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Conserved domains on  [gi|237823848|pdb|3FMO|A]
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Chain A, Nuclear pore complex protein Nup214

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ANAPC4_WD40 super family cl14918
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 155-216 7.64e-05

Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,


The actual alignment was detected with superfamily member pfam12894:

Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 41.49  E-value: 7.64e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
3FMO_A        155 MKWNPTVpSMVAVCLADGSIAVL----QVTETVKVCATlpsTVAVTSVCWSPKGKQLAVGKQNGTV 216
Cdd:pfam12894   1 MSWCPTM-DLIALATEDGELLLHrlnwQRVWTLSPDKE---DLEVTSLAWRPDGKLLAVGYSDGTV 62
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 94-265 1.30e-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.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 43.48  E-value: 1.30e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A       94 PIHHLALSCDNLTLSACMMSSEygsiIAFFDVRTFsneakQQKRPFAYHKllkdagGMVIDMKWNPTvPSMVAVCLADGS 173
Cdd:cd00200  95 YVSSVAFSPDGRILSSSSRDKT----IKVWDVETG-----KCLTTLRGHT------DWVNSVAFSPD-GTFVASSSQDGT 158

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A      174 IAVLQVtETVKVCATLPS-TVAVTSVCWSPKGKQLAVGKQNGTVVQY-LPTLQEKKVIPCppfyesdHPVRVLDVLWIGT 251
Cdd:cd00200 159 IKLWDL-RTGKCVATLTGhTGEVNSVAFSPDGEKLLSSSSDGTIKLWdLSTGKCLGTLRG-------HENGVNSVAFSPD 230

                       170
                ....*....|....
3FMO_A      252 YVFAIVyAAADGTL 265
Cdd:cd00200 231 GYLLAS-GSEDGTI 243
 
Name Accession Description Interval E-value
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 155-216 7.64e-05

Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 41.49  E-value: 7.64e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
3FMO_A        155 MKWNPTVpSMVAVCLADGSIAVL----QVTETVKVCATlpsTVAVTSVCWSPKGKQLAVGKQNGTV 216
Cdd:pfam12894   1 MSWCPTM-DLIALATEDGELLLHrlnwQRVWTLSPDKE---DLEVTSLAWRPDGKLLAVGYSDGTV 62
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 94-265 1.30e-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: 43.48  E-value: 1.30e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A       94 PIHHLALSCDNLTLSACMMSSEygsiIAFFDVRTFsneakQQKRPFAYHKllkdagGMVIDMKWNPTvPSMVAVCLADGS 173
Cdd:cd00200  95 YVSSVAFSPDGRILSSSSRDKT----IKVWDVETG-----KCLTTLRGHT------DWVNSVAFSPD-GTFVASSSQDGT 158

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A      174 IAVLQVtETVKVCATLPS-TVAVTSVCWSPKGKQLAVGKQNGTVVQY-LPTLQEKKVIPCppfyesdHPVRVLDVLWIGT 251
Cdd:cd00200 159 IKLWDL-RTGKCVATLTGhTGEVNSVAFSPDGEKLLSSSSDGTIKLWdLSTGKCLGTLRG-------HENGVNSVAFSPD 230

                       170
                ....*....|....
3FMO_A      252 YVFAIVyAAADGTL 265
Cdd:cd00200 231 GYLLAS-GSEDGTI 243
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 94-216 1.93e-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: 43.09  E-value: 1.93e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A       94 PIHHLALSCDNLTLSACmmSSEygSIIAFFDVRTFsneakQQKRPFAYHKllkdagGMVIDMKWNPTvPSMVAVCLADGS 173
Cdd:cd00200 179 EVNSVAFSPDGEKLLSS--SSD--GTIKLWDLSTG-----KCLGTLRGHE------NGVNSVAFSPD-GYLLASGSEDGT 242

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
3FMO_A      174 IAVLQVtETVKVCATLPS-TVAVTSVCWSPKGKQLAVGKQNGTV 216
Cdd:cd00200 243 IRVWDL-RTGECVQTLSGhTNSVTSLAWSPDGKRLASGSADGTI 285
WD40 COG2319
WD40 repeat [General function prediction only];
143-265 1.08e-03

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 41.05  E-value: 1.08e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A      143 KLLKDAGGMVIDMKWNPTvPSMVAVCLADGSIAVLQVtETVKVCATLP-STVAVTSVCWSPKGKQLAVGKQNGTVVQY-L 220
Cdd:COG2319 282 RTLTGHSGGVNSVAFSPD-GKLLASGSDDGTVRLWDL-ATGKLLRTLTgHTGAVRSVAFSPDGKTLASGSDDGTVRLWdL 359

