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Conserved domains on  [gi|85102469|ref|XP_961333|]
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replication factor-A protein 1 [Neurospora crassa OR74A]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RFA1 super family cl28407
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
2-604 0e+00

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


The actual alignment was detected with superfamily member TIGR00617:

Pssm-ID: 333227  Cd Length: 608  Bit Score: 708.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469     2 AGQITQGALDAMFNDPDRAQQQfPVPILQCLQIKTLDSKNGGagatERFRIVLSDLKNYVQCMMATQTNHLVHDGLLQRG 81
Cdd:TIGR00617   1 AVSLSNGAIALIMTNGEANGYP-PDPVLQVLDLKPINGAQDP----RRYRIVISDGIYYSKAMLATQLNPLVREGELQEG 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469    82 CIVRLKQYQAQCL--KGKNILIVLDLEVIQS-LGCPEKMGDPQPLGPR----------SAEPQQNPNLGSTGFYGVKSEP 148
Cdd:TIGR00617  76 TIIRLTKFEVNTIgkDGRKVLIVYELEVVKPeLKVRDKIGNPVTYEKYldswheeqvlASKPATNPANPPNAKAPKNEVA 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   149 T--QDTKPQFPRQMPSRNAsggQGSSTIYPIEGLSPFSHKWTIKARVTSKSDIKTWHKASGEGKLFSVNFLDESGEIRAT 226
Cdd:TIGR00617 156 SynNAANPERGNAPPAPNS---GSTRRVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDESGEIRAT 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   227 GFNDQVDQFYDLLQEGQVYYISTpCRVQLAKKQWSNLPNDYELTFERDTVIEKAEDQTSVPQVRFNFVNIQELQDVERDA 306
Cdd:TIGR00617 233 AFNEQADKFYDIIQEGKVYYISK-GSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETAIPKIQFNFVKIDDIGGYEGNS 311
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   307 TVDIIGVLKEVQEVTQIVSKTTQKPYDKRELTLVDNTGYSVRCTIWGKTATNFDAQPESIVAFKGTKVSDFGGRSLSLLS 386
Cdd:TIGR00617 312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFDVSVQPVIAIKGVRVSDFGGKSLSTGG 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   387 SGTMAIDPDIPEAHHLKGWYDSSGRNNTFATHNNMQTlGGATGRKDDAKTISQVKEENLGTNEAPDYFALKATVVFIKQD 466
Cdd:TIGR00617 392 SSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMS-GRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPD 470
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   467 NFAYPGCRSEGCNRKVTDMGDGTWRCEKCQINHDRPQYRYIMSVNVNDHTGQLWLSCFDDTARVIMGKSADELMEIRETD 546
Cdd:TIGR00617 471 NALYRACPSEDCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELKEED 550
                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 85102469   547 ETRLPAEFEQANCRKLNFRCRAKMDTFGEQQRIRYQVMSVAPLDYKMEGNKLNELINS 604
Cdd:TIGR00617 551 PDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVDPVNYRAEAKYLLQEIEK 608
 
Name Accession Description Interval E-value
rpa1 TIGR00617
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
2-604 0e+00

