Citrus Sinensis ID: 008606

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560
METIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
ccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccEEEEEEEEEEccccccccccccccEEEEEEEcccccEEEEEEEcHHHHHHHHccccccEEEEEEEEEEccccccccccccEEEEEccccEEEEcccccccccccccccccHHHHHHcccccEEEEEEEEEEEcccEEEEEcccccEEEEEEEEccccccEEEEEccccHHHHHHHHHHHccccccccEEEEcccEEEEcccccccccccEEEEEccccHHHHHHHHHHHcccccccEEEccHHHcccccccHHcccHHHHHHHcccccccccEEEEEEEEEEEEccccEEEccccccccccccEEEEccccEEEEccccccccccEEEEEEEEEEEEccccEEEEEEHHHHHHHHcccHHHHHHHHHHcccHHHHHHHHHHHcccEEEEEEEEEEEEEccEEEEEEEEEEEEEccHHHHHHHHHHHHHHHHHc
ccEEEccHcHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccEEEEEEEEEcccEEEEEccEEEEEEEEEEEcccccEEEEEEEHHHHHHHHHHcccccEEEEEccEEEEccHHHccccccEEEEcccccEEEEcccccccccEEEEEEEEHHHHcccccccEEEEEEEEEEccccEEEEEccccccccEEEEEEEccccEEEEEEEcccHHHccHHHHHHHccccccEEEEEEEEEEcccccEEEcccccEEEEccccHHHHHHHHHHHHHcccccccccccccccccccccccEEHHHHHHHcccccccccEEEEEEEEEEEcccccccccccccccccccccEEEEccccEEEcccccccccccEEEEEEEEEccccccEEEEccHHHHHHHHcccHHHHHHHHHHcccHHHHHHHHHHccccEEEEEEEEEEcccccccEEEEEEEEEccccHHHHHHHHHHHHHHHHcc
metiildcepignpkifseseltaqktipsnnlpqpvrvnnysapnsgtfnlqnsgtfnsqnpgsfstpnsgtfrapnagsivrsfqptvqppyqpppnfrnhgpilkneapariipiaalnpyqgRWAIKARVTAKGdlrrynnargdgkvfsfdlldsdggeirvTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTvdlcteeddsipkqqfsfRHISEIesaennsiVDVIGIVIsvnpsvpilrkngMETQRRILNlkdtsgrsvELTLWGDFCNKEGQKLQEMVDVGFFPVlsvksgkvndfsgksigtipstqlfinpdfaeAHELREWFdsggknaaTVSISREIaaggakneIHKTVSQIKneglgrsekpdwVTVRAFITFIKsdsfcytacplmigdrqcnkkvtqsgnrwqcdrcnqeideCDYRYLLQAQIQDQTGLTWVTAFQEsgeeilgcpakELYMLKYelqddvrfgEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
metiildcepignpKIFSESELTAQKTipsnnlpqpvRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAalnpyqgrwAIKARVtakgdlrrynnargdgkvfsfdlldsdggeIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRIlnlkdtsgrsvELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIaaggakneihktvsqikneglgrsekpdwVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTqsgnrwqcdrCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKeelygdeqrvkitviradqvnyssesrylldlisksfrk
METIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFqptvqppyqpppNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAEnnsivdvigivisvnPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
****ILDC**************************************************************************************************LKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEE*******QFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAA************************PDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLI******
METIILDCEPIGN*******************************************************************************************************PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSI*******GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSF**
METIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCN********RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
METIILDCEPIGNPKIF***********************************************************************************************ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGK*******************IHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
METIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query560 2.2.26 [Sep-21-2011]
Q6NY74601 Replication protein A 70 yes no 0.857 0.798 0.364 1e-89
P27694616 Replication protein A 70 yes no 0.808 0.735 0.382 8e-86
Q5R7Q4616 Replication protein A 70 yes no 0.808 0.735 0.380 9e-85
Q8VEE4623 Replication protein A 70 yes no 0.767 0.690 0.378 8e-82
Q5FW17609 Replication protein A 70 yes no 0.764 0.702 0.376 5e-81
Q01588609 Replication protein A 70 N/A no 0.764 0.702 0.378 7e-81
P22336621 Replication factor A prot yes no 0.780 0.703 0.360 8e-81
Q5ZJJ2614 Replication protein A 70 yes no 0.814 0.742 0.373 5e-78
Q24492603 Replication protein A 70 yes no 0.746 0.693 0.365 4e-74
Q92372609 Replication factor A prot yes no 0.771 0.709 0.328 1e-72
>sp|Q6NY74|RFA1_DANRE Replication protein A 70 kDa DNA-binding subunit OS=Danio rerio GN=rpa1 PE=1 SV=1 Back     alignment and function desciption
 Score =  330 bits (847), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 185/508 (36%), Positives = 290/508 (57%), Gaps = 28/508 (5%)

Query: 61  QNPGSFSTPN---SGTFRAPNAGS--IVRSFQP---TVQPPYQPPPNFRNHGPILKNEAP 112
           Q PG    P     G  +AP+       R  QP   +    Y+P        P+     P
Sbjct: 106 QMPGKIGDPTPYVEGQSKAPSTAPAPTARPLQPQNGSDGSTYRPSAQSFGKKPMAAPNTP 165

Query: 113 ---ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTC 169
              ++++PIA+LNPYQ +W I+ARVT K  +R ++N+RGDGK+FS +L+D + GEIR T 
Sbjct: 166 GGSSKVVPIASLNPYQSKWTIRARVTNKSAIRTWSNSRGDGKLFSMELVD-ESGEIRATG 224

Query: 170 FNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIP 229
           FN  VD+F+ +IE G+V+ ISKG+LK A K F+ LKN++E+ L   +++  C + +D +P
Sbjct: 225 FNNEVDKFFSLIEQGKVFYISKGTLKIANKQFSSLKNDYEMTLNGETSIIPCEDSND-VP 283

Query: 230 KQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVE 289
             Q  F  I+++ES E ++I+DVIG+  +      I+ KN  E  +R + L D SGR ++
Sbjct: 284 MLQCDFVSIADLESREKDTILDVIGVCKNAEDVARIMTKNSREVSKRNIQLIDMSGRVIQ 343

Query: 290 LTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAH 349
           LT+WG           E  D    P+L++K  +++DF G+S+ T+ S+ + INPD  EA+
Sbjct: 344 LTMWGSDA--------ETFDGSGQPILAIKGARLSDFGGRSLSTLYSSTVMINPDIPEAY 395

Query: 350 ELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITF 409
           +LR W+D  G      S++     GG  N   KT++++KNE LG  +K D+ +  A I +
Sbjct: 396 KLRGWYDKEGHALDGQSMTELRGPGGGGNTNWKTLAEVKNEHLGHGDKADYFSCIATIVY 455

Query: 410 IKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGL 468
           I+ ++  Y ACP     + CNKKV  Q    ++C++C++E  +  YR +L A I D    
Sbjct: 456 IRKENCLYQACP----SKDCNKKVVDQQNGMFRCEKCDKEFPDFKYRLMLSANIADFGDN 511

Query: 469 TWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDE 528
            WVT FQ++ E +LG  +  L  LK    ++  F E+ +   FN ++FR ++K E Y DE
Sbjct: 512 QWVTCFQDTAETLLGQNSSYLGQLKD--TNEAAFDEVFQHANFNTFVFRNRVKLETYNDE 569

Query: 529 QRVKITVIRADQVNYSSESRYLLDLISK 556
            R+K+TV+ A  V++   S+ L+  I K
Sbjct: 570 SRIKVTVVDAKPVDHREYSKRLIINIRK 597
Plays an essential role in several cellular processes in DNA metabolism including replication, recombination and DNA repair. Binds and subsequently stabilizes single-stranded DNA intermediates and thus prevents complementary DNA from reannealing.
Danio rerio (taxid: 7955)
>sp|P27694|RFA1_HUMAN Replication protein A 70 kDa DNA-binding subunit OS=Homo sapiens GN=RPA1 PE=1 SV=2 Back     alignment and function description
>sp|Q5R7Q4|RFA1_PONAB Replication protein A 70 kDa DNA-binding subunit OS=Pongo abelii GN=RPA1 PE=2 SV=1 Back     alignment and function description
>sp|Q8VEE4|RFA1_MOUSE Replication protein A 70 kDa DNA-binding subunit OS=Mus musculus GN=Rpa1 PE=2 SV=1 Back     alignment and function description
>sp|Q5FW17|RFA1_XENTR Replication protein A 70 kDa DNA-binding subunit OS=Xenopus tropicalis GN=rpa1 PE=2 SV=1 Back     alignment and function description
>sp|Q01588|RFA1_XENLA Replication protein A 70 kDa DNA-binding subunit OS=Xenopus laevis GN=rpa1 PE=1 SV=1 Back     alignment and function description
>sp|P22336|RFA1_YEAST Replication factor A protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFA1 PE=1 SV=1 Back     alignment and function description
>sp|Q5ZJJ2|RFA1_CHICK Replication protein A 70 kDa DNA-binding subunit OS=Gallus gallus GN=RPA1 PE=2 SV=1 Back     alignment and function description
>sp|Q24492|RFA1_DROME Replication protein A 70 kDa DNA-binding subunit OS=Drosophila melanogaster GN=RpA-70 PE=1 SV=1 Back     alignment and function description
>sp|Q92372|RFA1_SCHPO Replication factor A protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ssb1 PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query560
225444784622 PREDICTED: replication protein A 70 kDa 0.939 0.845 0.752 0.0
255546005 670 replication factor A 1, rfa1, putative [ 0.994 0.831 0.742 0.0
449488185623 PREDICTED: replication protein A 70 kDa 0.944 0.849 0.739 0.0
449446612 694 PREDICTED: replication protein A 70 kDa 0.928 0.749 0.742 0.0
33621259637 RPA 70kDa subunit [Pisum sativum] 0.960 0.844 0.706 0.0
42570719617 replication factor A1 [Arabidopsis thali 0.964 0.875 0.699 0.0
15225129640 replication factor A1 [Arabidopsis thali 0.964 0.843 0.699 0.0
297831712640 hypothetical protein ARALYDRAFT_899421 [ 0.964 0.843 0.697 0.0
356556324637 PREDICTED: replication protein A 70 kDa 0.958 0.843 0.707 0.0
224122534502 predicted protein [Populus trichocarpa] 0.846 0.944 0.740 0.0
>gi|225444784|ref|XP_002278273.1| PREDICTED: replication protein A 70 kDa DNA-binding subunit [Vitis vinifera] gi|297738589|emb|CBI27834.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  872 bits (2254), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/557 (75%), Positives = 475/557 (85%), Gaps = 31/557 (5%)

