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Conserved domains on  [gi|21537031|gb|AAM61372|]
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putative replication factor A [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 69-162 1.95e-40

RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro.


:

Pssm-ID: 239924  Cd Length: 95  Bit Score: 135.42  E-value: 1.95e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031  69 TVVIVGRISRMENRITQVDFVVDDGTGWVDCVRWCHA-RQETEEMEAVKLGMYVRLHGHLKIFQGKRSVNVFSVRPVTDF 147
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDdNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTDF 80

                        90
                ....*....|....*
gi 21537031 148 NEIVHHFTECMYVHM 162
Cdd:cd04478  81 NEVTYHLLEVIYVHL 95
RPA_C pfam08784
Replication protein A C terminal; This domain corresponds to the C terminal of the single ...
 161-270 2.46e-37

Replication protein A C terminal; This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.


:

Pssm-ID: 400920  Cd Length: 106  Bit Score: 127.88  E-value: 2.46e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031   161 HMYNTKLRGGSITQDTATPRPQMPYSTMPTPAKPYQTGPSNQFPNqfNDSMHGVKQTVLNYLNQPMHivSEAGVHCDIIA 240
Cdd:pfam08784   1 HLFLTKGASGSSGGGATTPAVSNGGSSMGTQGAYSGGDASVVNAN--NGGLTPLQDQVLNLIKQPPN--GNEGVHVDEIA 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 21537031   241 RELRIPLLQVKEALEQLSNDGCIYSTLDET 270
Cdd:pfam08784  77 QRLGLPVNDVKQAVDFLSNEGHIYSTIDDD 106
 
Name Accession Description Interval E-value
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 69-162 1.95e-40

RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro.


Pssm-ID: 239924  Cd Length: 95  Bit Score: 135.42  E-value: 1.95e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031  69 TVVIVGRISRMENRITQVDFVVDDGTGWVDCVRWCHA-RQETEEMEAVKLGMYVRLHGHLKIFQGKRSVNVFSVRPVTDF 147
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDdNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTDF 80

                        90
                ....*....|....*
gi 21537031 148 NEIVHHFTECMYVHM 162
Cdd:cd04478  81 NEVTYHLLEVIYVHL 95
RPA_C pfam08784
Replication protein A C terminal; This domain corresponds to the C terminal of the single ...
 161-270 2.46e-37

Replication protein A C terminal; This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.


Pssm-ID: 400920  Cd Length: 106  Bit Score: 127.88  E-value: 2.46e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031   161 HMYNTKLRGGSITQDTATPRPQMPYSTMPTPAKPYQTGPSNQFPNqfNDSMHGVKQTVLNYLNQPMHivSEAGVHCDIIA 240
Cdd:pfam08784   1 HLFLTKGASGSSGGGATTPAVSNGGSSMGTQGAYSGGDASVVNAN--NGGLTPLQDQVLNLIKQPPN--GNEGVHVDEIA 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 21537031   241 RELRIPLLQVKEALEQLSNDGCIYSTLDET 270
Cdd:pfam08784  77 QRLGLPVNDVKQAVDFLSNEGHIYSTIDDD 106
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 14-275 5.55e-31

Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair];


Pssm-ID: 227560 [Multi-domain]  Cd Length: 258  Bit Score: 115.84  E-value: 5.55e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031  14 GGGFMPSQATTQAHESSSslkNRDVRTLLPLTLKQLSSAS-TTGESNFSIDGVDIKTVVIVGRISRMENRITQVDFVVDD 92
Cdd:COG5235  15 RGQIFGTGSPPPMDRSEG---GYIVNTLRPVTIKQILSCDqDETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIED 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031  93 GTGWVDCVRWCHARQETEEMEAVKLGMYVRLHGHLKIFQGKRSVNVFSVRPVTDFNEIVHHFTECMYVHMYNTklrggsi 172
Cdd:COG5235  92 GTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYT------- 164

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031 173 tqdtatprpQMPYSTMPTPAKPYQTGPSNQFPNQFNDSMHGVKQTVLNYLNQpmhIVSEAGVHCDIIAREL--RIPLLQV 250
Cdd:COG5235 165 ---------RQLQRPLEEEVKNDGQSLFAKLDNDTSSGSSRLQEDILECYRR---NQDENGLHINVVIKMLsqSYSEDET 232

                       250       260
                ....*....|....*....|....*
gi 21537031 251 KEALEQLSNDGCIYSTLDETCFKST 275
Cdd:COG5235 233 RVNIDVLLRDGHIYPTVDGNEFKTT 257
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 70-144 3.15e-08

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 49.54  E-value: 3.15e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21537031    70 VVIVGRISRME-NRITQVDFVVDDGTGWVDCVRWCHARQEteEMEAVKLGMYVRLHGHLKIFQGKR-SVNVFSVRPV 144
Cdd:pfam01336   1 VTVAGRVTSIRrSGGKLLFLTLRDGTGSIQVVVFKEEAEK--LAKKLKEGDVVRVTGKVKKRKGGElELVVEEIELL 75
 
Name Accession Description Interval E-value
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 69-162 1.95e-40

RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro.