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  Cd Length: 608  Bit Score: 708.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469     2 AGQITQGALDAMFNDPDRAQQQfPVPILQCLQIKTLDSKNGGagatERFRIVLSDLKNYVQCMMATQTNHLVHDGLLQRG 81
Cdd:TIGR00617   1 AVSLSNGAIALIMTNGEANGYP-PDPVLQVLDLKPINGAQDP----RRYRIVISDGIYYSKAMLATQLNPLVREGELQEG 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469    82 CIVRLKQYQAQCL--KGKNILIVLDLEVIQS-LGCPEKMGDPQPLGPR----------SAEPQQNPNLGSTGFYGVKSEP 148
Cdd:TIGR00617  76 TIIRLTKFEVNTIgkDGRKVLIVYELEVVKPeLKVRDKIGNPVTYEKYldswheeqvlASKPATNPANPPNAKAPKNEVA 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   149 T--QDTKPQFPRQMPSRNAsggQGSSTIYPIEGLSPFSHKWTIKARVTSKSDIKTWHKASGEGKLFSVNFLDESGEIRAT 226
Cdd:TIGR00617 156 SynNAANPERGNAPPAPNS---GSTRRVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDESGEIRAT 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   227 GFNDQVDQFYDLLQEGQVYYISTpCRVQLAKKQWSNLPNDYELTFERDTVIEKAEDQTSVPQVRFNFVNIQELQDVERDA 306
Cdd:TIGR00617 233 AFNEQADKFYDIIQEGKVYYISK-GSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETAIPKIQFNFVKIDDIGGYEGNS 311
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   307 TVDIIGVLKEVQEVTQIVSKTTQKPYDKRELTLVDNTGYSVRCTIWGKTATNFDAQPESIVAFKGTKVSDFGGRSLSLLS 386
Cdd:TIGR00617 312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFDVSVQPVIAIKGVRVSDFGGKSLSTGG 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   387 SGTMAIDPDIPEAHHLKGWYDSSGRNNTFATHNNMQTlGGATGRKDDAKTISQVKEENLGTNEAPDYFALKATVVFIKQD 466
Cdd:TIGR00617 392 SSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMS-GRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPD 470
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   467 NFAYPGCRSEGCNRKVTDMGDGTWRCEKCQINHDRPQYRYIMSVNVNDHTGQLWLSCFDDTARVIMGKSADELMEIRETD 546
Cdd:TIGR00617 471 NALYRACPSEDCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELKEED 550
                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 85102469   547 ETRLPAEFEQANCRKLNFRCRAKMDTFGEQQRIRYQVMSVAPLDYKMEGNKLNELINS 604
Cdd:TIGR00617 551 PDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVDPVNYRAEAKYLLQEIEK 608
Rep_fac-A_C pfam08646
Replication factor-A C terminal domain; This domain is found at the C terminal of replication ...
453-598 2.41e-82

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: 312238  Cd Length: 146  Bit Score: 258.31  E-value: 2.41e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   453 YFALKATVVFIKQDNFAYPGCRSEGCNRKVTDMGDGTWRCEKCQINHDRPQYRYIMSVNVNDHTGQLWLSCFDDTARVIM 532
Cdd:pfam08646   1 YFSVKATVVFIKQDNFWYPACPSEDCNKKVVEQGDGTWRCEKCDKNFPEPKYRYILSINISDHTGQLWVTLFNEAAEKIL 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85102469   533 GKSADELMEIRETDETRLPAEFEQANCRKLNFRCRAKMDTFGEQQRIRYQVMSVAPLDYKMEGNKL 598
Cdd:pfam08646  81 GKSADELGKLKEEDENEFEDIFQKANFREYIFRLRVKQETYNDESRVRYTVMSVAPVDYKKESKRL 146
RPA1_DBD_C cd04476
RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding ...
437-602 6.83e-73

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  Cd Length: 166  Bit Score: 234.12  E-value: 6.83e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 437 ISQVKEENLGTNEAPDYFALKATVVFIKQDNFAYPGCRseGCNRKVTDMGDGTWRCEKCQINHDRPQYRYIMSVNVNDHT 516
Cdd:cd04476   1 IAEIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP--GCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHT 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 517 GQLWLSCFDDTARVIMGKSADELMEIRETDETRLPAEFEQANCRKLNFRCRAKMDTFGEQQRIRYQVMSVAPLDYKMEGN 596
Cdd:cd04476  79 GEAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQDLVGKTFLFRVSVKEETYNDEGRIRYTVVKVAPVDYKKESK 158

                ....*.
gi 85102469 597 KLNELI 602
Cdd:cd04476 159 RLIQSI 164
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
132-469 5.03e-32

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


Pssm-ID: 224515  Cd Length: 407  Bit Score: 128.38  E-value: 5.03e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 132 QNPNLGSTGFYGVKSEPTQDTKPQFPRqMPSRNAsggQGSSTIYPIEGLSPFSHkwtikARVTSKSDIKTWHKASGEGKL 211
Cdd:COG1599 124 AYTSLYRGGKRLSVGRVGSVADVDDEE-DEARES---EDAREIGEESLLSPYQK-----ARVVVGSEIKTFDNQGGESKV 194
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 212 FSVNFLDEsgEIRATGFNDQVDqfydlLQEGQVYYISTpCRVQLAKKQWSNlPNDYELTFERDT--VIEKAEDQTSVPQV 289
Cdd:COG1599 195 FSNELEDE--ERGVIVFTDWDP-----SQDGDVYRIEG-ARVKTKNKQPEE-NLAEELVLRVEVrvAIEKAEREEFVDEV 265
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 290 RFNfVNIQELQdverDATVDIIGVlkevqEVTQIVSKTTQKPYDKRELTLVDNTGYsVRCTIWGKTATnFDAQPESIVAF 369
Cdd:COG1599 266 KES-VSLVEAD----GAVVDVTRV-----PECERVVRKGGCKGHGKDIGLDDLTGK-IRVTLWGDATE-VLINEESVEAL 333
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 370 KGTKVSDFGGrslsllssgtMAIDPDIPEAHHLKGWYDSSGRNNTFATHnnmqtlggatgrkddaKTISQVKEENLGTNE 449
Cdd:COG1599 334 KGINVEDASG----------IALSALDTEAVALEIWYDILGKYLRVTGD----------------AREDRYLIENLVESS 387
                       330       340
                ....*....|....*....|
gi 85102469 450 APDYFALKATVVFIKQDNFA 469
Cdd:COG1599 388 TWDDVDVRAEIEALKEEEEA 407
PRK12366 PRK12366
replication factor A; Reviewed
188-544 1.78e-10

replication factor A; Reviewed


Pssm-ID: 237078  Cd Length: 637  Bit Score: 63.53  E-value: 1.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  188 TIKARVTSKSDIKTWHKASGEGKLFSVNFLDESGEIRATGFNDQVDQFYDlLQEGQVYYISTpCRVqlaKKQWSNLPND- 266
Cdd:PRK12366 295 DVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILEN-LKEGDAVKIEN-CKV---RTYYDNEGEKr 369
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  267 YELTFERDTVIEKaEDQTSVPQVRFNFVNIQELQDVERDAT-VDIIGVLKEVQEVtQIVSKTTQKPYDKRELTLVDNTGy 345
Cdd:PRK12366 370 VDLNAGYSSEIIK-DESISFEEIEEKIYKIKDILNLEEDDNdITVIARVVEDYPV-NEFERSDGSKGKVRNIELADGTG- 446
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  346 SVRCTIWgKTATNFDAQPESIVAFKGTKVSDFGGR-SLSLLSSGTMAIDPDIPEAhhlkgwydssgrnntfathnnmqtl 424
Cdd:PRK12366 447 SIRLTLW-DDDAEIEIKEGDAIKILHPYVKENGDYlDLSIGRYGRIEINPEGEII------------------------- 500
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  425 ggatgrKDDAKTISQVKEEnlgtneapDYFALKATVVFIKQDNFAYPGCRSegCNRKVtDMGDGTWRCEKCQINhdRPQY 504
Cdd:PRK12366 501 ------KSNRKFIADLEED--------DTVEIRGTVVDIRKQKIILYLCPN--CRKRV-EEVDGEYICEFCGEV--EPNE 561
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 85102469  505 RYIMSVNVNDHTGQLWLSCFDDTARVIMGKSADELMEIRE 544
Cdd:PRK12366 562 LLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELNL 601
 
Name Accession Description Interval E-value
rpa1 TIGR00617
replication factor-a protein 1 (rpa1); All proteins in this family for which functions are ...
2-604 0e+00

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  Cd Length: 608  Bit Score: 708.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469     2 AGQITQGALDAMFNDPDRAQQQfPVPILQCLQIKTLDSKNGGagatERFRIVLSDLKNYVQCMMATQTNHLVHDGLLQRG 81
Cdd:TIGR00617   1 AVSLSNGAIALIMTNGEANGYP-PDPVLQVLDLKPINGAQDP----RRYRIVISDGIYYSKAMLATQLNPLVREGELQEG 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469    82 CIVRLKQYQAQCL--KGKNILIVLDLEVIQS-LGCPEKMGDPQPLGPR----------SAEPQQNPNLGSTGFYGVKSEP 148
Cdd:TIGR00617  76 TIIRLTKFEVNTIgkDGRKVLIVYELEVVKPeLKVRDKIGNPVTYEKYldswheeqvlASKPATNPANPPNAKAPKNEVA 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   149 T--QDTKPQFPRQMPSRNAsggQGSSTIYPIEGLSPFSHKWTIKARVTSKSDIKTWHKASGEGKLFSVNFLDESGEIRAT 226
Cdd:TIGR00617 156 SynNAANPERGNAPPAPNS---GSTRRVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDESGEIRAT 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   227 GFNDQVDQFYDLLQEGQVYYISTpCRVQLAKKQWSNLPNDYELTFERDTVIEKAEDQTSVPQVRFNFVNIQELQDVERDA 306
Cdd:TIGR00617 233 AFNEQADKFYDIIQEGKVYYISK-GSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETAIPKIQFNFVKIDDIGGYEGNS 311
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   307 TVDIIGVLKEVQEVTQIVSKTTQKPYDKRELTLVDNTGYSVRCTIWGKTATNFDAQPESIVAFKGTKVSDFGGRSLSLLS 386
Cdd:TIGR00617 312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFDVSVQPVIAIKGVRVSDFGGKSLSTGG 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   387 SGTMAIDPDIPEAHHLKGWYDSSGRNNTFATHNNMQTlGGATGRKDDAKTISQVKEENLGTNEAPDYFALKATVVFIKQD 466
Cdd:TIGR00617 392 SSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMS-GRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPD 470
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   467 NFAYPGCRSEGCNRKVTDMGDGTWRCEKCQINHDRPQYRYIMSVNVNDHTGQLWLSCFDDTARVIMGKSADELMEIRETD 546
Cdd:TIGR00617 471 NALYRACPSEDCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELKEED 550
                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 85102469   547 ETRLPAEFEQANCRKLNFRCRAKMDTFGEQQRIRYQVMSVAPLDYKMEGNKLNELINS 604
Cdd:TIGR00617 551 PDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVDPVNYRAEAKYLLQEIEK 608
Rep_fac-A_C pfam08646
Replication factor-A C terminal domain; This domain is found at the C terminal of replication ...
453-598 2.41e-82

