NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|56550086|ref|NP_001008397|]
View 

WD repeat and HMG-box DNA-binding protein 1 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
 308-591 4.12e-123

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


:

Pssm-ID: 463539  Cd Length: 288  Bit Score: 376.53  E-value: 4.12e-123
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    308 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 385
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    386 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 465
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    466 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 542
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 56550086    543 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 591
Cdd:pfam12341  239 LLLRkgGKSDTYWPVGVSE--DKLRCIICKGGeKYPGFLPRPLLSELPLKLP 288
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 891-953 5.55e-25

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


:

Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 98.48  E-value: 5.55e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56550086  891 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 953
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 5-165 3.24e-22

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: 98.18  E-value: 3.24e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    5 QQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIP 82
Cdd:cd00200  127 CLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSS 196

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086   83 VEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWH 159
Cdd:cd00200  197 SDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWS 270


                 ....*.
gi 56550086  160 PTCGRI 165
Cdd:cd00200  271 PDGKRL 276
 
Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
 308-591 4.12e-123

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


Pssm-ID: 463539  Cd Length: 288  Bit Score: 376.53  E-value: 4.12e-123
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    308 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 385
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    386 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 465
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    466 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 542
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 56550086    543 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 591
Cdd:pfam12341  239 LLLRkgGKSDTYWPVGVSE--DKLRCIICKGGeKYPGFLPRPLLSELPLKLP 288
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 891-953 5.55e-25

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 98.48  E-value: 5.55e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56550086  891 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 953
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 5-165 3.24e-22

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: 98.18  E-value: 3.24e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    5 QQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIP 82
Cdd:cd00200  127 CLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSS 196

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086   83 VEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWH 159
Cdd:cd00200  197 SDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWS 270


                 ....*.
gi 56550086  160 PTCGRI 165
Cdd:cd00200  271 PDGKRL 276
WD40 COG2319
WD40 repeat [General function prediction only];
7-160 1.09e-18

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 89.59  E-value: 1.09e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    7 KTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCAISwplLQKCNDVINAksicrLAWQPkSGKLLAIPVE-K 85
Cdd:COG2319  156 RTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRT---LTGHTGAVRS-----VAFSP-DGKLLASGSAdG 226

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56550086   86 SVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 160
Cdd:COG2319  227 TVRLWDLATGKLLRTLTGH--SGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSG-GVNSVAFSP 298
HMG smart00398
high mobility group;
894-951 2.15e-09

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 54.63  E-value: 2.15e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 56550086     894 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKGETA 951
Cdd:smart00398    4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 2-40 3.61e-08

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: 50.39  E-value: 3.61e-08
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 56550086       2 DSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 40
Cdd:smart00320    1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
3-40 3.80e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 50.04  E-value: 3.80e-08
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 56550086      3 SSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 40
Cdd:pfam00400    1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
893-988 2.69e-04

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 43.31  E-value: 2.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086  893 QRPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetaSEGTEAKKRKRVVDESDETEN 972
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                         90
                 ....*....|....*.
gi 56550086  973 QEEKAKENLNLSKKQK 988
Cdd:COG5648  147 PIGPFIENEPKIRPKV 162
 
Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
 308-591 4.12e-123

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


Pssm-ID: 463539  Cd Length: 288  Bit Score: 376.53  E-value: 4.12e-123
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    308 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 385
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    386 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 465
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    466 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 542
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 56550086    543 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 591
Cdd:pfam12341  239 LLLRkgGKSDTYWPVGVSE--DKLRCIICKGGeKYPGFLPRPLLSELPLKLP 288
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 891-953 5.55e-25

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 98.48  E-value: 5.55e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56550086  891 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 953
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 5-165 3.24e-22

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: 98.18  E-value: 3.24e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    5 QQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIP 82
Cdd:cd00200  127 CLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSS 196

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086   83 VEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWH 159
Cdd:cd00200  197 SDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWS 270


