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Conserved domains on  [gi|15219131|ref|NP_175703|]
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Nucleic acid-binding, OB-fold-like protein [Arabidopsis thaliana]

Protein Classification

replication protein A OB-fold DNA-binding domain-containing protein; single-stranded DNA-binding protein( domain architecture ID 10138922)

replication protein A (RPA) OB-fold DNA-binding domain-containing protein| single-stranded DNA (ssDNA)-binding protein plays a key role in DNA replication, recombination, and repair

Graphical summary

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List of domain hits

 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 ...
 275-428 4.39e-39

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: 140.52  E-value: 4.39e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 275 IAELKASFEVEKVK-----IICSILSIDLDySWYYYAHIKCNKKVFKSKKTlssgakkiIYRCDKCATDVTSIEARYWLH 349
Cdd:cd04476   1 IAEIKEENLGEGEKpdyftVKATIVFIKPD-NWWYPACPGCNKKVVEEGNG--------TYRCEKCNKSVPNPEYRYILS 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 350 LDIMDNTGESKLMLFDSFVEPIIGCPATELLDVTNEQIDEpqpLPDVVKNIIGKTYQFLVCVEQDNISR-GNDEYKVAEV 428
Cdd:cd04476  72 LNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDA---FPDAIQDLVGKTFLFRVSVKEETYNDeGRIRYTVVKV 148
RPA1_DBD_B_like cd04481
RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB ...
 138-242 2.69e-31

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: 116.99  E-value: 2.69e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 138 NVIGQLVNVGEIQLLDVQGKPTKKIDFQLRDTDDNRLPCSLWGKFADQIH-KVSKESVGGIVICLIRWAKLGHYKEIRSI 216
Cdd:cd04481   1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDaKFQSAGNGEPVVAVLRFWKIKEYKGPKSL 80

                        90       100
                ....*....|....*....|....*.
gi 15219131 217 SNAFDASEVFINPILTEVEEFKNLLP 242
Cdd:cd04481  81 SNSFGASKVYINPDIPEVPEIKMSLK 106
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 21-106 3.10e-28

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, 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-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


:

Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 107.72  E-value: 3.10e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131  21 CIQVKILHAWNHYTKGSGMSYEMMLADEDGNKIQAGIKKEHLLKLQRYVKIGHWTIIEEFSVTKASGLYRSTTHPYRINI 100
Cdd:cd04480   1 KICVRVLRLWDVYNNASGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHPYKIKF 80


                ....*.
gi 15219131 101 QSSTRF 106
Cdd:cd04480  81 MSDTVV 86
 
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 ...
 275-428 4.39e-39

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: 140.52  E-value: 4.39e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 275 IAELKASFEVEKVK-----IICSILSIDLDySWYYYAHIKCNKKVFKSKKTlssgakkiIYRCDKCATDVTSIEARYWLH 349
Cdd:cd04476   1 IAEIKEENLGEGEKpdyftVKATIVFIKPD-NWWYPACPGCNKKVVEEGNG--------TYRCEKCNKSVPNPEYRYILS 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 350 LDIMDNTGESKLMLFDSFVEPIIGCPATELLDVTNEQIDEpqpLPDVVKNIIGKTYQFLVCVEQDNISR-GNDEYKVAEV 428
Cdd:cd04476  72 LNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDA---FPDAIQDLVGKTFLFRVSVKEETYNDeGRIRYTVVKV 148
RPA1_DBD_B_like cd04481
RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB ...
 138-242 2.69e-31

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: 116.99  E-value: 2.69e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 138 NVIGQLVNVGEIQLLDVQGKPTKKIDFQLRDTDDNRLPCSLWGKFADQIH-KVSKESVGGIVICLIRWAKLGHYKEIRSI 216
Cdd:cd04481   1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDaKFQSAGNGEPVVAVLRFWKIKEYKGPKSL 80

                        90       100
                ....*....|....*....|....*.
gi 15219131 217 SNAFDASEVFINPILTEVEEFKNLLP 242
Cdd:cd04481  81 SNSFGASKVYINPDIPEVPEIKMSLK 106
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 21-106 3.10e-28

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, 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-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 107.72  E-value: 3.10e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131  21 CIQVKILHAWNHYTKGSGMSYEMMLADEDGNKIQAGIKKEHLLKLQRYVKIGHWTIIEEFSVTKASGLYRSTTHPYRINI 100
Cdd:cd04480   1 KICVRVLRLWDVYNNASGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHPYKIKF 80


                ....*.
gi 15219131 101 QSSTRF 106
Cdd:cd04480  81 MSDTVV 86
rpa1 TIGR00617
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
 9-450 4.06e-20

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: 94.03  E-value: 4.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131     9 AIKNLKPFKTSWCIQVKI-----LHAWnHYTKGSGMSYEMMLADEDGnKIQAGIKKEHLLKLQRYVKIGHWTIIEEFSVT 83
Cdd:TIGR00617 182 PIASLSPYQNKWTIKARVtnkseIRTW-SNARGEGKLFNVELLDESG-EIRATAFNEQADKFYDIIQEGKVYYISKGSLK 259

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131    84 KASGLYRSTTHPYRINIQSSTRF------SNSPTISdeiwLDLVNFNDVlsGTLDQNKLVNVIGQLVNVGEIQLLDVQ-- 155
Cdd:TIGR00617 260 PANKQFTNLGNDYEMTLDRDTVIeecedeTAIPKIQ----FNFVKIDDI--GGYEGNSLVDVIGIVQSVSPTQTITSRkn 333

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131   156 GKPTKKIDFQLRDTDDNRLPCSLWGKFADQIhKVSKESVggIVICLIRWAKLGHykeiRSISNAFdASEVFINPILTEVE 235
Cdd:TIGR00617 334 NKEFPKRDITLVDDSGKSVRVTLWGDDATKF-DVSVQPV--IAIKGVRVSDFGG----KSLSTGG-SSTIIVNPDIPEAE 405

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131   236 EFKNLLPSDGLALtimepKPRFQPLRVREERSKQF-ERKTIAELKAS----------FEVEKVkiicsILSIDLDYSWYY 304
Cdd:TIGR00617 406 KLKGWYDNEGKGT-----MASSISDMMSGRVGGSNaERKTIAEIQAEnlgksdkpdyFSVKAT-----ISYLKPDNALYR 475

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131   305 YAHIK-CNKKVFkskktlssGAKKIIYRCDKCATDVTSIEARYWLHLDIMDNTGESKLMLFDSFVEPIIGCPATELLDVT 383
Cdd:TIGR00617 476 ACPSEdCNKKVV--------DQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELK 547

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15219131   384 NEqidEPQPLPDVVKNIIGKTYQFLVCVEQDNIsrgNDEYKVAevLTSQninqalpindSVNPVDHS 450
Cdd:TIGR00617 548 EE---DPDEFEAIFQEAQFVPYIFRLRVKQDTY---NDESRQK--YTVM----------SVDPVNYR 596
Rep_fac-A_C pfam08646
Replication factor-A C terminal domain; This domain is found at the C terminal of replication ...
 310-451 1.67e-12

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: 64.94  E-value: 1.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131   310 CNKKVFKSkktlSSGAkkiiYRCDKCATDVTSIEARYWLHLDIMDNTGESKLMLFDSFVEPIIGCPATELLDVTNEqidE 389
Cdd:pfam08646  26 CNKKVVEQ----GDGT----WRCEKCDKNFPEPKYRYILSINVSDHTGQLWVTLFNEAAEKILGKSADELMKLKEE---D 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15219131   390 PQPLPDVVKNIIGKTYQFLVCVEQDNIsrgNDEYKV-AEVLtsqninqalpindSVNPVDHSS 451
Cdd:pfam08646  95 ENEFEAIFQKATFREYIFRLRVKQETY---NDESRVrYTVM-------------SVAPVDYKK 141
DUF223 pfam02721
Domain of unknown function DUF223;
42-136 1.10e-11

Domain of unknown function DUF223;


Pssm-ID: 145722  Cd Length: 95  Bit Score: 61.16  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131    42 EMMLADEDGNKIQAGIKKEHLLKLQRYVKIGHWTIIEEFSVTKASGLYRSTTHPYRINIQSSTRFSNSPTISDEIWLDLV 121
Cdd:pfam02721   1 GLILADENGDKIEATIRRRLAAFYADRISEGEWKTITTFVVRPNSGSYRITSHEYGILFMDQTVVTKSDTRETVLFNNLT 80

                          90
                  ....*....|....*
gi 15219131   122 NFNDVLSGTLDQNKL 136
Cdd:pfam02721  81 PFDYIIEDTVDKNVL 95
 
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 ...
 275-428 4.39e-39

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: 140.52  E-value: 4.39e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 275 IAELKASFEVEKVK-----IICSILSIDLDySWYYYAHIKCNKKVFKSKKTlssgakkiIYRCDKCATDVTSIEARYWLH 349
Cdd:cd04476   1 IAEIKEENLGEGEKpdyftVKATIVFIKPD-NWWYPACPGCNKKVVEEGNG--------TYRCEKCNKSVPNPEYRYILS 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 350 LDIMDNTGESKLMLFDSFVEPIIGCPATELLDVTNEQIDEpqpLPDVVKNIIGKTYQFLVCVEQDNISR-GNDEYKVAEV 428
Cdd:cd04476  72 LNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDA---FPDAIQDLVGKTFLFRVSVKEETYNDeGRIRYTVVKV 148
RPA1_DBD_B_like cd04481
RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB ...
 138-242 2.69e-31

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: 116.99  E-value: 2.69e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131 138 NVIGQLVNVGEIQLLDVQGKPTKKIDFQLRDTDDNRLPCSLWGKFADQIH-KVSKESVGGIVICLIRWAKLGHYKEIRSI 216
Cdd:cd04481   1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDaKFQSAGNGEPVVAVLRFWKIKEYKGPKSL 80

