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Conserved domains on  [gi|1841656269|ref|XP_034229611|]
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replication protein A 70 kDa DNA-binding subunit B-like [Prunus dulcis]

Protein Classification

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 ...
 138-247 1.53e-14

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 cd04476:

Pssm-ID: 471953 [Multi-domain]  Cd Length: 166  Bit Score: 70.80  E-value: 1.53e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269 138 CRAAITRFDTRNgWWYKACPSCFKQLRTAaHRDELLCPKHNN--QIPLPWFKVSLVLEDSTDETNAIIIGRPAEQLFRIS 215
Cdd:cd04476    20 VKATIVFIKPDN-WWYPACPGCNKKVVEE-GNGTYRCEKCNKsvPNPEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKS 97

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1841656269 216 CNELVVQRgFTDQQQLPDAILQTRGQVKNFQL 247
Cdd:cd04476    98 AEELLELK-EEDPDAFPDAIQDLVGKTFLFRV 128
rpa1 super family cl36710
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
 23-219 1.11e-11

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: 65.91  E-value: 1.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269  23 VRITLWGNTAKTFDSQalqqlTSPIfAAFTSLKVKQFQGKivlnsSVSTL----IFINPDIQELAAYKTIFNDSTHAIkm 98
Cdd:TIGR00617 352 VRVTLWGDDATKFDVS-----VQPV-IAIKGVRVSDFGGK-----SLSTGgsstIIVNPDIPEAEKLKGWYDNEGKGT-- 418

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269  99 MPSSATQLMTPQ---HLEAAKKLY-VQELNVLdpetHKDTP--ILCRAAITRFDTRNgWWYKACPS--CFKQLrTAAHRD 170
Cdd:TIGR00617 419 MASSISDMMSGRvggSNAERKTIAeIQAENLG----KSDKPdyFSVKATISYLKPDN-ALYRACPSedCNKKV-VDQGDG 492

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1841656269 171 ELLCPKHNNQIPLPWFKVSLVLE--DSTDETNAIIIGRPAEQLFRISCNEL 219
Cdd:TIGR00617 493 TYRCEKCNKNFAEFKYRYILQISisDETGQLWVTAFNDQAEQILGKSAAEL 543
 
Name Accession Description Interval E-value
RPA1_DBD_C cd04476
RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding ...
 138-247 1.53e-14

RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, 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-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding.


Pssm-ID: 239922 [Multi-domain]  Cd Length: 166  Bit Score: 70.80  E-value: 1.53e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269 138 CRAAITRFDTRNgWWYKACPSCFKQLRTAaHRDELLCPKHNN--QIPLPWFKVSLVLEDSTDETNAIIIGRPAEQLFRIS 215
Cdd:cd04476    20 VKATIVFIKPDN-WWYPACPGCNKKVVEE-GNGTYRCEKCNKsvPNPEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKS 97

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1841656269 216 CNELVVQRgFTDQQQLPDAILQTRGQVKNFQL 247
Cdd:cd04476    98 AEELLELK-EEDPDAFPDAIQDLVGKTFLFRV 128
rpa1 TIGR00617
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
 23-219 1.11e-11

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: 65.91  E-value: 1.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269  23 VRITLWGNTAKTFDSQalqqlTSPIfAAFTSLKVKQFQGKivlnsSVSTL----IFINPDIQELAAYKTIFNDSTHAIkm 98
Cdd:TIGR00617 352 VRVTLWGDDATKFDVS-----VQPV-IAIKGVRVSDFGGK-----SLSTGgsstIIVNPDIPEAEKLKGWYDNEGKGT-- 418

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269  99 MPSSATQLMTPQ---HLEAAKKLY-VQELNVLdpetHKDTP--ILCRAAITRFDTRNgWWYKACPS--CFKQLrTAAHRD 170
Cdd:TIGR00617 419 MASSISDMMSGRvggSNAERKTIAeIQAENLG----KSDKPdyFSVKATISYLKPDN-ALYRACPSedCNKKV-VDQGDG 492

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1841656269 171 ELLCPKHNNQIPLPWFKVSLVLE--DSTDETNAIIIGRPAEQLFRISCNEL 219
Cdd:TIGR00617 493 TYRCEKCNKNFAEFKYRYILQISisDETGQLWVTAFNDQAEQILGKSAAEL 543
RPA1_DBD_B cd04475
RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding ...
 23-81 5.39e-10

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: 56.05  E-value: 5.39e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1841656269  23 VRITLWGNTAKTFDSQalqqlTSPIfAAFTSLKVKQFQGKiVLNSSVSTLIFINPDIQE 81
Cdd:cd04475    41 VELTLWGEQAELFDGS-----ENPV-IAIKGVKVSEFNGK-SLSTGSSSTIIINPDIPE 92
REPA_OB_2 pfam16900
Replication protein A OB domain; Replication protein A contains two OB domains in it's DNA ...
 23-76 2.71e-06

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: 45.49  E-value: 2.71e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1841656269  23 VRITLWGNTAKTFDSQalqqlTSPIFaAFTSLKVKQFQGKivlnsSVSTL----IFIN 76
Cdd:pfam16900  52 VRLTLWGKEAEQFDSS-----ENPVV-AFKGVKVSDFGGR-----SLSTLssstLFIN 98
Rep_fac-A_C pfam08646
Replication factor-A C terminal domain; This domain is found at the C terminal of replication ...
 138-223 1.46e-03

Replication factor-A C terminal domain; This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA.