                 ....*.
gi 56550086  160 PTCGRI 165
Cdd:cd00200  271 PDGKRL 276
WD40 COG2319
WD40 repeat [General function prediction only];
7-160 1.09e-18

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 89.59  E-value: 1.09e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    7 KTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCAISwplLQKCNDVINAksicrLAWQPkSGKLLAIPVE-K 85
Cdd:COG2319  156 RTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRT---LTGHTGAVRS-----VAFSP-DGKLLASGSAdG 226

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56550086   86 SVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 160
Cdd:COG2319  227 TVRLWDLATGKLLRTLTGH--SGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSG-GVNSVAFSP 298
WD40 COG2319
WD40 repeat [General function prediction only];
7-160 1.17e-17

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 86.50  E-value: 1.17e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    7 KTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCAISWPLlqkcndviNAKSICRLAWQPkSGKLLAI-PVEK 85
Cdd:COG2319  198 RTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTG--------HSGSVRSVAFSP-DGRLLASgSADG 268

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56550086   86 SVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 160
Cdd:COG2319  269 TVRLWDLATGELLRTLTGH--SGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTG-AVRSVAFSP 340
WD40 COG2319
WD40 repeat [General function prediction only];
5-160 3.68e-17

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 84.96  E-value: 3.68e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    5 QQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCaisWPLLQKCNDVINAksicrLAWQPkSGKLLAIPVE 84
Cdd:COG2319  238 LLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGEL---LRTLTGHSGGVNS-----VAFSP-DGKLLASGSD 308

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56550086   85 -KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVK-HEKgyAICGLAWHP 160
Cdd:COG2319  309 dGTVRLWDLATGKLLRTLTGH--TGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTgHTG--AVTSVAFSP 382
WD40 COG2319
WD40 repeat [General function prediction only];
8-160 4.34e-16

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 81.50  E-value: 4.34e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    8 TFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCAISWPLLQkcnDVINAksicrLAWQPkSGKLLAI-PVEKS 86
Cdd:COG2319  115 TLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHS---GAVTS-----VAFSP-DGKLLASgSDDGT 185

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56550086   87 VKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 160
Cdd:COG2319  186 VRLWDLATGKLLRTLTGH--TGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSG-SVRSVAFSP 256
WD40 COG2319
WD40 repeat [General function prediction only];
2-160 6.42e-14

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 74.95  E-value: 6.42e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    2 DSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCAiswPLLQKCNDVINAksicrLAWQPKSGKLLAI 81
Cdd:COG2319   67 AGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATGLLL---RTLTGHTGAVRS-----VAFSPDGKTLASG 138

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56550086   82 PVEKSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 160
Cdd:COG2319  139 SADGTVRLWDLATGKLLRTLTGH--SGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTG-AVRSVAFSP 214
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 4-165 1.13e-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: 72.75  E-value: 1.13e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    4 SQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCAISwpLLQKCNDVinaksICrLAWQPKSGKLLAIPV 83
Cdd:cd00200   42 ELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRT--LTGHTSYV-----SS-VAFSPDGRILSSSSR 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086   84 EKSVKLYRRESWSHQFDLSDnfISQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKHEKGYaICGLAWHPTCG 163
Cdd:cd00200  114 DKTIKVWDVETGKCLTTLRG--HTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGE-VNSVAFSPDGE 190


                 ..
gi 56550086  164 RI 165
Cdd:cd00200  191 KL 192
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 7-135 4.93e-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: 70.83  E-value: 4.93e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    7 KTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCAISwplLQKCNDVINAksicrLAWQPKSGKLLAIPVEKS 86
Cdd:cd00200  171 ATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGT---LRGHENGVNS-----VAFSPDGYLLASGSEDGT 242

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 56550086   87 VKLYRRESWSHQFDLS--DNFISQtlniVTWSPCGQYLAAGSINGLIIVWN 135
Cdd:cd00200  243 IRVWDLRTGECVQTLSghTNSVTS----LAWSPDGKRLASGSADGTIRIWD 289
WD40 COG2319
WD40 repeat [General function prediction only];
7-138 3.70e-12

