NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|445647578|gb|ELZ00552|]
View 

replication factor A [Natrialba asiatica DSM 12278]

Protein Classification

PRK07218 family protein( domain architecture ID 11482639)

PRK07218 family protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK07218 PRK07218
Single-stranded DNA binding protein;
1-423 0e+00

Single-stranded DNA binding protein;


:

Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 688.28  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578   1 MELDDHAEDLASDLGVDKEEVKSDLQNLVEYSVPVDEAKQSLRRKYGDGASGGssTPSSREIGEITPEDGNVTVTCTVLT 80
Cdd:PRK07218   2 MKLDPHAEELASDLGVDKEEVKEELENLVAYSVPIDEAKQSIRRKYGGGGSGG--TPSSKDIKELSTDDKNVTVTGRVLT 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  81 AGKRSIRYQGSDHVIVEGELADETGTIDYTAWEDFGLSPGDTITAGNAGVREWDGEPELNIGESTSLSFVDESLQITQEI 160
Cdd:PRK07218  80 IGERSIRYQGDDHVIYEGILADETGTISYTAWKDFGLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSLPPYSI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 161 GGDATLADLQTGDRARAVEVTVLECERRTIDGRDGETEILSGVFGDESGRLPFTNWDPAPEIEDGGPVRIENAYVQEFRG 240
Cdd:PRK07218 160 GGDKKLIDLGPGDRGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPLPEIEIGASIRIEDAYVREFRG 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 241 VPEINVSEFSTVTELDREIEVGADTTTMAIREAVETGGIYDVELVGNVIAVRDGSGLIQRCPECYRVIQKGQCRTHGDVD 320
Cdd:PRK07218 240 VPSVNVSEFTTVEALDREVSVSKDPPRLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGRVIQKGQCRSHGAVE 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 321 GIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDDALEQAREAMDQSVVADTIRERIVGHEFSVRGHLSVDEYGANLD 400
Cdd:PRK07218 320 GEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRERLVGREYRVRGNLSVDEYGANLV 399

                        410       420
                 ....*....|....*....|...
gi 445647578 401 AERFGESDDDPQVRARAFLEEVE 423
Cdd:PRK07218 400 AESFWVPDDDPAKRAVALLAEVG 422
 
Name Accession Description Interval E-value
PRK07218 PRK07218
Single-stranded DNA binding protein;
1-423 0e+00

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 688.28  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578   1 MELDDHAEDLASDLGVDKEEVKSDLQNLVEYSVPVDEAKQSLRRKYGDGASGGssTPSSREIGEITPEDGNVTVTCTVLT 80
Cdd:PRK07218   2 MKLDPHAEELASDLGVDKEEVKEELENLVAYSVPIDEAKQSIRRKYGGGGSGG--TPSSKDIKELSTDDKNVTVTGRVLT 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  81 AGKRSIRYQGSDHVIVEGELADETGTIDYTAWEDFGLSPGDTITAGNAGVREWDGEPELNIGESTSLSFVDESLQITQEI 160
Cdd:PRK07218  80 IGERSIRYQGDDHVIYEGILADETGTISYTAWKDFGLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSLPPYSI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 161 GGDATLADLQTGDRARAVEVTVLECERRTIDGRDGETEILSGVFGDESGRLPFTNWDPAPEIEDGGPVRIENAYVQEFRG 240
Cdd:PRK07218 160 GGDKKLIDLGPGDRGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPLPEIEIGASIRIEDAYVREFRG 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 241 VPEINVSEFSTVTELDREIEVGADTTTMAIREAVETGGIYDVELVGNVIAVRDGSGLIQRCPECYRVIQKGQCRTHGDVD 320
Cdd:PRK07218 240 VPSVNVSEFTTVEALDREVSVSKDPPRLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGRVIQKGQCRSHGAVE 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 321 GIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDDALEQAREAMDQSVVADTIRERIVGHEFSVRGHLSVDEYGANLD 400
Cdd:PRK07218 320 GEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRERLVGREYRVRGNLSVDEYGANLV 399

                        410       420
                 ....*....|....*....|...
gi 445647578 401 AERFGESDDDPQVRARAFLEEVE 423
Cdd:PRK07218 400 AESFWVPDDDPAKRAVALLAEVG 422
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
163-425 1.26e-87

