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Conserved domains on  [gi|767979579|ref|XP_011534675|]
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WD repeat and HMG-box DNA-binding protein 1 isoform X2 [Homo sapiens]

Protein Classification

Graphical summary

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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 ...
 68-351 1.42e-125

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: 1.42e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579   68 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 145
Cdd:pfam12341   1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579  146 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 225
Cdd:pfam12341  81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579  226 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 302
Cdd:pfam12341 161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767979579  303 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 351
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 ...
 651-713 4.03e-24

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: 95.79  E-value: 4.03e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767979579 651 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 713
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
 
Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
 68-351 1.42e-125

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: 1.42e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579   68 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 145
Cdd:pfam12341   1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579  146 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 225
Cdd:pfam12341  81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579  226 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 302
Cdd:pfam12341 161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767979579  303 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 351
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 ...
 651-713 4.03e-24

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: 95.79  E-value: 4.03e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767979579 651 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 713
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
HMG smart00398
high mobility group;
654-711 6.20e-09

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 53.09  E-value: 6.20e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 767979579   654 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKGETA 711
Cdd:smart00398   4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
653-748 9.09e-04

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 41.39  E-value: 9.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579 653 QRPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetaSEGTEAKKRKRVVDESDETEN 732
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                         90
                 ....*....|....*.
gi 767979579 733 QEEKAKENLNLSKKQK 748
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 ...
 68-351 1.42e-125

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: 1.42e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579   68 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 145
Cdd:pfam12341   1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579  146 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 225
Cdd:pfam12341  81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579  226 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 302
Cdd:pfam12341 161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767979579  303 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 351
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 ...
 651-713 4.03e-24

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: 95.79  E-value: 4.03e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767979579 651 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 713
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
HMG smart00398
high mobility group;
654-711 6.20e-09

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 53.09  E-value: 6.20e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 767979579   654 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKGETA 711
Cdd:smart00398   4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 654-720 1.05e-07

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: 49.22  E-value: 1.05e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767979579 654 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetasegtEAKKR 720
Cdd:cd21994    1 RPMSAYMLWLNENREKIKKENPGIS-VTEISKKAGEIWKELDEEDKEKWEQKAE--------KAKER 58
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 654-707 1.83e-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: 45.59  E-value: 1.83e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767979579 654 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAK 707
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKKENPDLS-FTEISKLLGERWKELSEEEKQPYEEKAK 53
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
653-748 9.09e-04

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 41.39  E-value: 9.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767979579 653 QRPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetaSEGTEAKKRKRVVDESDETEN 732
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                         90
                 ....*....|....*.
gi 767979579 733 QEEKAKENLNLSKKQK 748
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 ...
 653-726 2.24e-03

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: 37.05  E-value: 2.24e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767979579 653 QRPKTGFQMWLEENRSNILSDNP--DFSDEADIIKEgmiRFRVLSTEERKVWANKAKgetasegTEAKKRKRVVDE 726
Cdd:cd22006    1 KKPKTAYFLWCKDQREEVKKENPnaDFSEVSKILGA---KWKNLSEEEKKPYEEKYK-------EEKEKYLKVVGE 66
 
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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