Pssm-ID: 462546 [Multi-domain]  Cd Length: 146  Bit Score: 38.74  E-value: 1.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269 138 CRAAITRFDTRNgWWYKACPS--CFKQLrTAAHRDELLCPKHNNQIPLPWFK--VSLVLEDSTDETNAIIIGRPAEQLFR 213
Cdd:pfam08646   4 VKATVVFIKQDN-FWYPACPSedCNKKV-VEQGDGTWRCEKCDKNFPEPKYRyiLSINVSDHTGQLWVTLFNEAAEKILG 81

                          90
                  ....*....|
gi 1841656269 214 ISCNELVVQR 223
Cdd:pfam08646  82 KSADELMKLK 91
 
Name Accession Description Interval E-value
RPA1_DBD_C cd04476
RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding ...
 138-247 1.53e-14

RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, 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-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding.


Pssm-ID: 239922 [Multi-domain]  Cd Length: 166  Bit Score: 70.80  E-value: 1.53e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269 138 CRAAITRFDTRNgWWYKACPSCFKQLRTAaHRDELLCPKHNN--QIPLPWFKVSLVLEDSTDETNAIIIGRPAEQLFRIS 215
Cdd:cd04476    20 VKATIVFIKPDN-WWYPACPGCNKKVVEE-GNGTYRCEKCNKsvPNPEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKS 97

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1841656269 216 CNELVVQRgFTDQQQLPDAILQTRGQVKNFQL 247
Cdd:cd04476    98 AEELLELK-EEDPDAFPDAIQDLVGKTFLFRV 128
rpa1 TIGR00617
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
 23-219 1.11e-11

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: 65.91  E-value: 1.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269  23 VRITLWGNTAKTFDSQalqqlTSPIfAAFTSLKVKQFQGKivlnsSVSTL----IFINPDIQELAAYKTIFNDSTHAIkm 98
Cdd:TIGR00617 352 VRVTLWGDDATKFDVS-----VQPV-IAIKGVRVSDFGGK-----SLSTGgsstIIVNPDIPEAEKLKGWYDNEGKGT-- 418

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269  99 MPSSATQLMTPQ---HLEAAKKLY-VQELNVLdpetHKDTP--ILCRAAITRFDTRNgWWYKACPS--CFKQLrTAAHRD 170
Cdd:TIGR00617 419 MASSISDMMSGRvggSNAERKTIAeIQAENLG----KSDKPdyFSVKATISYLKPDN-ALYRACPSedCNKKV-VDQGDG 492

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1841656269 171 ELLCPKHNNQIPLPWFKVSLVLE--DSTDETNAIIIGRPAEQLFRISCNEL 219
Cdd:TIGR00617 493 TYRCEKCNKNFAEFKYRYILQISisDETGQLWVTAFNDQAEQILGKSAAEL 543
RPA1_DBD_B cd04475
RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding ...
 23-81 5.39e-10

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: 56.05  E-value: 5.39e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1841656269  23 VRITLWGNTAKTFDSQalqqlTSPIfAAFTSLKVKQFQGKiVLNSSVSTLIFINPDIQE 81
Cdd:cd04475    41 VELTLWGEQAELFDGS-----ENPV-IAIKGVKVSEFNGK-SLSTGSSSTIIINPDIPE 92
RPA1_DBD_B_like cd04481
RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB ...
 15-89 6.69e-07

RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity 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 RPA 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.


Pssm-ID: 239927 [Multi-domain]  Cd Length: 106  Bit Score: 47.27  E-value: 6.69e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1841656269  15 IENIRKENVRITLWGNTAKTFDSQALQQLTS-PIFAAFTSLKVKQFQGKIVL-NSSVSTLIFINPDIQELAAYKTIF 89
Cdd:cd04481    29 IRDLSDERLKCTLWGEYAEEFDAKFQSAGNGePVVAVLRFWKIKEYKGPKSLsNSFGASKVYINPDIPEVPEIKMSL 105
REPA_OB_2 pfam16900
Replication protein A OB domain; Replication protein A contains two OB domains in it's DNA ...
 23-76 2.71e-06

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: 45.49  E-value: 2.71e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1841656269  23 VRITLWGNTAKTFDSQalqqlTSPIFaAFTSLKVKQFQGKivlnsSVSTL----IFIN 76
Cdd:pfam16900  52 VRLTLWGKEAEQFDSS-----ENPVV-AFKGVKVSDFGGR-----SLSTLssstLFIN 98
Rep_fac-A_C pfam08646
Replication factor-A C terminal domain; This domain is found at the C terminal of replication ...
 138-223 1.46e-03

Replication factor-A C terminal domain; This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA.


Pssm-ID: 462546 [Multi-domain]  Cd Length: 146  Bit Score: 38.74  E-value: 1.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841656269 138 CRAAITRFDTRNgWWYKACPS--CFKQLrTAAHRDELLCPKHNNQIPLPWFK--VSLVLEDSTDETNAIIIGRPAEQLFR 213
Cdd:pfam08646   4 VKATVVFIKQDN-FWYPACPSedCNKKV-VEQGDGTWRCEKCDKNFPEPKYRyiLSINVSDHTGQLWVTLFNEAAEKILG 81

                          90
                  ....*....|
gi 1841656269 214 ISCNELVVQR 223
Cdd:pfam08646  82 KSADELMKLK 91
 
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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