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


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 268.47  E-value: 1.26e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 163 DATLADLQTGDRARAVEVTVLEC-ERRTIDGRDG-ETEILSGVFGDESGRLPFTNWDPA--PEIEDGGPVRIENAYVQEF 238
Cdd:COG1599   21 EVKISDLSPGDRDVNVEGRVLEIgEERTFDRKDGsEGRVQSGVIGDETGRIRFTLWDDKadLELEEGDVVRIENAYVREF 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 239 RGVPEINVSEFSTVTELDREIEVGADTTTMAIREAVETGGiydVELVGNVIAVRDGSGLIQRCPECYRVIQK-GQCRTHG 317
Cdd:COG1599  101 NGGPELNLGERTTIEKLDEDVEVIPDEERTPIGDIEPGGT---VSVTGTIVSVRPGSGFIKRCPECNRVLQDdGQCREHG 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 318 DVDGIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDDALEQAREAMDQSVVADTIRERIVGHEFSVRGHLSvDEYGa 397
Cdd:COG1599  178 KVRGEYDLRIKAVLDDGTGTIRVVLWGELTEELYGIDLGDAIEIADDALDQGVVAEEIREKLLGRYYRVRGNLS-DRYG- 255

                        250       260
                 ....*....|....*....|....*...
gi 445647578 398 nLDAERFGESDDDPQVRARAFLEEVERV 425
Cdd:COG1599  256 -LLADSIELSADDPAERAEELLAEVEGD 282
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 178-255 9.01e-15

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 69.19  E-value: 9.01e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 178 VEVTVLEC-ERRTIDGRDGETEILSGVFGDESGRLPFTNWDP--APEIEDGGPVRIENAYVQEFRGVPEINVSEFSTVTE 254
Cdd:cd04491    2 VEGKVLSIsEPREFTRDGSEGKVQSGLVGDETGTIRFTLWDEkaADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81


                 .
gi 445647578 255 L 255
Cdd:cd04491   82 L 82
 
Name Accession Description Interval E-value
PRK07218 PRK07218
Single-stranded DNA binding protein;
1-423 0e+00

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 688.28  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578   1 MELDDHAEDLASDLGVDKEEVKSDLQNLVEYSVPVDEAKQSLRRKYGDGASGGssTPSSREIGEITPEDGNVTVTCTVLT 80
Cdd:PRK07218   2 MKLDPHAEELASDLGVDKEEVKEELENLVAYSVPIDEAKQSIRRKYGGGGSGG--TPSSKDIKELSTDDKNVTVTGRVLT 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  81 AGKRSIRYQGSDHVIVEGELADETGTIDYTAWEDFGLSPGDTITAGNAGVREWDGEPELNIGESTSLSFVDESLQITQEI 160
Cdd:PRK07218  80 IGERSIRYQGDDHVIYEGILADETGTISYTAWKDFGLSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDSSLPPYSI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 161 GGDATLADLQTGDRARAVEVTVLECERRTIDGRDGETEILSGVFGDESGRLPFTNWDPAPEIEDGGPVRIENAYVQEFRG 240
Cdd:PRK07218 160 GGDKKLIDLGPGDRGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPLPEIEIGASIRIEDAYVREFRG 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 241 VPEINVSEFSTVTELDREIEVGADTTTMAIREAVETGGIYDVELVGNVIAVRDGSGLIQRCPECYRVIQKGQCRTHGDVD 320
Cdd:PRK07218 240 VPSVNVSEFTTVEALDREVSVSKDPPRLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGRVIQKGQCRSHGAVE 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 321 GIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDDALEQAREAMDQSVVADTIRERIVGHEFSVRGHLSVDEYGANLD 400
Cdd:PRK07218 320 GEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRERLVGREYRVRGNLSVDEYGANLV 399

                        410       420
                 ....*....|....*....|...
gi 445647578 401 AERFGESDDDPQVRARAFLEEVE 423
Cdd:PRK07218 400 AESFWVPDDDPAKRAVALLAEVG 422
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
163-425 1.26e-87

