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Conserved domains on  [gi|386781235|ref|NP_001247405|]
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tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 3 [Homo sapiens]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 1000017)

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 ...
 4-154 3.48e-13

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: 67.75  E-value: 3.48e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386781235   4 DVAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTQpGLLLSSSGDGTLRLWEYRSGRQLHCC-- 81
Cdd:cd00200  140 SVAFSPDGTFVASSSQDGTIKL-WDLRTGKCVATLTGHTGEVNSVAFSPDG-EKLLSSSSDGTIKLWDLSTGKCLGTLrg 217

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 386781235  82 HLASLQELVdpqapqkFAASRiafwcqENCVALLCDGTpvVYIFQLDARRQQLVYRqqlAFQHQVWDVAFEET 154
Cdd:cd00200  218 HENGVNSVA-------FSPDG------YLLASGSEDGT--IRVWDLRTGECVQTLS---GHTNSVTSLAWSPD 272
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 4-154 3.48e-13

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: 67.75  E-value: 3.48e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386781235   4 DVAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTQpGLLLSSSGDGTLRLWEYRSGRQLHCC-- 81
Cdd:cd00200  140 SVAFSPDGTFVASSSQDGTIKL-WDLRTGKCVATLTGHTGEVNSVAFSPDG-EKLLSSSSDGTIKLWDLSTGKCLGTLrg 217

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 386781235  82 HLASLQELVdpqapqkFAASRiafwcqENCVALLCDGTpvVYIFQLDARRQQLVYRqqlAFQHQVWDVAFEET 154
Cdd:cd00200  218 HENGVNSVA-------FSPDG------YLLASGSEDGT--IRVWDLRTGECVQTLS---GHTNSVTSLAWSPD 272
WD40 COG2319
WD40 repeat [General function prediction only];
4-79 6.19e-10

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 58.77  E-value: 6.19e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386781235   4 DVAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTQpGLLLSSSGDGTLRLWEYRSGRQLH 79
Cdd:COG2319  167 SVAFSPDGKLLASGSDDGTVRL-WDLATGKLLRTLTGHTGAVRSVAFSPDG-KLLASGSADGTVRLWDLATGKLLR 240
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 40-71 1.96e-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: 1.96e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 386781235    40 GHTEFVSRISVVPTQPgLLLSSSGDGTLRLWE 71
Cdd:smart00320  10 GHTGPVTSVAFSPDGK-YLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
40-71 3.64e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 34.63  E-value: 3.64e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 386781235   40 GHTEFVSRISVVPTQPgLLLSSSGDGTLRLWE 71
Cdd:pfam00400   9 GHTGSVTSLAFSPDGK-LLASGSDDGTVKVWD 39
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 4-154 3.48e-13

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: 67.75  E-value: 3.48e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386781235   4 DVAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTQpGLLLSSSGDGTLRLWEYRSGRQLHCC-- 81
Cdd:cd00200  140 SVAFSPDGTFVASSSQDGTIKL-WDLRTGKCVATLTGHTGEVNSVAFSPDG-EKLLSSSSDGTIKLWDLSTGKCLGTLrg 217

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 386781235  82 HLASLQELVdpqapqkFAASRiafwcqENCVALLCDGTpvVYIFQLDARRQQLVYRqqlAFQHQVWDVAFEET 154
Cdd:cd00200  218 HENGVNSVA-------FSPDG------YLLASGSEDGT--IRVWDLRTGECVQTLS---GHTNSVTSLAWSPD 272
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 5-79 2.80e-10

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: 59.27  E-value: 2.80e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 386781235   5 VAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTQPgLLLSSSGDGTLRLWEYRSGRQLH 79
Cdd:cd00200   15 VAFSPDGKLLATGSGDGTIKV-WDLETGELLRTLKGHTGPVRDVAASADGT-YLASGSSDKTIRLWDLETGECVR 87
WD40 COG2319
WD40 repeat [General function prediction only];
4-79 6.19e-10

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 58.77  E-value: 6.19e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386781235   4 DVAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTQpGLLLSSSGDGTLRLWEYRSGRQLH 79
Cdd:COG2319  167 SVAFSPDGKLLASGSDDGTVRL-WDLATGKLLRTLTGHTGAVRSVAFSPDG-KLLASGSADGTVRLWDLATGKLLR 240
WD40 COG2319
WD40 repeat [General function prediction only];
3-79 7.11e-10