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
3FMO_A      221 PTLQEKKVIpcppfyeSDHPVRVLDVLWI--GTYvfaIVYAAADGTL 265
Cdd:COG2319 360 ATGELLRTL-------TGHTGAVTSVAFSpdGRT---LASGSADGTV 396
 
Name Accession Description Interval E-value
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 155-216 7.64e-05

Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 41.49  E-value: 7.64e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
3FMO_A        155 MKWNPTVpSMVAVCLADGSIAVL----QVTETVKVCATlpsTVAVTSVCWSPKGKQLAVGKQNGTV 216
Cdd:pfam12894   1 MSWCPTM-DLIALATEDGELLLHrlnwQRVWTLSPDKE---DLEVTSLAWRPDGKLLAVGYSDGTV 62
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 94-265 1.30e-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: 43.48  E-value: 1.30e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A       94 PIHHLALSCDNLTLSACMMSSEygsiIAFFDVRTFsneakQQKRPFAYHKllkdagGMVIDMKWNPTvPSMVAVCLADGS 173
Cdd:cd00200  95 YVSSVAFSPDGRILSSSSRDKT----IKVWDVETG-----KCLTTLRGHT------DWVNSVAFSPD-GTFVASSSQDGT 158

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A      174 IAVLQVtETVKVCATLPS-TVAVTSVCWSPKGKQLAVGKQNGTVVQY-LPTLQEKKVIPCppfyesdHPVRVLDVLWIGT 251
Cdd:cd00200 159 IKLWDL-RTGKCVATLTGhTGEVNSVAFSPDGEKLLSSSSDGTIKLWdLSTGKCLGTLRG-------HENGVNSVAFSPD 230

                       170
                ....*....|....
3FMO_A      252 YVFAIVyAAADGTL 265
Cdd:cd00200 231 GYLLAS-GSEDGTI 243
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 94-216 1.93e-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: 43.09  E-value: 1.93e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A       94 PIHHLALSCDNLTLSACmmSSEygSIIAFFDVRTFsneakQQKRPFAYHKllkdagGMVIDMKWNPTvPSMVAVCLADGS 173
Cdd:cd00200 179 EVNSVAFSPDGEKLLSS--SSD--GTIKLWDLSTG-----KCLGTLRGHE------NGVNSVAFSPD-GYLLASGSEDGT 242

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
3FMO_A      174 IAVLQVtETVKVCATLPS-TVAVTSVCWSPKGKQLAVGKQNGTV 216
Cdd:cd00200 243 IRVWDL-RTGECVQTLSGhTNSVTSLAWSPDGKRLASGSADGTI 285
WD40 COG2319
WD40 repeat [General function prediction only];
143-265 1.08e-03

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 41.05  E-value: 1.08e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A      143 KLLKDAGGMVIDMKWNPTvPSMVAVCLADGSIAVLQVtETVKVCATLP-STVAVTSVCWSPKGKQLAVGKQNGTVVQY-L 220
Cdd:COG2319 282 RTLTGHSGGVNSVAFSPD-GKLLASGSDDGTVRLWDL-ATGKLLRTLTgHTGAVRSVAFSPDGKTLASGSDDGTVRLWdL 359

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
3FMO_A      221 PTLQEKKVIpcppfyeSDHPVRVLDVLWI--GTYvfaIVYAAADGTL 265
Cdd:COG2319 360 ATGELLRTL-------TGHTGAVTSVAFSpdGRT---LASGSADGTV 396
WD40 COG2319
WD40 repeat [General function prediction only];
164-265 1.79e-03

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 40.28  E-value: 1.79e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3FMO_A      164 MVAVCLADGSIAVLQVtETVKVCATLP-STVAVTSVCWSPKGKQLAVGKQNGTVVQY-LPTLQEKKVIPcppfyesDHPV 241
Cdd:COG2319 176 LLASGSDDGTVRLWDL-ATGKLLRTLTgHTGAVRSVAFSPDGKLLASGSADGTVRLWdLATGKLLRTLT-------GHSG 247

                        90       100
                ....*....|....*....|....*.
3FMO_A      242 RVLDVLWI--GTYvfaIVYAAADGTL 265
Cdd:COG2319 248 SVRSVAFSpdGRL---LASGSADGTV 270
 
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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