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


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 268.47  E-value: 1.26e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 163 DATLADLQTGDRARAVEVTVLEC-ERRTIDGRDG-ETEILSGVFGDESGRLPFTNWDPA--PEIEDGGPVRIENAYVQEF 238
Cdd:COG1599   21 EVKISDLSPGDRDVNVEGRVLEIgEERTFDRKDGsEGRVQSGVIGDETGRIRFTLWDDKadLELEEGDVVRIENAYVREF 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 239 RGVPEINVSEFSTVTELDREIEVGADTTTMAIREAVETGGiydVELVGNVIAVRDGSGLIQRCPECYRVIQK-GQCRTHG 317
Cdd:COG1599  101 NGGPELNLGERTTIEKLDEDVEVIPDEERTPIGDIEPGGT---VSVTGTIVSVRPGSGFIKRCPECNRVLQDdGQCREHG 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 318 DVDGIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDDALEQAREAMDQSVVADTIRERIVGHEFSVRGHLSvDEYGa 397
Cdd:COG1599  178 KVRGEYDLRIKAVLDDGTGTIRVVLWGELTEELYGIDLGDAIEIADDALDQGVVAEEIREKLLGRYYRVRGNLS-DRYG- 255

                        250       260
                 ....*....|....*....|....*...
gi 445647578 398 nLDAERFGESDDDPQVRARAFLEEVERV 425
Cdd:COG1599  256 -LLADSIELSADDPAERAEELLAEVEGD 282
PRK07217 PRK07217
replication factor A; Reviewed
 202-404 4.04e-48

replication factor A; Reviewed


Pssm-ID: 235970 [Multi-domain]  Cd Length: 311  Bit Score: 167.12  E-value: 4.04e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 202 GVFGDESGRLPFTNWDPA--PEIEDGGPVRIENAYVQEFRGVPEINVSEFSTVTELDREIEVGADTTtmaireavetggi 279
Cdd:PRK07217 106 GLLGDETGTIKFTKWAKSdlPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDIEVGDDEV------------- 172

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 280 ydvELVGNVIAVRDGSGLIQRCPE--CYRVIQKGQCRTHGDVDGIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDD 357
Cdd:PRK07217 173 ---EVEGALVDIQSGSGLIKRCPEedCTRVLQNGRCSEHGKVEGEFDLRIKGVLDDGEEVQEVIFNREATEELTGITLEE 249

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 445647578 358 ALEQAREAMDQSVVADTIRERIVGHEFSVRGHL--------SVDEYGANLDAERF 404
Cdd:PRK07217 250 AKQMAMDALDTGVVLDELKEKLLGRYYRVTGPTlgrylladSVEPLTGPVDAEEL 304
PRK06386 PRK06386
replication factor A; Reviewed
 61-410 3.85e-29

replication factor A; Reviewed


Pssm-ID: 235790 [Multi-domain]  Cd Length: 358  Bit Score: 116.93  E-value: 3.85e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  61 EIGEITPEDGNVTVTCTVLTAGKRSIRYQGSDHVIVEGELADETGTIDYTAWE-DFGLSPGDTITAGNAGVREWDGEPEL 139
Cdd:PRK06386   4 KISDINAARQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEfPDAVKSGDVIEIKYCYSKEYNGKIRI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 140 NI-GESTSLSFVDESLQITQEIgGDATLADLQTGDRARAVEVTVLECERRTIDGRDGETEILSGVFGDESGRLPFTNWdp 218
Cdd:PRK06386  84 YFdSRSEVMLKPDENIEVKRTY-KLVKIRDLSLVTPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTARVRISSF-- 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 219 APEIEDGGPVRIENAYVQEFRGVPEINVSEFSTVTELDREIEVGADTTTMA-IREAVetGGIydvELVGNVIAVRDGSGL 297
Cdd:PRK06386 161 GKPLEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDINLESRNIFIFeIKSPV--GGI---TIMGFIVSVGQGSRI 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 298 IQRCPECYRVIQKGQCRTHGDVDGIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDDALEQAREAMDQSVvadtIRE 377
Cdd:PRK06386 236 FTKCSVCNKIIEDGVCKDHPDAPVYLDIFGYFTISDGTGFVTCYANKDSFLPYININENEFARKASSMNPNML----IKK 311

                        330       340       350
                 ....*....|....*....|....*....|...
gi 445647578 378 RIVGHEFSVRGHLSVDEYGANLDAERFGESDDD 410
Cdd:PRK06386 312 NLLGKCFSVTGDLRKKDDEIDMNVISAKSITAD 344
PRK12366 PRK12366
replication factor A; Reviewed
 68-394 7.19e-15

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 76.62  E-value: 7.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  68 EDGN-VTVTCTVLT-AGKRSIRYQGSDHVIVEGELADETGTIDYTAWED-----FGLSPGDTITAGNAGVREWDG----- 135
Cdd:PRK12366 289 EDGEeVDVKGRIIAiSDKREVERDDRTAEVQDIELADGTGRVRVSFWGEkakilENLKEGDAVKIENCKVRTYYDnegek 368