                        90       100
                ....*....|....*....|....*.
gi 15219131 217 SNAFDASEVFINPILTEVEEFKNLLP 242
Cdd:cd04481  81 SNSFGASKVYINPDIPEVPEIKMSLK 106
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 21-106 3.10e-28

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, 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-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 107.72  E-value: 3.10e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131  21 CIQVKILHAWNHYTKGSGMSYEMMLADEDGNKIQAGIKKEHLLKLQRYVKIGHWTIIEEFSVTKASGLYRSTTHPYRINI 100
Cdd:cd04480   1 KICVRVLRLWDVYNNASGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHPYKIKF 80


                ....*.
gi 15219131 101 QSSTRF 106
Cdd:cd04480  81 MSDTVV 86
rpa1 TIGR00617
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
 9-450 4.06e-20

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: 94.03  E-value: 4.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131     9 AIKNLKPFKTSWCIQVKI-----LHAWnHYTKGSGMSYEMMLADEDGnKIQAGIKKEHLLKLQRYVKIGHWTIIEEFSVT 83
Cdd:TIGR00617 182 PIASLSPYQNKWTIKARVtnkseIRTW-SNARGEGKLFNVELLDESG-EIRATAFNEQADKFYDIIQEGKVYYISKGSLK 259

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131    84 KASGLYRSTTHPYRINIQSSTRF------SNSPTISdeiwLDLVNFNDVlsGTLDQNKLVNVIGQLVNVGEIQLLDVQ-- 155
Cdd:TIGR00617 260 PANKQFTNLGNDYEMTLDRDTVIeecedeTAIPKIQ----FNFVKIDDI--GGYEGNSLVDVIGIVQSVSPTQTITSRkn 333

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131   156 GKPTKKIDFQLRDTDDNRLPCSLWGKFADQIhKVSKESVggIVICLIRWAKLGHykeiRSISNAFdASEVFINPILTEVE 235
Cdd:TIGR00617 334 NKEFPKRDITLVDDSGKSVRVTLWGDDATKF-DVSVQPV--IAIKGVRVSDFGG----KSLSTGG-SSTIIVNPDIPEAE 405

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131   236 EFKNLLPSDGLALtimepKPRFQPLRVREERSKQF-ERKTIAELKAS----------FEVEKVkiicsILSIDLDYSWYY 304
Cdd:TIGR00617 406 KLKGWYDNEGKGT-----MASSISDMMSGRVGGSNaERKTIAEIQAEnlgksdkpdyFSVKAT-----ISYLKPDNALYR 475

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131   305 YAHIK-CNKKVFkskktlssGAKKIIYRCDKCATDVTSIEARYWLHLDIMDNTGESKLMLFDSFVEPIIGCPATELLDVT 383
Cdd:TIGR00617 476 ACPSEdCNKKVV--------DQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELK 547

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15219131   384 NEqidEPQPLPDVVKNIIGKTYQFLVCVEQDNIsrgNDEYKVAevLTSQninqalpindSVNPVDHS 450
Cdd:TIGR00617 548 EE---DPDEFEAIFQEAQFVPYIFRLRVKQDTY---NDESRQK--YTVM----------SVDPVNYR 596
Rep_fac-A_C pfam08646
Replication factor-A C terminal domain; This domain is found at the C terminal of replication ...
 310-451 1.67e-12

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: 64.94  E-value: 1.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131   310 CNKKVFKSkktlSSGAkkiiYRCDKCATDVTSIEARYWLHLDIMDNTGESKLMLFDSFVEPIIGCPATELLDVTNEqidE 389
Cdd:pfam08646  26 CNKKVVEQ----GDGT----WRCEKCDKNFPEPKYRYILSINVSDHTGQLWVTLFNEAAEKILGKSADELMKLKEE---D 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15219131   390 PQPLPDVVKNIIGKTYQFLVCVEQDNIsrgNDEYKV-AEVLtsqninqalpindSVNPVDHSS 451
Cdd:pfam08646  95 ENEFEAIFQKATFREYIFRLRVKQETY---NDESRVrYTVM-------------SVAPVDYKK 141
DUF223 pfam02721
Domain of unknown function DUF223;
42-136 1.10e-11

Domain of unknown function DUF223;


Pssm-ID: 145722  Cd Length: 95  Bit Score: 61.16  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219131    42 EMMLADEDGNKIQAGIKKEHLLKLQRYVKIGHWTIIEEFSVTKASGLYRSTTHPYRINIQSSTRFSNSPTISDEIWLDLV 121
Cdd:pfam02721   1 GLILADENGDKIEATIRRRLAAFYADRISEGEWKTITTFVVRPNSGSYRITSHEYGILFMDQTVVTKSDTRETVLFNNLT 80

                          90
                  ....*....|....*
gi 15219131   122 NFNDVLSGTLDQNKL 136
Cdd:pfam02721  81 PFDYIIEDTVDKNVL 95
 
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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