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: 312238  Cd Length: 146  Bit Score: 258.31  E-value: 2.41e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   453 YFALKATVVFIKQDNFAYPGCRSEGCNRKVTDMGDGTWRCEKCQINHDRPQYRYIMSVNVNDHTGQLWLSCFDDTARVIM 532
Cdd:pfam08646   1 YFSVKATVVFIKQDNFWYPACPSEDCNKKVVEQGDGTWRCEKCDKNFPEPKYRYILSINISDHTGQLWVTLFNEAAEKIL 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85102469   533 GKSADELMEIRETDETRLPAEFEQANCRKLNFRCRAKMDTFGEQQRIRYQVMSVAPLDYKMEGNKL 598
Cdd:pfam08646  81 GKSADELGKLKEEDENEFEDIFQKANFREYIFRLRVKQETYNDESRVRYTVMSVAPVDYKKESKRL 146
RPA1_DBD_C cd04476
RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding ...
437-602 6.83e-73

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  Cd Length: 166  Bit Score: 234.12  E-value: 6.83e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 437 ISQVKEENLGTNEAPDYFALKATVVFIKQDNFAYPGCRseGCNRKVTDMGDGTWRCEKCQINHDRPQYRYIMSVNVNDHT 516
Cdd:cd04476   1 IAEIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP--GCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHT 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 517 GQLWLSCFDDTARVIMGKSADELMEIRETDETRLPAEFEQANCRKLNFRCRAKMDTFGEQQRIRYQVMSVAPLDYKMEGN 596
Cdd:cd04476  79 GEAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQDLVGKTFLFRVSVKEETYNDEGRIRYTVVKVAPVDYKKESK 158

                ....*.
gi 85102469 597 KLNELI 602
Cdd:cd04476 159 RLIQSI 164
REPA_OB_2 pfam16900
Replication protein A OB domain; Replication protein A contains two OB domains in it's DNA ...
296-393 2.94e-54

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: 318990  Cd Length: 98  Bit Score: 181.83  E-value: 2.94e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   296 IQELQDVERDATVDIIGVLKEVQEVTQIVSKTTQKPYDKRELTLVDNTGYSVRCTIWGKTATNFDAQPESIVAFKGTKVS 375
Cdd:pfam16900   1 ISDLENVEKDSIVDVIGVVKSVGPVTEITSKSTGKETQKRELTLVDDSGRSVRLTLWGKEAEQFDSSENPVVAFKGVRVS 80
                          90
                  ....*....|....*...
gi 85102469   376 DFGGRSLSLLSSGTMAID 393
Cdd:pfam16900  81 DFGGRSLSTISSSTLKIN 98
RPA1_DBD_A cd04474
RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding ...
176-278 1.64e-51

RPA1_DBD_A: A subfamily of OB folds corresponding 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 human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) 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. 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: 239920  Cd Length: 104  Bit Score: 174.74  E-value: 1.64e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 176 PIEGLSPFSHKWTIKARVTSKSDIKTWHKASGEGKLFSVNFLDE-SGEIRATGFNDQVDQFYDLLQEGQVYYISTpCRVQ 254
Cdd:cd04474   1 PISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEdGGEIRATFFNDAVDKFYDLLEVGKVYYISK-GSVK 79
                        90       100
                ....*....|....*....|....
gi 85102469 255 LAKKQWSNLPNDYELTFERDTVIE 278
Cdd:cd04474  80 VANKKFNTLKNDYEITFNRDTSII 103
RPA1_DBD_B cd04475
RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding ...
307-407 2.08e-46

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  Cd Length: 101  Bit Score: 160.44  E-value: 2.08e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 307 TVDIIGVLKEVQEVTQIVSKTTQKPYDKRELTLVDNTGYSVRCTIWGKTATNFDAQPESIVAFKGTKVSDFGGRSLSLLS 386
Cdd:cd04475   1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSENPVIAIKGVKVSEFNGKSLSTGS 80
                        90       100
                ....*....|....*....|.
gi 85102469 387 SGTMAIDPDIPEAHHLKGWYD 407
Cdd:cd04475  81 SSTIIINPDIPEAHKLRGWYD 101
RPA1N cd04477
RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 ...
8-109 1.46e-39

RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain 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). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C.


Pssm-ID: 239923  Cd Length: 97  Bit Score: 141.18  E-value: 1.46e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   8 GALDAMFNDPDRaqQQFPVPILQCLQIKTLDSKNGgagATERFRIVLSDLKNYVQCMMATQTNHLVHDGLLQRGCIVRLK 87
Cdd:cd04477   1 GALAAIFNGEDR--SNVIKPVLQVLNIKKIDSSNG---SSERYRILLSDGVYYVQAMLATQLNPLVESGQLQRGSIIRLK 75
                        90       100
                ....*....|....*....|..
gi 85102469  88 QYQAQCLKGKNILIVLDLEVIQ 109
Cdd:cd04477  76 RFICNVIKGKRILIILDLEVVQ 97
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
132-469 5.03e-32

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


Pssm-ID: 224515  Cd Length: 407  Bit Score: 128.38  E-value: 5.03e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 132 QNPNLGSTGFYGVKSEPTQDTKPQFPRqMPSRNAsggQGSSTIYPIEGLSPFSHkwtikARVTSKSDIKTWHKASGEGKL 211
Cdd:COG1599 124 AYTSLYRGGKRLSVGRVGSVADVDDEE-DEARES---EDAREIGEESLLSPYQK-----ARVVVGSEIKTFDNQGGESKV 194
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 212 FSVNFLDEsgEIRATGFNDQVDqfydlLQEGQVYYISTpCRVQLAKKQWSNlPNDYELTFERDT--VIEKAEDQTSVPQV 289
Cdd:COG1599 195 FSNELEDE--ERGVIVFTDWDP-----SQDGDVYRIEG-ARVKTKNKQPEE-NLAEELVLRVEVrvAIEKAEREEFVDEV 265
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 290 RFNfVNIQELQdverDATVDIIGVlkevqEVTQIVSKTTQKPYDKRELTLVDNTGYsVRCTIWGKTATnFDAQPESIVAF 369
Cdd:COG1599 266 KES-VSLVEAD----GAVVDVTRV-----PECERVVRKGGCKGHGKDIGLDDLTGK-IRVTLWGDATE-VLINEESVEAL 333
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 370 KGTKVSDFGGrslsllssgtMAIDPDIPEAHHLKGWYDSSGRNNTFATHnnmqtlggatgrkddaKTISQVKEENLGTNE 449
Cdd:COG1599 334 KGINVEDASG----------IALSALDTEAVALEIWYDILGKYLRVTGD----------------AREDRYLIENLVESS 387
                       330       340
                ....*....|....*....|
gi 85102469 450 APDYFALKATVVFIKQDNFA 469
Cdd:COG1599 388 TWDDVDVRAEIEALKEEEEA 407
Rep-A_N pfam04057
Replication factor-A protein 1, N-terminal domain;
5-110 4.08e-19

Replication factor-A protein 1, N-terminal domain;


Pssm-ID: 281980  Cd Length: 99  Bit Score: 84.29  E-value: 4.08e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469     5 ITQGALDAMFNDPDRAQQqfpvPILQCLQIKTLDSKNGGagatERFRIVLSDLKNYVQCMMATQTNHLVHDGLLQRGCIV 84
Cdd:pfam04057   1 LTPGAIAAILATGDASDK----PVLQVVDLKPINSGNSP----ERYRFLLSDGKNKSKAMLATQLNPLVISGKLQNGSIV 72
                          90       100
                  ....*....|....*....|....*..
gi 85102469    85 RLKQYQAQCLK-GKNILIVLDLEVIQS 110
Cdd:pfam04057  73 QLTDYTVNDIKeGRRILIVLELEVLVS 99
RPA1_DBD_B_like cd04481
RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB ...
309-403 2.92e-12

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  Cd Length: 106  Bit Score: 64.99  E-value: 2.92e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 309 DIIGVLKEVQEVTQIVSKTtqKPYDKRELTLVDNTGYSVRCTIWGKTATNFDA------QPESIVA-FKGTKVSDFGG-R 380
Cdd:cd04481   1 DVIGVIVDVGPLEELPPVN--KPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAkfqsagNGEPVVAvLRFWKIKEYKGpK 78
                        90       100
                ....*....|....*....|....
gi 85102469 381 SLSLLSSGT-MAIDPDIPEAHHLK 403
Cdd:cd04481  79 SLSNSFGASkVYINPDIPEVPEIK 102
PRK12366 PRK12366
replication factor A; Reviewed
188-544 1.78e-10

replication factor A; Reviewed


Pssm-ID: 237078  Cd Length: 637  Bit Score: 63.53  E-value: 1.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  188 TIKARVTSKSDIKTWHKASGEGKLFSVNFLDESGEIRATGFNDQVDQFYDlLQEGQVYYISTpCRVqlaKKQWSNLPND- 266
Cdd:PRK12366 295 DVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILEN-LKEGDAVKIEN-CKV---RTYYDNEGEKr 369
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  267 YELTFERDTVIEKaEDQTSVPQVRFNFVNIQELQDVERDAT-VDIIGVLKEVQEVtQIVSKTTQKPYDKRELTLVDNTGy 345
Cdd:PRK12366 370 VDLNAGYSSEIIK-DESISFEEIEEKIYKIKDILNLEEDDNdITVIARVVEDYPV-NEFERSDGSKGKVRNIELADGTG- 446
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  346 SVRCTIWgKTATNFDAQPESIVAFKGTKVSDFGGR-SLSLLSSGTMAIDPDIPEAhhlkgwydssgrnntfathnnmqtl 424
Cdd:PRK12366 447 SIRLTLW-DDDAEIEIKEGDAIKILHPYVKENGDYlDLSIGRYGRIEINPEGEII------------------------- 500
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  425 ggatgrKDDAKTISQVKEEnlgtneapDYFALKATVVFIKQDNFAYPGCRSegCNRKVtDMGDGTWRCEKCQINhdRPQY 504
Cdd:PRK12366 501 ------KSNRKFIADLEED--------DTVEIRGTVVDIRKQKIILYLCPN--CRKRV-EEVDGEYICEFCGEV--EPNE 561
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 85102469  505 RYIMSVNVNDHTGQLWLSCFDDTARVIMGKSADELMEIRE 544
Cdd:PRK12366 562 LLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELNL 601
PRK12366 PRK12366
replication factor A; Reviewed
174-371 4.44e-09

replication factor A; Reviewed


Pssm-ID: 237078  Cd Length: 637  Bit Score: 59.29  E-value: 4.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  174 IYPIEGLSPFSHKWTIKARVTSKSDIKTWHKASG-EGKLFSVNFLDESGEIRATGFNDQVDQFYDlLQEGQVYYIsTPCR 252
Cdd:PRK12366  63 DFKISDIEEGQINVEITGRIIEISNIKTFTRKDGsTGKLANITIADNTGTIRLTLWNDNAKLLKG-LKEGDVIKI-ENAR 140
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  253 VqlakKQWSnlpNDYELTFERDTVIEKAE--DQTSVPQVRFNFvNIQELQDvERDATvdIIGVLKEVQEVTQIvSKTTQK 330
Cdd:PRK12366 141 S----RKWN---NDVELNSGSETRIDKLEkyDESRYPIIKENY-DIPELEP-NLSAT--IEGEVTKAYPIKEF-TRKDGS 208
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 85102469  331 PYDKRELTLVDNTGySVRCTIWGKTaTNFDAQPESIVAFKG 371
Cdd:PRK12366 209 EGKLKSFILKDDTG-SIRVTLWNDL-TDIEVNKGDIVRVKG 247
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
187-277 3.96e-07