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 58.77  E-value: 7.11e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 386781235   3 LDVAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTqpG-LLLSSSGDGTLRLWEYRSGRQLH 79
Cdd:COG2319  250 RSVAFSPDGRLLASGSADGTVRL-WDLATGELLRTLTGHSGGVNSVAFSPD--GkLLASGSDDGTVRLWDLATGKLLR 324
WD40 COG2319
WD40 repeat [General function prediction only];
5-79 4.83e-09

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 56.07  E-value: 4.83e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386781235   5 VAVSPDDRFILTADRDEKIRVsW-AAAPHSIESFcLGHTEFVSRISVVPTqpG-LLLSSSGDGTLRLWEYRSGRQLH 79
Cdd:COG2319  126 VAFSPDGKTLASGSADGTVRL-WdLATGKLLRTL-TGHSGAVTSVAFSPD--GkLLASGSDDGTVRLWDLATGKLLR 198
WD40 COG2319
WD40 repeat [General function prediction only];
5-79 6.54e-09

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 55.69  E-value: 6.54e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 386781235   5 VAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPtQPGLLLSSSGDGTLRLWEYRSGRQLH 79
Cdd:COG2319  294 VAFSPDGKLLASGSDDGTVRL-WDLATGKLLRTLTGHTGAVRSVAFSP-DGKTLASGSDDGTVRLWDLATGELLR 366
WD40 COG2319
WD40 repeat [General function prediction only];
5-70 1.93e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 54.53  E-value: 1.93e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386781235   5 VAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTQPgLLLSSSGDGTLRLW 70
Cdd:COG2319  336 VAFSPDGKTLASGSDDGTVRL-WDLATGELLRTLTGHTGAVTSVAFSPDGR-TLASGSADGTVRLW 399
WD40 COG2319
WD40 repeat [General function prediction only];
5-79 2.04e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 54.53  E-value: 2.04e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 386781235   5 VAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTQpGLLLSSSGDGTLRLWEYRSGRQLH 79
Cdd:COG2319   84 VAFSPDGRLLASASADGTVRL-WDLATGLLLRTLTGHTGAVRSVAFSPDG-KTLASGSADGTVRLWDLATGKLLR 156
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 2-85 2.80e-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: 50.41  E-value: 2.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386781235   2 LLDVAVSPDDRFILTADRDEKIRVSWAAAPHSIESFcLGHTEFVSRISVVPTQPgLLLSSSGDGTLRLWEYRSGRQLHC- 80
Cdd:cd00200   54 VRDVAASADGTYLASGSSDKTIRLWDLETGECVRTL-TGHTSYVSSVAFSPDGR-ILSSSSRDKTIKVWDVETGKCLTTl 131


                 ....*.
gi 386781235  81 -CHLAS 85
Cdd:cd00200  132 rGHTDW 137
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 5-71 5.44e-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: 46.56  E-value: 5.44e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386781235   5 VAVSPDDRFILTADRDEKIRVsWAAAPHSIESFCLGHTEFVSRISVVPTqPGLLLSSSGDGTLRLWE 71
Cdd:cd00200  225 VAFSPDGYLLASGSEDGTIRV-WDLRTGECVQTLSGHTNSVTSLAWSPD-GKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 40-80 9.74e-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: 39.63  E-value: 9.74e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 386781235  40 GHTEFVSRISVVPtQPGLLLSSSGDGTLRLWEYRSGRQLHC 80
Cdd:cd00200    7 GHTGGVTCVAFSP-DGKLLATGSGDGTIKVWDLETGELLRT 46
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 40-71 1.96e-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: 1.96e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 386781235    40 GHTEFVSRISVVPTQPgLLLSSSGDGTLRLWE 71
Cdd:smart00320  10 GHTGPVTSVAFSPDGK-YLASGSDDGTIKLWD 40
WD40 pfam00400
WD domain, G-beta repeat;
40-71 3.64e-03

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 34.63  E-value: 3.64e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 386781235   40 GHTEFVSRISVVPTQPgLLLSSSGDGTLRLWE 71
Cdd:pfam00400   9 GHTGSVTSLAFSPDGK-LLASGSDDGTVKVWD 39
 
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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