Query: 1   METIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNS 60
           METII +CE IGNPK+ +ES  TAQK  P  N  + V V N                   
Sbjct: 94  METIIPECEIIGNPKMNTESHSTAQKEFPGGNRARSVGVTN------------------- 134

Query: 61  QNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAA 120
                            N G+ + SF+P+VQPP+QPPPN+++HG ILKNEAPARIIPIAA
Sbjct: 135 -----------NNLSVQNGGNKMPSFRPSVQPPFQPPPNYKSHGTILKNEAPARIIPIAA 183

Query: 121 LNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEI 180
           LNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY+ 
Sbjct: 184 LNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYDT 243

Query: 181 IEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISE 240
           IEVG+VYLISKGSLKPAQKNFNHLKNEWEIFLEA+S+V+LC +ED SIPKQQFSFR ISE
Sbjct: 244 IEVGKVYLISKGSLKPAQKNFNHLKNEWEIFLEASSSVELCPDEDGSIPKQQFSFRPISE 303

Query: 241 IESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE 300
           IE+ ENNSI+DVIGIVISVNPSVPILRKNGMETQRRI+NLKD SGRS+ELT+WG+FCN+E
Sbjct: 304 IENVENNSILDVIGIVISVNPSVPILRKNGMETQRRIVNLKDGSGRSIELTMWGEFCNRE 363

Query: 301 GQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGK 360
           G +LQEM+D G FPVL+VKSGKVNDFSGKS+GTI +TQLFINPDF EA  LREWFD GGK
Sbjct: 364 GHQLQEMIDSGSFPVLAVKSGKVNDFSGKSVGTISATQLFINPDFTEACNLREWFDRGGK 423

Query: 361 NAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTAC 420
           NAA+ SISR+I   G++NEI KTVSQIK+EGLGRS+KPDWVTV+A I+FIK+D+FCY AC
Sbjct: 424 NAASQSISRDIMPAGSRNEIRKTVSQIKDEGLGRSDKPDWVTVKATISFIKTDTFCYAAC 483

Query: 421 PLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGE 479
           PLMIGDRQCNKKVT+SGN RWQCDRCNQE ++CDYRYLLQAQ+QD TGLTWVTAFQE+GE
Sbjct: 484 PLMIGDRQCNKKVTRSGNTRWQCDRCNQEFEDCDYRYLLQAQVQDHTGLTWVTAFQEAGE 543

Query: 480 EILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRAD 539
           EILGC AKELY+LKYE +DD RFGEIIRSR+ NQ+LFRLKIKEE+YG+EQRVKITV++AD
Sbjct: 544 EILGCSAKELYLLKYEEEDDFRFGEIIRSRLLNQFLFRLKIKEEMYGEEQRVKITVVKAD 603

Query: 540 QVNYSSESRYLLDLISK 556
           +VNY+SESR+LLDLISK
Sbjct: 604 KVNYTSESRHLLDLISK 620

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255546005|ref|XP_002514062.1| replication factor A 1, rfa1, putative [Ricinus communis] gi|223546518|gb|EEF48016.1| replication factor A 1, rfa1, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|449488185|ref|XP_004157962.1| PREDICTED: replication protein A 70 kDa DNA-binding subunit-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449446612|ref|XP_004141065.1| PREDICTED: replication protein A 70 kDa DNA-binding subunit-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|33621259|gb|AAQ23194.1| RPA 70kDa subunit [Pisum sativum] Back     alignment and taxonomy information
>gi|42570719|ref|NP_973433.1| replication factor A1 [Arabidopsis thaliana] gi|330250915|gb|AEC06009.1| replication factor A1 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|15225129|ref|NP_178690.1| replication factor A1 [Arabidopsis thaliana] gi|4584356|gb|AAD25150.1| putative replication protein A1 [Arabidopsis thaliana] gi|26452416|dbj|BAC43293.1| putative replication protein A1 [Arabidopsis thaliana] gi|29029004|gb|AAO64881.1| At2g06510 [Arabidopsis thaliana] gi|330250916|gb|AEC06010.1| replication factor A1 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297831712|ref|XP_002883738.1| hypothetical protein ARALYDRAFT_899421 [Arabidopsis lyrata subsp. lyrata] gi|297329578|gb|EFH59997.1| hypothetical protein ARALYDRAFT_899421 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|356556324|ref|XP_003546476.1| PREDICTED: replication protein A 70 kDa DNA-binding subunit-like [Glycine max] Back     alignment and taxonomy information
>gi|224122534|ref|XP_002330505.1| predicted protein [Populus trichocarpa] gi|222872439|gb|EEF09570.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query560
TAIR|locus:2054577640 RPA1A "replication protein A 1 0.958 0.839 0.673 2.2e-201
UNIPROTKB|Q9AVL8654 OsRPA70a "Replication protein 0.973 0.833 0.588 1.7e-176
TAIR|locus:2163553 853 RPA70C [Arabidopsis thaliana ( 0.808 0.531 0.587 2.1e-154
TAIR|locus:2134766 784 AT4G19130 [Arabidopsis thalian 0.921 0.658 0.524 1.3e-148
UNIPROTKB|Q65XV7 951 P0016H04.11 "Os05g0111000 prot 0.967 0.569 0.450 4.8e-129
ZFIN|ZDB-GENE-030912-3601 rpa1 "replication protein A1" 0.764 0.712 0.373 3.2e-81
UNIPROTKB|P27694616 RPA1 "Replication protein A 70 0.782 0.711 0.371 7.1e-77
UNIPROTKB|Q5ZJJ2614 RPA1 "Replication protein A 70 0.762 0.695 0.371 3.6e-76
MGI|MGI:1915525623 Rpa1 "replication protein A1" 0.766 0.688 0.366 6.3e-76
UNIPROTKB|Q0VCV0616 RPA1 "Replication protein A1, 0.753 0.685 0.365 1.7e-75
TAIR|locus:2054577 RPA1A "replication protein A 1A" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1949 (691.1 bits), Expect = 2.2e-201, P = 2.2e-201
 Identities = 376/558 (67%), Positives = 451/558 (80%)

Query:     1 METIILDCEPIGNPKIFSESELTAQKTIP-SNNLPQPVRVNNYSAPN-SGTFNLQNSGTF 58
             METI+   E IGNP IF E++  AQKT   + N+P P RV  ++ P    + N       
Sbjct:    98 METIVQQSETIGNPTIFGETDTEAQKTFSGTGNIPPPNRVV-FNEPMVQHSVNRAPPRGV 156

Query:    59 NSQNPGSFSTPNSGTFRAPNAGSIVRSFXXXXXXXXXXXXNFRNHGPILKNEAPARIIPI 118
             N QN  + +TP+   FR P   S+  S+            ++RNHGPI+KNEAPAR+IPI
Sbjct:   157 NIQNQAN-NTPS---FR-P---SVQPSYQPPA--------SYRNHGPIMKNEAPARVIPI 200

Query:   119 AALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY 178
             AALNPYQGRWAIKARVTAKGD+RRYNNA+GDGKVFSFDLLD DGGEIRVTCFNA+VDRFY
Sbjct:   201 AALNPYQGRWAIKARVTAKGDIRRYNNAKGDGKVFSFDLLDYDGGEIRVTCFNALVDRFY 260

Query:   179 EIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHI 238
             ++ EVG+VYLISKGSLKPAQKNFNHLKNEWEIFLE+TSTV+LC +ED SIPKQQFSFR I
Sbjct:   261 DVTEVGKVYLISKGSLKPAQKNFNHLKNEWEIFLESTSTVELCPDEDGSIPKQQFSFRPI 320

Query:   239 SEIESAEXXXXXXXXXXXXXXXPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCN 298
             S+IE+AE               PSVPILRKNGMET RRILNLKD SG++VE+TLWG+FCN
Sbjct:   321 SDIENAENNTILDVIGVVTSVNPSVPILRKNGMETHRRILNLKDESGKAVEVTLWGEFCN 380

Query:   299 KEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSG 358
             ++G++L+EMVD  F PVL++K+GKV+DFSGKS+GTI STQLFINPDF EAH+LR WFD G
Sbjct:   381 RDGRQLEEMVDSAFHPVLAIKAGKVSDFSGKSVGTISSTQLFINPDFPEAHKLRTWFDYG 440

Query:   359 GKNAATVSISREIAAGG-AKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCY 417
             GK+ A+ SISR+   GG ++NEI K VSQIK EGLGRS+KPDW+TV+A I+FIK+DSFCY
Sbjct:   441 GKDTASFSISRDTMPGGVSRNEIRKNVSQIKEEGLGRSDKPDWITVKATISFIKTDSFCY 500

Query:   418 TACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQE 476
             TACPLMIGD+QCNKKVT+SG NRW CDRCNQE DECDYRYLLQ QIQD TGLTW+TAFQE
Sbjct:   501 TACPLMIGDKQCNKKVTRSGTNRWLCDRCNQESDECDYRYLLQVQIQDHTGLTWITAFQE 560

Query:   477 SGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVI 536
             +GEEI+GCPAK+LY +KYEL+ +  F EI+R R+F+QY+ +LKIKEE YGDEQRVK+TV+
Sbjct:   561 TGEEIMGCPAKKLYAMKYELEKEEEFAEIVRDRLFHQYMLKLKIKEESYGDEQRVKMTVV 620

Query:   537 RADQVNYSSESRYLLDLI 554
             + D+VNY+SES+Y+LDL+
Sbjct:   621 KVDKVNYTSESKYMLDLL 638
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM;IEA
GO:0006260 "DNA replication" evidence=IEA;ISS
GO:0000790 "nuclear chromatin" evidence=IDA
GO:0007131 "reciprocal meiotic recombination" evidence=IGI;RCA
GO:0007141 "male meiosis I" evidence=IMP
GO:0009555 "pollen development" evidence=IMP
GO:0048232 "male gamete generation" evidence=IMP
GO:0051026 "chiasma assembly" evidence=IMP
GO:0000724 "double-strand break repair via homologous recombination" evidence=RCA
GO:0006312 "mitotic recombination" evidence=RCA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA
GO:0007062 "sister chromatid cohesion" evidence=RCA
GO:0007129 "synapsis" evidence=RCA
GO:0007140 "male meiosis" evidence=RCA
GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA
GO:0009560 "embryo sac egg cell differentiation" evidence=RCA
GO:0009640 "photomorphogenesis" evidence=RCA
GO:0009793 "embryo development ending in seed dormancy" evidence=RCA
GO:0009845 "seed germination" evidence=RCA
GO:0009909 "regulation of flower development" evidence=RCA
GO:0009933 "meristem structural organization" evidence=RCA
GO:0010162 "seed dormancy process" evidence=RCA
GO:0010182 "sugar mediated signaling pathway" evidence=RCA
GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA
GO:0010332 "response to gamma radiation" evidence=RCA
GO:0016444 "somatic cell DNA recombination" evidence=RCA
GO:0016567 "protein ubiquitination" evidence=RCA
GO:0019915 "lipid storage" evidence=RCA
GO:0032204 "regulation of telomere maintenance" evidence=RCA
GO:0032504 "multicellular organism reproduction" evidence=RCA
GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA
GO:0043247 "telomere maintenance in response to DNA damage" evidence=RCA
GO:0043687 "post-translational protein modification" evidence=RCA
GO:0045132 "meiotic chromosome segregation" evidence=RCA
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA
GO:0050826 "response to freezing" evidence=RCA
UNIPROTKB|Q9AVL8 OsRPA70a "Replication protein A 70kDa" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2163553 RPA70C [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2134766 AT4G19130 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q65XV7 P0016H04.11 "Os05g0111000 protein" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030912-3 rpa1 "replication protein A1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q5ZJJ2 RPA1 "Replication protein A 70 kDa DNA-binding subunit" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
MGI|MGI:1915525 Rpa1 "replication protein A1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|Q0VCV0 RPA1 "Replication protein A1, 70kDa" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00016477001
SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (622 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00031357001
SubName- Full=Chromosome chr11 scaffold_56, whole genome shotgun sequence; (277 aa)
   •••• 0.603
GSVIVG00022496001
SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (330 aa)
   •••• 0.584
GSVIVG00032340001
SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (268 aa)
   •••• 0.561
GSVIVG00006013001
RecName- Full=DNA polymerase; EC=2.7.7.7; (1126 aa)
   • •• 0.560
GSVIVG00006228001
SubName- Full=Chromosome chr1 scaffold_166, whole genome shotgun sequence; (739 aa)
   •••  0.521
GSVIVG00024178001
RecName- Full=Proliferating cell nuclear antigen;; This protein is an auxiliary protein of DNA [...] (266 aa)
   •••• 0.489
GSVIVG00019349001
RecName- Full=Ribonucleoside-diphosphate reductase; EC=1.17.4.1;; Provides the precursors neces [...] (790 aa)
   •  • 0.482
GSVIVG00002439001
RecName- Full=DNA primase; EC=2.7.7.-; (457 aa)
   •••• 0.458
GSVIVG00035935001
SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (721 aa)
   •••  0.450
GSVIVG00028109001
SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (718 aa)
   •••  0.446

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query560
TIGR00617608 TIGR00617, rpa1, replication factor-a protein 1 (r 0.0
pfam08646146 pfam08646, Rep_fac-A_C, Replication factor-A C ter 2e-67
cd04476166 cd04476, RPA1_DBD_C, RPA1_DBD_C: A subfamily of OB 3e-60
cd04474104 cd04474, RPA1_DBD_A, RPA1_DBD_A: A subfamily of OB 1e-48
cd04475101 cd04475, RPA1_DBD_B, RPA1_DBD_B: A subfamily of OB 2e-32
COG1599407 COG1599, RFA1, Single-stranded DNA-binding replica 1e-13
PRK12366637 PRK12366, PRK12366, replication factor A; Reviewed 4e-13
cd04481106 cd04481, RPA1_DBD_B_like, RPA1_DBD_B_like: A subgr 1e-08
pfam0133675 pfam01336, tRNA_anti, OB-fold nucleic acid binding 1e-05
PRK12366637 PRK12366, PRK12366, replication factor A; Reviewed 5e-05
cd0352475 cd03524, RPA2_OBF_family, RPA2_OBF_family: A famil 6e-05
PRK12366 637 PRK12366, PRK12366, replication factor A; Reviewed 1e-04
PRK07211485 PRK07211, PRK07211, replication factor A; Reviewed 7e-04
>gnl|CDD|233055 TIGR00617, rpa1, replication factor-a protein 1 (rpa1) Back     alignment and domain information 
 Score =  534 bits (1377), Expect = 0.0
 Identities = 221/544 (40%), Positives = 316/544 (58%), Gaps = 35/544 (6%)

Query: 16  IFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFR 75
           I  E E+   +    + +  PV    Y         L +    N  NP +   P +    
Sbjct: 97  IVYELEVVKPELKVRDKIGNPVTYEKYLDSWHEEQVLASKPATNPANPPNAKAPKNEVAS 156

Query: 76  APNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVT 135
             NA +  R            PP   +           R++PIA+L+PYQ +W IKARVT
Sbjct: 157 YNNAANPERGN---------APPAPNSGSTR-------RVMPIASLSPYQNKWTIKARVT 200

Query: 136 AKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK 195
            K ++R ++NARG+GK+F+ +LLD + GEIR T FN   D+FY+II+ G+VY ISKGSLK
Sbjct: 201 NKSEIRTWSNARGEGKLFNVELLD-ESGEIRATAFNEQADKFYDIIQEGKVYYISKGSLK 259

Query: 196 PAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGI 255
           PA K F +L N++E+ L+  + ++ C E++ +IPK QF+F  I +I   E NS+VDVIGI
Sbjct: 260 PANKQFTNLGNDYEMTLDRDTVIEEC-EDETAIPKIQFNFVKIDDIGGYEGNSLVDVIGI 318

Query: 256 VISVNPSVPIL-RKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP 314
           V SV+P+  I  RKN  E  +R + L D SG+SV +TLWGD   K         DV   P
Sbjct: 319 VQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATK--------FDVSVQP 370

Query: 315 VLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAG 374
           V+++K  +V+DF GKS+ T  S+ + +NPD  EA +L+ W+D+ GK     SIS  ++  
Sbjct: 371 VIAIKGVRVSDFGGKSLSTGGSSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGR 430

Query: 375 -GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKV 433
            G  N   KT+++I+ E LG+S+KPD+ +V+A I+++K D+  Y ACP       CNKKV
Sbjct: 431 VGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSE----DCNKKV 486

Query: 434 TQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYML 492
              G+  ++C++CN+   E  YRY+LQ  I D+TG  WVTAF +  E+ILG  A EL  L
Sbjct: 487 VDQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGEL 546

Query: 493 KYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLD 552
           K E  D   F  I +   F  Y+FRL++K++ Y DE R K TV+  D VNY +E++YLL 
Sbjct: 547 KEE--DPDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVDPVNYRAEAKYLLQ 604

Query: 553 LISK 556
            I K
Sbjct: 605 EIEK 608

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]. Length = 608
>gnl|CDD|149635 pfam08646, Rep_fac-A_C, Replication factor-A C terminal domain Back     alignment and domain information
>gnl|CDD|239922 cd04476, RPA1_DBD_C, 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) Back     alignment and domain information
>gnl|CDD|239920 cd04474, RPA1_DBD_A, 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) Back     alignment and domain information
>gnl|CDD|239921 cd04475, RPA1_DBD_B, 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) Back     alignment and domain information
>gnl|CDD|224515 COG1599, RFA1, Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed Back     alignment and domain information
>gnl|CDD|239927 cd04481, RPA1_DBD_B_like, 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) Back     alignment and domain information
>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain Back     alignment and domain information
>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed Back     alignment and domain information
>gnl|CDD|239601 cd03524, RPA2_OBF_family, 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) Back     alignment and domain information
>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed Back     alignment and domain information
>gnl|CDD|180887 PRK07211, PRK07211, replication factor A; Reviewed Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 560
TIGR00617608 rpa1 replication factor-a protein 1 (rpa1). This f 100.0
PRK12366637 replication factor A; Reviewed 100.0
PRK08402355 replication factor A; Reviewed 100.0
cd04476166 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor 100.0
PRK07218423 replication factor A; Provisional 100.0
PF08646146 Rep_fac-A_C: Replication factor-A C terminal domai 100.0
PRK06386358 replication factor A; Reviewed 100.0
PRK12366 637 replication factor A; Reviewed 100.0
PRK07211485 replication factor A; Reviewed 99.98
PRK07211485 replication factor A; Reviewed 99.97
PRK15491374 replication factor A; Provisional 99.97
cd04474104 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor 99.95
PRK14699484 replication factor A; Provisional 99.95
PRK15491374 replication factor A; Provisional 99.94
PRK14699484 replication factor A; Provisional 99.91
cd04475101 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor 99.86
cd04481106 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc 99.82
cd0448086 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of unc 99.78
PF0272195 DUF223: Domain of unknown function DUF223; InterPr 99.67
PRK07217311 replication factor A; Reviewed 99.62
PRK08402355 replication factor A; Reviewed 99.58
KOG0851246 consensus Single-stranded DNA-binding replication 99.28
cd04497138 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f 99.08
PRK06386358 replication factor A; Reviewed 99.07
COG1599407 RFA1 Single-stranded DNA-binding replication prote 99.06
PRK07218423 replication factor A; Provisional 99.04
cd0449182 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil 98.84
PRK06461129 single-stranded DNA-binding protein; Reviewed 98.83
cd0449182 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil 98.75
PRK06461129 single-stranded DNA-binding protein; Reviewed 98.71
PRK07217311 replication factor A; Reviewed 98.18
TIGR00617 608 rpa1 replication factor-a protein 1 (rpa1). This f 98.16
COG1599407 RFA1 Single-stranded DNA-binding replication prote 98.13
cd04474104 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor 97.93
PF0133675 tRNA_anti-codon: OB-fold nucleic acid binding doma 97.73
PF02765146 POT1: Telomeric single stranded DNA binding POT1/C 97.44
cd04475101 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor 97.3
cd0352475 RPA2_OBF_family RPA2_OBF_family: A family of oligo 96.74
KOG3416134 consensus Predicted nucleic acid binding protein [ 96.58
KOG3416134 consensus Predicted nucleic acid binding protein [ 96.5
cd04497138 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f 95.97
cd0352475 RPA2_OBF_family RPA2_OBF_family: A family of oligo 95.7
cd0448392 hOBFC1_like hOBFC1_like: A subfamily of OB folds s 95.44
PF0133675 tRNA_anti-codon: OB-fold nucleic acid binding doma 95.35
cd04481106 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc 95.12
PF154891144 CTC1: CST, telomere maintenance, complex subunit C 94.98
cd0449079 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds 94.87
cd0448875 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f 94.37
cd0448584 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp 94.27
cd0447895 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor 92.6
cd0448584 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp 92.29
cd0448978 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol 91.6
PTZ00401550 aspartyl-tRNA synthetase; Provisional 91.44
cd0449079 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds 91.39
PRK06751173 single-stranded DNA-binding protein; Provisional 91.22
cd0449283 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol 90.47
PF02765146 POT1: Telomeric single stranded DNA binding POT1/C 90.14
PRK02801101 primosomal replication protein N; Provisional 90.05
PF1132584 DUF3127: Domain of unknown function (DUF3127); Int 89.46
PF14951389 DUF4503: Domain of unknown function (DUF4503) 89.3
PF1507286 DUF4539: Domain of unknown function (DUF4539) 88.99
PRK07275162 single-stranded DNA-binding protein; Provisional 88.84
PRK07459121 single-stranded DNA-binding protein; Provisional 88.74
cd04322108 LysRS_N LysRS_N: N-terminal, anticodon recognition 88.45
PRK07772186 single-stranded DNA-binding protein; Provisional 88.01
KOG0851246 consensus Single-stranded DNA-binding replication 87.94
PRK05733172 single-stranded DNA-binding protein; Provisional 87.82
cd0449283 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol 87.7
cd0448978 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol 87.68
PLN02850530 aspartate-tRNA ligase 87.65
PRK05813219 single-stranded DNA-binding protein; Provisional 87.59
PRK07373449 DNA polymerase III subunit alpha; Reviewed 87.25
COG5235258 RFA2 Single-stranded DNA-binding replication prote 87.16
PRK08763164 single-stranded DNA-binding protein; Provisional 86.6
cd04320102 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r 86.43
PRK13480314 3'-5' exoribonuclease YhaM; Provisional 86.31
PRK07274131 single-stranded DNA-binding protein; Provisional 86.05
PRK09010177 single-stranded DNA-binding protein; Provisional 86.05
PRK13480314 3'-5' exoribonuclease YhaM; Provisional 86.02
cd04496100 SSB_OBF SSB_OBF: A subfamily of OB folds similar t 85.97
PRK08486182 single-stranded DNA-binding protein; Provisional 85.91
PRK06293161 single-stranded DNA-binding protein; Provisional 85.44
cd0447895 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor 85.3
cd04495100 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds 85.11
PRK13732175 single-stranded DNA-binding protein; Provisional 84.55
PRK06752112 single-stranded DNA-binding protein; Validated 84.2
PRK07373449 DNA polymerase III subunit alpha; Reviewed 84.1
PF09104143 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide 83.95
cd0448482 polC_OBF polC_OBF: A subfamily of OB folds corresp 83.38
PF1374299 tRNA_anti_2: OB-fold nucleic acid binding domain 82.98
PRK06863168 single-stranded DNA-binding protein; Provisional 82.85
PRK08182148 single-stranded DNA-binding protein; Provisional 82.78
cd0410085 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant 82.05
cd0432384 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, a 81.67
PRK05159437 aspC aspartyl-tRNA synthetase; Provisional 81.39
PRK056731135 dnaE DNA polymerase III subunit alpha; Validated 81.27
PF00436104 SSB: Single-strand binding protein family; InterPr 81.07
TIGR00621164 ssb single stranded DNA-binding protein (ssb). Thi 80.83
cd0448086 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of unc 80.26
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1) Back     alignment and domain information 
Probab=100.00  E-value=2.7e-100  Score=847.70  Aligned_cols=442  Identities=46%  Similarity=0.818  Sum_probs=406.4

Q ss_pred             CCCCCCCccCCCCCCcceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHH
Q 008606           99 NFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY  178 (560)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~  178 (560)
                      .+.+.+|..+..++.+++||++|+||+++|+|+|||++||++|+|++++|+|++|+|+|+| +|++|+|+||++.+++|+
T Consensus       164 ~~~~~~~~~~~~~~~~~~pI~~L~py~~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~D-egg~Irat~f~~~~dkf~  242 (608)
T TIGR00617       164 ERGNAPPAPNSGSTRRVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLD-ESGEIRATAFNEQADKFY  242 (608)
T ss_pred             ccCCCCCCccccCCcceEEHHHCCCCCCceEEEEEEEeccccceecCCCCCceeeEEEEec-CCCeEEEEECchHHHHHh
Confidence            4445555333344557999999999999999999999999999999999999999999999 999999999999999999


Q ss_pred             hhcccCcEEEEeeeEEecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEE
Q 008606          179 EIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVIS  258 (560)
Q Consensus       179 ~~l~eG~vY~Is~~~V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~  258 (560)
                      ++|++|+||+|++|+|++++++|++++|+|||.|+.+|+|++|.| ...||.+.|+|++|+||.+...+.+|||||+|++
T Consensus       243 ~~l~eG~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d-~~~iP~~~~~f~~i~dI~~~~~~~~VDVIGvV~~  321 (608)
T TIGR00617       243 DIIQEGKVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECED-ETAIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQS  321 (608)
T ss_pred             hhcccCCEEEECceEEEEccccccCCCCCEEEEECCCeEEEECCC-cccCCcccccceEHHHhhhhcCCCCccEEEEEeE
Confidence            999999999999999999999999999999999999999999975 4459999999999999999877889999999999


Q ss_pred             ecCceeEeec-cCceeeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCceecccCCe
Q 008606          259 VNPSVPILRK-NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPST  337 (560)
Q Consensus       259 V~~~~~i~~k-~G~~~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~sLs~~~~S  337 (560)
                      |+++.+|++| +|++..||+|+|+|+||.+|+|||||++|..+        +...++||+|+++||++|+|++||++++|
T Consensus       322 v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~~--------~~~~~~Vva~kg~~V~~f~g~sLs~~~~S  393 (608)
T TIGR00617       322 VSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKF--------DVSVQPVIAIKGVRVSDFGGKSLSTGGSS  393 (608)
T ss_pred             ecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhhc--------CCCCCCEEEEEeEEEEecCCceEeccCCc
Confidence            9999999854 78999999999999999999999999999874        34578999999999999999999999999


Q ss_pred             EEEECCChHHHHHHHHHHhcCCCccceeeccccccc-CCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeE
Q 008606          338 QLFINPDFAEAHELREWFDSGGKNAATVSISREIAA-GGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFC  416 (560)
Q Consensus       338 ~i~iNPdipEa~~L~~w~~~~g~~~~~~sls~~~~~-~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~  416 (560)
                      +|++|||+||+++|+.||+++|....+.+++...+. .+.+...+|||+||+++.+|.+++++||.|+|+|++|+.|+||
T Consensus       394 ~i~iNPdipEa~~L~~w~~~~g~~~~~~s~~~~~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~  473 (608)
T TIGR00617       394 TIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNAL  473 (608)
T ss_pred             eEEECCCcHHHHHHHHHHHhcCCCccceeehhccccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeE
Confidence            999999999999999999999987766666543322 1344678999999999999999999999999999999999999


Q ss_pred             EeCCCCCcCccccCceeeecC-CeeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhc
Q 008606          417 YTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYE  495 (560)
Q Consensus       417 Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e  495 (560)
                      |+|||+.    .|+|||...+ +.|+|++|++++++|.|||+|++.|+||||++|+++||+.|++|||++|+||.+++  
T Consensus       474 Y~ACp~~----~CnKKV~~~~~g~~~CekC~~~~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~--  547 (608)
T TIGR00617       474 YRACPSE----DCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELK--  547 (608)
T ss_pred             eccCChh----hCCCccccCCCCCEECCCCCCCCCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHH--
Confidence            9999942    3999999876 49999999999999999999999999999999999999999999999999999999  


Q ss_pred             cCChhHHHHHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEeeeCChHHHHHHHHHHHHh
Q 008606          496 LQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK  556 (560)
Q Consensus       496 ~~d~~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~~~vd~~~e~~~ll~~i~~  556 (560)
                      ++++++|+++|.++.|++|.|+|+++.++||||.|+|++|++++|+||++|+++||+.|++
T Consensus       548 ~~~~~~~~~i~~~~~~~~~~f~~~~k~e~yn~e~r~~~~v~~~~~vd~~~e~~~L~~~i~~  608 (608)
T TIGR00617       548 EEDPDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVDPVNYRAEAKYLLQEIEK  608 (608)
T ss_pred             hcCHHHHHHHHHHhhCcEEEEEEEEEEcccCCEeeEEEEEEEeeeCCHHHHHHHHHHHhcC
Confidence            6788999999999999999999999999999999999999999999999999999999974

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
>PRK12366 replication factor A; Reviewed Back     alignment and domain information
>PRK08402 replication factor A; Reviewed Back     alignment and domain information
>cd04476 RPA1_DBD_C 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) Back     alignment and domain information
>PRK07218 replication factor A; Provisional Back     alignment and domain information
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing Back     alignment and domain information
>PRK06386 replication factor A; Reviewed Back     alignment and domain information
>PRK12366 replication factor A; Reviewed Back     alignment and domain information
>PRK07211 replication factor A; Reviewed Back     alignment and domain information
>PRK07211 replication factor A; Reviewed Back     alignment and domain information
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>cd04474 RPA1_DBD_A 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) Back     alignment and domain information
>PRK14699 replication factor A; Provisional Back     alignment and domain information
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>PRK14699 replication factor A; Provisional Back     alignment and domain information
>cd04475 RPA1_DBD_B 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) Back     alignment and domain information
>cd04481 RPA1_DBD_B_like 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) Back     alignment and domain information
>cd04480 RPA1_DBD_A_like 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) Back     alignment and domain information
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding Back     alignment and domain information
>PRK07217 replication factor A; Reviewed Back     alignment and domain information
>PRK08402 replication factor A; Reviewed Back     alignment and domain information
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair] Back     alignment and domain information
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP) Back     alignment and domain information
>PRK06386 replication factor A; Reviewed Back     alignment and domain information
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07218 replication factor A; Provisional Back     alignment and domain information
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB) Back     alignment and domain information
>PRK06461 single-stranded DNA-binding protein; Reviewed Back     alignment and domain information
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB) Back     alignment and domain information
>PRK06461 single-stranded DNA-binding protein; Reviewed Back     alignment and domain information
>PRK07217 replication factor A; Reviewed Back     alignment and domain information
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1) Back     alignment and domain information
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>cd04474 RPA1_DBD_A 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) Back     alignment and domain information
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands Back     alignment and domain information
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold [] Back     alignment and domain information
>cd04475 RPA1_DBD_B 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) Back     alignment and domain information
>cd03524 RPA2_OBF_family 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) Back     alignment and domain information
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only] Back     alignment and domain information
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only] Back     alignment and domain information
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP) Back     alignment and domain information
>cd03524 RPA2_OBF_family 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) Back     alignment and domain information
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1) Back     alignment and domain information
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands Back     alignment and domain information
>cd04481 RPA1_DBD_B_like 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) Back     alignment and domain information
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1 Back     alignment and domain information
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit Back     alignment and domain information
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG Back     alignment and domain information
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE) Back     alignment and domain information
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32) Back     alignment and domain information
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE) Back     alignment and domain information
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit Back     alignment and domain information
>PTZ00401 aspartyl-tRNA synthetase; Provisional Back     alignment and domain information
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit Back     alignment and domain information
>PRK06751 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1) Back     alignment and domain information
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold [] Back     alignment and domain information
>PRK02801 primosomal replication protein N; Provisional Back     alignment and domain information
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function Back     alignment and domain information
>PF14951 DUF4503: Domain of unknown function (DUF4503) Back     alignment and domain information
>PF15072 DUF4539: Domain of unknown function (DUF4539) Back     alignment and domain information
>PRK07275 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07459 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS) Back     alignment and domain information
>PRK07772 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair] Back     alignment and domain information
>PRK05733 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1) Back     alignment and domain information
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit Back     alignment and domain information
>PLN02850 aspartate-tRNA ligase Back     alignment and domain information
>PRK05813 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07373 DNA polymerase III subunit alpha; Reviewed Back     alignment and domain information
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK08763 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS) Back     alignment and domain information
>PRK13480 3'-5' exoribonuclease YhaM; Provisional Back     alignment and domain information
>PRK07274 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK09010 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK13480 3'-5' exoribonuclease YhaM; Provisional Back     alignment and domain information
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB) Back     alignment and domain information
>PRK08486 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06293 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32) Back     alignment and domain information
>cd04495 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds corresponding to the third OB fold (OB3) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD Back     alignment and domain information
>PRK13732 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06752 single-stranded DNA-binding protein; Validated Back     alignment and domain information
>PRK07373 DNA polymerase III subunit alpha; Reviewed Back     alignment and domain information
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel Back     alignment and domain information
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC) Back     alignment and domain information
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain Back     alignment and domain information
>PRK06863 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08182 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs) Back     alignment and domain information
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs Back     alignment and domain information
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional Back     alignment and domain information
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated Back     alignment and domain information
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids Back     alignment and domain information
>TIGR00621 ssb single stranded DNA-binding protein (ssb) Back     alignment and domain information
>cd04480 RPA1_DBD_A_like 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) Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query560
4gop_C444 Structure And Conformational Change Of A Replicatio 1e-79
1fgu_A252 Ssdna-Binding Domain Of The Large Subunit Of Replic 1e-48
1jmc_A246 Single Stranded Dna-Binding Domain Of Human Replica 1e-47
1l1o_C181 Structure Of The Human Replication Protein A (Rpa) 1e-24
1ynx_A114 Solution Structure Of Dna Binding Domain A (Dbd-A) 3e-22
>pdb|4GOP|C Chain C, Structure And Conformational Change Of A Replication Protein A Heterotrimer Bound To Ssdna Length = 444 Back     alignment and structure 
Iteration: 1

 Score =  294 bits (752), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 166/450 (36%), Positives = 246/450 (54%), Gaps = 22/450 (4%)
Query: 115 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV 174
           I PI  L+PYQ RW IKARVT+K D+R ++N RG+GK+FS +LLD D GEI+ T FN  V
Sbjct: 3   IYPIEGLSPYQNRWTIKARVTSKSDIRHWSNQRGEGKLFSVNLLD-DSGEIKATGFNDAV 61
Query: 175 DRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFS 234
           DRFY +++   VYLISK  +  A+K F++L+NE+EI  E ++ ++ CT+  D +P+ ++ 
Sbjct: 62  DRFYPLLQENHVYLISKARVNIAKKQFSNLQNEYEITFENSTEIEECTDATD-VPEVKYE 120
Query: 235 FRHISEIESAEXXXXXXXXXXXXXXXPSVPILRKNGME-TQRRILNLKDTSGRSVELTLW 293
           F  I+E+ES E                   I+ K      Q+R L L D   RSV+LTLW
Sbjct: 121 FVRINELESVEANQQCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTLW 180
Query: 294 GDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELRE 353
           G    K  +       V   PVL+ K  KV DF G+S+    S+ + INPD  E+H LR 
Sbjct: 181 G----KTAETFPTNAGVDEKPVLAFKGVKVGDFGGRSLSMFSSSTMLINPDITESHVLRG 236
Query: 354 WFDSGGKNA--------ATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRA 405
           W+D+ G +A             +      GA     +T+ Q+K+E LG SEKPD+  VRA
Sbjct: 237 WYDNDGAHAQFQPYTNGGVGGGAMGGGGAGANMAERRTIVQVKDENLGMSEKPDYFNVRA 296
Query: 406 FITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQD 464
            + +IK ++  YTAC        CNKKV     N W+C++C++     +YRY+L   + D
Sbjct: 297 TVVYIKQENLYYTAC----ASEGCNKKVNLDHENNWRCEKCDRSYATPEYRYILSTNVAD 352
Query: 465 QTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEEL 524
            TG  W++ F E   +++G  A EL+ L+ E + +  F   +       Y+F  + K + 
Sbjct: 353 ATGQMWLSGFNEDATQLIGMSAGELHKLREESESE--FSAALHRAANRMYMFNCRAKMDT 410
Query: 525 YGDEQRVKITVIRADQVNYSSESRYLLDLI 554
           + D  RV+ T+ RA  V+++     L+D I
Sbjct: 411 FNDTARVRYTISRAAPVDFAKAGMELVDAI 440
>pdb|1FGU|A Chain A, Ssdna-Binding Domain Of The Large Subunit Of Replication Protein A Length = 252 Back     alignment and structure
>pdb|1JMC|A Chain A, Single Stranded Dna-Binding Domain Of Human Replication Protein A Bound To Single Stranded Dna, Rpa70 Subunit, Residues 183-420 Length = 246 Back     alignment and structure
>pdb|1L1O|C Chain C, Structure Of The Human Replication Protein A (Rpa) Trimerization Core Length = 181 Back     alignment and structure
>pdb|1YNX|A Chain A, Solution Structure Of Dna Binding Domain A (Dbd-A) Of S.Cerevisiae Replication Protein A (Rpa) Length = 114 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query560
1jmc_A246 Protein (replication protein A (RPA)); human ssDNA 1e-70
1l1o_C181 Replication protein A 70 kDa DNA-binding subunit; 3e-64
3u50_C172 Telomerase-associated protein 82; TEB1, processivi 5e-51
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 4e-40
2k50_A115 Replication factor A related protein; uncharacteri 1e-13
2k50_A115 Replication factor A related protein; uncharacteri 3e-09
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 1e-13
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 7e-07
3dm3_A105 Replication factor A; probably plays AN essential 2e-06
3e0e_A97 Replication protein A; structural genomics, PSI-2, 2e-05
>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding replication protein A(RPA), single stranded DNA-binding protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A Length = 246 Back     alignment and structure
 Score =  225 bits (575), Expect = 1e-70
 Identities = 103/250 (41%), Positives = 157/250 (62%), Gaps = 11/250 (4%)

Query: 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 172
           ++++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D   GEIR T FN 
Sbjct: 6   SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDES-GEIRATAFNE 64

Query: 173 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 232
            VD+F+ +IEV +VY  SKG+LK A K F  +KN++E+     ++V  C ++   +P  Q
Sbjct: 65  QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDDHH-LPTVQ 123

Query: 233 FSFRHISEIESAENNSIVDVIGIVISVNPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 291
           F F  I ++E+   +S+VD+IGI  S   +  I +R N  E  +R + L DTSG+ V  T
Sbjct: 124 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 183

Query: 292 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 351
           LWG+  +K     Q        PVL++K  +V+DF G+S+  + S+ +  NPD  EA++L
Sbjct: 184 LWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKL 235

