NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1379652078|ref|XP_024626309|]
View 

WD repeat-containing protein 20 isoform X1 [Medicago truncatula]

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

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];
307-527 7.50e-23

WD40 repeat [General function prediction only];


:

Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 100.76  E-value: 7.50e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 307 QGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAW 386
Cdd:COG2319   204 TGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRT 283

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 387 GEGHNSWVSGVAFdsywsSPnsndNGETITyrfgSVGQDTQLLLWELEMDEIVVPLRrgppGGSPTFGSPTFSAGSQ--- 463
Cdd:COG2319   284 LTGHSGGVNSVAF-----SP----DGKLLA----SGSDDGTVRLWDLATGKLLRTLT----GHTGAVRSVAFSPDGKtla 346

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1379652078 464 SSHWDNAVPLgtlqpapsmRDVPKISPLVAHRVHTEPLSSLIFTQES--VLTACREGHIKIWTRPG 527
Cdd:COG2319   347 SGSDDGTVRL---------WDLATGELLRTLTGHTGAVTSVAFSPDGrtLASGSADGTVRLWDLAT 403
Nup160 super family cl26448
Nucleoporin Nup120/160; Nup120 is conserved from fungi to plants to humans, and is homologous ...
 154-433 4.02e-06

Nucleoporin Nup120/160; Nup120 is conserved from fungi to plants to humans, and is homologous with the Nup160 of vertebrates. The nuclear core complex, or NPC, mediates macromolecular transport across the nuclear envelope. Deletion of the NUP120 gene causes clustering of NPCs at one side of the nuclear envelope, moderate nucleolar fragmentation and slower cell growth. The vertebrate NPC is estimated to contain between 30 and 60 different proteins. most of which are not known. Two important ones in creating the nucleoporin basket are Nup98 and Nup153, and Nup120, in conjunction with Nup 133, interacts with these two and itself plays a role in mRNA export. Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. The phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. The entire Nup107-160 sub-complex is stable throughout the cell cycle, thus it seems unlikely that phosphorylation affects interactions within the Nup107-160 sub-complex, but rather that it regulates the association of the sub-complex with the NPC and other proteins.


The actual alignment was detected with superfamily member pfam11715:

Pssm-ID: 432020 [Multi-domain]  Cd Length: 540  Bit Score: 49.38  E-value: 4.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 154 VFNAGDAILISDLNSQDKDPIKS--IHFSNSN-PVCHAFdQDaKDGHDLLIgLF----SGDVYSVSLRQqlqdvgkkivg 226
Cdd:pfam11715  57 VLTDGRVLELVDLSLKSSLANLTlrLDFPSPIlPSCVCF-TD-SEDGDVLI-VIvttaSVHLYSLRLRP----------- 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 227 AHHYNKDGILNNSRCTCISWVP--------------GGDGAFVVAHADGNLYVYEKNKDGA---------GESSFPILKD 283
Cdd:pfam11715 123 DFFRLPDAIFGDLGDWCKSYVPssfsgfskpgrlvaVSPLELLVSLADGGLLKLTRSSDGGawkestfepASWLQSLSGL 202

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 284 QTLFSVAHARYSKSNPiarwHICQGSINSISFSADGAYLATVGRDGYLRVFDY-TKEHLVCG----------------GK 346
Cdd:pfam11715 203 LGWLADPTIRYSGSSV----ALSLSAAPAVTTVGGQNFLFTLSLDHTLRVWDLlTGKCLATIdlldlelpqdssswltLD 278

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 347 SYYGGLLCCAWSMDGKYILT--GGEDDLVQVWSMEdrkvvawgEGHNSWVSGVAFDSYW----SSPNSNDNGETITYRFG 420
Cdd:pfam11715 279 PAPSSLIRVSGSFRAYLVLTysPSSNGQFKFWKVK--------SNDTSELSLVDLFTDQtirpADPDSLGFWTLADFALT 350

                         330
                  ....*....|...
gi 1379652078 421 SvgQDTQLLLWEL 433
Cdd:pfam11715 351 S--SEKGFELWTL 361
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
307-527 7.50e-23