Pssm-ID: 239924  Cd Length: 95  Bit Score: 135.42  E-value: 1.95e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031  69 TVVIVGRISRMENRITQVDFVVDDGTGWVDCVRWCHA-RQETEEMEAVKLGMYVRLHGHLKIFQGKRSVNVFSVRPVTDF 147
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDdNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTDF 80

                        90
                ....*....|....*
gi 21537031 148 NEIVHHFTECMYVHM 162
Cdd:cd04478  81 NEVTYHLLEVIYVHL 95
RPA_C pfam08784
Replication protein A C terminal; This domain corresponds to the C terminal of the single ...
 161-270 2.46e-37

Replication protein A C terminal; This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.


Pssm-ID: 400920  Cd Length: 106  Bit Score: 127.88  E-value: 2.46e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031   161 HMYNTKLRGGSITQDTATPRPQMPYSTMPTPAKPYQTGPSNQFPNqfNDSMHGVKQTVLNYLNQPMHivSEAGVHCDIIA 240
Cdd:pfam08784   1 HLFLTKGASGSSGGGATTPAVSNGGSSMGTQGAYSGGDASVVNAN--NGGLTPLQDQVLNLIKQPPN--GNEGVHVDEIA 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 21537031   241 RELRIPLLQVKEALEQLSNDGCIYSTLDET 270
Cdd:pfam08784  77 QRLGLPVNDVKQAVDFLSNEGHIYSTIDDD 106
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 14-275 5.55e-31

Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair];


Pssm-ID: 227560 [Multi-domain]  Cd Length: 258  Bit Score: 115.84  E-value: 5.55e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031  14 GGGFMPSQATTQAHESSSslkNRDVRTLLPLTLKQLSSAS-TTGESNFSIDGVDIKTVVIVGRISRMENRITQVDFVVDD 92
Cdd:COG5235  15 RGQIFGTGSPPPMDRSEG---GYIVNTLRPVTIKQILSCDqDETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIED 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031  93 GTGWVDCVRWCHARQETEEMEAVKLGMYVRLHGHLKIFQGKRSVNVFSVRPVTDFNEIVHHFTECMYVHMYNTklrggsi 172
Cdd:COG5235  92 GTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYT------- 164

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031 173 tqdtatprpQMPYSTMPTPAKPYQTGPSNQFPNQFNDSMHGVKQTVLNYLNQpmhIVSEAGVHCDIIAREL--RIPLLQV 250
Cdd:COG5235 165 ---------RQLQRPLEEEVKNDGQSLFAKLDNDTSSGSSRLQEDILECYRR---NQDENGLHINVVIKMLsqSYSEDET 232

                       250       260
                ....*....|....*....|....*
gi 21537031 251 KEALEQLSNDGCIYSTLDETCFKST 275
Cdd:COG5235 233 RVNIDVLLRDGHIYPTVDGNEFKTT 257
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 70-144 3.15e-08

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 49.54  E-value: 3.15e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21537031    70 VVIVGRISRME-NRITQVDFVVDDGTGWVDCVRWCHARQEteEMEAVKLGMYVRLHGHLKIFQGKR-SVNVFSVRPV 144
Cdd:pfam01336   1 VTVAGRVTSIRrSGGKLLFLTLRDGTGSIQVVVFKEEAEK--LAKKLKEGDVVRVTGKVKKRKGGElELVVEEIELL 75
RPA2_OBF_family cd03524
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold ...
 72-143 1.16e-07

RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1).


Pssm-ID: 239601 [Multi-domain]  Cd Length: 75  Bit Score: 48.13  E-value: 1.16e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21537031  72 IVGRISRMENRITQ---VDFVVDDGTG-WVDCVRWchaRQETEEMEA-VKLGMYVRLHGHLKIFQGKRSVNVFSVRP 143
Cdd:cd03524   2 IVGIVVAVEEIRTEgkvLIFTLTDGTGgTIRVTLF---GELAEELENlLKEGQVVYIKGKVKKFRGRLQLIVESIEL 75
hOBFC1_like cd04483
hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein ...
 72-141 3.84e-07

hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. 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). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.


Pssm-ID: 239929  Cd Length: 92  Bit Score: 47.04  E-value: 3.84e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21537031  72 IVGRISRMENRITQVDFVVDDGTGWVDCVRW-----------------CHARQETEEMEAV-KLGMYVRLHGHLKIFQGK 133
Cdd:cd04483   2 ILGTVVSRRERETFYSFGVDDGTGVVNCVCWknlsyaevssrsdaariLKSALMALKQAKVlEIGDLLRVRGSIRTYRGE 81


                ....*...
gi 21537031 134 RSVNVFSV 141
Cdd:cd04483  82 REINASVV 89
 
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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