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Conserved domains on  [gi|119631243|gb|EAX10838|]
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oligonucleotide/oligosaccharide-binding fold containing 2A, isoform CRA_d [Homo sapiens]

Protein Classification

SOSS complex subunit B family protein( domain architecture ID 10139587)

SOSS complex subunit B family protein that contains an OB-fold nucleic acid binding domain; such as human SOSS complex subunit B2 (SSB2/NABP1), a component of the SOSS multiprotein complex that functions downstream of the MRN complex to promote DNA repair and G2/M checkpoint

Gene Ontology:  GO:0006281|GO:0005634|GO:0070876|GO:0003697
PubMed:  19683501|19683490

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 22-99 8.36e-21

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: 82.29  E-value: 8.36e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  22 NVVFIVLEIGRV-TKTKDGHE--VRSCKVADKTGSITISVWDE-IGGLIQPGDIIRLTRGYASMWKGCLTLYTGRGGELQ 97
Cdd:cd04491    1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                 ..
gi 119631243  98 KI 99
Cdd:cd04491   81 KL 82
 
Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 22-99 8.36e-21

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: 82.29  E-value: 8.36e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  22 NVVFIVLEIGRV-TKTKDGHE--VRSCKVADKTGSITISVWDE-IGGLIQPGDIIRLTRGYASMWKGCLTLYTGRGGELQ 97
Cdd:cd04491    1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                 ..
gi 119631243  98 KI 99
Cdd:cd04491   81 KL 82
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 11-110 1.17e-16

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 72.76  E-value: 1.17e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDG-HEVRSCKVADKTGSITISVWDEIGGLIQPGDIIRLTRGYASMWKGCLT 87
Cdd:PRK06461   7 IKDLKPGMERVNVTVRVLEVGepKVIQTKGGpRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQ 86

                         90       100
                 ....*....|....*....|...
gi 119631243  88 LYTGRGGELQKIGEfcmvySEVP 110
Cdd:PRK06461  87 LNVGKYGSISESDD-----EEVP 104
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
11-101 6.71e-13

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 65.47  E-value: 6.71e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDGHE--VRSCKVADKTGSITISVWDEIGGL-IQPGDIIRLTRGYASMWKGC 85
Cdd:COG1599   24 ISDLSPGDRDVNVEGRVLEIGeeRTFDRKDGSEgrVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVREFNGG 103

                         90
                 ....*....|....*.
gi 119631243  86 LTLYTGRGGELQKIGE 101
Cdd:COG1599  104 PELNLGERTTIEKLDE 119
 
Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 22-99 8.36e-21

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: 82.29  E-value: 8.36e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  22 NVVFIVLEIGRV-TKTKDGHE--VRSCKVADKTGSITISVWDE-IGGLIQPGDIIRLTRGYASMWKGCLTLYTGRGGELQ 97
Cdd:cd04491    1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                 ..
gi 119631243  98 KI 99
Cdd:cd04491   81 KL 82
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 11-110 1.17e-16

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 72.76  E-value: 1.17e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDG-HEVRSCKVADKTGSITISVWDEIGGLIQPGDIIRLTRGYASMWKGCLT 87
Cdd:PRK06461   7 IKDLKPGMERVNVTVRVLEVGepKVIQTKGGpRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQ 86

                         90       100
                 ....*....|....*....|...
gi 119631243  88 LYTGRGGELQKIGEfcmvySEVP 110
Cdd:PRK06461  87 LNVGKYGSISESDD-----EEVP 104
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
11-101 6.71e-13

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 65.47  E-value: 6.71e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDGHE--VRSCKVADKTGSITISVWDEIGGL-IQPGDIIRLTRGYASMWKGC 85
Cdd:COG1599   24 ISDLSPGDRDVNVEGRVLEIGeeRTFDRKDGSEgrVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVREFNGG 103

                         90
                 ....*....|....*.
gi 119631243  86 LTLYTGRGGELQKIGE 101
Cdd:COG1599  104 PELNLGERTTIEKLDE 119
PRK12366 PRK12366
replication factor A; Reviewed
 11-102 1.91e-08

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 53.51  E-value: 1.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDGHE--VRSCKVADKTGSITISVWDEIGGLI---QPGDIIRLTRGYASMWK 83
Cdd:PRK12366  66 ISDIEEGQINVEITGRIIEISniKTFTRKDGSTgkLANITIADNTGTIRLTLWNDNAKLLkglKEGDVIKIENARSRKWN 145

                         90
                 ....*....|....*....
gi 119631243  84 GCLTLYTGRGGELQKIGEF 102
Cdd:PRK12366 146 NDVELNSGSETRIDKLEKY 164
PRK07218 PRK07218
Single-stranded DNA binding protein;
11-84 1.83e-07

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 50.39  E-value: 1.83e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIGRVTKTKDG--HEVRSCKVADKTGSITISVWDEIGGliQPGDIIRLTRGYASMWKG 84
Cdd:PRK07218  61 IKELSTDDKNVTVTGRVLTIGERSIRYQGddHVIYEGILADETGTISYTAWKDFGL--SPGDTVTIGNAGVREWDG 134
YhaM COG3481
3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily ...
 10-88 3.89e-06

3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily [Translation, ribosomal structure and biogenesis]; 3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 442704 [Multi-domain]  Cd Length: 316  Bit Score: 46.34  E-value: 3.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  10 FIRDIKPGlKNLNVVFIVLEIgRVTKTKDGHEVRSCKVADKTGSITISVWD---EIGGLIQPGDIIRLtRGYASMWKGCL 86
Cdd:COG3481    6 FIKDLKPG-EEVDGFFLIKSK-ELRTTKNGKPYLSLTLQDKTGTIEAKIWDaseEDIEEFQPGDVVKV-RGKVQEYQGRL 82