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 100.76  E-value: 7.50e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 307 QGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAW 386
Cdd:COG2319   204 TGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRT 283

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 387 GEGHNSWVSGVAFdsywsSPnsndNGETITyrfgSVGQDTQLLLWELEMDEIVVPLRrgppGGSPTFGSPTFSAGSQ--- 463
Cdd:COG2319   284 LTGHSGGVNSVAF-----SP----DGKLLA----SGSDDGTVRLWDLATGKLLRTLT----GHTGAVRSVAFSPDGKtla 346

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1379652078 464 SSHWDNAVPLgtlqpapsmRDVPKISPLVAHRVHTEPLSSLIFTQES--VLTACREGHIKIWTRPG 527
Cdd:COG2319   347 SGSDDGTVRL---------WDLATGELLRTLTGHTGAVTSVAFSPDGrtLASGSADGTVRLWDLAT 403
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 308-523 5.31e-19

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: 87.39  E-value: 5.31e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 308 GSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAWG 387
Cdd:cd00200    10 GGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 388 EGHNSWVSGVAFdsywsspnsNDNGETITyrfgSVGQDTQLLLWELEMDEIVVPLR--RGP-----PGGSPTFGSptfsa 460
Cdd:cd00200    90 TGHTSYVSSVAF---------SPDGRILS----SSSRDKTIKVWDVETGKCLTTLRghTDWvnsvaFSPDGTFVA----- 151

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1379652078 461 gsqSSHWDNAVplgtlqpapSMRDVPKISPLVAHRVHTEPLSSLIF--TQESVLTACREGHIKIW 523
Cdd:cd00200   152 ---SSSQDGTI---------KLWDLRTGKCVATLTGHTGEVNSVAFspDGEKLLSSSSDGTIKLW 204
Nup160 pfam11715
Nucleoporin Nup120/160; Nup120 is conserved from fungi to plants to humans, and is homologous ...
 154-433 4.02e-06

Nucleoporin Nup120/160; Nup120 is conserved from fungi to plants to humans, and is homologous with the Nup160 of vertebrates. The nuclear core complex, or NPC, mediates macromolecular transport across the nuclear envelope. Deletion of the NUP120 gene causes clustering of NPCs at one side of the nuclear envelope, moderate nucleolar fragmentation and slower cell growth. The vertebrate NPC is estimated to contain between 30 and 60 different proteins. most of which are not known. Two important ones in creating the nucleoporin basket are Nup98 and Nup153, and Nup120, in conjunction with Nup 133, interacts with these two and itself plays a role in mRNA export. Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. The phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. The entire Nup107-160 sub-complex is stable throughout the cell cycle, thus it seems unlikely that phosphorylation affects interactions within the Nup107-160 sub-complex, but rather that it regulates the association of the sub-complex with the NPC and other proteins.


Pssm-ID: 432020 [Multi-domain]  Cd Length: 540  Bit Score: 49.38  E-value: 4.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 154 VFNAGDAILISDLNSQDKDPIKS--IHFSNSN-PVCHAFdQDaKDGHDLLIgLF----SGDVYSVSLRQqlqdvgkkivg 226
Cdd:pfam11715  57 VLTDGRVLELVDLSLKSSLANLTlrLDFPSPIlPSCVCF-TD-SEDGDVLI-VIvttaSVHLYSLRLRP----------- 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 227 AHHYNKDGILNNSRCTCISWVP--------------GGDGAFVVAHADGNLYVYEKNKDGA---------GESSFPILKD 283
Cdd:pfam11715 123 DFFRLPDAIFGDLGDWCKSYVPssfsgfskpgrlvaVSPLELLVSLADGGLLKLTRSSDGGawkestfepASWLQSLSGL 202

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 284 QTLFSVAHARYSKSNPiarwHICQGSINSISFSADGAYLATVGRDGYLRVFDY-TKEHLVCG----------------GK 346
Cdd:pfam11715 203 LGWLADPTIRYSGSSV----ALSLSAAPAVTTVGGQNFLFTLSLDHTLRVWDLlTGKCLATIdlldlelpqdssswltLD 278

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 347 SYYGGLLCCAWSMDGKYILT--GGEDDLVQVWSMEdrkvvawgEGHNSWVSGVAFDSYW----SSPNSNDNGETITYRFG 420
Cdd:pfam11715 279 PAPSSLIRVSGSFRAYLVLTysPSSNGQFKFWKVK--------SNDTSELSLVDLFTDQtirpADPDSLGFWTLADFALT 350

                         330
                  ....*....|...
gi 1379652078 421 SvgQDTQLLLWEL 433
Cdd:pfam11715 351 S--SEKGFELWTL 361
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 296-335 1.11e-04

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: 39.60  E-value: 1.11e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1379652078  296 KSNPIARWHICQGSINSISFSADGAYLATVGRDGYLRVFD 335
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
307-335 2.73e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 35.78  E-value: 2.73e-03
                          10        20
                  ....*....|....*....|....*....
gi 1379652078 307 QGSINSISFSADGAYLATVGRDGYLRVFD 335
Cdd:pfam00400  11 TGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
 
Name Accession Description Interval E-value
WD40 COG2319
WD40 repeat [General function prediction only];
307-527 7.50e-23

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 100.76  E-value: 7.50e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 307 QGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAW 386
Cdd:COG2319   204 TGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRT 283

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 387 GEGHNSWVSGVAFdsywsSPnsndNGETITyrfgSVGQDTQLLLWELEMDEIVVPLRrgppGGSPTFGSPTFSAGSQ--- 463
Cdd:COG2319   284 LTGHSGGVNSVAF-----SP----DGKLLA----SGSDDGTVRLWDLATGKLLRTLT----GHTGAVRSVAFSPDGKtla 346

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1379652078 464 SSHWDNAVPLgtlqpapsmRDVPKISPLVAHRVHTEPLSSLIFTQES--VLTACREGHIKIWTRPG 527
Cdd:COG2319   347 SGSDDGTVRL---------WDLATGELLRTLTGHTGAVTSVAFSPDGrtLASGSADGTVRLWDLAT 403
WD40 COG2319
WD40 repeat [General function prediction only];
308-523 1.09e-19

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 91.51  E-value: 1.09e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 308 GSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAWG 387
Cdd:COG2319    79 AAVLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTL 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 388 EGHNSWVSGVAFdsywsSPnsndNGETITyrfgSVGQDTQLLLWELEMDEIVVPLRrgppGGSPTFGSPTFSAGSQ---S 464
Cdd:COG2319   159 TGHSGAVTSVAF-----SP----DGKLLA----SGSDDGTVRLWDLATGKLLRTLT----GHTGAVRSVAFSPDGKllaS 221

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1379652078 465 SHWDNAVPLgtlqpapsmRDVPKISPLVAHRVHTEPLSSLIFTQ--ESVLTACREGHIKIW 523
Cdd:COG2319   222 GSADGTVRL---------WDLATGKLLRTLTGHSGSVRSVAFSPdgRLLASGSADGTVRLW 273
WD40 COG2319
WD40 repeat [General function prediction only];
299-434 1.70e-19

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 90.74  E-value: 1.70e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 299 PIARWHICQGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSM 378
Cdd:COG2319   280 LLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDL 359

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1379652078 379 EDRKVVAWGEGHNSWVSGVAFdsywsSPNSNdngetityRFGSVGQDTQLLLWELE 434
Cdd:COG2319   360 ATGELLRTLTGHTGAVTSVAF-----SPDGR--------TLASGSADGTVRLWDLA 402
WD40 COG2319
WD40 repeat [General function prediction only];
299-471 3.13e-19

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 89.97  E-value: 3.13e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 299 PIARWHICQGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSM 378
Cdd:COG2319   238 LLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDL 317

