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Conserved domains on  [gi|6324147|ref|NP_014217|]
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chromatin-binding/pre-rRNA-processing protein IPI3 [Saccharomyces cerevisiae S288C]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 12822048)

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

 Zoom to residue level

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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 ...
 108-226 2.85e-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: 58.50  E-value: 2.85e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  108 PYLLLGStESGKLYIWELNSGILLNVkPMAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHD 187
Cdd:cd00200  22 KLLATGS-GDGTIKVWDLETGELLRT-LKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL--------ETGECVRTLTG 91

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 6324147  188 HTLPVTDFQVSSSqGKFLSCTdtklftvSQDATIRCYDL 226
Cdd:cd00200  92 HTSYVSSVAFSPD-GRILSSS-------SRDKTIKVWDV 122
WD40 super family cl43672
WD40 repeat [General function prediction only];
109-383 1.06e-05

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: 47.98  E-value: 1.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  109 YLLLGStESGKLYIWELNSGILLNVKPmAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHDH 188
Cdd:COG2319 134 TLASGS-ADGTVRLWDLATGKLLRTLT-GHSGAVTSVAFSPDGKLLASGSDDGTVRLWDL--------ATGKLLRTLTGH 203

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  189 TLPVTDFQVsSSQGKFlsctdtkLFTVSQDATIRCYDLsligskkkqkanendvsigKTPVLLATFTTP-YSIKSIVLDP 267
Cdd:COG2319 204 TGAVRSVAF-SPDGKL-------LASGSADGTVRLWDL-------------------ATGKLLRTLTGHsGSVRSVAFSP 256

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  268 ADRACYIGTAEGCFSLnlfYKLKGNAIVNLL--QSAGVNTVqkgrVFSLVQRNSLTGGENEDL---DAlyAMGQLVCE-N 341
Cdd:COG2319 257 DGRLLASGSADGTVRL---WDLATGELLRTLtgHSGGVNSV----AFSPDGKLLASGSDDGTVrlwDL--ATGKLLRTlT 327

                       250       260       270       280
                ....*....|....*....|....*....|....*....|..
gi 6324147  342 VLNSNVSCLEISMDGTLLLIGDTEGKVSIAEIYSKQIIRTIQ 383
Cdd:COG2319 328 GHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLT 369
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 108-226 2.85e-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: 58.50  E-value: 2.85e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  108 PYLLLGStESGKLYIWELNSGILLNVkPMAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHD 187
Cdd:cd00200  22 KLLATGS-GDGTIKVWDLETGELLRT-LKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL--------ETGECVRTLTG 91

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 6324147  188 HTLPVTDFQVSSSqGKFLSCTdtklftvSQDATIRCYDL 226
Cdd:cd00200  92 HTSYVSSVAFSPD-GRILSSS-------SRDKTIKVWDV 122
WD40 COG2319
WD40 repeat [General function prediction only];
110-227 5.86e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 51.84  E-value: 5.86e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  110 LLLGSTESGKLYIWELNSGILLNVKPmAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHDHT 189
Cdd:COG2319 260 LLASGSADGTVRLWDLATGELLRTLT-GHSGGVNSVAFSPDGKLLASGSDDGTVRLWDL--------ATGKLLRTLTGHT 330

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 6324147  190 LPVTDFQVsSSQGKFlsctdtkLFTVSQDATIRCYDLS 227
Cdd:COG2319 331 GAVRSVAF-SPDGKT-------LASGSDDGTVRLWDLA 360
WD40 COG2319
WD40 repeat [General function prediction only];
109-383 1.06e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 47.98  E-value: 1.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  109 YLLLGStESGKLYIWELNSGILLNVKPmAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHDH 188
Cdd:COG2319 134 TLASGS-ADGTVRLWDLATGKLLRTLT-GHSGAVTSVAFSPDGKLLASGSDDGTVRLWDL--------ATGKLLRTLTGH 203

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  189 TLPVTDFQVsSSQGKFlsctdtkLFTVSQDATIRCYDLsligskkkqkanendvsigKTPVLLATFTTP-YSIKSIVLDP 267
Cdd:COG2319 204 TGAVRSVAF-SPDGKL-------LASGSADGTVRLWDL-------------------ATGKLLRTLTGHsGSVRSVAFSP 256

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  268 ADRACYIGTAEGCFSLnlfYKLKGNAIVNLL--QSAGVNTVqkgrVFSLVQRNSLTGGENEDL---DAlyAMGQLVCE-N 341
Cdd:COG2319 257 DGRLLASGSADGTVRL---WDLATGELLRTLtgHSGGVNSV----AFSPDGKLLASGSDDGTVrlwDL--ATGKLLRTlT 327

                       250       260       270       280
                ....*....|....*....|....*....|....*....|..
gi 6324147  342 VLNSNVSCLEISMDGTLLLIGDTEGKVSIAEIYSKQIIRTIQ 383
Cdd:COG2319 328 GHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLT 369
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 178-225 9.88e-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: 34.21  E-value: 9.88e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 6324147     178 DPKPLCILHDHTLPVTDFQVSSSQGKFLSCtdtklftvSQDATIRCYD 225
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASG--------SDDGTIKLWD 40
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 108-226 2.85e-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: 58.50  E-value: 2.85e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  108 PYLLLGStESGKLYIWELNSGILLNVkPMAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHD 187
Cdd:cd00200  22 KLLATGS-GDGTIKVWDLETGELLRT-LKGHTGPVRDVAASADGTYLASGSSDKTIRLWDL--------ETGECVRTLTG 91

