVKI--LKTASFMFDLNG----ITSMDVSPNKKFVALSSNDN 283
Cdd:cd00200   93 TSYVSS-VAFSPDGRILSSSSRDKT--------------IKVwdVETGKCLTTLRGhtdwVNSVAFSPDGTFVASSSQDG 157

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 6319912   284 LVAIVSVEKLKLVQLVPRvHESTITKVTFSPDSRYLASTSMGNTINV 330
Cdd:cd00200  158 TIKLWDLRTGKCVATLTG-HTGEVNSVAFSPDGEKLLSSSSDGTIKL 203
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 171-330 8.36e-05

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: 45.79  E-value: 8.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   171 VNDLHFAPNG-ILLSYITSNSLEVASVRDGNFVARKTDfdKNLVLSNIRFLNDNTLLVAASLSNSdgVSLLKLGvSSKGV 249
Cdd:cd00200   12 VTCVAFSPDGkLLATGSGDGTIKVWDLETGELLRTLKG--HTGPVRDVAASADGTYLASGSSDKT--IRLWDLE-TGECV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319912   250 KILKTasfmfDLNGITSMDVSPNKKFVALSSNDNLVAIVSVEKLKLVQlVPRVHESTITKVTFSPDSRYLASTSMGNTIN 329
Cdd:cd00200   87 RTLTG-----HTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLT-TLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160


                 .
gi 6319912   330 V 330
Cdd:cd00200  161 L 161
COG4946 COG4946
Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown] ...
 264-333 1.35e-04

Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown];


Pssm-ID: 443973 [Multi-domain]  Cd Length: 1072  Bit Score: 46.19  E-value: 1.35e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6319912   264 ITSMDVSPNKKFVALSSNDNLVAIVSVEKLKLVQLVPRVHESTITKVTFSPDSRYLA-STSMGNTINVLKL 333
Cdd:COG4946  391 VFNPVWSPDGKKIAFTDNRGRLWVVDLASGKVRKVDTDGYGDGISDLAWSPDSKWLAySKPGPNQLSQIFL 461
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 303-330 6.34e-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: 35.37  E-value: 6.34e-03
                            10        20
                    ....*....|....*....|....*...
gi 6319912      303 HESTITKVTFSPDSRYLASTSMGNTINV 330
Cdd:smart00320   11 HTGPVTSVAFSPDGKYLASGSDDGTIKL 38
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH