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Conserved domains on  [gi|18391179|ref|NP_563874|]
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Nucleic acid-binding, OB-fold-like protein [Arabidopsis thaliana]

Protein Classification

single stranded DNA-binding domain-containing protein( domain architecture ID 489)

single stranded DNA-binding domain-containing protein may bind preferentially to single-stranded DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA_2b-aaRSs_OBF_like super family cl09930
Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with ...
 14-115 6.47e-19

Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism. This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B, of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases.


The actual alignment was detected with superfamily member PRK06461:

Pssm-ID: 471953 [Multi-domain]  Cd Length: 129  Bit Score: 76.61  E-value: 6.47e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179   14 TKVNELRPGTNGHSLNVKVVNT---KMVMQRGGGRpmgpqsrqmRIAECLVGDETGIIIFTARNDQVDMMKEGSVVTLRN 90
Cdd:PRK06461   5 TKIKDLKPGMERVNVTVRVLEVgepKVIQTKGGPR---------TISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIEN 75

                         90       100
                 ....*....|....*....|....*
gi 18391179   91 AKIDMYKGSMRLAVDRWGRVEVAEE 115
Cdd:PRK06461  76 AWTTLYRGKVQLNVGKYGSISESDD 100
 
Name Accession Description Interval E-value
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 14-115 6.47e-19

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 76.61  E-value: 6.47e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179   14 TKVNELRPGTNGHSLNVKVVNT---KMVMQRGGGRpmgpqsrqmRIAECLVGDETGIIIFTARNDQVDMMKEGSVVTLRN 90
Cdd:PRK06461   5 TKIKDLKPGMERVNVTVRVLEVgepKVIQTKGGPR---------TISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIEN 75

                         90       100
                 ....*....|....*....|....*
gi 18391179   91 AKIDMYKGSMRLAVDRWGRVEVAEE 115
Cdd:PRK06461  76 AWTTLYRGKVQLNVGKYGSISESDD 100
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 55-112 4.60e-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: 63.03  E-value: 4.60e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 18391179  55 RIAECLVGDETGIIIFTARNDQV-DMMKEGSVVTLRNAKIDMYKGSMRLAVDRWGRVEV 112
Cdd:cd04491  23 KVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
14-131 3.71e-10

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


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 56.22  E-value: 3.71e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179  14 TKVNELRPGTNGHSLNVKVVNT---KMVMQRGGGrpmgpqsrQMRIAECLVGDETGIIIFTARNDQVDM-MKEGSVVTLR 89
Cdd:COG1599  22 VKISDLSPGDRDVNVEGRVLEIgeeRTFDRKDGS--------EGRVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIE 93

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 18391179  90 NAKIDMYKGSMRLAVDRWGRVEVAEEptDITVKDDNNLSLIE 131
Cdd:COG1599  94 NAYVREFNGGPELNLGERTTIEKLDE--DVEVIPDEERTPIG 133
 
Name Accession Description Interval E-value
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 14-115 6.47e-19

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 76.61  E-value: 6.47e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179   14 TKVNELRPGTNGHSLNVKVVNT---KMVMQRGGGRpmgpqsrqmRIAECLVGDETGIIIFTARNDQVDMMKEGSVVTLRN 90
Cdd:PRK06461   5 TKIKDLKPGMERVNVTVRVLEVgepKVIQTKGGPR---------TISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIEN 75

                         90       100
                 ....*....|....*....|....*
gi 18391179   91 AKIDMYKGSMRLAVDRWGRVEVAEE 115
Cdd:PRK06461  76 AWTTLYRGKVQLNVGKYGSISESDD 100
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 55-112 4.60e-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: 63.03  E-value: 4.60e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 18391179  55 RIAECLVGDETGIIIFTARNDQV-DMMKEGSVVTLRNAKIDMYKGSMRLAVDRWGRVEV 112
Cdd:cd04491  23 KVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
14-131 3.71e-10

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


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 56.22  E-value: 3.71e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179  14 TKVNELRPGTNGHSLNVKVVNT---KMVMQRGGGrpmgpqsrQMRIAECLVGDETGIIIFTARNDQVDM-MKEGSVVTLR 89
Cdd:COG1599  22 VKISDLSPGDRDVNVEGRVLEIgeeRTFDRKDGS--------EGRVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIE 93

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 18391179  90 NAKIDMYKGSMRLAVDRWGRVEVAEEptDITVKDDNNLSLIE 131
Cdd:COG1599  94 NAYVREFNGGPELNLGERTTIEKLDE--DVEVIPDEERTPIG 133
PRK07217 PRK07217
replication factor A; Reviewed
 60-139 3.18e-07

replication factor A; Reviewed


Pssm-ID: 235970 [Multi-domain]  Cd Length: 311  Bit Score: 47.71  E-value: 3.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179   60 LVGDETGIIIFT--ARNDQVDmMKEGSVVTLRNAKIDMYKGSMRLAVDRWGRVEVAEEptDITVKDDNnlSLIEYELVSV 137
Cdd:PRK07217 107 LLGDETGTIKFTkwAKSDLPE-LEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDE--DIEVGDDE--VEVEGALVDI 181


                 ..
gi 18391179  138 ET 139
Cdd:PRK07217 182 QS 183
PRK06386 PRK06386
replication factor A; Reviewed
 60-139 5.84e-06

replication factor A; Reviewed


Pssm-ID: 235790 [Multi-domain]  Cd Length: 358  Bit Score: 44.12  E-value: 5.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179   60 LVGDETGIIIFTARNDQvDMMKEGSVVTLRNAKIDMYKGSMRLAVDrwGRVEVAEEPtDITVKDDNNLSLIEYELVSVET 139
Cdd:PRK06386  42 IIGDETGTVPFTAWEFP-DAVKSGDVIEIKYCYSKEYNGKIRIYFD--SRSEVMLKP-DENIEVKRTYKLVKIRDLSLVT 117
PRK07218 PRK07218
Single-stranded DNA binding protein;
14-120 2.00e-05

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 42.69  E-value: 2.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179   14 TKVNELRPGTNGHSLNVKV--VNTKMVMQRGGgrpmgpqsrQMRIAECLVGDETGIIIFTARnDQVDMMKEGSVVTLRNA 91
Cdd:PRK07218 163 KKLIDLGPGDRGVNVEARVleLEHREIDGRDG---------ETTILSGVLADETGRLPFTDW-DPLPEIEIGASIRIEDA 232

                         90       100
                 ....*....|....*....|....*....
gi 18391179   92 KIDMYKGSMRLAVDRWGRVEVAEEPTDIT 120
Cdd:PRK07218 233 YVREFRGVPSVNVSEFTTVEALDREVSVS 261
PRK07218 PRK07218
Single-stranded DNA binding protein;
1-131 5.94e-03

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 35.37  E-value: 5.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18391179    1 MAEATSALRK----------PVFTKVNELRPGTNGHSLNVKVVNTkmvmqrgGGRPMGPQSRQMRIAECLVGDETGIIIF 70
Cdd:PRK07218  36 IDEAKQSIRRkyggggsggtPSSKDIKELSTDDKNVTVTGRVLTI-------GERSIRYQGDDHVIYEGILADETGTISY 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18391179   71 TARNDQvdMMKEGSVVTLRNAKIDMYKGSMRLAVDRWGRVEVAEEPTDITVKDDNNLSLIE 131
Cdd:PRK07218 109 TAWKDF--GLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSLPPYSIGGDKKLID 167
 
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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