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 6324147  188 HTLPVTDFQVSSSqGKFLSCTdtklftvSQDATIRCYDL 226
Cdd:cd00200  92 HTSYVSSVAFSPD-GRILSSS-------SRDKTIKVWDV 122
WD40 COG2319
WD40 repeat [General function prediction only];
110-227 5.86e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 51.84  E-value: 5.86e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  110 LLLGSTESGKLYIWELNSGILLNVKPmAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHDHT 189
Cdd:COG2319 260 LLASGSADGTVRLWDLATGELLRTLT-GHSGGVNSVAFSPDGKLLASGSDDGTVRLWDL--------ATGKLLRTLTGHT 330

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 6324147  190 LPVTDFQVsSSQGKFlsctdtkLFTVSQDATIRCYDLS 227
Cdd:COG2319 331 GAVRSVAF-SPDGKT-------LASGSDDGTVRLWDLA 360
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 150-227 9.88e-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: 47.71  E-value: 9.88e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324147  150 NGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHDHTLPVTDFQVSSSqgkflsctDTKLFTVSQDATIRCYDLS 227
Cdd:cd00200  20 DGKLLATGSGDGTIKVWDL--------ETGELLRTLKGHTGPVRDVAASAD--------GTYLASGSSDKTIRLWDLE 81
WD40 COG2319
WD40 repeat [General function prediction only];
109-383 1.06e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 47.98  E-value: 1.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  109 YLLLGStESGKLYIWELNSGILLNVKPmAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHDH 188
Cdd:COG2319 134 TLASGS-ADGTVRLWDLATGKLLRTLT-GHSGAVTSVAFSPDGKLLASGSDDGTVRLWDL--------ATGKLLRTLTGH 203

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  189 TLPVTDFQVsSSQGKFlsctdtkLFTVSQDATIRCYDLsligskkkqkanendvsigKTPVLLATFTTP-YSIKSIVLDP 267
Cdd:COG2319 204 TGAVRSVAF-SPDGKL-------LASGSADGTVRLWDL-------------------ATGKLLRTLTGHsGSVRSVAFSP 256

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  268 ADRACYIGTAEGCFSLnlfYKLKGNAIVNLL--QSAGVNTVqkgrVFSLVQRNSLTGGENEDL---DAlyAMGQLVCE-N 341
Cdd:COG2319 257 DGRLLASGSADGTVRL---WDLATGELLRTLtgHSGGVNSV----AFSPDGKLLASGSDDGTVrlwDL--ATGKLLRTlT 327

                       250       260       270       280
                ....*....|....*....|....*....|....*....|..
gi 6324147  342 VLNSNVSCLEISMDGTLLLIGDTEGKVSIAEIYSKQIIRTIQ 383
Cdd:COG2319 328 GHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLT 369
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 110-226 2.38e-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: 46.17  E-value: 2.38e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  110 LLLGSTESGKLYIWELNSGILLNVKPmAHYQSITKIKSILNGKYIITSGNDSRVIIWqtvDLvsasnDDPKPLCILHDHT 189
Cdd:cd00200 149 FVASSSQDGTIKLWDLRTGKCVATLT-GHTGEVNSVAFSPDGEKLLSSSSDGTIKLW---DL-----STGKCLGTLRGHE 219

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 6324147  190 LPVTDFQVSSSQGKFLSCtdtklftvSQDATIRCYDL 226
Cdd:cd00200 220 NGVNSVAFSPDGYLLASG--------SEDGTIRVWDL 248
WD40 COG2319
WD40 repeat [General function prediction only];
110-226 5.80e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 45.67  E-value: 5.80e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324147  110 LLLGSTESGKLYIWELNSGILLNVkPMAHYQSITKIKSILNGKYIITSGNDSRVIIWQTvdlvsasnDDPKPLCILHDHT 189
Cdd:COG2319  92 LLASASADGTVRLWDLATGLLLRT-LTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDL--------ATGKLLRTLTGHS 162

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 6324147  190 LPVTDFQVSSSqGKFlsctdtkLFTVSQDATIRCYDL 226
Cdd:COG2319 163 GAVTSVAFSPD-GKL-------LASGSDDGTVRLWDL 191
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 109-167 2.94e-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: 2.94e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 6324147  109 YLLLGSTESGKLYIWELNSGILLNVKPmAHYQSITKIKSILNGKYIITSGNDSRVIIWQ 167
Cdd:cd00200 232 YLLASGSEDGTIRVWDLRTGECVQTLS-GHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 178-225 9.88e-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: 34.21  E-value: 9.88e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 6324147     178 DPKPLCILHDHTLPVTDFQVSSSQGKFLSCtdtklftvSQDATIRCYD 225
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASG--------SDDGTIKLWD 40
 
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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