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 136 EPELNIGESTSLSfVDESLQ---ITQEIGGDATLADLQTGDRARAVEVTVLEC-ERRTIDGRDGET-EILSGVFGDESGR 210
Cdd:PRK12366 369 RVDLNAGYSSEII-KDESISfeeIEEKIYKIKDILNLEEDDNDITVIARVVEDyPVNEFERSDGSKgKVRNIELADGTGS 447

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 211 LPFTNWDPAPEIE--DGGPVRIENAYVQEFRGVPEINVSEFSTVTELDREIEVGADTTTMAIREAVETggiydVELVGNV 288
Cdd:PRK12366 448 IRLTLWDDDAEIEikEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGEIIKSNRKFIADLEEDDT-----VEIRGTV 522

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 289 IAVRDGSGLIQRCPECYR----VIQKGQCRTHGDVDGIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDDALEQARE 364
Cdd:PRK12366 523 VDIRKQKIILYLCPNCRKrveeVDGEYICEFCGEVEPNELLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELNLE 602

                        330       340       350
                 ....*....|....*....|....*....|
gi 445647578 365 AMdqsvvadtirERIVGHEFSVRGHLSVDE 394
Cdd:PRK12366 603 AL----------EDLLGEEVVFYGNVSFRN 622
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 178-255 9.01e-15

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 69.19  E-value: 9.01e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 178 VEVTVLEC-ERRTIDGRDGETEILSGVFGDESGRLPFTNWDP--APEIEDGGPVRIENAYVQEFRGVPEINVSEFSTVTE 254
Cdd:cd04491    2 VEGKVLSIsEPREFTRDGSEGKVQSGLVGDETGTIRFTLWDEkaADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81


                 .
gi 445647578 255 L 255
Cdd:cd04491   82 L 82
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 167-258 2.05e-11

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 61.21  E-value: 2.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 167 ADLQTGDRARAVEVTVLEC-ERRTIDGRDGETEILSGVFGDESGRLPFTNW-DPAPEIEDGGPVRIENAYVQEFRGVPEI 244
Cdd:PRK06461   8 KDLKPGMERVNVTVRVLEVgEPKVIQTKGGPRTISEAVVGDETGRVKLTLWgEQAGSLKEGEVVEIENAWTTLYRGKVQL 87

                         90
                 ....*....|....
gi 445647578 245 NVSEFSTVTELDRE 258
Cdd:PRK06461  88 NVGKYGSISESDDE 101
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 73-150 4.72e-11

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 58.79  E-value: 4.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  73 TVTCTVLTAG-KRSIRYQGSDHVIVEGELADETGTIDYTAWED---FGLSPGDTITAGNAGVREWDGEPELNIGESTSLS 148
Cdd:cd04491    1 SVEGKVLSISePREFTRDGSEGKVQSGLVGDETGTIRFTLWDEkaaDDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                 ..
gi 445647578 149 FV 150
Cdd:cd04491   81 KL 82
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 58-153 5.63e-11

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 60.05  E-value: 5.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  58 SSREIGEITPEDGNVTVTCTVLTAG-KRSIRYQGSDHVIVEGELADETGTIDYTAWEDFG--LSPGDTITAGNAGVREWD 134
Cdd:PRK06461   3 MITKIKDLKPGMERVNVTVRVLEVGePKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQAgsLKEGEVVEIENAWTTLYR 82

                         90
                 ....*....|....*....
gi 445647578 135 GEPELNIGESTSLSFVDES 153
Cdd:PRK06461  83 GKVQLNVGKYGSISESDDE 101
PRK14699 PRK14699
replication factor A; Provisional
 59-360 1.17e-08

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 56.93  E-value: 1.17e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  59 SREIGEITPEDGNVTVTCTVLTA--GKRSIRYQGSDHVIVEGELADETGTIDYTAWEDFG-------LSPGDTITAGNAG 129
Cdd:PRK14699  57 SVKIENITPESGPVNFIARVVSVfdTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMAdlikagkIKAGQTLQISGYA 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 130 VREWDGePELNIGESTSLSFVDESLQItqeIGGDATLADLQTGDRARAVEVTVLE-CERRTIDGRDGET-EILSGVFGDE 207
Cdd:PRK14699 137 KQGYSG-VEVNIGNNGVLTESEEEIDV---AANSQKIKDIKDGMGDLNLTGKVLEiSEIRTFQRKDGTSgKVGNLLLGDE 212