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: 307482  Cd Length: 75  Bit Score: 49.15  E-value: 3.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   187 WTIKARVTSKSdiktwhkaSGEGKLFSVNFLDESGEIRATGFNDQVDQFYDLLQEGQVYYIStpCRVQLAKKqwsnlpND 266
Cdd:pfam01336   1 VTVAGRVTSIR--------RSGGKLLFLTLRDGTGSIQVVVFKEEAEKLAKKLKEGDVVRVT--GKVKKRPG------GE 64
                          90
                  ....*....|.
gi 85102469   267 YELTFERDTVI 277
Cdd:pfam01336  65 LELVVEEIELL 75
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
188-279 6.04e-06

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  Cd Length: 82  Bit Score: 45.69  E-value: 6.04e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 188 TIKARVTSKSDIKTWHKASGEGKLFSVNFLDESGEIRATGFNDQVDqfyDLLQEGQVYYISTpCRVqlakKQWSnlpNDY 267
Cdd:cd04491   1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETGTIRFTLWDEKAA---DDLEPGDVVRIEN-AYV----REFN---GRL 69
                        90
                ....*....|..
gi 85102469 268 ELTFERDTVIEK 279
Cdd:cd04491  70 ELSVGKNSEIEK 81
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
216-277 3.00e-05

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  Cd Length: 86  Bit Score: 43.78  E-value: 3.00e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85102469 216 FLDESGE-IRATGFNDQVDQFYDLLQEGQVYYISTpCRVQLAKKQWSNLPNDYELTFERDTVI 277
Cdd:cd04480  25 LVDEKGNrIHATIPKRLAAKFRPLLKEGKWYTISN-FEVAPNTGSYRPTDHPYKIKFMSDTVV 86
PRK14699 PRK14699
replication factor A; Provisional
173-356 3.11e-04

replication factor A; Provisional


Pssm-ID: 173162  Cd Length: 484  Bit Score: 43.45  E-value: 3.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  173 TIYPIEGLSPFSHKWTIKARVTSKSDIKTWHKASGE-GKLFSVNFLDESGEIRATGFNDQVDQFYDLLQEGQVYYISTPC 251
Cdd:PRK14699 275 EFTPIEDIKADMNNINISGRVLDISEVRTFEKKDGSpGRVGNLLLGDSTGKIRLTLWDEKTNFLDEIDFDETVEVLNAYS 354
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  252 RVQLAKKQwsnlpndYELTFERDTVIEKAEDQTsvpQVRFNFVNIQEL---QDVERDATVDIIGVLKEVQE---VTQIVS 325
Cdd:PRK14699 355 RENTFSQQ-------VELNLGARGIIQKSEKKV---EYREKFTDIADIipgESYSVQGKVSEIGELREFERedgTENVVA 424
                        170       180       190
                 ....*....|....*....|....*....|.
gi 85102469  326 KttqkpydkreLTLVDNTGySVRCTIWGKTA 356
Cdd:PRK14699 425 N----------LQLKDETG-SIRLTLWGEQA 444
RPA2_OBF_family cd03524
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold ...
188-269 3.48e-04

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  Cd Length: 75  Bit Score: 40.42  E-value: 3.48e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469 188 TIKARVTSKSDIKTWhkasgeGKLFSVNFLDESGE-IRATGFNDQVDQFYDLLQEGQVYYIStpCRVQLAKKQWSNLPND 266
Cdd:cd03524   1 TIVGIVVAVEEIRTE------GKVLIFTLTDGTGGtIRVTLFGELAEELENLLKEGQVVYIK--GKVKKFRGRLQLIVES 72

                ...
gi 85102469 267 YEL 269
Cdd:cd03524  73 IEL 75
PRK15491 PRK15491
replication factor A; Provisional
177-352 4.83e-04

replication factor A; Provisional


Pssm-ID: 185388  Cd Length: 374  Bit Score: 42.56  E-value: 4.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  177 IEGLSPFSHKWTIKARVTSKSDIKTWHKASG-EGKLFSVNFLDESGEIRATGFNDQVdqfyDLLQEGQvyyISTPCRVQL 255
Cdd:PRK15491  60 IADINESSSNVNFTAKVVSIFEPKEFNRNDGtTGRVGNIIVADETGSIRLTLWDDLA----DLIKTGD---IEVGKSLNI 132
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  256 ---AKKQWSNLpndyELTFERDTVIEKAEDQTSVPqvrfnfVNIQELQDVER-DATVDIIGVLKEVQEVtqivsKTTQK- 330
Cdd:PRK15491 133 sgyAKEGYSGI----EVNIGRYGGISESDENVKAS------INSQKISDIKDgDSDINIVGKVLDISDV-----RTFQKk 197
                        170       180
                 ....*....|....*....|....*
gi 85102469  331 ---PYDKRELTLVDNTGySVRCTIW 352
Cdd:PRK15491 198 dgsQGRVRNITIGDETG-KIRVTLW 221
PRK12366 PRK12366
replication factor A; Reviewed
174-342 8.80e-04