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 379 EDRKVVAWGEGHNSWVSGVAFdsywsSPnsndNGETItyrfGSVGQDTQLLLWELEMDEIVVPLRrgppGGSPTFGSPTF 458
Cdd:COG2319   318 ATGKLLRTLTGHTGAVRSVAF-----SP----DGKTL----ASGSDDGTVRLWDLATGELLRTLT----GHTGAVTSVAF 380

                         170
                  ....*....|....*.
gi 1379652078 459 SAGSQ---SSHWDNAV 471
Cdd:COG2319   381 SPDGRtlaSGSADGTV 396
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 308-523 5.31e-19

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: 87.39  E-value: 5.31e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 308 GSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAWG 387
Cdd:cd00200    10 GGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 388 EGHNSWVSGVAFdsywsspnsNDNGETITyrfgSVGQDTQLLLWELEMDEIVVPLR--RGP-----PGGSPTFGSptfsa 460
Cdd:cd00200    90 TGHTSYVSSVAF---------SPDGRILS----SSSRDKTIKVWDVETGKCLTTLRghTDWvnsvaFSPDGTFVA----- 151

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1379652078 461 gsqSSHWDNAVplgtlqpapSMRDVPKISPLVAHRVHTEPLSSLIF--TQESVLTACREGHIKIW 523
Cdd:cd00200   152 ---SSSQDGTI---------KLWDLRTGKCVATLTGHTGEVNSVAFspDGEKLLSSSSDGTIKLW 204
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 307-434 1.01e-12

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: 68.90  E-value: 1.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 307 QGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVcggkSYYGG----LLCCAWSMDGKYILTGGEDDLVQVWSMEDRK 382
Cdd:cd00200    51 TGPVRDVAASADGTYLASGSSDKTIRLWDLETGECV----RTLTGhtsyVSSVAFSPDGRILSSSSRDKTIKVWDVETGK 126

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1379652078 383 VVAWGEGHNSWVSGVAFDSywsspnsndNGETITyrfgSVGQDTQLLLWELE 434
Cdd:cd00200   127 CLTTLRGHTDWVNSVAFSP---------DGTFVA----SSSQDGTIKLWDLR 165
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 307-432 1.46e-12

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: 68.52  E-value: 1.46e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 307 QGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAW 386
Cdd:cd00200   177 TGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQT 256

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1379652078 387 GEGHNSWVSGVAFdsywsSPNSNdngetityRFGSVGQDTQLLLWE 432
Cdd:cd00200   257 LSGHTNSVTSLAW-----SPDGK--------RLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 307-403 1.77e-12

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: 68.13  E-value: 1.77e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 307 QGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAW 386
Cdd:cd00200   135 TDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGT 214

                          90
                  ....*....|....*....
gi 1379652078 387 GEGHNSWVSGVAF--DSYW 403
Cdd:cd00200   215 LRGHENGVNSVAFspDGYL 233
WD40 COG2319
WD40 repeat [General function prediction only];
300-523 5.57e-10

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 61.47  E-value: 5.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 300 IARWHICQGSINSISFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSME 379
Cdd:COG2319    29 LLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLA 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 380 DRKVVAWGEGHNSWVSGVAFdsywsSPnsndNGETITyrfgSVGQDTQLLLWELEMDEIVVPLRrgppGGSPTFGSPTFS 459
Cdd:COG2319   109 TGLLLRTLTGHTGAVRSVAF-----SP----DGKTLA----SGSADGTVRLWDLATGKLLRTLT----GHSGAVTSVAFS 171

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1379652078 460 AGSQ---SSHWDNAVPLgtlqpapsmRDVPKISPLVAHRVHTEPLSSLIFTQES--VLTACREGHIKIW 523
Cdd:COG2319   172 PDGKllaSGSDDGTVRL---------WDLATGKLLRTLTGHTGAVRSVAFSPDGklLASGSADGTVRLW 231
Nup160 pfam11715
Nucleoporin Nup120/160; Nup120 is conserved from fungi to plants to humans, and is homologous ...
 154-433 4.02e-06