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 208 SGRLPFTNWDPAPE----IEDGGPVRIENAYVQE--FRGVPEINVSEFSTVTELDREIEVGADTTTMAireavetggiyD 281
Cdd:PRK14699 213 TGTLRVTLWDDKTDflnqIEYGDTVELINAYAREnaFTQKVELQVGNRSIIRKSEKKVEYEEEFTPIE-----------D 281

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 445647578 282 VELVGNVIAVrdgSGliqrcpecyRVIQKGQCRTHGDVDGIDDLRVKAILDDGTGTVTVVLDDELTADVYGGTLDDALE 360
Cdd:PRK14699 282 IKADMNNINI---SG---------RVLDISEVRTFEKKDGSPGRVGNLLLGDSTGKIRLTLWDEKTNFLDEIDFDETVE 348
PRK07211 PRK07211
single-stranded DNA binding protein;
92-279 2.00e-08

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 56.30  E-value: 2.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  92 DHVIVEGELADETGTIDYTAWEDFGLSPGDTITAGNA---GVREWDGEPELNIgeSTSLSFVDESLQITQEIGGDATLAD 168
Cdd:PRK07211  89 DGRVINVEVADETGSVRVAFWDEQAVAAEEELEVGQVlriKGRPKDGYNGLEV--SVDKVEPDPDAEIDVQIGDTYTVED 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 169 LQTGDRARAVEVTVLECER-RTIDGRDG-ETEILSGVFGDESGRLPFTNWDP----APEIEDGGPVRIENAYVQEFRGVP 242
Cdd:PRK07211 167 LSLGLSDVTLVGVVLDTDSvRTFDRDDGsEGRVSNLTVGDETGRVRVTLWDDradlAEELDAGESVEIVDGYVRERDGSL 246

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 445647578 243 EINVSEFSTVTELDREIEVGADTT---TMAIREAVETGGI 279
Cdd:PRK07211 247 ELHVGDRGAVEEVDEDVEYVPDTTpieSLEIDETVDIAGV 286
PRK12366 PRK12366
replication factor A; Reviewed
 99-359 1.51e-06

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 50.43  E-value: 1.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  99 ELADETGTIDYTAWED-----FGLSPGDTITAGNAGVREWDGEPELNIGESTS---LSFVDESLqiTQEIGGDATLADLQ 170
Cdd:PRK12366 105 TIADNTGTIRLTLWNDnakllKGLKEGDVIKIENARSRKWNNDVELNSGSETRidkLEKYDESR--YPIIKENYDIPELE 182

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 171 TGDRArAVEVTVLEC-ERRTIDGRDGETEIL-SGVFGDESGRLPFTNWDPAPEIE--DGGPVRIENAYVQEFRGVPEINV 246
Cdd:PRK12366 183 PNLSA-TIEGEVTKAyPIKEFTRKDGSEGKLkSFILKDDTGSIRVTLWNDLTDIEvnKGDIVRVKGYVKQGYRTGLEISA 261

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 247 SEFSTVTELDREIEVGADTTTMAIREAVEtgGIYdVELVGNVIAVRDGsgliqrcpecyRVIQKGqcrthgdvDGIDDLR 326
Cdd:PRK12366 262 NNIEILEKLEKEEKELEIVNIEELTEFED--GEE-VDVKGRIIAISDK-----------REVERD--------DRTAEVQ 319

                        250       260       270
                 ....*....|....*....|....*....|...
gi 445647578 327 vKAILDDGTGTVTVVLDDELTADVYGGTLDDAL 359
Cdd:PRK12366 320 -DIELADGTGRVRVSFWGEKAKILENLKEGDAV 351
PRK15491 PRK15491
replication factor A; Provisional
 61-269 2.02e-06

replication factor A; Provisional


Pssm-ID: 185388 [Multi-domain]  Cd Length: 374  Bit Score: 49.50  E-value: 2.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  61 EIGEITPEDGNVTVTCTVLT--AGKRSIRYQGSDHVIVEGELADETGTIDYTAWEDFG--LSPGDTITAGNAGVREWDGE 136
Cdd:PRK15491  59 KIADINESSSNVNFTAKVVSifEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLAdlIKTGDIEVGKSLNISGYAKE 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 137 ----PELNIGESTSLSFVDESLQITQEIGGdatLADLQTGDRARAVEVTVLEC-ERRTIDGRDGETEILSGV-FGDESGR 210
Cdd:PRK15491 139 gysgIEVNIGRYGGISESDENVKASINSQK---ISDIKDGDSDINIVGKVLDIsDVRTFQKKDGSQGRVRNItIGDETGK 215