                 ..
gi 119631243  87 TL 88
Cdd:COG3481   83 QL 84
PRK14699 PRK14699
replication factor A; Provisional
 11-79 4.31e-06

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 46.53  E-value: 4.31e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDGH--EVRSCKVADKTGSITISVWDEIGGL---IQPGDIIRLTRGYA 79
Cdd:PRK14699 169 IKDIKDGMGDLNLTGKVLEISeiRTFQRKDGTsgKVGNLLLGDETGTLRVTLWDDKTDFlnqIEYGDTVELINAYA 244
PRK12366 PRK12366
replication factor A; Reviewed
 20-94 2.46e-05

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 44.27  E-value: 2.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  20 NLNVVFIVLEIGRVT--KTKDGHE--VRSCKVADKTGSITISVWDEIGGL-IQPGDIIRLTRGYASMWKGCLTLYTGRGG 94
Cdd:PRK12366 410 DITVIARVVEDYPVNefERSDGSKgkVRNIELADGTGSIRLTLWDDDAEIeIKEGDAIKILHPYVKENGDYLDLSIGRYG 489
PRK07211 PRK07211
single-stranded DNA binding protein;
11-101 2.54e-05

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 43.98  E-value: 2.54e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDGHE--VRSCKVADKTGSITISVWDEIGGL---IQPGDIIRLTRGYASMWK 83
Cdd:PRK07211 164 VEDLSLGLSDVTLVGVVLDTDsvRTFDRDDGSEgrVSNLTVGDETGRVRVTLWDDRADLaeeLDAGESVEIVDGYVRERD 243

                         90
                 ....*....|....*...
gi 119631243  84 GCLTLYTGRGGELQKIGE 101
Cdd:PRK07211 244 GSLELHVGDRGAVEEVDE 261
PRK15491 PRK15491
replication factor A; Provisional
 11-101 2.75e-05

replication factor A; Provisional


Pssm-ID: 185388 [Multi-domain]  Cd Length: 374  Bit Score: 43.72  E-value: 2.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIGRVTK--TKDGHE--VRSCKVADKTGSITISVWDEIGGLIQPGDI-----IRLTrGYASM 81
Cdd:PRK15491  60 IADINESSSNVNFTAKVVSIFEPKEfnRNDGTTgrVGNIIVADETGSIRLTLWDDLADLIKTGDIevgksLNIS-GYAKE 138

                         90       100
                 ....*....|....*....|
gi 119631243  82 WKGCLTLYTGRGGELQKIGE 101
Cdd:PRK15491 139 GYSGIEVNIGRYGGISESDE 158
PRK15491 PRK15491
replication factor A; Provisional
 11-79 3.60e-05

replication factor A; Provisional


Pssm-ID: 185388 [Multi-domain]  Cd Length: 374  Bit Score: 43.33  E-value: 3.60e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDGHE--VRSCKVADKTGSITISVWDEIGGL---IQPGDIIRLTRGYA 79
Cdd:PRK15491 169 ISDIKDGDSDINIVGKVLDISdvRTFQKKDGSQgrVRNITIGDETGKIRVTLWDGKTDLadkLENGDSVEIINGYA 244
PRK07211 PRK07211
single-stranded DNA binding protein;
11-74 5.63e-05

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 43.21  E-value: 5.63e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIGRV-TKTKDGHE----VRSCKVADKTGSITISVWDEIG----GLIQPGDIIRL 74
Cdd:PRK07211  56 IADIEPGMDEVKFLAKVLSIGDLrTFERDGEDedgrVINVEVADETGSVRVAFWDEQAvaaeEELEVGQVLRI 128
PRK07218 PRK07218
Single-stranded DNA binding protein;
13-84 1.13e-04

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 41.92  E-value: 1.13e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119631243  13 DIKPGLKNLNVVFIVLEIG-RVTKTKDGH-EVRSCKVADKTGSITISVWDEIGGlIQPGDIIRLTRGYASMWKG 84
Cdd:PRK07218 167 DLGPGDRGVNVEARVLELEhREIDGRDGEtTILSGVLADETGRLPFTDWDPLPE-IEIGASIRIEDAYVREFRG 239
PRK14699 PRK14699
replication factor A; Provisional
 11-61 4.60e-04

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 40.37  E-value: 4.60e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 119631243  11 IRDIKPGLKNLNVVFIVLEIG--RVTKTKDGHEVRSCKV--ADKTGSITISVWDE 61
Cdd:PRK14699 279 IEDIKADMNNINISGRVLDISevRTFEKKDGSPGRVGNLllGDSTGKIRLTLWDE 333
PRK12366 PRK12366
replication factor A; Reviewed
 23-80 2.10e-03

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 38.49  E-value: 2.10e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119631243  23 VVFIVLEIGRVTKtKDGHE--VRSCKVADKTGSITISVWDEIGGL-IQPGDIIRLtRGYAS 80
Cdd:PRK12366 192 EVTKAYPIKEFTR-KDGSEgkLKSFILKDDTGSIRVTLWNDLTDIeVNKGDIVRV-KGYVK 250
PRK08402 PRK08402
replication factor A; Reviewed
 7-74 3.00e-03

replication factor A; Reviewed


Pssm-ID: 169427 [Multi-domain]  Cd Length: 355  Bit Score: 37.86  E-value: 3.00e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119631243   7 PLIFIRDIKPGLKNLNVVFIVLEI--GRVTKTKDGH--EVRSCKVADKTGSITISVWD----EIGGLIQPGDIIRL 74
Cdd:PRK08402  61 PLMHISDLVPGMRGVNIVGRVLRKypPREYTKKDGStgRVASLIIYDDTGRARVVLWDakvaKYYNKINVGDVIKV 136
 
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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