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Conserved domains on  [gi|195972894|ref|NP_689977|]
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meiosis-specific with OB domain-containing protein isoform 2 [Homo sapiens]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 13514490)

single-stranded DNA (ssDNA)-binding protein plays a key role in DNA replication, recombination, and repair

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA1_DBD_B cd04475
RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding ...
 167-270 1.14e-18

RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can.


:

Pssm-ID: 239921 [Multi-domain]  Cd Length: 101  Bit Score: 80.71  E-value: 1.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894 167 IINVLAAVKSVGEPKYFTT-SDRRKGQRCEVRLYDETESSFAMTCWDNESILLAQSWmprETVIFASDVRINFDkfrNCM 245
Cdd:cd04475    1 IVDVIGVVKSVGPVTTITTkSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSE---NPVIAIKGVKVSEF---NGK 74

                         90       100
                 ....*....|....*....|....*
gi 195972894 246 TATVISKTIITTNPDIPEANILLNF 270
Cdd:cd04475   75 SLSTGSSSTIIINPDIPEAHKLRGW 99
rpa1 super family cl36710
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
 149-406 6.85e-10

replication factor-a protein 1 (rpa1); All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1, RPA2 and RPA3 that bind ssDNA and function in the recognition of DNA damage for nucleotide excision repairThis family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00617:

Pssm-ID: 273177 [Multi-domain]  Cd Length: 608  Bit Score: 60.90  E-value: 6.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  149 DYYSLGDIvanGHSLNGRIINVLAAVKSVGEPKYFTTS-DRRKGQRCEVRLYDETESSFAMTCWDNESILLAqswMPRET 227
Cdd:TIGR00617 297 NFVKIDDI---GGYEGNSLVDVIGIVQSVSPTQTITSRkNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFD---VSVQP 370

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  228 VIFASDVRIN-FDKFrncmTATVISKTIITTNPDIPEANILLN-FIRENKETnvlDDEIDSYFKESINLSTIVDVYTVEQ 305
Cdd:TIGR00617 371 VIAIKGVRVSdFGGK----SLSTGGSSTIIVNPDIPEAEKLKGwYDNEGKGT---MASSISDMMSGRVGGSNAERKTIAE 443

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  306 LKGKALkneGKAD-PSYGILYAYISTLNIDDettkVVRNRCSS--CGYIVNEASN---MCTTCNKNSLDFKSVFLsfhVL 379
Cdd:TIGR00617 444 IQAENL---GKSDkPDYFSVKATISYLKPDN----ALYRACPSedCNKKVVDQGDgtyRCEKCNKNFAEFKYRYI---LQ 513

                         250       260
                  ....*....|....*....|....*..
gi 195972894  380 IDLTDHTGTLHsCSLTGSVAEETLGCT 406
Cdd:TIGR00617 514 ISISDETGQLW-VTAFNDQAEQILGKS 539
 
Name Accession Description Interval E-value
RPA1_DBD_B cd04475
RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding ...
 167-270 1.14e-18

RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can.


Pssm-ID: 239921 [Multi-domain]  Cd Length: 101  Bit Score: 80.71  E-value: 1.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894 167 IINVLAAVKSVGEPKYFTT-SDRRKGQRCEVRLYDETESSFAMTCWDNESILLAQSWmprETVIFASDVRINFDkfrNCM 245
Cdd:cd04475    1 IVDVIGVVKSVGPVTTITTkSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSE---NPVIAIKGVKVSEF---NGK 74

                         90       100
                 ....*....|....*....|....*
gi 195972894 246 TATVISKTIITTNPDIPEANILLNF 270
Cdd:cd04475   75 SLSTGSSSTIIINPDIPEAHKLRGW 99
rpa1 TIGR00617
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
 149-406 6.85e-10

replication factor-a protein 1 (rpa1); All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1, RPA2 and RPA3 that bind ssDNA and function in the recognition of DNA damage for nucleotide excision repairThis family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273177 [Multi-domain]  Cd Length: 608  Bit Score: 60.90  E-value: 6.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  149 DYYSLGDIvanGHSLNGRIINVLAAVKSVGEPKYFTTS-DRRKGQRCEVRLYDETESSFAMTCWDNESILLAqswMPRET 227
Cdd:TIGR00617 297 NFVKIDDI---GGYEGNSLVDVIGIVQSVSPTQTITSRkNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFD---VSVQP 370

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  228 VIFASDVRIN-FDKFrncmTATVISKTIITTNPDIPEANILLN-FIRENKETnvlDDEIDSYFKESINLSTIVDVYTVEQ 305
Cdd:TIGR00617 371 VIAIKGVRVSdFGGK----SLSTGGSSTIIVNPDIPEAEKLKGwYDNEGKGT---MASSISDMMSGRVGGSNAERKTIAE 443

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  306 LKGKALkneGKAD-PSYGILYAYISTLNIDDettkVVRNRCSS--CGYIVNEASN---MCTTCNKNSLDFKSVFLsfhVL 379
Cdd:TIGR00617 444 IQAENL---GKSDkPDYFSVKATISYLKPDN----ALYRACPSedCNKKVVDQGDgtyRCEKCNKNFAEFKYRYI---LQ 513

                         250       260
                  ....*....|....*....|....*..
gi 195972894  380 IDLTDHTGTLHsCSLTGSVAEETLGCT 406
Cdd:TIGR00617 514 ISISDETGQLW-VTAFNDQAEQILGKS 539
REPA_OB_2 pfam16900
Replication protein A OB domain; Replication protein A contains two OB domains in it's DNA ...
 164-229 1.82e-03

Replication protein A OB domain; Replication protein A contains two OB domains in it's DNA binding region. This is the second of the OB domains.