replication factor A; Reviewed


Pssm-ID: 237078  Cd Length: 637  Bit Score: 41.96  E-value: 8.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  174 IYPIEGLSPFSHKW---TIKARVTSKSDIKTWHKASG-EGKLFSVNFLDESGEIRATGFNDQVDQfydLLQEGQVYYIST 249
Cdd:PRK12366 395 IYKIKDILNLEEDDndiTVIARVVEDYPVNEFERSDGsKGKVRNIELADGTGSIRLTLWDDDAEI---EIKEGDAIKILH 471
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  250 PcrvqLAKKQwsnlpNDY-ELTFERDTVIEKAEDQTSVPQVRfnfVNIQELQDverDATVDIIGVLKEVQEVTQIVSKTt 328
Cdd:PRK12366 472 P----YVKEN-----GDYlDLSIGRYGRIEINPEGEIIKSNR---KFIADLEE---DDTVEIRGTVVDIRKQKIILYLC- 535
                        170
                 ....*....|....
gi 85102469  329 qkPYDKRELTLVDN 342
Cdd:PRK12366 536 --PNCRKRVEEVDG 547
dnaE PRK06920
DNA polymerase III DnaE; Reviewed
197-281 1.30e-03

DNA polymerase III DnaE; Reviewed


Pssm-ID: 180749  Cd Length: 1107  Bit Score: 41.71  E-value: 1.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469   197 SDIKTWHKASGEGKLFsVNFLDESGEIRATGFNDQVDQFYDLLQEGQVYYISTPCRVQLAKKQWsnLPNDYELTFERDTV 276
Cdd:PRK06920  953 TSVKVIRTKKGQKMAF-ITFCDQNDEMEAVVFPETYIHFSDKLQEGAIVLVDGTIELRNHKLQW--IVNGLYPLEEMDAY 1029

                  ....*
gi 85102469   277 IEKAE 281
Cdd:PRK06920 1030 EEKKD 1034
RPA2_OBF_family cd03524
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold ...
320-380 2.27e-03

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  Cd Length: 75  Bit Score: 37.73  E-value: 2.27e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85102469 320 VTQIVSKTTQKPYDKreLTLVDNTGYSVRCTIWGKTA--TNFDAQPESIVAFKGtKVSDFGGR 380
Cdd:cd03524   6 VVAVEEIRTEGKVLI--FTLTDGTGGTIRVTLFGELAeeLENLLKEGQVVYIKG-KVKKFRGR 65
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
172-248 2.30e-03

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794  Cd Length: 681  Bit Score: 40.90  E-value: 2.30e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 85102469  172 STIYPIEGLSPFSHKwTIKARVTSKSdiktwhKASGEGKLFSVNFLDESGEIRATGFNDQVDQFYDLLQEGQVYYIS 248
Cdd:PRK10917  48 TRLKPIAELRPGEKV-TVEGEVLSAE------VVFGKRRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVGKRVAVY 117
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
139-254 4.69e-03

DNA polymerase III, alpha subunit [Replication, recombination and repair];


Pssm-ID: 223660  Cd Length: 1139  Bit Score: 39.96  E-value: 4.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85102469  139 TGFYgVKSEPTQDTKPQFPRQMpsrnasggqgsSTIYPIEGLSPFSHKWTIKARVTSKSDIKTwhKASGEGKLFsVNFLD 218
Cdd:COG0587  943 LGLY-LSGHPLDFLYEDLLARG-----------LTPIRLLDLVEDGRRVVLAGGIVAVRQRPT--KAKGNKMAF-LTLED 1007
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 85102469  219 ESGEIRATGFNDQVDQFYDLLQEGQVYYIStpCRVQ 254
Cdd:COG0587 1008 ETGILEVVVFPSEYERYRRLLLEGRLLIVK--GKVQ 1041
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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