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 69.55  E-value: 3.70e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    7 KTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDQTCAISWPllqkcndvINAKSICRLAWQPKsGKLLAIPVE-K 85
Cdd:COG2319  282 RTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLT--------GHTGAVRSVAFSPD-GKTLASGSDdG 352

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 56550086   86 SVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLAAGSINGLIIVWNVET 138
Cdd:COG2319  353 TVRLWDLATGELLRTLTGH--TGAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
HMG smart00398
high mobility group;
894-951 2.15e-09

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 54.63  E-value: 2.15e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 56550086     894 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKGETA 951
Cdd:smart00398    4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 2-40 3.61e-08

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: 50.39  E-value: 3.61e-08
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 56550086       2 DSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 40
Cdd:smart00320    1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
3-40 3.80e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 50.04  E-value: 3.80e-08
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 56550086      3 SSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 40
Cdd:pfam00400    1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 894-960 5.53e-08

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 50.37  E-value: 5.53e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56550086  894 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetasegtEAKKR 960
Cdd:cd21994    1 RPMSAYMLWLNENREKIKKENPGIS-VTEISKKAGEIWKELDEEDKEKWEQKAE--------KAKER 58
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 4-91 3.98e-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: 52.72  E-value: 3.98e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086    4 SQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAI 81
Cdd:cd00200  210 KCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRT----------GECVQTLSGhtNSVTSLAWSPDGKRLASG 279

                         90
                 ....*....|
gi 56550086   82 PVEKSVKLYR 91
Cdd:cd00200  280 SADGTIRIWD 289
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 894-947 1.03e-06

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 46.74  E-value: 1.03e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 56550086  894 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAK 947
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKKENPDLS-FTEISKLLGERWKELSEEEKQPYEEKAK 53
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
893-988 2.69e-04

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 43.31  E-value: 2.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086  893 QRPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetaSEGTEAKKRKRVVDESDETEN 972
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                         90
                 ....*....|....*.
gi 56550086  973 QEEKAKENLNLSKKQK 988
Cdd:COG5648  147 PIGPFIENEPKIRPKV 162
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 893-966 9.85e-04

first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438822 [Multi-domain]  Cd Length: 68  Bit Score: 38.59  E-value: 9.85e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56550086  893 QRPKTGFQMWLEENRSNILSDNP--DFSDEADIIKEgmiRFRVLSTEERKVWANKAKgetasegTEAKKRKRVVDE 966
Cdd:cd22006    1 KKPKTAYFLWCKDQREEVKKENPnaDFSEVSKILGA---KWKNLSEEEKKPYEEKYK-------EEKEKYLKVVGE 66
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 69-158 1.40e-03

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: 38.80  E-value: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086     69 LAWQPKSgKLLAIPVEK-SVKLYRReSWSHQFDLSDNFISQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKH 147
Cdd:pfam12894    1 MSWCPTM-DLIALATEDgELLLHRL-NWQRVWTLSPDKEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSA 78

                           90
                   ....*....|.
gi 56550086    148 EKGYAICgLAW 158
Cdd:pfam12894   79 GSDLITC-LGW 88
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
 70-161 1.48e-03

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 462552 [Multi-domain]  Cd Length: 194  Bit Score: 40.72  E-value: 1.48e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56550086     70 AWQPKSGKLLAI--PVEKSVKLYrreswSHQFDLSDNFISQTLNIVTWSPCGQYLAA---GSINGLIIVWNVETKDCMER 144
Cdd:pfam08662   66 AWSPNGKEFAVIygYMPAKVSFF-----DLKGNVIHSFGEQPRNTIFWSPFGRLVLLagfGNLAGDIEFWDVVNKKKIAT 140

                           90
                   ....*....|....*..
gi 56550086    145 VKHEKGyaiCGLAWHPT 161
Cdd:pfam08662  141 AEASNA---TLCEWSPD 154
 
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