Pssm-ID: 465304 [Multi-domain]  Cd Length: 98  Bit Score: 37.40  E-value: 1.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 195972894  164 NGRIINVLAAVKSVGEPKYFTT-SDRRKGQRCEVRLYDETESSFAMTCWDNEsillAQSW-MPRETVI 229
Cdd:pfam16900   9 KDSIVDVIGVVKSVGPVTEITSkSTGKETDKRELTLVDDSGRSVRLTLWGKE----AEQFdSSENPVV 72
 
Name Accession Description Interval E-value
RPA1_DBD_B cd04475
RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding ...
 167-270 1.14e-18

RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can.


Pssm-ID: 239921 [Multi-domain]  Cd Length: 101  Bit Score: 80.71  E-value: 1.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894 167 IINVLAAVKSVGEPKYFTT-SDRRKGQRCEVRLYDETESSFAMTCWDNESILLAQSWmprETVIFASDVRINFDkfrNCM 245
Cdd:cd04475    1 IVDVIGVVKSVGPVTTITTkSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSE---NPVIAIKGVKVSEF---NGK 74

                         90       100
                 ....*....|....*....|....*
gi 195972894 246 TATVISKTIITTNPDIPEANILLNF 270
Cdd:cd04475   75 SLSTGSSSTIIINPDIPEAHKLRGW 99
rpa1 TIGR00617
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
 149-406 6.85e-10

replication factor-a protein 1 (rpa1); All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1, RPA2 and RPA3 that bind ssDNA and function in the recognition of DNA damage for nucleotide excision repairThis family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273177 [Multi-domain]  Cd Length: 608  Bit Score: 60.90  E-value: 6.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  149 DYYSLGDIvanGHSLNGRIINVLAAVKSVGEPKYFTTS-DRRKGQRCEVRLYDETESSFAMTCWDNESILLAqswMPRET 227
Cdd:TIGR00617 297 NFVKIDDI---GGYEGNSLVDVIGIVQSVSPTQTITSRkNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFD---VSVQP 370

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  228 VIFASDVRIN-FDKFrncmTATVISKTIITTNPDIPEANILLN-FIRENKETnvlDDEIDSYFKESINLSTIVDVYTVEQ 305
Cdd:TIGR00617 371 VIAIKGVRVSdFGGK----SLSTGGSSTIIVNPDIPEAEKLKGwYDNEGKGT---MASSISDMMSGRVGGSNAERKTIAE 443

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894  306 LKGKALkneGKAD-PSYGILYAYISTLNIDDettkVVRNRCSS--CGYIVNEASN---MCTTCNKNSLDFKSVFLsfhVL 379
Cdd:TIGR00617 444 IQAENL---GKSDkPDYFSVKATISYLKPDN----ALYRACPSedCNKKVVDQGDgtyRCEKCNKNFAEFKYRYI---LQ 513

                         250       260
                  ....*....|....*....|....*..
gi 195972894  380 IDLTDHTGTLHsCSLTGSVAEETLGCT 406
Cdd:TIGR00617 514 ISISDETGQLW-VTAFNDQAEQILGKS 539
REPA_OB_2 pfam16900
Replication protein A OB domain; Replication protein A contains two OB domains in it's DNA ...
 164-229 1.82e-03

Replication protein A OB domain; Replication protein A contains two OB domains in it's DNA binding region. This is the second of the OB domains.


Pssm-ID: 465304 [Multi-domain]  Cd Length: 98  Bit Score: 37.40  E-value: 1.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 195972894  164 NGRIINVLAAVKSVGEPKYFTT-SDRRKGQRCEVRLYDETESSFAMTCWDNEsillAQSW-MPRETVI 229
Cdd:pfam16900   9 KDSIVDVIGVVKSVGPVTEITSkSTGKETDKRELTLVDDSGRSVRLTLWGKE----AEQFdSSENPVV 72
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 169-256 9.15e-03

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 35.29  E-value: 9.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 195972894 169 NVLAAVKSVGEPKYFTTsDRRKGQRCEVRLYDETeSSFAMTCWDNESILLAQswmPRETVIFaSDVRInfDKFRNCMTAT 248
Cdd:cd04491    1 SVEGKVLSISEPREFTR-DGSEGKVQSGLVGDET-GTIRFTLWDEKAADDLE---PGDVVRI-ENAYV--REFNGRLELS 72


                 ....*...
gi 195972894 249 VISKTIIT 256
Cdd:cd04491   73 VGKNSEIE 80
 
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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