Nucleoporin Nup120/160; Nup120 is conserved from fungi to plants to humans, and is homologous with the Nup160 of vertebrates. The nuclear core complex, or NPC, mediates macromolecular transport across the nuclear envelope. Deletion of the NUP120 gene causes clustering of NPCs at one side of the nuclear envelope, moderate nucleolar fragmentation and slower cell growth. The vertebrate NPC is estimated to contain between 30 and 60 different proteins. most of which are not known. Two important ones in creating the nucleoporin basket are Nup98 and Nup153, and Nup120, in conjunction with Nup 133, interacts with these two and itself plays a role in mRNA export. Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. The phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. The entire Nup107-160 sub-complex is stable throughout the cell cycle, thus it seems unlikely that phosphorylation affects interactions within the Nup107-160 sub-complex, but rather that it regulates the association of the sub-complex with the NPC and other proteins.


Pssm-ID: 432020 [Multi-domain]  Cd Length: 540  Bit Score: 49.38  E-value: 4.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 154 VFNAGDAILISDLNSQDKDPIKS--IHFSNSN-PVCHAFdQDaKDGHDLLIgLF----SGDVYSVSLRQqlqdvgkkivg 226
Cdd:pfam11715  57 VLTDGRVLELVDLSLKSSLANLTlrLDFPSPIlPSCVCF-TD-SEDGDVLI-VIvttaSVHLYSLRLRP----------- 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 227 AHHYNKDGILNNSRCTCISWVP--------------GGDGAFVVAHADGNLYVYEKNKDGA---------GESSFPILKD 283
Cdd:pfam11715 123 DFFRLPDAIFGDLGDWCKSYVPssfsgfskpgrlvaVSPLELLVSLADGGLLKLTRSSDGGawkestfepASWLQSLSGL 202

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 284 QTLFSVAHARYSKSNPiarwHICQGSINSISFSADGAYLATVGRDGYLRVFDY-TKEHLVCG----------------GK 346
Cdd:pfam11715 203 LGWLADPTIRYSGSSV----ALSLSAAPAVTTVGGQNFLFTLSLDHTLRVWDLlTGKCLATIdlldlelpqdssswltLD 278

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 347 SYYGGLLCCAWSMDGKYILT--GGEDDLVQVWSMEdrkvvawgEGHNSWVSGVAFDSYW----SSPNSNDNGETITYRFG 420
Cdd:pfam11715 279 PAPSSLIRVSGSFRAYLVLTysPSSNGQFKFWKVK--------SNDTSELSLVDLFTDQtirpADPDSLGFWTLADFALT 350

                         330
                  ....*....|...
gi 1379652078 421 SvgQDTQLLLWEL 433
Cdd:pfam11715 351 S--SEKGFELWTL 361
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 296-335 1.11e-04

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: 39.60  E-value: 1.11e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1379652078  296 KSNPIARWHICQGSINSISFSADGAYLATVGRDGYLRVFD 335
Cdd:smart00320   1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
307-335 2.73e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 35.78  E-value: 2.73e-03
                          10        20
                  ....*....|....*....|....*....
gi 1379652078 307 QGSINSISFSADGAYLATVGRDGYLRVFD 335
Cdd:pfam00400  11 TGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 350-377 4.86e-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: 34.98  E-value: 4.86e-03
                           10        20
                   ....*....|....*....|....*...
gi 1379652078  350 GGLLCCAWSMDGKYILTGGEDDLVQVWS 377
Cdd:smart00320  13 GPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Nsa1_WDR74-like cd22850
Ribosome biogenesis protein Nsa1 and similar proteins; Ribosome biogenesis protein Nsa1 ...
 238-380 5.46e-03

Ribosome biogenesis protein Nsa1 and similar proteins; Ribosome biogenesis protein Nsa1 (Nop7-associated 1) from fungi and WDR74 (WD repeat-containing protein 74) from mammals and plants, are homologous essential factors for ribosome assembly. In cooperation with the assembly factor Rix7/NVL2, Nsa1/WDR74 participates in an early cleavage of the pre-rRNA processing pathway. Rix7/NVL2 is a type II double ring, AAA-ATPase, that may mediate the release of Nsa1/WDR74 from nucleolar pre-60S particles. Nsa1/WDR74 contains an N-terminal seven-bladed beta-propeller WD40 domain that associates with the D1-AAA domain of the AAA-ATPase Rix7/NVL2, and a flexible lysine-rich C-terminus that extends outward from the WD40 domain, and is required for nucleolar localization.