Query: 352 REWFDSGGKN 361
           R WFD+ G+ 
Sbjct: 236 RGWFDAEGQA 245
>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB, ssDNA binding protein, OB-fold; 2.80A {Homo sapiens} SCOP: b.40.4.3 Length = 181 Back     alignment and structure
>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae} Length = 114 Back     alignment and structure
>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Length = 115 Back     alignment and structure
>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Length = 115 Back     alignment and structure
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Length = 119 Back     alignment and structure
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Length = 119 Back     alignment and structure
>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii} Length = 105 Back     alignment and structure
>3e0e_A Replication protein A; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.60A {Methanococcus maripaludis} PDB: 2k5v_A Length = 97 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query560
4gop_C444 Putative uncharacterized protein; OB fold, ssDNA b 100.0
1jmc_A246 Protein (replication protein A (RPA)); human ssDNA 100.0
1l1o_C181 Replication protein A 70 kDa DNA-binding subunit; 100.0
3u50_C172 Telomerase-associated protein 82; TEB1, processivi 100.0
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 99.97
3dm3_A105 Replication factor A; probably plays AN essential 99.39
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 99.36
2k50_A115 Replication factor A related protein; uncharacteri 99.35
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 99.34
3e0e_A97 Replication protein A; structural genomics, PSI-2, 99.3
3dm3_A105 Replication factor A; probably plays AN essential 99.24
2k50_A115 Replication factor A related protein; uncharacteri 99.15
3e0e_A97 Replication protein A; structural genomics, PSI-2, 99.01
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 98.96
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 98.87
1wjj_A145 Hypothetical protein F20O9.120; DNA-binding protei 98.78
1jmc_A246 Protein (replication protein A (RPA)); human ssDNA 98.74
1xjv_A294 Protection of telomeres 1; protein-DNA complex, si 98.64
1jb7_A495 Telomere-binding protein alpha subunit; DNA-protei 98.55
1wjj_A145 Hypothetical protein F20O9.120; DNA-binding protei 98.55
2kbn_A109 Conserved protein; nucleic acid binding protein, b 98.52
2kbn_A109 Conserved protein; nucleic acid binding protein, b 98.38
4gop_C 444 Putative uncharacterized protein; OB fold, ssDNA b 98.36
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 98.18
1xjv_A294 Protection of telomeres 1; protein-DNA complex, si 98.11
1qzg_A187 Protection of telomeres protein 1; protrein-DNA co 97.75
3u58_A213 Tetrahymena TEB1 AB; tetrahymena, telomerase, TEB1 97.6
1miu_A738 BRCA2, breast cancer type 2 susceptibility protein 97.36
1jb7_A 495 Telomere-binding protein alpha subunit; DNA-protei 97.21
3u4v_A117 Telomerase-associated protein 82; TEB1, processivi 96.97
3mxn_A157 RECQ-mediated genome instability protein 1; bloom 95.3
1se8_A301 Single-strand binding protein; DNA binding protein 95.17
2fxq_A264 Single-strand binding protein; strand beta-sheet e 94.49
4hik_A143 Protection of telomeres protein 1; specificity, pl 94.17
3ebe_A200 Protein MCM10 homolog; OB-fold, zinc finger, CCCH, 93.66
3kdf_D132 Replication protein A 32 kDa subunit; wheat GERM c 92.34
4gop_B136 Putative uncharacterized protein; OB fold, ssDNA b 92.11
3u4z_A109 Telomerase-associated protein 82; TEB1, processivi 91.37
1txy_A104 Primosomal replication protein N; OB fold, dimer, 91.37
3en2_A101 Probable primosomal replication protein N; PRIB RS 90.72
3fhw_A115 Primosomal replication protein N; PRIB BPR162 X-RA 90.57
3ebe_A200 Protein MCM10 homolog; OB-fold, zinc finger, CCCH, 90.24
3koj_A108 Uncharacterized protein YCF41; single-strand bindi 89.79
3eiv_A199 Single-stranded DNA-binding protein 2; DNA damage, 89.78
4gop_B136 Putative uncharacterized protein; OB fold, ssDNA b 89.35
2vw9_A134 Single-stranded DNA binding protein; DNA replicati 88.9
4dni_A257 Fusion protein of RNA-editing complex proteins MP 88.23
3kf6_A159 Protein STN1; OB fold, chromosomal protein, DNA-bi 88.2
1qzg_A187 Protection of telomeres protein 1; protrein-DNA co 88.19
2pi2_A270 Replication protein A 32 kDa subunit; FULL-length 87.44
3i7f_A548 Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-bi 86.86
3ulp_A124 Single-strand binding protein; OB-fold, DNA bindin 86.85
1v1q_A134 Primosomal replication protein N; primosome, DNA r 86.62
3vdy_A116 SSB, single-stranded DNA-binding protein SSBB; OB 86.46
3tqy_A158 Single-stranded DNA-binding protein; DNA replicati 86.03
1z9f_A153 Single-strand binding protein; TM0604, single stra 85.83
3k8a_A103 Putative primosomal replication protein; beta-barr 85.42
3kdf_D132 Replication protein A 32 kDa subunit; wheat GERM c 85.24
1eov_A487 ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy 84.96
3afp_A168 Single-stranded DNA-binding protein; OB-fold, quat 84.58
1qvc_A145 Single stranded DNA binding protein monomer; beta- 82.95
3u58_A213 Tetrahymena TEB1 AB; tetrahymena, telomerase, TEB1 82.85
>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis} Back     alignment and structure
Probab=100.00  E-value=3.1e-94  Score=778.84  Aligned_cols=433  Identities=39%  Similarity=0.704  Sum_probs=402.4

Q ss_pred             cceeccccCCCCCceEEEEEEEEecccceeccCCCCCcEEEEEEEeCCCCeEEEEEcchhHHHHHhhcccCcEEEEeeeE
Q 008606          114 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  193 (560)
Q Consensus       114 ~~~pI~~L~p~~~~w~Ik~RV~~k~~ir~~~n~~g~gkvf~~~L~D~~g~~I~at~~~~~~~kf~~~l~eG~vY~Is~~~  193 (560)
                      +++||++|+|++++|+|+|||++||++|.|++++|+|++|+|+|+|+.| +|+|++|++++++|++.|++|+||+|++|.
T Consensus         2 ~~~~I~~L~p~~~~w~I~~rV~~k~~ir~~~~~~~~g~~~~~~L~De~G-~I~at~~~~~~~~f~~~l~eG~vy~Is~~~   80 (444)
T 4gop_C            2 PIYPIEGLSPYQNRWTIKARVTSKSDIRHWSNQRGEGKLFSVNLLDDSG-EIKATGFNDAVDRFYPLLQENHVYLISKAR   80 (444)
T ss_dssp             -CCCSTTCCTTCCSCEEEEECCEECCCEEEECSSCEEEEEEEEEECSSC-EEEEEEETHHHHHHTTTCCTTCEEEEESCE
T ss_pred             CceeHHHCCCCCcceEEEEEEEEccCcceecCCCCCceEEEEEEEcCCC-EEEEEEeHHHHHHHHHheecCCEEEEcCCE
Confidence            5899999999999999999999999999999998899999999999777 999999999999999999999999999999


Q ss_pred             EecCCCccccCCCeeEEEEcccceEEeccCCCCCCCcccccccCccchhcccCCceeEEEEEEEEecCceeEeec-cCce
Q 008606          194 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK-NGME  272 (560)
Q Consensus       194 V~~a~~~y~~~~~~yeI~f~~~T~I~~~~d~~~~iP~~~f~f~~i~dI~~~~~~~~VDVIGvV~~V~~~~~i~~k-~G~~  272 (560)
                      |++++++|++++|+|||.|+.+|+|+++++ +..||...|+|++|++|.+...+.+|||||+|++|+++++|++| +|++
T Consensus        81 V~~~~~~y~~~~~~~ei~~~~~T~V~~~~d-~~~iP~~~~~f~~i~~i~~~~~~~~vDViG~V~~v~~~~~i~~k~~g~~  159 (444)
T 4gop_C           81 VNIAKKQFSNLQNEYEITFENSTEIEECTD-ATDVPEVKYEFVRINELESVEANQQCDVIGILDSYGELSEIVSKASQRP  159 (444)
T ss_dssp             EEECCGGGCSCCCSEEEEECTTCEEEECSC-CSSSCCCCCCBCCGGGGGGSCSSCCCBEEEEEEEECCCEEECCTTTCSC
T ss_pred             EEecCCccccCCCCEEEEEcCCcEEEEccC-cccCcceeecccCHHHHhccCCCCceEEEEEEEEcCCcEEEEEccCCce
Confidence            999999999999999999999999999975 45799999999999999998889999999999999999999988 7888


Q ss_pred             eeEEEEEEecCCCcEEEEEEeCcchhhhhhhHHhhhccCCccEEEEEEEEEecCCCceecccCCeEEEECCChHHHHHHH
Q 008606          273 TQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELR  352 (560)
Q Consensus       273 ~~kr~i~L~D~Sg~~I~vtLWg~~a~~~~~~l~~~~~~~~~~VV~l~~~rV~~f~G~sLs~~~~S~i~iNPdipEa~~L~  352 (560)
                      ..+|+|+|.|+||.+|+|||||++|..|...   .+ .+.++||+|+++||++|+|++||+.++|+|++|||+||+.+|+
T Consensus       160 ~~kr~i~L~D~sg~~i~~tLWg~~A~~f~~~---~~-~~~~~VV~i~~~kV~~f~G~~ls~~~~s~i~inPdipea~~l~  235 (444)
T 4gop_C          160 VQKRELTLVDQGNRSVKLTLWGKTAETFPTN---AG-VDEKPVLAFKGVKVGDFGGRSLSMFSSSTMLINPDITESHVLR  235 (444)
T ss_dssp             EEEEEEEEECTTCBEEEEEEEHHHHHTSTTS---TT-SSSCCEEEEESCEEECTTSSEEECCTTCEEEESCSSHHHHHHH
T ss_pred             eeEEEEEEEeCCCCEEEEEEEhhhhhhhhhh---hc-cCCCCEEEEEeEEEeecCCeEEeccccceEEECCCCHHHHHHH
Confidence            9999999999999999999999999886431   11 3578999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCccceeeccccc------c--cCCCccchhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCc
Q 008606          353 EWFDSGGKNAATVSISREI------A--AGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMI  424 (560)
Q Consensus       353 ~w~~~~g~~~~~~sls~~~------~--~~~~~~~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~  424 (560)
                      .||++.|.+..+.+++...      +  ..+.+...+|||+||+++.+|.+++++||.|+|+|+.|+.++|||+|||.+ 
T Consensus       236 ~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kti~~i~~~~~g~~~~~~~~~v~atI~~i~~~~~~Y~aC~~~-  314 (444)
T 4gop_C          236 GWYDNDGAHAQFQPYTNGGVGGGAMGGGGAGANMAERRTIVQVKDENLGMSEKPDYFNVRATVVYIKQENLYYTACASE-  314 (444)
T ss_dssp             HHHHHHTTTSCCBCCCCCC---------CTTCCSSEECCHHHHHHTTTTSSSSCEEEEEEEEEEEECCTTCEEEECCST-
T ss_pred             HHHHcCCCCcccccccccccccccccccccccccccceeHHHHhhhccCCCCCCcEEEEEEEEEEEcCCceEEccCCcc-
Confidence            9999999888888876543      1  122356789999999999999999999999999999999999999999921 


