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Conserved domains on  [gi|1063685975|ref|NP_001322201|]
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Nucleic acid-binding, OB-fold-like protein [Arabidopsis thaliana]

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 ...
 17-74 2.00e-14

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: 62.26  E-value: 2.00e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063685975  17 RISECIVGDETGVIVFTARNDQV-DLMKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEV 74
Cdd:cd04491    23 KVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81
 
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 ...
 17-74 2.00e-14

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: 62.26  E-value: 2.00e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063685975  17 RISECIVGDETGVIVFTARNDQV-DLMKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEV 74
Cdd:cd04491    23 KVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 17-86 1.88e-13

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 61.21  E-value: 1.88e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063685975  17 RISECIVGDETGVIVFTARNDQVDLMKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEVTE----PASFKVKEDT 86
Cdd:PRK06461   40 TISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDdeevPEAEEIPEET 113
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
17-92 9.51e-07

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


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 45.05  E-value: 9.51e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063685975  17 RISECIVGDETGVIVFTARNDQVDL-MKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEVTEpASFKVKEDTNMSLIE 92
Cdd:COG1599    58 RVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVREFNGGPELNLGERTTIEKLD-EDVEVIPDEERTPIG 133
 
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 ...
 17-74 2.00e-14

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: 62.26  E-value: 2.00e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063685975  17 RISECIVGDETGVIVFTARNDQV-DLMKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEV 74
Cdd:cd04491    23 KVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 17-86 1.88e-13

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 61.21  E-value: 1.88e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063685975  17 RISECIVGDETGVIVFTARNDQVDLMKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEVTE----PASFKVKEDT 86
Cdd:PRK06461   40 TISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDdeevPEAEEIPEET 113
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
17-92 9.51e-07

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


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 45.05  E-value: 9.51e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063685975  17 RISECIVGDETGVIVFTARNDQVDL-MKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEVTEpASFKVKEDTNMSLIE 92
Cdd:COG1599    58 RVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVREFNGGPELNLGERTTIEKLD-EDVEVIPDEERTPIG 133
PRK06386 PRK06386
replication factor A; Reviewed
 22-98 6.73e-06

replication factor A; Reviewed


Pssm-ID: 235790 [Multi-domain]  Cd Length: 358  Bit Score: 42.58  E-value: 6.73e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063685975  22 IVGDETGVIVFTARNDQvDLMKEGSTVTLRNAKIDMYKGSMRLAVDkwGRVEVTepasfkVKEDTNMSLIE-YELVNV 98
Cdd:PRK06386   42 IIGDETGTVPFTAWEFP-DAVKSGDVIEIKYCYSKEYNGKIRIYFD--SRSEVM------LKPDENIEVKRtYKLVKI 110
PRK07217 PRK07217
replication factor A; Reviewed
 22-68 3.39e-03

replication factor A; Reviewed


Pssm-ID: 235970 [Multi-domain]  Cd Length: 311  Bit Score: 34.99  E-value: 3.39e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063685975  22 IVGDETGVIVFT--ARNDQVDLmKEGSTVTLRNAKIDMYKGSMRLAVDK 68
Cdd:PRK07217  107 LLGDETGTIKFTkwAKSDLPEL-EEGKSYLLKNVVTDEYQGRFSVKLNR 154
PRK07218 PRK07218
Single-stranded DNA binding protein;
14-77 4.92e-03

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 34.60  E-value: 4.92e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063685975  14 RQLRISECIVGDETGVIVFTARnDQVDLMKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEVTEP 77
Cdd:PRK07218  194 GETTILSGVLADETGRLPFTDW-DPLPEIEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDR 256
PRK07218 PRK07218
Single-stranded DNA binding protein;
12-87 8.99e-03

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 33.83  E-value: 8.99e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063685975  12 QARQLRISECIVGDETGVIVFTARNDqVDLMKeGSTVTLRNAKIDMYKGSMRLAVDKWGRVEVTEPASFKVKEDTN 87
Cdd:PRK07218   88 QGDDHVIYEGILADETGTISYTAWKD-FGLSP-GDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSLPPYSIGG 161
 
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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