Pssm-ID: 439302 [Multi-domain]  Cd Length: 333  Bit Score: 39.15  E-value: 5.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 238 NSRCTCISWVPGGDGAFVVAHADGNLYVYEKNK-DGAGESSFPILKDQTlfsvahaRYSKSNPIarwhicqgsINSISFS 316
Cdd:cd22850    34 SNAVQRLSLVDRSDPLLLVARRNGNGEVYVLSPvDGELFELLSSIEGLT-------RSKEEDKF---------VGLHLLR 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1379652078 317 ADGAYLATvGRDGYLRVFD---YTKEHLVCGGKSYYGGLLCC--AWSMDGKYILTGGEDDLVQVWSMED 380
Cdd:cd22850    98 SLGLLTCA-TKSGLLHIIDledSKKDSLEVKAPLTLPGFLSAfrVNPTDEGVFAYGGKENDLKLWDLEK 165
Nsa1 cd22858
Ribosome Biogenesis Protein Nsa1; Ribosome biogenesis protein Nsa1 (Nop7-associated 1) from ...
 308-382 6.08e-03

Ribosome Biogenesis Protein Nsa1; Ribosome biogenesis protein Nsa1 (Nop7-associated 1) from fungi is an essential factor for ribosome assembly. In cooperation with the assembly factor Rix7, Nsa1 participates in an early cleavage of the pre-rRNA processing pathway. Rix7 is a type II double ring, AAA-ATPase, that may mediate the release of Nsa1 from nucleolar pre-60S particles. The release of Nsa1 from a discrete preribosomal particle may trigger the progression of 60S ribosome biogenesis. Nsa1 is essential for cell viability in yeast. It contains an N-terminal seven-bladed beta-propeller WD40 domain that associates with the D1-AAA domain of the AAA-ATPase Rix7, and a flexible lysine-rich C-terminus that extends outward from the WD40 domain, and is required for nucleolar localization.


Pssm-ID: 439304  Cd Length: 399  Bit Score: 39.12  E-value: 6.08e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1379652078 308 GSINSISFSADGaYLATVGRDGYLRVFDY-TKEHLVcggKSYYGGLLCCAWsmdgkyILTGGEDDLVQVWSMEDRK 382
Cdd:cd22858   308 GAVSAVDVFEDK-YLATGGLDRYLRVFDLeTRELLA---KVYVGSKISSVL------LLDDEDIELPESEKKKKKK 373
WD40 COG2319
WD40 repeat [General function prediction only];
314-523 7.81e-03

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 38.74  E-value: 7.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 314 SFSADGAYLATVGRDGYLRVFDYTKEHLVCGGKSYYGGLLCCAWSMDGKYILTGGEDDLVQVWSMEDRKVVAWGEGHNSW 393
Cdd:COG2319     1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1379652078 394 VSGVAFDSywsspnsndNGETITyrfgSVGQDTQLLLWELEMDEIVVPLRrgppGGSPTFGSPTFSAGSQ---SSHWDNA 470
Cdd:COG2319    81 VLSVAFSP---------DGRLLA----SASADGTVRLWDLATGLLLRTLT----GHTGAVRSVAFSPDGKtlaSGSADGT 143

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1379652078 471 VPLgtlqpapsmRDVPKISPLVAHRVHTEPLSSLIFTQ--ESVLTACREGHIKIW 523
Cdd:COG2319   144 VRL---------WDLATGKLLRTLTGHSGAVTSVAFSPdgKLLASGSDDGTVRLW 189
 
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