Q ss_pred             CccccCceeeecCC-eeecCcCCCccCCceeEEEEEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHH
Q 008606          425 GDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFG  503 (560)
Q Consensus       425 ~~~~C~KKv~~~~~-~~~C~kC~~~~~~~~~rY~l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~  503 (560)
                         .|+|||...++ .|+|++|++..++|.|||+|++.|+||||++|+++||+.|++|||++|+||.+++  ++|+..++
T Consensus       315 ---~C~kkv~~~~~g~~~C~~C~~~~~~~~~ry~l~~~v~D~Tg~~~~~~F~~~a~~llG~sa~el~~~~--~~d~~~~~  389 (444)
T 4gop_C          315 ---GCNKKVNLDHENNWRCEKCDRSYATPEYRYILSTNVADATGQMWLSGFNEDATQLIGMSAGELHKLR--EESESEFS  389 (444)
T ss_dssp             ---TCCCBEEECTTSCEEETTTTEEESSCEEEECEEEEEEETTEEEEEEECHHHHHHHTTSCHHHHHHHH--TTCHHHHH
T ss_pred             ---cCCCccccCCCccEECCCCCCcCccccEEEEEEEEEEeCCCCEEEEEehHHHHHHcCCCHHHHHHHH--hcChHHHH
Confidence               39999987654 8999999999889999999999999999999999999999999999999999998  67899999


Q ss_pred             HHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEEeeeCChHHHHHHHHHHHHhhh
Q 008606          504 EIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSF  558 (560)
Q Consensus       504 ~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~~~~vd~~~e~~~ll~~i~~~~  558 (560)
                      ++|++++|++|+|+|+++.++|+|+.|+|++|++++|+||++|+++||++|++|+
T Consensus       390 ~~~~~~~~k~~~f~~~~k~~~y~~~~r~~~~v~~~~~~d~~~~~~~l~~~i~~~~  444 (444)
T 4gop_C          390 AALHRAANRMYMFNCRAKMDTFNDTARVRYTISRAAPVDFAKAGMELVDAIRAYM  444 (444)
T ss_dssp             HHHHTTSSCEEEEEEEEEEEEETTEEEEEEEEEEEEECCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHhhCcEEEEEEEEEeeeeCCeeEEEEEEEEeeeCCHHHHHHHHHHHHHhhC
Confidence            9999999999999999999999999999999999999999999999999999984
>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding replication protein A(RPA), single stranded DNA-binding protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A Back     alignment and structure
>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB, ssDNA binding protein, OB-fold; 2.80A {Homo sapiens} SCOP: b.40.4.3 Back     alignment and structure
>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii} Back     alignment and structure
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Back     alignment and structure
>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Back     alignment and structure
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Back     alignment and structure
>3e0e_A Replication protein A; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.60A {Methanococcus maripaludis} PDB: 2k5v_A Back     alignment and structure
>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii} Back     alignment and structure
>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Back     alignment and structure
>3e0e_A Replication protein A; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.60A {Methanococcus maripaludis} PDB: 2k5v_A Back     alignment and structure
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum} Back     alignment and structure
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum} Back     alignment and structure
>1wjj_A Hypothetical protein F20O9.120; DNA-binding protein-related, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.40.4.3 Back     alignment and structure
>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding replication protein A(RPA), single stranded DNA-binding protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A Back     alignment and structure
>1xjv_A Protection of telomeres 1; protein-DNA complex, single-stranded DNA, transcription/DNA complex; 1.73A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 3kjo_A 3kjp_A Back     alignment and structure
>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions, DNA HYDR sodium ION, quadruplex DNA, DNA-binding protein-DNA complex; 1.86A {Sterkiella nova} SCOP: b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1kix_A 1otc_A* 2i0q_A 1ph6_A 1ph1_A 1phj_A* 1ph3_A 1pa6_A 1ph4_A 1ph7_A 1ph8_A 1ph9_A 1ph5_A* 1ph2_A* 1k8g_A Back     alignment and structure
>1wjj_A Hypothetical protein F20O9.120; DNA-binding protein-related, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.40.4.3 Back     alignment and structure
>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_A Back     alignment and structure
>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_A Back     alignment and structure
>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis} Back     alignment and structure
>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>1xjv_A Protection of telomeres 1; protein-DNA complex, single-stranded DNA, transcription/DNA complex; 1.73A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 3kjo_A 3kjp_A Back     alignment and structure
>1qzg_A Protection of telomeres protein 1; protrein-DNA complex, single-stranded telomeric DNA, DNA binding protein/DNA complex; HET: TMP; 1.90A {Schizosaccharomyces pombe} SCOP: b.40.4.3 PDB: 1qzh_A Back     alignment and structure
>3u58_A Tetrahymena TEB1 AB; tetrahymena, telomerase, TEB1, processivity factor, DNA BIND protein-DNA complex; HET: DNA; 2.61A {Tetrahymena thermophila} Back     alignment and structure
>1miu_A BRCA2, breast cancer type 2 susceptibility protein; tumor suppressor, breast cancer susceptibility, DNA-binding; 3.10A {Mus musculus} SCOP: a.170.1.1 a.171.1.1 b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1iyj_B 1mje_A Back     alignment and structure
>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions, DNA HYDR sodium ION, quadruplex DNA, DNA-binding protein-DNA complex; 1.86A {Sterkiella nova} SCOP: b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1kix_A 1otc_A* 2i0q_A 1ph6_A 1ph1_A 1phj_A* 1ph3_A 1pa6_A 1ph4_A 1ph7_A 1ph8_A 1ph9_A 1ph5_A* 1ph2_A* 1k8g_A Back     alignment and structure
>3u4v_A Telomerase-associated protein 82; TEB1, processivity factor, DNA BIND protein; 1.80A {Tetrahymena thermophila} Back     alignment and structure
>3mxn_A RECQ-mediated genome instability protein 1; bloom syndrome, helicase, RMI, topoisomerase, replication PR replication; 1.55A {Homo sapiens} PDB: 4day_A 3nbh_A Back     alignment and structure
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3 Back     alignment and structure
>2fxq_A Single-strand binding protein; strand beta-sheet extended loops, DNA binding protein; 1.85A {Thermus aquaticus} PDB: 2ihe_A 2cwa_A 2ihf_A Back     alignment and structure
>4hik_A Protection of telomeres protein 1; specificity, plasticity, promiscuity, OB-fold, ssDNA binding stranded telomeric DNA; HET: DNA; 1.64A {Schizosaccharomyces pombe} PDB: 4hid_A* 4him_A* 4hio_A* 4hj5_A* 4hj7_A* 4hj8_A* 4hj9_A* 4hja_A* Back     alignment and structure
>3ebe_A Protein MCM10 homolog; OB-fold, zinc finger, CCCH, DNA replication, metal-binding, zinc-finger, replication; 2.30A {Xenopus laevis} PDB: 3h15_A Back     alignment and structure
>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_A 1quq_A 1l1o_B Back     alignment and structure
>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis} Back     alignment and structure
>3u4z_A Telomerase-associated protein 82; TEB1, processivity factor, DNA BIND protein; 2.30A {Tetrahymena thermophila} Back     alignment and structure
>1txy_A Primosomal replication protein N; OB fold, dimer, DNA binding protein; 2.00A {Escherichia coli} SCOP: b.40.4.3 PDB: 1woc_A 2pnh_A 4apv_A Back     alignment and structure
>3en2_A Probable primosomal replication protein N; PRIB RSR213C NESG X-RAY Q8XZT7 Q8XZT7_ralso, structural genomics, PSI-2; 2.30A {Ralstonia solanacearum} Back     alignment and structure
>3fhw_A Primosomal replication protein N; PRIB BPR162 X-RAY NESG, structural genomics, PSI-2, protein initiative; 1.90A {Bordetella parapertussis} PDB: 3dm4_A 3klw_A Back     alignment and structure
>3ebe_A Protein MCM10 homolog; OB-fold, zinc finger, CCCH, DNA replication, metal-binding, zinc-finger, replication; 2.30A {Xenopus laevis} PDB: 3h15_A Back     alignment and structure
>3koj_A Uncharacterized protein YCF41; single-strand binding protein family, PF00436, SNR59A, NESG, structural genomics, PSI-2; 1.90A {Synechococcus elongatus pcc 6301} Back     alignment and structure
>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor} Back     alignment and structure
>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis} Back     alignment and structure
>2vw9_A Single-stranded DNA binding protein; DNA replication, single-stranded DNA, single-stranded DNA binding protein, oligonucleotide/oligosaccharide binding fold, OB-fold; 2.30A {Helicobacter pylori} Back     alignment and structure
>4dni_A Fusion protein of RNA-editing complex proteins MP MP18; krepa3, krepa6, editosome, protein/RNA binding, protein BIND binding protein; 2.55A {Trypanosoma brucei} Back     alignment and structure
>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1qzg_A Protection of telomeres protein 1; protrein-DNA complex, single-stranded telomeric DNA, DNA binding protein/DNA complex; HET: TMP; 1.90A {Schizosaccharomyces pombe} SCOP: b.40.4.3 PDB: 1qzh_A Back     alignment and structure
>2pi2_A Replication protein A 32 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2z6k_A 1dpu_A 1z1d_A Back     alignment and structure
>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding, aminoacyl-tRNA synthetase, LI nucleotide-binding, protein biosynthesis; 2.80A {Entamoeba histolytica} Back     alignment and structure
>3ulp_A Single-strand binding protein; OB-fold, DNA binding, single-stranded DNA, apicoplast, DNA B protein-DNA complex; HET: DNA; 2.10A {Plasmodium falciparum} Back     alignment and structure
>1v1q_A Primosomal replication protein N; primosome, DNA replication, DNA binding; 2.1A {Escherichia coli} SCOP: b.40.4.3 PDB: 2ccz_A Back     alignment and structure
>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis} Back     alignment and structure
>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii} Back     alignment and structure
>1z9f_A Single-strand binding protein; TM0604, single stranded DNA-binding protein, structural GENO joint center for structural genomics, JCSG; 2.30A {Thermotoga maritima} Back     alignment and structure
>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold, DNA binding protein; 2.70A {Neisseria gonorrhoeae fa 1090} Back     alignment and structure
>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_A 1quq_A 1l1o_B Back     alignment and structure
>1eov_A ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA synthetase, tRNA ligase, APO-enzyme, OB-fold,; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.1 d.104.1.1 PDB: 1asy_A* 1asz_A* Back     alignment and structure
>3afp_A Single-stranded DNA-binding protein; OB-fold, quaternary structure and stability, changes on oligomerisation, water-bridges, DNA damage; 2.05A {Mycobacterium leprae} PDB: 3afq_A 1ue1_A 1ue5_A 1ue6_A 1ue7_A 1x3e_A 1x3f_A 1x3g_A 3a5u_A* Back     alignment and structure
>1qvc_A Single stranded DNA binding protein monomer; beta-barrel; 2.20A {Escherichia coli} SCOP: b.40.4.3 PDB: 1kaw_A 1eyg_A 1sru_A Back     alignment and structure
>3u58_A Tetrahymena TEB1 AB; tetrahymena, telomerase, TEB1, processivity factor, DNA BIND protein-DNA complex; HET: DNA; 2.61A {Tetrahymena thermophila} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 560
d1l1oc_178 b.40.4.3 (C:) Replication protein A 70 KDa subunit 4e-65
d1jmca2122 b.40.4.3 (A:299-420) Replication protein A 70 KDa 7e-39
d1jmca1116 b.40.4.3 (A:183-298) Replication protein A 70 KDa 1e-37
d1o7ia_115 b.40.4.3 (A:) Archaeal ssDNA-binding protein {Arch 1e-15
>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Length = 178 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  208 bits (530), Expect = 4e-65
 Identities = 62/176 (35%), Positives = 99/176 (56%), Gaps = 7/176 (3%)

Query: 382 KTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RW 440
           KT+ ++K+E LG+ +KPD+ +  A + +++ ++  Y ACP     + CNKKV    N  +
Sbjct: 5   KTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPT----QDCNKKVIDQQNGLY 60

Query: 441 QCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDV 500
           +C++C+ E     YR +L   I D     WVT FQES E ILG  A  L  LK   +++ 
Sbjct: 61  RCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK--DKNEQ 118

Query: 501 RFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 556
            F E+ ++  F  ++FR+++K E Y DE R+K TV+    V+Y    R L+  I +
Sbjct: 119 AFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMSIRR 174
>d1jmca2 b.40.4.3 (A:299-420) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Length = 122 Back     information, alignment and structure
>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Length = 116 Back     information, alignment and structure
>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Length = 115 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query560
d1l1oc_178 Replication protein A 70 KDa subunit (RPA70) {Huma 100.0
d1jmca2122 Replication protein A 70 KDa subunit (RPA70) {Huma 99.96
d1jmca1116 Replication protein A 70 KDa subunit (RPA70) {Huma 99.96
d1o7ia_115 Archaeal ssDNA-binding protein {Archaeon Sulfolobu 99.44
d1o7ia_115 Archaeal ssDNA-binding protein {Archaeon Sulfolobu 99.0
d1wjja_145 Hypothetical protein At4g28440 (F20O9.120) {Thale 98.68
d1wjja_145 Hypothetical protein At4g28440 (F20O9.120) {Thale 98.62
d1jmca1116 Replication protein A 70 KDa subunit (RPA70) {Huma 98.43
d1xjva1140 Protection of telomeres protein 1, Pot1 {Human (Ho 98.27
d1jmca2122 Replication protein A 70 KDa subunit (RPA70) {Huma 97.67
d1jb7a1169 Telomere end binding protein alpha subunit {Oxytri 97.58
d1qzga_170 Protection of telomeres protein 1, Pot1 {Fission y 97.22
d1se8a_231 ssDNA-binding protein {Deinococcus radiodurans [Ta 96.12
d1xjva1140 Protection of telomeres protein 1, Pot1 {Human (Ho 95.31
d1jb7a1169 Telomere end binding protein alpha subunit {Oxytri 93.57
d1eova1134 Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S 93.25
d1xjva2151 Protection of telomeres protein 1, Pot1 {Human (Ho 93.23
d1v1qa_111 Primosomal replication protein N, PriB {Escherichi 90.71
d1e1oa1143 Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g 88.13
d1gm5a2180 RecG "wedge" domain {Thermotoga maritima [TaxId: 2 88.12
d1c0aa1106 Aspartyl-tRNA synthetase (AspRS) {Escherichia coli 87.6
d1jb7a2124 Telomere end binding protein alpha subunit {Oxytri 87.3
d1n9wa193 Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph 86.29
d1ue1a_118 ssDNA-binding protein {Mycobacterium tuberculosis 85.41
d2pi2a1128 Replication protein A 32 KDa subunit (RPA32) fragm 84.73
d1qvca_145 ssDNA-binding protein {Escherichia coli [TaxId: 56 84.35
d1b8aa1103 Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ 84.27
d1iyjb5138 OB-fold domains of BRCA2 {Rat (Rattus norvegicus) 84.03
d1l0wa1104 Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph 82.61
d1jb7a2124 Telomere end binding protein alpha subunit {Oxytri 82.55
d1qzga_170 Protection of telomeres protein 1, Pot1 {Fission y 80.99
>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=7e-44  Score=335.76  Aligned_cols=174  Identities=36%  Similarity=0.656  Sum_probs=160.9

Q ss_pred             chhhhHHHHhhcCCCCCCCCceEEEEEEEEEEeCCCeEEeCCCCCcCccccCceeeecC-CeeecCcCCCccCCceeEEE
Q 008606          379 EIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECDYRYL  457 (560)
Q Consensus       379 ~~~ktI~~I~~~~~g~~e~~~~~~v~atI~~I~~d~~~Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~~~~~~~rY~  457 (560)
                      ..+|||+||+++.+|.+++|+||+|+|+|+.|+.++|||+|||+.    .|+|||+..+ +.|+|++|++..++|.|||+
T Consensus         2 ~~~kti~~i~~e~lg~~~k~d~f~v~a~I~~i~~~~~~Y~aCp~~----~C~KKv~~~~~g~~~C~kC~~~~~~~~~ry~   77 (178)
T d1l1oc_           2 TNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPTQ----DCNKKVIDQQNGLYRCEKCDTEFPNFKYRMI   77 (178)
T ss_dssp             CCBCCHHHHHHHTTTSSSSCEEEEEEEEEEEECCSTTEEEBCCST----TCCCBCEEETTTEEEETTTTEEESSCCEEEE
T ss_pred             CccccHHHHHhccCCCCCCCCEEEEEEEEEEEeCCCeEEcCCCCc----ccCCccccCCCCcEECCCCCCcCCCceEEEE
Confidence            468999999999999999999999999999999999999999943    5999998655 48999999999999999999


Q ss_pred             EEEEEEeCCCeEEEEEehhhhhhhcCCCHHHHHHhhhccCChhHHHHHHHHhcCCeEEEEEEEeeeecCCeeeEEEEEEE
Q 008606          458 LQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIR  537 (560)
Q Consensus       458 l~~~i~D~Tgs~~~~~Fd~~ae~llG~sA~el~~~~~e~~d~~~~~~~l~~~~~k~~~fkvkvk~e~y~~e~r~k~~v~~  537 (560)
                      |++.|+|+||++|+++||+.|++|||++|+||.++.  ++++..++++++++.|++|.|+++++.++||++.|+|++|++
T Consensus        78 l~~~i~D~Tg~~~~~~F~~~a~~l~G~sA~EL~~~~--~~d~~~~~~~~~~l~~k~~~f~~~~k~~~yn~e~r~k~~v~~  155 (178)
T d1l1oc_          78 LSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK--DKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMD  155 (178)
T ss_dssp             EEEEEECSSCEEEEEEEHHHHHHHHSSCHHHHHHHT--TSCHHHHHHHHHHTTTCEEEEEEEEECCCC-----CEEEEEE
T ss_pred             EEEEEecCCCCEEEEEehhhHHHHhCCCHHHHHHHh--hcCHHHHHHHHHHhcCcEEEEEEEEEecccCCeeEEEEEEEE
Confidence            999999999999999999999999999999999998  678999999999999999999999999999999999999999


Q ss_pred             eeeCChHHHHHHHHHHHHhhh
Q 008606          538 ADQVNYSSESRYLLDLISKSF  558 (560)
Q Consensus       538 ~~~vd~~~e~~~ll~~i~~~~  558 (560)
                      ++|+||++|+++|++.|++|.
T Consensus       156 i~pvd~~~e~~~L~~~I~~~~  176 (178)
T d1l1oc_         156 VKPVDYREYGRRLVMSIRRSA  176 (178)
T ss_dssp             EEECCHHHHHHHHHHHHHHHH
T ss_pred             eEeCCHHHHHHHHHHHHHHhh
Confidence            999999999999999999985
>d1jmca2 b.40.4.3 (A:299-420) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1xjva1 b.40.4.3 (A:6-145) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jmca2 b.40.4.3 (A:299-420) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jb7a1 b.40.4.3 (A:36-204) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]} Back     information, alignment and structure
>d1qzga_ b.40.4.3 (A:) Protection of telomeres protein 1, Pot1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Back     information, alignment and structure
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1xjva1 b.40.4.3 (A:6-145) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jb7a1 b.40.4.3 (A:36-204) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]} Back     information, alignment and structure
>d1eova1 b.40.4.1 (A:71-204) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1xjva2 b.40.4.3 (A:149-299) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]} Back     information, alignment and structure
>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1c0aa1 b.40.4.1 (A:1-106) Aspartyl-tRNA synthetase (AspRS) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jb7a2 b.40.4.3 (A:205-328) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]} Back     information, alignment and structure
>d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]} Back     information, alignment and structure
>d1ue1a_ b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d2pi2a1 b.40.4.3 (A:44-171) Replication protein A 32 KDa subunit (RPA32) fragment {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1b8aa1 b.40.4.1 (A:1-103) Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococcus kodakaraensis [TaxId: 311400]} Back     information, alignment and structure
>d1iyjb5 b.40.4.3 (B:2980-3117) OB-fold domains of BRCA2 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1l0wa1 b.40.4.1 (A:1-104) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]} Back     information, alignment and structure
>d1jb7a2 b.40.4.3 (A:205-328) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]} Back     information, alignment and structure
>d1qzga_ b.40.4.3 (A:) Protection of telomeres protein 1, Pot1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Back     information, alignment and structure