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 445647578 211 LPFTNWDP----APEIEDGGPVRIENAYVQ--EFRGVPEINVSEFSTVTELDREIEVGADTTTMA 269
Cdd:PRK15491 216 IRVTLWDGktdlADKLENGDSVEIINGYARtnNYSQEVEIQIGNHGSLRKTDRNVEYEEDFTPIA 280
PRK12366 PRK12366
replication factor A; Reviewed
 62-347 2.36e-05

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 46.58  E-value: 2.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578  62 IGEITPEDgNVTVTCTVLTA--GKRSIRYQGSDHVIVEGELADETGTIDYTAWED---FGLSPGDTITagnagVREWDGE 136
Cdd:PRK12366 178 IPELEPNL-SATIEGEVTKAypIKEFTRKDGSEGKLKSFILKDDTGSIRVTLWNDltdIEVNKGDIVR-----VKGYVKQ 251

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 137 PELNiGESTSLSFVD--ESLQITQEIGGDATLADLQTGDRARAVEVT---VLECERRTIDGRDGETEILSGVFGDESGRL 211
Cdd:PRK12366 252 GYRT-GLEISANNIEilEKLEKEEKELEIVNIEELTEFEDGEEVDVKgriIAISDKREVERDDRTAEVQDIELADGTGRV 330

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 212 PFTNWDPAPEIED----GGPVRIENAYVQEFRGVPEINVSEFST--VTELDREIEVGADTTTMAIreaVETGGIYDVELV 285
Cdd:PRK12366 331 RVSFWGEKAKILEnlkeGDAVKIENCKVRTYYDNEGEKRVDLNAgySSEIIKDESISFEEIEEKI---YKIKDILNLEED 407

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 445647578 286 GNVIAVRdgsgliqrcpecYRVIQKGQCRTHGDVDGIDDLRVKAILDDGTGTVTVVLDDELT 347
Cdd:PRK12366 408 DNDITVI------------ARVVEDYPVNEFERSDGSKGKVRNIELADGTGSIRLTLWDDDA 457
PRK08402 PRK08402
replication factor A; Reviewed
 193-422 7.51e-05

replication factor A; Reviewed


Pssm-ID: 169427 [Multi-domain]  Cd Length: 355  Bit Score: 44.79  E-value: 7.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 193 RDGETEILSG-VFGDESGRLPFTNWDPA-----PEIEDGGPVRIENAYVQE-FRGVPEINVS---------EFSTVTELD 256
Cdd:PRK08402  93 KDGSTGRVASlIIYDDTGRARVVLWDAKvakyyNKINVGDVIKVIDAQVREsLSGLPELHINfrariilnpDDPRVEEIP 172

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 257 REIEVGADTTTMAIREAVETGGIYdVELVGNV-----IAVRDGsgliqrCPECYRVIQKGQ------CRTHGDVDGIDDL 325
Cdd:PRK08402 173 PLEEVRSYNYTRKKIGELEGGERF-VEVRGTIakvyrVLVYDA------CPECRRKVDYDPatdtwiCPEHGEVEPIKIT 245

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445647578 326 RVKAILDDGTGTVTVVLDDELTADVYGGTLDDALEQAREAMDQSVVADTIRER--------IVGHEFSVRGHLSVDEY-G 396
Cdd:PRK08402 246 ILDFGLDDGTGYIRVTLFGDDAAELLGVEPEEIAEKLKELIEMGLTPKEAARKlaeeefynIIGREIVVRGNVIEDRFlG 325

                        250       260
                 ....*....|....*....|....*..
gi 445647578 397 ANLDAERFGESDDDPQV-RARAFLEEV 422
Cdd:PRK08402 326 LILKASSWDEVDYKREIeRVRAELEEL 352
YhaM_OBF_like cd04492
YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and ...
 203-256 6.60e-04

YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.


Pssm-ID: 239938 [Multi-domain]  Cd Length: 83  Bit Score: 38.34  E-value: 6.60e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 445647578 203 VFGDESGRLPFTNWDPAPE----IEDGGPVRIEnAYVQEFRGVPEINVSEFSTVTELD 256
Cdd:cd04492   24 TLQDKTGEIEAKLWDASEEdeekFKPGDIVHVK-GRVEEYRGRLQLKIQRIRLVTEED 80
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH