Citrus Sinensis ID: 006263

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Local Sequence Feature Prediction

Residue Number Marker
--------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-------570-------580-------590-------600-------610-------620-------630-------640-------650---
Protein Sequence
MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
Secondary Structure (PSIPRED)
ccccccHHHHHHHHccccccccEEEEEEEEEEcccccEEEEEEEcccHHHHHHccccccccccccccccccEEEEEEEEEEEccccEEEEEEEEEEEccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEcccccccccccccEEEEEEEEEccccEEEEEEcccHHHccccccccccEEEEcccEEcccccccccccccEEEEEccccEEEEcccccccccccccccccHHHHHccccccEEEEEEEEEEEcccEEEEcccccEEEEEEEEEEcccccEEEEcccHHHHHHHHcccccccccccccEEEEcccEEEccccccccccccEEEEEccccHHHHHHHHHHHcccccccEEEcccccccccccccccHHHHHHHHccccccccccEEEEEEEEEEEEccccEEEccccccccccccEEEEEcccEEEEccccccccccEEEEEEEEEEEEccccEEEEEEHHHHHHHHcccHHHHHHHHHHcccHHHHHHHHHHHcccEEEEEEEEEEEEEccEEEEEEEEEEEEcccHHHHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHccccccccEEEEEEEEEcccccccEEEEEcccHHHHHHHHHHHHHHHHHcccEcccEEEEEEEEEEEEccccEEEEEEEEEEEcccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccEEEEEEEEEcccEEEEEccEEEEEEEEEEEcccccEEEEEEEHHHHHHHHHHcccccEEEEEccEEEEccHHHccccccEEEEcccccEEEEcccccccccEEEEEEEEHHHHcccccccEEEEEEEEEEccccEEEEEccccEcccEEEEEEEccccEEEEEEEcccHHHccHHHHHHHccccccEEEEEEEEEEcccccEEEcccccEEEEccccHHHHHHHHHHHHHcccccccccccccccccccccccEEHHHHHHccccccccccEEEEEEEEEEEcccccccccccccccccccccEEEEccccEEEcccccccccccEEEEEEEEEEcccccEEEEccHHHHHHHHcccHHHHHHHHHccccHHHHHHHHHHccccEEEEEEEEEEcccccccEEEEEEEEEccccHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mpvnltpnsislinggdvnskplVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDrvktgqvkkgsVVQLIDYICSTVQNRKIIVVLNMETIIldcepignpkifseseltaqktipsnnlpqpvrvnnysapnsgtfnlqnsgtfnsqnpgsfstpnsgtfrapnagsivrsfqptvqppyqpppnfrnhgpilkneapariipiaalnpyqgRWAIKARVTAKGdlrrynnargdgkvfsfdlldsdggeirvTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTvdlcteeddsipkqqfsfRHISEIesaennsiVDVIGIVIsvnpsvpilrkngMETQRRILNlkdtsgrsvELTLWGDFCNKEGQKLQEMVDVGFFPVlsvksgkvndfsgksigtipstqlfinpdfaeAHELREWFdsggknaaTVSISREIaaggakneIHKTVSQIKneglgrsekpdwVTVRAFITFIKsdsfcytacplmigdrqcnkkvtqsgnrwqcdrcnqeideCDYRYLLQAQIQDQTGLTWVTAFQEsgeeilgcpakELYMLKYelqddvrfgEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
Flexible Loop (DISEMBL)
mpvnltpnsislinggdvnskplVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATqlndrvktgqvkkGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKtipsnnlpqpvRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAalnpyqgrwAIKARVtakgdlrrynnargdgkvfsfdlldsdggeIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRIlnlkdtsgrsvELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIaaggakneihktvsqikneglgrsekpdwVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTqsgnrwqcdrCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKeelygdeqrvkitviradqvnyssesrylldlisksfrk
Low Complexity Region (SEG)
MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFqptvqppyqpppNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAEnnsivdvigivisvnPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
Disordered region (IsUnstruct)
***********LINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIF*****************************************************************************************LKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEE*******QFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAA************************PDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLI******
Disordered Region (DISOPRED)
**VNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNP*******************************************************************************************************IAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAA*************KNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSF**
Disordered Region (DISEMBL)
MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCN********RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
Disordered Region (DISPRO)
****LTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKI************************************************************************************************ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGG********************IHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	653	2.2.26 [Sep-21-2011]
Q6NY74	601	Replication protein A 70	yes	no	0.898	0.976	0.339	2e-97
P27694	616	Replication protein A 70	yes	no	0.905	0.959	0.348	5e-97
Q5R7Q4	616	Replication protein A 70	yes	no	0.898	0.952	0.349	3e-95
Q8VEE4	623	Replication protein A 70	yes	no	0.894	0.937	0.335	1e-93
Q5FW17	609	Replication protein A 70	yes	no	0.905	0.970	0.339	8e-92
Q01588	609	Replication protein A 70	N/A	no	0.900	0.965	0.340	3e-91
Q5ZJJ2	614	Replication protein A 70	yes	no	0.917	0.975	0.337	9e-90
Q92372	609	Replication factor A prot	yes	no	0.909	0.975	0.302	1e-85
P22336	621	Replication factor A prot	yes	no	0.848	0.892	0.307	6e-83
Q24492	603	Replication protein A 70	yes	no	0.877	0.950	0.318	1e-81

>sp|Q6NY74|RFA1_DANRE Replication protein A 70 kDa DNA-binding subunit OS=Danio rerio GN=rpa1 PE=1 SV=1

 Score =  357 bits (915), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 224/659 (33%), Positives = 363/659 (55%), Gaps = 72/659 (10%)

Query: 1   MPVNLTPNSI-SLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLAT 56
           M V L+  +I SL  G +VN+ P++Q ++I+ I  G+   R+R ++SD + T  + ML+T
Sbjct: 1   MTVRLSEGAIESLSKGTEVNN-PILQCVNIRKIDGGNGVSRFRVMMSDGLHTMSSFMLST 59

Query: 57  QLNDRVKTGQVKKGSVVQLIDYICSTVQN-RKIIVVLNMETI-ILDCEP--IGNPKIFSE 112
           QLN   +  Q+    V  L   + + +++ R+++V+L++E +   D  P  IG+P  + E
Sbjct: 60  QLNPMAEQNQLATNCVCVLKRSVTNVLKDGRRVVVILDIEVLKSADQMPGKIGDPTPYVE 119

Query: 113 SELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTF-RAPN 171
            +  A  T P              AP +     QN       + GS   P++ +F + P 
Sbjct: 120 GQSKAPSTAP--------------APTARPLQPQNG------SDGSTYRPSAQSFGKKPM 159

Query: 172 AGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKG 231
           A             P  P                ++++PIA+LNPYQ +W I+ARVT K 
Sbjct: 160 AA------------PNTPG-------------GSSKVVPIASLNPYQSKWTIRARVTNKS 194

Query: 232 DLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQ 291
            +R ++N+RGDGK+FS +L+D + GEIR T FN  VD+F+ +IE G+V+ ISKG+LK A 
Sbjct: 195 AIRTWSNSRGDGKLFSMELVD-ESGEIRATGFNNEVDKFFSLIEQGKVFYISKGTLKIAN 253

Query: 292 KNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVIS 351
           K F+ LKN++E+ L   +++  C + +D +P  Q  F  I+++ES E ++I+DVIG+  +
Sbjct: 254 KQFSSLKNDYEMTLNGETSIIPCEDSND-VPMLQCDFVSIADLESREKDTILDVIGVCKN 312

Query: 352 VNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV 411
                 I+ KN  E  +R + L D SGR ++LT+WG           E  D    P+L++
Sbjct: 313 AEDVARIMTKNSREVSKRNIQLIDMSGRVIQLTMWGSDA--------ETFDGSGQPILAI 364

Query: 412 KSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKN 471
           K  +++DF G+S+ T+ S+ + INPD  EA++LR W+D  G      S++     GG  N
Sbjct: 365 KGARLSDFGGRSLSTLYSSTVMINPDIPEAYKLRGWYDKEGHALDGQSMTELRGPGGGGN 424

Query: 472 EIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSG 530
              KT++++KNE LG  +K D+ +  A I +I+ ++  Y ACP     + CNKKV  Q  
Sbjct: 425 TNWKTLAEVKNEHLGHGDKADYFSCIATIVYIRKENCLYQACP----SKDCNKKVVDQQN 480

Query: 531 NRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQ 590
             ++C++C++E  +  YR +L A I D     WVT FQ++ E +LG  +  L  LK    
Sbjct: 481 GMFRCEKCDKEFPDFKYRLMLSANIADFGDNQWVTCFQDTAETLLGQNSSYLGQLKD--T 538

Query: 591 DDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
           ++  F E+ +   FN ++FR ++K E Y DE R+K+TV+ A  V++   S+ L+  I K
Sbjct: 539 NEAAFDEVFQHANFNTFVFRNRVKLETYNDESRIKVTVVDAKPVDHREYSKRLIINIRK 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

 Score =  355 bits (912), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 227/651 (34%), Positives = 360/651 (55%), Gaps = 60/651 (9%)

Query: 11  SLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQLNDRVKTGQV 67
           +++  GD N KP++QV++I+ I  G++  RYR L+SD ++T  + MLATQLN  V+  Q+
Sbjct: 12  AIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQL 71

Query: 68  KKGSVVQLIDYICSTVQN-RKIIVVLNMETIILDCEPIGNPKIFSESELTAQKTIPSNNL 126
               V Q+  +I +T+++ R++++++ +E ++   E +G                     
Sbjct: 72  SSNCVCQIHRFIVNTLKDGRRVVILMELE-VLKSAEAVG--------------------- 109

Query: 127 PQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPP 186
              V++ N    N G    Q +    + +P + S P       P  GS       TV   
Sbjct: 110 ---VKIGNPVPYNEGLGQPQVAPPAPAASPAASSRPQ------PQNGS--SGMGSTVSKA 158

Query: 187 YQPPPNF-RNHGPILKNEA---PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGD 242
           Y     F +  GP L + +    ++++PIA+L PYQ +W I ARVT K  +R ++N+RG+
Sbjct: 159 YGASKTFGKAAGPSLSHTSGGTQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGE 218

Query: 243 GKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWE 302
           GK+FS +L+D + GEIR T FN  VD+F+ +IEV +VY  SKG+LK A K F  +KN++E
Sbjct: 219 GKLFSLELVD-ESGEIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYE 277

Query: 303 IFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPI-LRK 361
           +     ++V  C E+D  +P  QF F  I ++E+   +S+VD+IGI  S   +  I +R 
Sbjct: 278 MTFNNETSVMPC-EDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRS 336

Query: 362 NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG 421
           N  E  +R + L DTSG+ V  TLWG+  +K     Q        PVL++K  +V+DF G
Sbjct: 337 NNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQ--------PVLAIKGARVSDFGG 388

Query: 422 KSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAG-GAKNEIHKTVSQI 480
           +S+  + S+ +  NPD  EA++LR WFD+ G+    VSIS   + G G  N   KT+ ++
Sbjct: 389 RSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVSISDLKSGGVGGSNTNWKTLYEV 448

Query: 481 KNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCN 539
           K+E LG+ +KPD+ +  A + +++ ++  Y ACP     + CNKKV  Q    ++C++C+
Sbjct: 449 KSENLGQGDKPDYFSSVATVVYLRKENCMYQACPT----QDCNKKVIDQQNGLYRCEKCD 504

Query: 540 QEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEII 599
            E     YR +L   I D     WVT FQES E ILG  A  L  LK   +++  F E+ 
Sbjct: 505 TEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKD--KNEQAFEEVF 562

Query: 600 RSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKS 650
           ++  F  ++FR+++K E Y DE R+K TV+    V+Y    R L+  I +S
Sbjct: 563 QNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMSIRRS 613

Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.

Homo sapiens (taxid: 9606)

>sp|Q5R7Q4|RFA1_PONAB Replication protein A 70 kDa DNA-binding subunit OS=Pongo abelii GN=RPA1 PE=2 SV=1

 Score =  350 bits (897), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 229/655 (34%), Positives = 359/655 (54%), Gaps = 68/655 (10%)

Query: 11  SLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQLNDRVKTGQV 67
           +++  GD N KP++QV++I+ I  G++  RYR L+SD ++T  + M ATQLN  V+  Q+
Sbjct: 12  AIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMSATQLNPLVEQEQL 71

Query: 68  KKGSVVQLIDYICSTVQN-RKIIVVLNMETIILDCE----PIGNPKIFSESELTAQKTIP 122
               V Q+  +I +T+++ R++++++ +E ++   E     IGNP  ++E          
Sbjct: 72  SSNCVCQINRFIVNTLKDGRRVVILMELE-VLKSAEVVGVKIGNPVPYNEG--------- 121

Query: 123 SNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPT 182
              L QP               +       S    S   P +GT     AGS       T
Sbjct: 122 ---LGQP--------------QVAPPAPAASPAASSRPQPQNGT---SGAGS-------T 154

Query: 183 VQPPYQPPPNF-RNHGPILKNEA---PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNN 238
           V   Y     F +  GP L + +    ++++PIA+L PYQ +W I ARVT K  +R ++N
Sbjct: 155 VSKAYGASKTFGKAAGPSLSHNSGGTQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSN 214

Query: 239 ARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLK 298
           +RG+ K+FS +L+D + GEIR T FN  VD+F+ +IEV +VY  SKG+LK A K F  +K
Sbjct: 215 SRGEEKLFSLELVD-ESGEIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVK 273

Query: 299 NEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPI 358
           N++E+     ++V  C E+D  +P  QF F  I ++E+   +S+VD+IGI  S   +  I
Sbjct: 274 NDYEMTFNNETSVMPC-EDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATKI 332

Query: 359 -LRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVN 417
            +R N  E  +R + L DTSG+ V  TLWG+  +K     Q        PVL++K  +V+
Sbjct: 333 TVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDGSRQ--------PVLAIKGARVS 384

Query: 418 DFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAG-GAKNEIHKT 476
           DF G+S+  + S+ +  NPD  EA++LR WFD+ G+    VSIS   + G G  N   KT
Sbjct: 385 DFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQALDGVSISDLKSGGVGGGNTNWKT 444

Query: 477 VSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQC 535
           + ++K+E LG+ +KPD+ +  A + +++ ++  Y ACP     + CNKKV  Q    ++C
Sbjct: 445 LYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPT----QDCNKKVIDQQNGLYRC 500

Query: 536 DRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRF 595
           ++C+ E     YR +L   I D     WVT FQES E ILG  A  L  LK   +++  F
Sbjct: 501 EKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKD--KNEQAF 558

Query: 596 GEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKS 650
            E+ ++  F  ++FR+++K E Y DE R+K TV+    V+Y    R L+  I +S
Sbjct: 559 EEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMSIRRS 613

It participates in a very early step in initiation. RP-A is a single-stranded DNA-binding protein.

Pongo abelii (taxid: 9601)

>sp|Q8VEE4|RFA1_MOUSE Replication protein A 70 kDa DNA-binding subunit OS=Mus musculus GN=Rpa1 PE=2 SV=1

 Score =  344 bits (883), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 218/649 (33%), Positives = 354/649 (54%), Gaps = 65/649 (10%)

Query: 21  KPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQLNDRVKTGQVKKGSVVQLID 77
           KP++QV++I+ I  G+   RYR L+SD ++T  + MLATQLN  V+ GQ+    V Q+  
Sbjct: 22  KPILQVINIRPISTGNRSPRYRLLMSDGLNTLSSFMLATQLNTLVEGGQLASNCVCQVHK 81

Query: 78  YICSTVQN-RKIIVVLNMETIILDCE----PIGNPKIFSES---ELTAQKTIPSNNLPQP 129
           +I +T+++ RK++V++++E ++   E     IGNP  ++E    +   Q+      +P P
Sbjct: 82  FIVNTLKDGRKVVVLMDLE-VMKSAEDVGLKIGNPVPYNEGYGQQQQQQQQQQQQAVPSP 140

Query: 130 VRVNNYSA----PNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQP 185
                  A    P +G+  + ++          F  P       P+ G+           
Sbjct: 141 ASAATPPASKPQPQNGSLGMGSTAAKAYGASKPFGKPAGTGLLQPSGGT----------- 189

Query: 186 PYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKV 245
                               ++++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+
Sbjct: 190 -------------------QSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKL 230

Query: 246 FSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFL 305
           FS +L+D + GEIR T FN  VD+F+ +IEV +VY  SKG+LK A K F+ +KN++E+  
Sbjct: 231 FSLELVD-ESGEIRATAFNEQVDKFFPLIEVNKVYYFSKGALKIANKQFSAVKNDYEMTF 289

Query: 306 EATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPI-LRKNGM 364
              ++V  C E+   +P  QF F  I ++ES   +++VD+IGI  S   S+ I ++ N  
Sbjct: 290 NNETSVLPC-EDGHHLPTVQFDFTGIGDLESKAKDALVDIIGICKSYEDSIKITVKSNNR 348

Query: 365 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSI 424
           E  +R + L D SG+ V  TLWG+  +K     Q        PV+++K  +V+DF G+S+
Sbjct: 349 EVAKRNIYLMDMSGKVVTTTLWGEDADKFDGSRQ--------PVMAIKGARVSDFGGRSL 400

Query: 425 GTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAG-GAKNEIHKTVSQIKNE 483
             + S+ + +NPD  EA++LR WFDS G+    VSIS   + G G  N   KT+ + K+E
Sbjct: 401 SVLSSSTVIVNPDIPEAYKLRGWFDSEGQALDGVSISDHRSGGAGGGNTNWKTLHEAKSE 460

Query: 484 GLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEI 542
            LG+ +K D+ +  A + F++ ++  Y ACP     + CNKKV  Q    ++C++C++E 
Sbjct: 461 NLGQGDKADYFSTVAAVVFLRKENCMYQACPT----QDCNKKVIDQQNGLYRCEKCDREF 516

Query: 543 DECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSR 602
               YR +L A I D     WVT FQES E ILG     +Y+ + + +++  F E+ ++ 
Sbjct: 517 PNFKYRMILSANIADFQENQWVTCFQESAEAILG--QNTMYLGELKEKNEQAFEEVFQNA 574

Query: 603 VFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSF 651
            F  + FR+++K E Y DE R+K TV+    V++    R L+  I K+ 
Sbjct: 575 NFRSFTFRIRVKLETYNDESRIKATVMDVKPVDFRDYGRRLIANIRKNM 623

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.

Mus musculus (taxid: 10090)

>sp|Q5FW17|RFA1_XENTR Replication protein A 70 kDa DNA-binding subunit OS=Xenopus tropicalis GN=rpa1 PE=2 SV=1

 Score =  338 bits (867), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 224/659 (33%), Positives = 355/659 (53%), Gaps = 68/659 (10%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQ 57
           +PV L+  +IS I GGD + KP +QV++I+ I  G+   RYR L+SD ++T  + MLATQ
Sbjct: 3   LPV-LSEGAISAILGGDSSCKPTLQVINIRSINTGNGPPRYRLLMSDGLNTLSSFMLATQ 61

Query: 58  LNDRVKTGQVKKGSVVQLIDYICSTVQN-RKIIVVLNMETII---LDCEPIGNPKIFSES 113
           LN  V    +    + Q+  +I + +++ R++I+V+ ME +    L    IGNP  +++ 
Sbjct: 62  LNFLVDNNLLATNCICQVSRFIVNNLKDGRRVIIVMEMEVLKSADLVKGKIGNPHPYNDG 121

Query: 114 ELTAQKTIPSNNLPQPV-RVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNA 172
           +   Q   P+     P  +  N SAP   + N   S  F                     
Sbjct: 122 QGPPQPAAPAPASAPPPSKPQNISAPPPPSMNRGASKLFG-------------------G 162

Query: 173 GSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGD 232
           GS+V +                         + ++++PIA+LNPYQ +W ++ARVT KG 
Sbjct: 163 GSVVNT----------------------PGGSQSKVVPIASLNPYQSKWTVRARVTNKGQ 200

Query: 233 LRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQK 292
           +R ++N+RG+GK+FS +++D + GEIR T FN   D+F+ +IEV +VY  SKG+LK A K
Sbjct: 201 IRTWSNSRGEGKLFSIEMVD-ESGEIRATAFNEQADKFFSLIEVNKVYYFSKGTLKIANK 259

Query: 293 NFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISV 352
            +  +KN++E+   + ++V  C +  D +P  QF F  I E+ES   ++++D+IGI  + 
Sbjct: 260 QYTSVKNDYEMTFNSETSVIPCDDSAD-VPMVQFEFVPIGELESKNKDTVLDIIGICKNA 318

Query: 353 NPSVPI-LRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV 411
                + +R N  E  +R +NL D+SG+ V  TLWG+  +K     Q        PV+++
Sbjct: 319 EEVTKVTIRSNNREVSKRNINLMDSSGKVVSTTLWGEDADKFDGSRQ--------PVVAI 370

Query: 412 KSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKN 471
           K  +++DF G+S+  + S+ + INPD  EA +LR WFDS G+     SIS      G  N
Sbjct: 371 KGARLSDFGGRSLSVLSSSTVMINPDIPEAFKLRAWFDSEGQVVEGTSISESRGGTGGGN 430

Query: 472 EIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSG 530
              K++ ++K E LG  EK D+ T  A I +++ ++  Y ACP     + CNKKV  Q  
Sbjct: 431 TNWKSLLEVKTENLGHGEKADYFTSVATIVYLRKENCLYQACP----SQDCNKKVIDQQN 486

Query: 531 NRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQ 590
             ++C++C++E     YR +L A I D     W+T FQES E ILG  A  L  LK   +
Sbjct: 487 GLFRCEKCDKEFPNYKYRLILSANIADFGENQWITCFQESAESILGQNATYLGELKE--K 544

Query: 591 DDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
           ++  + E+ ++  F  Y FR+++K E Y DE R+K T +    V++   SR L+  I K
Sbjct: 545 NEQAYDEVFQNANFRSYTFRIRVKLETYNDESRIKATAMDVKPVDHKEYSRRLIMNIRK 603

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.

Xenopus tropicalis (taxid: 8364)

>sp|Q01588|RFA1_XENLA Replication protein A 70 kDa DNA-binding subunit OS=Xenopus laevis GN=rpa1 PE=1 SV=1

 Score =  336 bits (862), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 223/655 (34%), Positives = 357/655 (54%), Gaps = 67/655 (10%)

Query: 5   LTPNSISLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQLNDR 61
           L+  +IS + GGD + KP +QV++I+ I  G+   RYR L+SD ++T  + MLATQLN  
Sbjct: 6   LSEGAISAMLGGDSSCKPTLQVINIRPINTGNGPPRYRLLMSDGLNTLSSFMLATQLNSL 65

Query: 62  VKTGQVKKGSVVQLIDYICSTVQN-RKIIVVLNMETII---LDCEPIGNPKIFSESELTA 117
           V    +    + Q+  +I + +++ R++I+V+ ++ +    L    IGNP+ +++ +   
Sbjct: 66  VDNNLLATNCICQVSRFIVNNLKDGRRVIIVMELDVLKSADLVMGKIGNPQPYNDGQPQP 125

Query: 118 QKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVR 177
               P+            SAP      LQN    NS  P S    N GT +    GS++ 
Sbjct: 126 AAPAPA------------SAPAPAPSKLQN----NSAPPPSM---NRGTSKLFGGGSLLN 166

Query: 178 SFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYN 237
           +                         + ++++PIA+LNPYQ +W ++ARVT KG +R ++
Sbjct: 167 T----------------------PGGSQSKVVPIASLNPYQSKWTVRARVTNKGQIRTWS 204

Query: 238 NARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHL 297
           N+RG+GK+FS +++D + GEIR T FN   D+F+ IIEV +VY  SKG+LK A K +  +
Sbjct: 205 NSRGEGKLFSIEMVD-ESGEIRATAFNEQADKFFSIIEVNKVYYFSKGTLKIANKQYTSV 263

Query: 298 KNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVP 357
           KN++E+   + ++V  C +  D +P  QF F  I E+ES   ++++D+IG+  +V     
Sbjct: 264 KNDYEMTFNSETSVIPCDDSAD-VPMVQFEFVSIGELESKNKDTVLDIIGVCKNVEEVTK 322

Query: 358 I-LRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKV 416
           + ++ N  E  +R ++L D+SG+ V  TLWG+  +K     Q        PV+++K  ++
Sbjct: 323 VTIKSNNREVSKRSIHLMDSSGKVVSTTLWGEDADKFDGSRQ--------PVVAIKGARL 374

Query: 417 NDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISR-EIAAGGAKNEIHK 475
           +DF G+S+  + S+ + INPD  EA +LR WFDS G+     SIS       G  N   K
Sbjct: 375 SDFGGRSLSVLSSSTVMINPDIPEAFKLRAWFDSEGQVVEGTSISESRGGGTGGGNTNWK 434

Query: 476 TVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQ 534
           ++ ++KNE LG  EK D+ T  A I +++ ++  Y ACP     + CNKKV  Q    ++
Sbjct: 435 SLLEVKNENLGHGEKADYFTSVATIVYLRKENCLYQACP----SQDCNKKVIDQQNGLFR 490

Query: 535 CDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVR 594
           C++CN+E     YR +L A I D     W+T FQES E ILG  A  L  LK   +++  
Sbjct: 491 CEKCNKEFPNFKYRLILSANIADFGENQWITCFQESAESILGQNATYLGELKE--KNEQA 548

Query: 595 FGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
           + E+ ++  F  Y FR ++K E Y DE R+K T +    V++   SR L+  I K
Sbjct: 549 YDEVFQNANFRSYTFRARVKLETYNDESRIKATAVDVKPVDHKEYSRRLIMNIRK 603

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.

Xenopus laevis (taxid: 8355)

>sp|Q5ZJJ2|RFA1_CHICK Replication protein A 70 kDa DNA-binding subunit OS=Gallus gallus GN=RPA1 PE=2 SV=1

 Score =  331 bits (849), Expect = 9e-90,   Method: Compositional matrix adjust.
 Identities = 223/661 (33%), Positives = 360/661 (54%), Gaps = 62/661 (9%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQ 57
           M V L+  +I+ I  G+   KP++QV++ + I  G+   RYR L+SD V+T  + MLATQ
Sbjct: 1   MSVRLSEGAIAAIMQGENVYKPVLQVINTRAIATGNGPPRYRVLMSDGVNTLSSFMLATQ 60

Query: 58  LNDRVKTGQVKKGSVVQLIDYICSTVQN-RKIIVVLNME---TIILDCEPIGNPKIFSES 113
           LN  V+  ++    + Q+  +I +++++ R+++++++++   T  +    +GNP  ++E 
Sbjct: 61  LNPLVEEERLSAHCICQVNRFIVNSLKDGRRVVILMDLDVLKTADMVGGTVGNPVPYNEG 120

Query: 114 ELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAG 173
           +   + + P+ N          +APN              Q  G+ S   S    AP   
Sbjct: 121 QGQQRSSAPTAN----------AAPNKP-----------QQQDGNLSVAGSA---APKYH 156

Query: 174 SIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDL 233
           +    F     P     P              ++++PIA+LNPYQ +W I ARVT KG +
Sbjct: 157 APSNQFSKASAPSSVKTPG----------GTQSKVVPIASLNPYQSKWTICARVTQKGQI 206

Query: 234 RRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKN 293
           R ++N+RG+GK+FS +L+D + GEIR T FN   D+F+ +IE+ +VY  +KG+LK A K 
Sbjct: 207 RTWSNSRGEGKLFSIELVD-ESGEIRATAFNDQADKFFPLIELNKVYYFTKGNLKTANKQ 265

Query: 294 FNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVN 353
           +  +KN++EI     ++V  C ++   +P  QF F  IS++E+   +SIVDVIGI  S  
Sbjct: 266 YTAVKNDYEITFNNETSVVPC-DDAQHLPSVQFDFVSISDLENTPKDSIVDVIGICKSYE 324

Query: 354 PSVPILRK-NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK 412
               I+ K +  E  +R ++L DTSG+ V  TLWG+    E +K     D    PV+++K
Sbjct: 325 DVTKIVVKASNREVSKRNVHLMDTSGKLVTATLWGN----EAEKF----DGSRQPVIAIK 376

Query: 413 SGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAK-- 470
             +V+DF G+S+  + S+ + +NPD  EA +LR WFDS G+     SIS ++  G A   
Sbjct: 377 GARVSDFGGRSLSVLSSSTVVVNPDSPEAFKLRGWFDSEGQLLECASIS-DVRGGSASGV 435

Query: 471 NEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QS 529
           N   KT+ + K+E LG+ +K D+ +    I  ++ ++  Y ACP     + CNKKV  Q 
Sbjct: 436 NTNWKTLYEAKSERLGQGDKADYFSCVGTIVHLRKENCMYQACP----SQDCNKKVIDQQ 491

Query: 530 GNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYEL 589
              ++C++C++E     YR +L   I D     WVT FQES E ILG  A  L  LK   
Sbjct: 492 NGLYRCEKCDREFPNFKYRMMLLVTIADSLDYQWVTCFQESAEFILGQSATFLGELKD-- 549

Query: 590 QDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
           +++  F E+ ++  FN Y F++++K E Y DE R+K T +    VNY   S+ L+  I +
Sbjct: 550 KNEQAFEEVFQNANFNTYEFKIRVKLETYNDESRIKATALDVKPVNYREYSKRLIASIRR 609

Query: 650 S 650
           +
Sbjct: 610 N 610

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.

Gallus gallus (taxid: 9031)

>sp|Q92372|RFA1_SCHPO Replication factor A protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ssb1 PE=1 SV=1

 Score =  318 bits (814), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 201/664 (30%), Positives = 340/664 (51%), Gaps = 70/664 (10%)

Query: 1   MPVNLTPNSISLINGGDVNS---KPLVQVMDIKLIGS-----TQERYRFLISDSVSTQHA 52
           M   L+  ++ +IN  D +S    P++QV+ +K + S       +RYR ++SDS++   +
Sbjct: 1   MAERLSVGALRIINTSDASSFPPNPILQVLTVKELNSNPTSGAPKRYRVVLSDSINYAQS 60

Query: 53  MLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVL--NMETIILDCEPIGNPKIF 110
           ML+TQLN  V   +++KG+ VQL  +  + ++ RKI++VL  N+ T +   + IGNP   
Sbjct: 61  MLSTQLNHLVAENKLQKGAFVQLTQFTVNVMKERKILIVLGLNVLTELGVMDKIGNPAGL 120

Query: 111 SESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAP 170
              +   Q         Q    NN SAP +G           S +  SF   N+      
Sbjct: 121 ETVDALRQ---------QQNEQNNASAPRTGI----------STSTNSFYGNNAAATAPA 161

Query: 171 NAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAK 230
               + +                        N     I PI  L+PYQ +W I+ARVT K
Sbjct: 162 PPPMMKKP--------------------AAPNSLSTIIYPIEGLSPYQNKWTIRARVTNK 201

Query: 231 GDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPA 290
            +++ ++N RG+GK+FS +LLD + GEIR T FN  VD FY+I++ G VY IS+  +  A
Sbjct: 202 SEVKHWHNQRGEGKLFSVNLLD-ESGEIRATGFNDQVDAFYDILQEGSVYYISRCRVNIA 260

Query: 291 QKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVI 350
           +K + +++NE+E+  E  + +    E+  ++P  +FSF  + E+     ++++DVIG++ 
Sbjct: 261 KKQYTNVQNEYELMFERDTEIRKA-EDQTAVPVAKFSFVSLQEVGDVAKDAVIDVIGVLQ 319

Query: 351 SVNPSVPIL-RKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVL 409
           +V P   I  R       +R + + D +G  + +TLWG        K      V    +L
Sbjct: 320 NVGPVQQITSRATSRGFDKRDITIVDQTGYEMRVTLWG--------KTAIEFSVSEESIL 371

Query: 410 SVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKN---AATVSISREIAA 466
           + K  KVNDF G+S+  + S+ + ++PD  E+H L+ W+D  G+    A    IS  ++ 
Sbjct: 372 AFKGVKVNDFQGRSLSMLTSSTMSVDPDIQESHLLKGWYDGQGRGQEFAKHSVISSTLST 431

Query: 467 GGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKV 526
            G   E  K +++++ E LG SE PD+ +++  I +I+  +  Y ACP       CNKKV
Sbjct: 432 TGRSAE-RKNIAEVQAEHLGMSETPDYFSLKGTIVYIRKKNVSYPACPAA----DCNKKV 486

Query: 527 TQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLK 586
              G  W+C++CN+E D   YRY++   + D TG  W+  F + G+ I+   A EL  L+
Sbjct: 487 FDQGGSWRCEKCNKEYDAPQYRYIITIAVGDHTGQLWLNVFDDVGKLIMHKTADELNDLQ 546

Query: 587 YELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDL 646
               D+  F   +    +  Y+F+ + K++ +  E RV+ TV+  +Q+++  ES+ L++ 
Sbjct: 547 E--NDENAFMNCMAEACYMPYIFQCRAKQDNFKGEMRVRYTVMSINQMDWKEESKRLINF 604

Query: 647 ISKS 650
           I  +
Sbjct: 605 IESA 608

Binds to single-stranded sequences.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P22336|RFA1_YEAST Replication factor A protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFA1 PE=1 SV=1

 Score =  309 bits (791), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 193/627 (30%), Positives = 331/627 (52%), Gaps = 73/627 (11%)

Query: 42  LISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRK--IIVVLNMETIIL 99
           +ISD +    A+L  Q   + ++ ++++G ++++I    + V+ RK  +++V + E +  
Sbjct: 49  MISDGIYHMKALLRNQAASKFQSMELQRGDIIRVIIAEPAIVRERKKYVLLVDDFELVQS 108

Query: 100 DCEPIGNPKIFSESELTAQ--KTIPSNNLPQPVRV-NNYSAPNSGTFNLQNSGTFNSQNP 156
             + +     F ++  +    +T+   ++     V N  +A N+G  ++ +S +  + N 
Sbjct: 109 RADMVNQTSTFLDNYFSEHPNETLKDEDITDSGNVANQTNASNAGVPDMLHSNSNLNANE 168

Query: 157 GSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNP 216
             F+  N                           PN +   PI           I  L+P
Sbjct: 169 RKFANEN---------------------------PNSQKTRPIF---------AIEQLSP 192

Query: 217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEV 276
           YQ  W IKARV+ KG+++ ++N RGDGK+F+ + LD+  GEIR T FN    +F EI++ 
Sbjct: 193 YQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDT-SGEIRATAFNDFATKFNEILQE 251

Query: 277 GRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIES 336
           G+VY +SK  L+PA+  F +L + +E+ L+  + ++ C +E + +PK  F+F  +  I++
Sbjct: 252 GKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDESN-VPKTHFNFIKLDAIQN 310

Query: 337 AENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWG----DFCNK 392
            E NS VDV+GI+ ++NP   +  + G +  RR + + D SG S+ + LW     DF   
Sbjct: 311 QEVNSNVDVLGIIQTINPHFELTSRAGKKFDRRDITIVDDSGFSISVGLWNQQALDFNLP 370

Query: 393 EGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGG 452
           EG             V ++K  +V DF GKS+    S+ L  NP+  EA+ L+ W+DS G
Sbjct: 371 EGS------------VAAIKGVRVTDFGGKSLSMGFSSTLIPNPEIPEAYALKGWYDSKG 418

Query: 453 KNAATVSISREIAAGG-AKNEIHK------TVSQIKNEGLGRSEKPDWVTVRAFITFIKS 505
           +NA  +++ +E   GG +   + K      T+++ + E LGRSEK D+ +V+A I+F+K 
Sbjct: 419 RNANFITLKQEPGMGGQSAASLTKFIAQRITIARAQAENLGRSEKGDFFSVKAAISFLKV 478

Query: 506 DSFCYTACPLMIGDRQCNKKV-TQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWV 564
           D+F Y AC     +  CNKKV  Q    W+C++C+      ++RY+L   I D+T   W+
Sbjct: 479 DNFAYPAC----SNENCNKKVLEQPDGTWRCEKCDTNNARPNWRYILTISIIDETNQLWL 534

Query: 565 TAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRV 624
           T F +  +++LG  A  L  LK E  D   F +I +S   N+Y FR++ +E+ Y D+ R+
Sbjct: 535 TLFDDQAKQLLGVDANTLMSLKEE--DPNEFTKITQSIQMNEYDFRIRAREDTYNDQSRI 592

Query: 625 KITVIRADQVNYSSESRYLLDLISKSF 651
           + TV     +NY +E+ YL D +SK+ 
Sbjct: 593 RYTVANLHSLNYRAEADYLADELSKAL 619

Binds to single-stranded sequences participating in DNA replication in addition to those mediating transcriptional repression (URS1) and activation (CAR1). Stimulates the activity of a cognate strand exchange protein (SEP1). It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the simian virus 40 origin of DNA replication.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q24492|RFA1_DROME Replication protein A 70 kDa DNA-binding subunit OS=Drosophila melanogaster GN=RpA-70 PE=1 SV=1

 Score =  305 bits (780), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 209/656 (31%), Positives = 332/656 (50%), Gaps = 83/656 (12%)

Query: 3   VNLTPNSISLINGGDVNSKPLVQVMDIKLIGST--QERYRFLISDS-VSTQHAMLATQLN 59
            +L+   I+ I  G+V   P++Q++ IK I S    ERYR LISD      +AMLA+QLN
Sbjct: 4   ASLSTGVIARIMHGEVVDAPVLQILAIKKINSAADSERYRILISDGKYFNSYAMLASQLN 63

Query: 60  DRVKTGQVKKGSVVQLIDYICSTV----QNRKIIVVLNMETIILDCEPIGNPKIFSESEL 115
                G++++ ++VQL  Y+ S V      ++++++  +  +        NP    +S++
Sbjct: 64  VMQHNGELEEFTIVQLDKYVTSLVGKDGAGKRVLIISELTVV--------NPGAEVKSKI 115

Query: 116 TAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSI 175
                       +PV   N +  +                P    T NS           
Sbjct: 116 G-----------EPVTYENAAKQDLA--------------PKPAVTSNS----------- 139

Query: 176 VRSFQPTVQPPYQPPPNFRNHGPILKNEA--PARIIPIAALNPYQGRWAIKARVTAKGDL 233
                   +P  +  P+  N+  I+ N +       PI++L+PYQ +W IKARVT+K  +
Sbjct: 140 --------KPIAKKEPSHNNNNNIVMNSSINSGMTHPISSLSPYQNKWVIKARVTSKSGI 191

Query: 234 RRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKN 293
           R ++NARG+GK+FS DL+D + GEIR T F    D+FY++I+V  VY ISK  LKPA K 
Sbjct: 192 RTWSNARGEGKLFSMDLMD-ESGEIRATAFKEQCDKFYDLIQVDSVYYISKCQLKPANKQ 250

Query: 294 FNHLKNEWEIFLEATSTVDLCTE-EDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISV 352
           ++ L N +E+     + V LC + +DD IP+ +++   IS++   EN + VD IGI   V
Sbjct: 251 YSSLNNAYEMTFSGETVVQLCEDTDDDPIPEIKYNLVPISDVSGMENKAAVDTIGICKEV 310

Query: 353 NPSVP-ILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV 411
                 + R    E ++R + L D S  ++ LTLWGD        +Q        PV+ V
Sbjct: 311 GELQSFVARTTNKEFKKRDITLVDMSNSAISLTLWGDDAVNFDGHVQ--------PVILV 362

Query: 412 KSGKVNDFSGKSIGTIPSTQLF-INPDFAEAHELREWFDSGGKNAATVSISREIAAGGAK 470
           K  ++N+F+G    ++    +  INPD  EAH+LR WFD+GG ++    +S     G   
Sbjct: 363 KGTRINEFNGGKSLSLGGGSIMKINPDIPEAHKLRGWFDNGGGDSVANMVSARTGGGSFS 422

Query: 471 NEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG 530
            E   T+   +   LG  +KPD+   +A +  +K ++  Y ACP       CNKKV   G
Sbjct: 423 TE-WMTLKDARARNLGSGDKPDYFQCKAVVHIVKQENAFYRACP----QSDCNKKVVDEG 477

Query: 531 N-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYEL 589
           N +++C++CN       YR L+   I D T   WV++F E GE++LG  ++E   +   L
Sbjct: 478 NDQFRCEKCNALFPNFKYRLLINMSIGDWTSNRWVSSFNEVGEQLLGHTSQE---VGEAL 534

Query: 590 QDDVRFGEIIRSRV-FNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLL 644
           ++D    E I S + F  ++F+L+ K E+YGD  R K+TV     +N+   +++LL
Sbjct: 535 ENDPAKAEQIFSALNFTSHIFKLRCKNEVYGDMTRNKLTVQSVAPINHKEYNKHLL 590

Participates in a very early step in DNA replication. RP-A is a single-stranded DNA-binding protein.

Drosophila melanogaster (taxid: 7227)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	653
225444784	622	PREDICTED: replication protein A 70 kDa	0.947	0.995	0.766	0.0
255546005	670	replication factor A 1, rfa1, putative [	0.995	0.970	0.764	0.0
449488185	623	PREDICTED: replication protein A 70 kDa	0.952	0.998	0.742	0.0
449446612	694	PREDICTED: replication protein A 70 kDa	0.938	0.883	0.745	0.0
297831712	640	hypothetical protein ARALYDRAFT_899421 [	0.969	0.989	0.701	0.0
15225129	640	replication factor A1 [Arabidopsis thali	0.969	0.989	0.699	0.0
33621259	637	RPA 70kDa subunit [Pisum sativum]	0.967	0.992	0.691	0.0
356556324	637	PREDICTED: replication protein A 70 kDa	0.964	0.989	0.695	0.0
42570719	617	replication factor A1 [Arabidopsis thali	0.931	0.985	0.700	0.0
115449015	656	Os02g0776800 [Oryza sativa Japonica Grou	0.970	0.966	0.588	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]

 Score = 1039 bits (2686), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 498/650 (76%), Positives = 565/650 (86%), Gaps = 31/650 (4%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLND 60
           MPVNLTPN+I+ INGGDVNSKPLVQV+DIKLIG++QERYRFL+SD+V+TQ AMLATQLND
Sbjct: 1   MPVNLTPNAIAAINGGDVNSKPLVQVLDIKLIGNSQERYRFLLSDAVATQQAMLATQLND 60

Query: 61  RVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKT 120
           RVK+GQV+KGSV+QLIDYICS VQNRKIIVVLNMETII +CE IGNPK+ +ES  TAQK 
Sbjct: 61  RVKSGQVRKGSVIQLIDYICSVVQNRKIIVVLNMETIIPECEIIGNPKMNTESHSTAQKE 120

Query: 121 IPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQ 180
            P  N  + V V N                                    N G+ + SF+
Sbjct: 121 FPGGNRARSVGVTN------------------------------NNLSVQNGGNKMPSFR 150

Query: 181 PTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAR 240
           P+VQPP+QPPPN+++HG ILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAR
Sbjct: 151 PSVQPPFQPPPNYKSHGTILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAR 210

Query: 241 GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNE 300
           GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY+ IEVG+VYLISKGSLKPAQKNFNHLKNE
Sbjct: 211 GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYDTIEVGKVYLISKGSLKPAQKNFNHLKNE 270

Query: 301 WEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILR 360
           WEIFLEA+S+V+LC +ED SIPKQQFSFR ISEIE+ ENNSI+DVIGIVISVNPSVPILR
Sbjct: 271 WEIFLEASSSVELCPDEDGSIPKQQFSFRPISEIENVENNSILDVIGIVISVNPSVPILR 330

Query: 361 KNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS 420
           KNGMETQRRI+NLKD SGRS+ELT+WG+FCN+EG +LQEM+D G FPVL+VKSGKVNDFS
Sbjct: 331 KNGMETQRRIVNLKDGSGRSIELTMWGEFCNREGHQLQEMIDSGSFPVLAVKSGKVNDFS 390

Query: 421 GKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQI 480
           GKS+GTI +TQLFINPDF EA  LREWFD GGKNAA+ SISR+I   G++NEI KTVSQI
Sbjct: 391 GKSVGTISATQLFINPDFTEACNLREWFDRGGKNAASQSISRDIMPAGSRNEIRKTVSQI 450

Query: 481 KNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCN 539
           K+EGLGRS+KPDWVTV+A I+FIK+D+FCY ACPLMIGDRQCNKKVT+SGN RWQCDRCN
Sbjct: 451 KDEGLGRSDKPDWVTVKATISFIKTDTFCYAACPLMIGDRQCNKKVTRSGNTRWQCDRCN 510

Query: 540 QEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEII 599
           QE ++CDYRYLLQAQ+QD TGLTWVTAFQE+GEEILGC AKELY+LKYE +DD RFGEII
Sbjct: 511 QEFEDCDYRYLLQAQVQDHTGLTWVTAFQEAGEEILGCSAKELYLLKYEEEDDFRFGEII 570

Query: 600 RSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
           RSR+ NQ+LFRLKIKEE+YG+EQRVKITV++AD+VNY+SESR+LLDLISK
Sbjct: 571 RSRLLNQFLFRLKIKEEMYGEEQRVKITVVKADKVNYTSESRHLLDLISK 620

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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]

 Score = 1016 bits (2627), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 513/671 (76%), Positives = 575/671 (85%), Gaps = 21/671 (3%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLND 60
           MPVNLTPN+IS+INGGDVN KPLVQV+DIK IGS QERYRFLISDSVSTQHAMLATQLND
Sbjct: 1   MPVNLTPNAISMINGGDVNMKPLVQVVDIKQIGSAQERYRFLISDSVSTQHAMLATQLND 60

Query: 61  RVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKT 120
           RVK G VKKGSVVQLIDYICS VQNRKIIVVLN+ETII +CE IGN K  ++  + AQK 
Sbjct: 61  RVKHGFVKKGSVVQLIDYICSEVQNRKIIVVLNLETIIPECEIIGNAKTLTD--MFAQKA 118

Query: 121 IPSNNLPQPVRV--NNYSAPNSGT--------FNLQNSG--------TFNSQNPGSFSTP 162
             + N  Q   V  NN SA N            +  N G        TF+SQN G+    
Sbjct: 119 SQNGNSVQSAGVGYNNSSARNHDNNVQNFQPPLSAHNQGSSMHNFRPTFSSQNHGNNMQN 178

Query: 163 NSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWA 222
            +    A N G+ ++SFQP VQPPY+PPPN+RNHG I+KNEAPARIIPIAALNPYQGRWA
Sbjct: 179 FTSNLSAQNYGNNIQSFQPNVQPPYRPPPNYRNHGAIMKNEAPARIIPIAALNPYQGRWA 238

Query: 223 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLI 282
           IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV+RFY++IEVGRVYLI
Sbjct: 239 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVERFYDVIEVGRVYLI 298

Query: 283 SKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSI 342
           SKGSLKPAQ+NFNHLKNEWEIFLEATSTVDLC + D+SIPKQQF+F+ ISEIE+ ENNSI
Sbjct: 299 SKGSLKPAQRNFNHLKNEWEIFLEATSTVDLCPDGDNSIPKQQFTFKTISEIENVENNSI 358

Query: 343 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVD 402
           +DVIGIVISVNPSVPILRKNGMETQRRILNLKD SGR++ELTLWGDFCNKEGQ+LQE+VD
Sbjct: 359 LDVIGIVISVNPSVPILRKNGMETQRRILNLKDGSGRNIELTLWGDFCNKEGQQLQEIVD 418

Query: 403 VGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISR 462
            G FPVL+VK+GKV+DFSGKS+GTI STQLFINPD  EAH L++WFD GG++ A+VSISR
Sbjct: 419 SGDFPVLAVKAGKVSDFSGKSLGTISSTQLFINPDIPEAHGLKDWFDRGGQHTASVSISR 478

Query: 463 EIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQC 522
           +I  GG+KNEI KTVSQIK+EGLGRS++PDWVTV A ITF+K+D+FCYTACPLMIGDRQC
Sbjct: 479 DILPGGSKNEIRKTVSQIKHEGLGRSDRPDWVTVSARITFVKTDTFCYTACPLMIGDRQC 538

Query: 523 NKKVTQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKE 581
           NKKVT SGN RWQCDRCNQE DECDYRYLLQ QIQD TGLTWVTAFQESGEEILG PAKE
Sbjct: 539 NKKVTSSGNSRWQCDRCNQEFDECDYRYLLQVQIQDHTGLTWVTAFQESGEEILGLPAKE 598

Query: 582 LYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESR 641
           LY LKYE+QDD +F ++IRSR+F Q+LFRLKIKEE+YGDEQRVKITV++A++VNYSSE R
Sbjct: 599 LYQLKYEMQDDTKFSDVIRSRLFQQFLFRLKIKEEMYGDEQRVKITVVKAEKVNYSSEGR 658

Query: 642 YLLDLISKSFR 652
           YLLDLIS+  R
Sbjct: 659 YLLDLISQCPR 669

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449488185|ref|XP_004157962.1| PREDICTED: replication protein A 70 kDa DNA-binding subunit-like [Cucumis sativus]

 Score =  986 bits (2549), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 485/653 (74%), Positives = 558/653 (85%), Gaps = 31/653 (4%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLND 60
           MPV+LTPN+IS I  GDVNSKPLVQV+DIKLIG+ QERY  LISD+VS + AMLATQLND
Sbjct: 1   MPVHLTPNAISAIVAGDVNSKPLVQVLDIKLIGNAQERYSLLISDAVSAEQAMLATQLND 60

Query: 61  RVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKT 120
            VKTG+VKKGSV+QLIDY+CS ++NRKIIVVL +ETIILDCE IGNPK  ++SE  AQK 
Sbjct: 61  VVKTGRVKKGSVIQLIDYVCSPIKNRKIIVVLCLETIILDCEIIGNPKSSAQSENFAQKA 120

Query: 121 IPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQ 180
            PS NL QP +V N                              G   A N    V+SFQ
Sbjct: 121 TPSVNLEQPAKVGN------------------------------GHLSARNPVHNVQSFQ 150

Query: 181 PTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAR 240
            TVQPPYQPPPN++NHG I+KNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNA+
Sbjct: 151 ATVQPPYQPPPNYKNHGAIIKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAK 210

Query: 241 GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNE 300
           GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYE+IEVG+VYLISKGSLKPA+K+FNHLKNE
Sbjct: 211 GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEVIEVGKVYLISKGSLKPARKDFNHLKNE 270

Query: 301 WEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILR 360
           WE+FLEA+STV+LC +EDD+IP+QQFSF+ ISEIE+AE NSI+DVIGIV S+NPS+P+LR
Sbjct: 271 WEVFLEASSTVELCPDEDDTIPRQQFSFKPISEIENAETNSILDVIGIVTSINPSIPVLR 330

Query: 361 KNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS 420
           KNGMETQRR++ LKD SGRSVELT+WGDFCNKEGQKLQE++  G  PVL+VKSGKV+DF+
Sbjct: 331 KNGMETQRRVVYLKDASGRSVELTMWGDFCNKEGQKLQEIIYSGLSPVLAVKSGKVSDFT 390

Query: 421 GKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQI 480
           GKSIGTI STQLFINPD  EAH LREW+D GGKN  ++SIS+EI  G AKN+I KTVSQI
Sbjct: 391 GKSIGTISSTQLFINPDLPEAHILREWYDGGGKNTTSLSISKEIVPGSAKNDIRKTVSQI 450

Query: 481 KNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCN 539
           K+EGLGR++KPDW+TV+A I+FIK+DSFCYTACPLMIGDRQCNKKVT+SGN +W CDRCN
Sbjct: 451 KDEGLGRADKPDWITVKATISFIKTDSFCYTACPLMIGDRQCNKKVTRSGNSKWVCDRCN 510

Query: 540 QEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEII 599
           QE ++CDYRYLLQAQIQD TGLTWVTAFQE+GEEILG   KELYMLKYE QDDV+FGEII
Sbjct: 511 QEFEDCDYRYLLQAQIQDHTGLTWVTAFQETGEEILGVSGKELYMLKYEEQDDVKFGEII 570

Query: 600 RSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFR 652
           RS++F+Q+LFRLKIKEE+YGDEQRVK TV++AD+VNYSSES+Y+LDL+SK  R
Sbjct: 571 RSKIFDQFLFRLKIKEEVYGDEQRVKNTVVKADRVNYSSESKYMLDLLSKFSR 623

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446612|ref|XP_004141065.1| PREDICTED: replication protein A 70 kDa DNA-binding subunit-like [Cucumis sativus]

 Score =  977 bits (2526), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 480/644 (74%), Positives = 552/644 (85%), Gaps = 31/644 (4%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLND 60
           MPV+LTPN+IS I  GDVNSKPLVQV+DIKLIG+ QERY  LISD+VS + AMLATQLND
Sbjct: 1   MPVHLTPNAISAIVAGDVNSKPLVQVLDIKLIGNAQERYSLLISDAVSAEQAMLATQLND 60

Query: 61  RVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKT 120
            VKTG+VKKGSV+QLIDY+CS ++NRKIIVVL +ETIILDCE IGNPK  ++SE  AQK 
Sbjct: 61  VVKTGRVKKGSVIQLIDYVCSPIKNRKIIVVLCLETIILDCEIIGNPKSSAQSENFAQKA 120

Query: 121 IPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQ 180
            PS NL QP +V N                              G   A N    V+SFQ
Sbjct: 121 TPSVNLEQPAKVGN------------------------------GHLSARNPVHNVQSFQ 150

Query: 181 PTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAR 240
            TVQPPYQPPPN++NHG I+KNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNA+
Sbjct: 151 ATVQPPYQPPPNYKNHGAIIKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAK 210

Query: 241 GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNE 300
           GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYE+IEVG+VYLISKGSLKPA+K+FNHLKNE
Sbjct: 211 GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEVIEVGKVYLISKGSLKPARKDFNHLKNE 270

Query: 301 WEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILR 360
           WE+FLEA+STV+LC +EDD+IP+QQFSF+ ISEIE+AE NSI+DVIGIV S+NPS+P+LR
Sbjct: 271 WEVFLEASSTVELCPDEDDTIPRQQFSFKPISEIENAETNSILDVIGIVTSINPSIPVLR 330

Query: 361 KNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS 420
           KNGMETQRR++ LKD SGRSVELT+WGDFCNKEGQKLQE++  G  PVL+VKSGKV+DF+
Sbjct: 331 KNGMETQRRVVYLKDASGRSVELTMWGDFCNKEGQKLQEIIYSGLSPVLAVKSGKVSDFT 390

Query: 421 GKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQI 480
           GKSIGTI STQLFINPD  EAH LREW+D GGKN  ++SIS+EI  G AKN+I KTVSQI
Sbjct: 391 GKSIGTISSTQLFINPDLPEAHILREWYDGGGKNTTSLSISKEIVPGSAKNDIRKTVSQI 450

Query: 481 KNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCN 539
           K+EGLGR++KPDW+TV+A I+FIK+DSFCYTACPLMIGDRQCNKKVT+SGN +W CDRCN
Sbjct: 451 KDEGLGRADKPDWITVKATISFIKTDSFCYTACPLMIGDRQCNKKVTRSGNSKWVCDRCN 510

Query: 540 QEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEII 599
           QE ++CDYRYLLQAQIQD TGLTWVTAFQE+GEEILG  AKELYMLKYE QDDV+FGEII
Sbjct: 511 QEFEDCDYRYLLQAQIQDHTGLTWVTAFQETGEEILGVSAKELYMLKYEEQDDVKFGEII 570

Query: 600 RSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYL 643
           RS++F+Q+LFRLKIKEE+YGDEQRVK TV++AD+VNYSSES+Y+
Sbjct: 571 RSKIFDQFLFRLKIKEEVYGDEQRVKNTVVKADRVNYSSESKYI 614

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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]

 Score =  951 bits (2457), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 460/656 (70%), Positives = 553/656 (84%), Gaps = 23/656 (3%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQER----YRFLISDSVSTQHAMLAT 56
           MPV+LTPN+I+ IN GDVN KPL+QV++IK+IG +QER    YRFLISD VS QHAM+A 
Sbjct: 1   MPVSLTPNAITAINDGDVNLKPLLQVLEIKMIGRSQERSQERYRFLISDGVSAQHAMVAV 60

Query: 57  QLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELT 116
           QLNDRVK+GQV+KGS+VQLIDYICS V+ RK+IVVLNMETI+   E IGNP IF E++  
Sbjct: 61  QLNDRVKSGQVEKGSIVQLIDYICSDVKGRKLIVVLNMETIVPHSETIGNPTIFGETDTE 120

Query: 117 AQKTIPS-NNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSI 175
           AQK + +  N+P P RV         + N       N QNP + STP             
Sbjct: 121 AQKPLSAVGNIPPPNRVVFNEPTAQHSVNRAPPRGVNIQNPAN-STP------------- 166

Query: 176 VRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRR 235
             SF+P+VQP YQPP ++RNHGPI+KNEAPAR+IPIAALNPYQGRWAIKARVTAKGD+RR
Sbjct: 167 --SFRPSVQPSYQPPASYRNHGPIMKNEAPARVIPIAALNPYQGRWAIKARVTAKGDIRR 224

Query: 236 YNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFN 295
           YNNA+GDGKV+SFDLLDSDGGEIRVTCFNAV DRFY++ EVG+VYLISKGSLKPAQKN+N
Sbjct: 225 YNNAKGDGKVYSFDLLDSDGGEIRVTCFNAVADRFYDVTEVGKVYLISKGSLKPAQKNYN 284

Query: 296 HLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPS 355
           HLKNEWEIFLE+TSTV+LC +ED SIP+QQFSFR IS+IE+AENN+I+DVIG+V SVNPS
Sbjct: 285 HLKNEWEIFLESTSTVELCPDEDGSIPRQQFSFRPISDIENAENNTILDVIGVVTSVNPS 344

Query: 356 VPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGK 415
           VPILRKNGMET RRILNLKD SG++VE+TLWG+FCN++G++L+EMVD  F PVL++K+GK
Sbjct: 345 VPILRKNGMETHRRILNLKDESGKAVEVTLWGEFCNRDGRQLEEMVDSAFHPVLAIKAGK 404

Query: 416 VNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGG-AKNEIH 474
           V+DFSGKS+GTI STQLFINPDF EAH+LR WFD GGK+ A+ SISR+   GG ++NEI 
Sbjct: 405 VSDFSGKSVGTISSTQLFINPDFPEAHKLRTWFDHGGKDTASFSISRDTMPGGVSRNEIR 464

Query: 475 KTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRW 533
           K+VSQIK EGLGRS+KPDW+TV+A I+FIK+DSFCYTACPLMIGD+QCNKKVT+SG NRW
Sbjct: 465 KSVSQIKEEGLGRSDKPDWITVKATISFIKTDSFCYTACPLMIGDKQCNKKVTRSGTNRW 524

Query: 534 QCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDV 593
            CDRCNQE DECDYRYLLQ QIQD TGLTW+TAFQE+GEEI+GCPAK+LY LKYEL+ + 
Sbjct: 525 LCDRCNQESDECDYRYLLQVQIQDHTGLTWITAFQETGEEIMGCPAKKLYALKYELEKEE 584

Query: 594 RFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
            F EI+R R+F+QY+ +LKIKEE YGDEQRVK+TV++ D++NY+SES+Y+LDL+ +
Sbjct: 585 EFAEIVRDRLFHQYMLKLKIKEESYGDEQRVKMTVVKVDKMNYTSESKYMLDLLVR 640

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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]

 Score =  950 bits (2455), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 459/656 (69%), Positives = 550/656 (83%), Gaps = 23/656 (3%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQER----YRFLISDSVSTQHAMLAT 56
           MPV+LTPN+I+ I+ GDVN KPL+QV++IK+IG +QER    YRFLISD VS QHAM+A 
Sbjct: 1   MPVSLTPNAITAIHDGDVNLKPLLQVLEIKMIGRSQERSQERYRFLISDGVSAQHAMVAV 60

Query: 57  QLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELT 116
           QLNDRVK+GQ +KGS+VQLIDYICS V+ RK+IVVLNMETI+   E IGNP IF E++  
Sbjct: 61  QLNDRVKSGQFEKGSIVQLIDYICSDVKGRKLIVVLNMETIVQQSETIGNPTIFGETDTE 120

Query: 117 AQKTIP-SNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSI 175
           AQKT   + N+P P RV         + N       N QN  + +TP             
Sbjct: 121 AQKTFSGTGNIPPPNRVVFNEPMVQHSVNRAPPRGVNIQNQAN-NTP------------- 166

Query: 176 VRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRR 235
             SF+P+VQP YQPP ++RNHGPI+KNEAPAR+IPIAALNPYQGRWAIKARVTAKGD+RR
Sbjct: 167 --SFRPSVQPSYQPPASYRNHGPIMKNEAPARVIPIAALNPYQGRWAIKARVTAKGDIRR 224

Query: 236 YNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFN 295
           YNNA+GDGKVFSFDLLD DGGEIRVTCFNA+VDRFY++ EVG+VYLISKGSLKPAQKNFN
Sbjct: 225 YNNAKGDGKVFSFDLLDYDGGEIRVTCFNALVDRFYDVTEVGKVYLISKGSLKPAQKNFN 284

Query: 296 HLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPS 355
           HLKNEWEIFLE+TSTV+LC +ED SIPKQQFSFR IS+IE+AENN+I+DVIG+V SVNPS
Sbjct: 285 HLKNEWEIFLESTSTVELCPDEDGSIPKQQFSFRPISDIENAENNTILDVIGVVTSVNPS 344

Query: 356 VPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGK 415
           VPILRKNGMET RRILNLKD SG++VE+TLWG+FCN++G++L+EMVD  F PVL++K+GK
Sbjct: 345 VPILRKNGMETHRRILNLKDESGKAVEVTLWGEFCNRDGRQLEEMVDSAFHPVLAIKAGK 404

Query: 416 VNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGG-AKNEIH 474
           V+DFSGKS+GTI STQLFINPDF EAH+LR WFD GGK+ A+ SISR+   GG ++NEI 
Sbjct: 405 VSDFSGKSVGTISSTQLFINPDFPEAHKLRTWFDYGGKDTASFSISRDTMPGGVSRNEIR 464

Query: 475 KTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRW 533
           K VSQIK EGLGRS+KPDW+TV+A I+FIK+DSFCYTACPLMIGD+QCNKKVT+SG NRW
Sbjct: 465 KNVSQIKEEGLGRSDKPDWITVKATISFIKTDSFCYTACPLMIGDKQCNKKVTRSGTNRW 524

Query: 534 QCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDV 593
            CDRCNQE DECDYRYLLQ QIQD TGLTW+TAFQE+GEEI+GCPAK+LY +KYEL+ + 
Sbjct: 525 LCDRCNQESDECDYRYLLQVQIQDHTGLTWITAFQETGEEIMGCPAKKLYAMKYELEKEE 584

Query: 594 RFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
            F EI+R R+F+QY+ +LKIKEE YGDEQRVK+TV++ D+VNY+SES+Y+LDL+ +
Sbjct: 585 EFAEIVRDRLFHQYMLKLKIKEESYGDEQRVKMTVVKVDKVNYTSESKYMLDLLVR 640

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|33621259|gb|AAQ23194.1| RPA 70kDa subunit [Pisum sativum]

 Score =  942 bits (2436), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 455/658 (69%), Positives = 544/658 (82%), Gaps = 26/658 (3%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLI----GSTQERYRFLISDSVSTQHAMLAT 56
           M VNLT ++I  I  GDVN+KPL+Q+++I  +     S Q+RYR L+SD+VS+ HAMLA 
Sbjct: 1   MSVNLTASAIPAIINGDVNAKPLLQILEISSVISNKNSQQQRYRVLLSDAVSSHHAMLAA 60

Query: 57  QLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELT 116
           QLND V TG+VK GS+VQL+DYIC+  QNRKII+VLNME+II DCE IG+PK F +SEL 
Sbjct: 61  QLNDLVTTGRVKNGSIVQLLDYICTLFQNRKIIMVLNMESIIPDCEIIGSPKPFVDSELP 120

Query: 117 AQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIV 176
            QK +  N       V +    N+      NS    +QN GS               + V
Sbjct: 121 VQKALRDNT------VGSSINSNNNNSYNSNSNILAAQNTGS---------------THV 159

Query: 177 RSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRY 236
           ++F+PT+QP Y+PPP ++  G ++KNEAPAR IPIAALNPYQGRWAI+ARVTAKGDLRRY
Sbjct: 160 QNFRPTIQPSYKPPPVYKGRGAVMKNEAPARTIPIAALNPYQGRWAIRARVTAKGDLRRY 219

Query: 237 NNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNH 296
           NNARGDGKVFSFDLLDSDGGEIRVTCFNA+VDRFY+ IEVG+VYLISKG+LKPAQKNFNH
Sbjct: 220 NNARGDGKVFSFDLLDSDGGEIRVTCFNAIVDRFYDSIEVGKVYLISKGNLKPAQKNFNH 279

Query: 297 LKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSV 356
           LKNEWEI L+  STV+LC +ED S PKQQFSFR IS+IE+ E+N+I+DVIG+V SVNPSV
Sbjct: 280 LKNEWEIMLDLNSTVELCPDEDGSYPKQQFSFRPISDIENVESNAILDVIGVVTSVNPSV 339

Query: 357 PILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKV 416
           PILRKNGMET RRILNLKD SGRSVELTLWG+FCN+EGQKLQEMVD G FP+L+VK+GKV
Sbjct: 340 PILRKNGMETLRRILNLKDNSGRSVELTLWGEFCNREGQKLQEMVDAGVFPILAVKAGKV 399

Query: 417 NDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKT 476
           N+FSGKSIG+I +TQLFINPDF EA  LR WFD  GK++A++SIS++I  GG KNEI KT
Sbjct: 400 NEFSGKSIGSISTTQLFINPDFPEAQSLRAWFDQVGKDSASLSISKDITHGGPKNEIRKT 459

Query: 477 VSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQC 535
           VSQI++EGLGRS+KPDW+T+RA I+F+K+D+FCYTACPLMIGDRQCNKKVT+SG+ RWQC
Sbjct: 460 VSQIRDEGLGRSDKPDWITIRATISFMKTDTFCYTACPLMIGDRQCNKKVTRSGDTRWQC 519

Query: 536 DRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRF 595
           DRCNQE +ECDYRYLLQAQIQD TGLTWVTAFQE GEEI+G PAKELY LKYE +DD RF
Sbjct: 520 DRCNQEFEECDYRYLLQAQIQDHTGLTWVTAFQEGGEEIMGYPAKELYALKYEQEDDERF 579

Query: 596 GEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK 653
           G+I++SR+FN ++FRLKIKEELYG+EQ+VK TV++AD+VNYS+ESRY+LDLISK  RK
Sbjct: 580 GDIVKSRLFNHFVFRLKIKEELYGEEQKVKSTVVKADKVNYSAESRYMLDLISKFGRK 637

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556324|ref|XP_003546476.1| PREDICTED: replication protein A 70 kDa DNA-binding subunit-like [Glycine max]

 Score =  922 bits (2382), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 459/660 (69%), Positives = 555/660 (84%), Gaps = 30/660 (4%)

Query: 1   MPVNLTPNSISLINGGDVNSKPLVQVMDIKLI------GSTQERYRFLISDSVSTQHAML 54
           M +NLT N+I  I GGDVN+KPLVQV+D+ L+         Q+RYR L+SD+V + HAML
Sbjct: 1   MSLNLTANAIPAIIGGDVNAKPLVQVLDVALVSNSNNSQQQQQRYRLLLSDAVFSHHAML 60

Query: 55  ATQLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESE 114
           ATQLNDRV+TG+V+KGSVVQL+DYIC+ ++NRKIIV+LNMETI+ + E IGNPK + +S+
Sbjct: 61  ATQLNDRVRTGRVQKGSVVQLLDYICTPLKNRKIIVILNMETIMDEFEIIGNPKPYMDSD 120

Query: 115 LTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGS 174
                 IP+      VR ++ ++ +S   NL  S   N+ + G  ++ N+          
Sbjct: 121 ------IPT------VRASDSASADSTVENLPRSYNSNNSSAGQNASHNN---------- 158

Query: 175 IVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLR 234
             ++F+PT+QPPYQPPP ++  GP++KNEAPARIIPIAALNPYQGRWAIKARVTAKGDLR
Sbjct: 159 -TQNFRPTIQPPYQPPPLYKGRGPVVKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLR 217

Query: 235 RYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNF 294
           RYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFY +IEVG+VY+ISKGSLKPAQKNF
Sbjct: 218 RYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYNVIEVGKVYMISKGSLKPAQKNF 277

Query: 295 NHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNP 354
           NHLKNEWEI LE++S V+LC +ED SIP+QQFSFR IS+IE+ +NNSI+DVIG+V SVNP
Sbjct: 278 NHLKNEWEILLESSSMVELCPDEDGSIPRQQFSFRPISDIENVDNNSILDVIGVVTSVNP 337

Query: 355 SVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG 414
           SVPILRKNGMETQRRIL+LKD+SG SVELTLWG+FCN+EGQ+LQ+MVD GFFP+L+VK+G
Sbjct: 338 SVPILRKNGMETQRRILSLKDSSGSSVELTLWGEFCNREGQQLQDMVDAGFFPILAVKTG 397

Query: 415 KVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIH 474
           KVNDFSGKSIG+I +TQLFINPDF EAH LREWF+  GK++A++SIS++I  G  KNE+ 
Sbjct: 398 KVNDFSGKSIGSISTTQLFINPDFPEAHSLREWFELVGKDSASLSISKDIIPGALKNEVR 457

Query: 475 KTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RW 533
           KTVSQIK+EGLGRS+KPDW+TVRA I FIK+D+FCYTACPLMIGDRQCNKKVT+ GN RW
Sbjct: 458 KTVSQIKDEGLGRSDKPDWITVRAAILFIKTDTFCYTACPLMIGDRQCNKKVTRLGNTRW 517

Query: 534 QCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDV 593
           QCDRCNQE +ECDYRYLLQ QI D TGL WVTAFQE+GEEI+   AK+LY LK+E QDD 
Sbjct: 518 QCDRCNQEFEECDYRYLLQVQILDGTGLAWVTAFQEAGEEIMDYSAKDLYFLKHEEQDDE 577

Query: 594 RFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSFRK 653
           +FGEII+SR+FNQ++FRLKIKEELYGDEQ+VKITV++AD+VNYSSESRY+LD ISK  R+
Sbjct: 578 KFGEIIKSRLFNQFMFRLKIKEELYGDEQKVKITVVKADKVNYSSESRYMLDTISKFCRQ 637

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42570719|ref|NP_973433.1| replication factor A1 [Arabidopsis thaliana] gi|330250915|gb|AEC06009.1| replication factor A1 [Arabidopsis thaliana]

 Score =  914 bits (2361), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 442/631 (70%), Positives = 528/631 (83%), Gaps = 23/631 (3%)

Query: 26  VMDIKLIGSTQER----YRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICS 81
           V++IK+IG +QER    YRFLISD VS QHAM+A QLNDRVK+GQ +KGS+VQLIDYICS
Sbjct: 3   VLEIKMIGRSQERSQERYRFLISDGVSAQHAMVAVQLNDRVKSGQFEKGSIVQLIDYICS 62

Query: 82  TVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQKTIP-SNNLPQPVRVNNYSAPNS 140
            V+ RK+IVVLNMETI+   E IGNP IF E++  AQKT   + N+P P RV        
Sbjct: 63  DVKGRKLIVVLNMETIVQQSETIGNPTIFGETDTEAQKTFSGTGNIPPPNRVVFNEPMVQ 122

Query: 141 GTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPIL 200
            + N       N QN  + +TP               SF+P+VQP YQPP ++RNHGPI+
Sbjct: 123 HSVNRAPPRGVNIQNQAN-NTP---------------SFRPSVQPSYQPPASYRNHGPIM 166

Query: 201 KNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRV 260
           KNEAPAR+IPIAALNPYQGRWAIKARVTAKGD+RRYNNA+GDGKVFSFDLLD DGGEIRV
Sbjct: 167 KNEAPARVIPIAALNPYQGRWAIKARVTAKGDIRRYNNAKGDGKVFSFDLLDYDGGEIRV 226

Query: 261 TCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDS 320
           TCFNA+VDRFY++ EVG+VYLISKGSLKPAQKNFNHLKNEWEIFLE+TSTV+LC +ED S
Sbjct: 227 TCFNALVDRFYDVTEVGKVYLISKGSLKPAQKNFNHLKNEWEIFLESTSTVELCPDEDGS 286

Query: 321 IPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRS 380
           IPKQQFSFR IS+IE+AENN+I+DVIG+V SVNPSVPILRKNGMET RRILNLKD SG++
Sbjct: 287 IPKQQFSFRPISDIENAENNTILDVIGVVTSVNPSVPILRKNGMETHRRILNLKDESGKA 346

Query: 381 VELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAE 440
           VE+TLWG+FCN++G++L+EMVD  F PVL++K+GKV+DFSGKS+GTI STQLFINPDF E
Sbjct: 347 VEVTLWGEFCNRDGRQLEEMVDSAFHPVLAIKAGKVSDFSGKSVGTISSTQLFINPDFPE 406

Query: 441 AHELREWFDSGGKNAATVSISREIAAGG-AKNEIHKTVSQIKNEGLGRSEKPDWVTVRAF 499
           AH+LR WFD GGK+ A+ SISR+   GG ++NEI K VSQIK EGLGRS+KPDW+TV+A 
Sbjct: 407 AHKLRTWFDYGGKDTASFSISRDTMPGGVSRNEIRKNVSQIKEEGLGRSDKPDWITVKAT 466

Query: 500 ITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECDYRYLLQAQIQDQ 558
           I+FIK+DSFCYTACPLMIGD+QCNKKVT+SG NRW CDRCNQE DECDYRYLLQ QIQD 
Sbjct: 467 ISFIKTDSFCYTACPLMIGDKQCNKKVTRSGTNRWLCDRCNQESDECDYRYLLQVQIQDH 526

Query: 559 TGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELY 618
           TGLTW+TAFQE+GEEI+GCPAK+LY +KYEL+ +  F EI+R R+F+QY+ +LKIKEE Y
Sbjct: 527 TGLTWITAFQETGEEIMGCPAKKLYAMKYELEKEEEFAEIVRDRLFHQYMLKLKIKEESY 586

Query: 619 GDEQRVKITVIRADQVNYSSESRYLLDLISK 649
           GDEQRVK+TV++ D+VNY+SES+Y+LDL+ +
Sbjct: 587 GDEQRVKMTVVKVDKVNYTSESKYMLDLLVR 617

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115449015|ref|NP_001048287.1| Os02g0776800 [Oryza sativa Japonica Group] gi|46805512|dbj|BAD16963.1| replication protein A 70kDa [Oryza sativa Japonica Group] gi|46806154|dbj|BAD17384.1| replication protein A 70kDa [Oryza sativa Japonica Group] gi|113537818|dbj|BAF10201.1| Os02g0776800 [Oryza sativa Japonica Group] gi|125583873|gb|EAZ24804.1| hypothetical protein OsJ_08582 [Oryza sativa Japonica Group] gi|215701492|dbj|BAG92916.1| unnamed protein product [Oryza sativa Japonica Group] gi|215715207|dbj|BAG94958.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  787 bits (2033), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/659 (58%), Positives = 506/659 (76%), Gaps = 25/659 (3%)

Query: 5   LTPNSISLINGGDVNSKPLVQVMDIKLI-----GSTQ-ERYRFLISDSVSTQHAMLATQL 58
           LTPN ++    GD N KP++Q+++++ +     G T+ ER+R ++SD  +   A+ A QL
Sbjct: 6   LTPNGVAAALAGDTNLKPVLQIVELRGVQVNGAGVTRGERFRAVVSDGTAASSALFAAQL 65

Query: 59  NDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQ 118
           +D  ++G +++GS+VQL +Y+ + V  R+IIV+LN+E ++ +CE IGNP   SE+     
Sbjct: 66  SDHARSGALRRGSIVQLSEYVINEVGPRRIIVILNLEVLVSECEIIGNPTALSET----- 120

Query: 119 KTIPSNNLPQPVRVNNYS-APNSGTF--NLQNSGTFNSQNPGSFSTP---NSGTFRAPNA 172
                + +P P RV  ++ AP  G    N  N+ T  S N   F      NS  F A   
Sbjct: 121 ----GSPIPNPTRVEQFNGAPQYGLMAGNSSNTTTKPSDNVPLFQNSMAGNSSNF-ATRP 175

Query: 173 GSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGD 232
              V  FQPTVQP Y+P PN++NHG I+KNEAPARIIPI+ALNPYQGRWAIKARVTAKGD
Sbjct: 176 SDKVPVFQPTVQPSYRPAPNYKNHGAIMKNEAPARIIPISALNPYQGRWAIKARVTAKGD 235

Query: 233 LRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQK 292
           +RRY+NA+GDGKVFSFDLLDSDGGEIRVTCFNA++DRFYE++EVG+VY++S+G+L+PAQK
Sbjct: 236 IRRYHNAKGDGKVFSFDLLDSDGGEIRVTCFNALLDRFYEVVEVGKVYVVSRGNLRPAQK 295

Query: 293 NFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISV 352
           N+NHL NEWEI LE  STVDLC +E+ SIP Q+F FR I+EIE A+NN+I+D+IG+V SV
Sbjct: 296 NYNHLNNEWEILLENGSTVDLCPDENSSIPTQRFDFRPINEIEDAQNNAILDIIGVVTSV 355

Query: 353 NPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK 412
           NP   I RKNGMETQ+R +NLKD SGRSVE+T+WGDFCN+EG +LQ MV+ G FPVL+VK
Sbjct: 356 NPCTTIQRKNGMETQKRTMNLKDMSGRSVEVTMWGDFCNREGSQLQGMVERGIFPVLAVK 415

Query: 413 SGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNE 472
           +GKV+DFSGKS+GTI STQLFINPD AEAH LR+WFDSGG++A+T SISR+I  G ++NE
Sbjct: 416 AGKVSDFSGKSVGTISSTQLFINPDSAEAHSLRQWFDSGGRDASTQSISRDITPGASRNE 475

Query: 473 IHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN- 531
           I KTV+QIK+EGLG  +KPDW+TV+A + F K++SF YTACP MIGDRQCNKKVT+S N 
Sbjct: 476 IRKTVAQIKDEGLGMGDKPDWITVKATVIFFKNESFFYTACPNMIGDRQCNKKVTKSTNG 535

Query: 532 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQD 591
            W CD+C++E +ECDYRYLLQ QIQD +G  WVTAFQE+G+E+LGC A EL  LK   ++
Sbjct: 536 NWTCDKCDREFEECDYRYLLQFQIQDHSGTAWVTAFQEAGQELLGCSATELNALKE--RE 593

Query: 592 DVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKS 650
           D RF + + + +F +YL RLK+KEE YGDE++VK T ++ ++V+ S ES++LLDLISKS
Sbjct: 594 DPRFADTMLNCLFQEYLLRLKVKEESYGDERKVKNTAVKVEKVDPSGESKFLLDLISKS 652

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	653
TAIR|locus:2054577	640	RPA1A "replication protein A 1	0.964	0.984	0.677	2e-237
UNIPROTKB|Q9AVL8	654	OsRPA70a "Replication protein	0.970	0.969	0.558	4.3e-196
TAIR|locus:2163553	853	RPA70C [Arabidopsis thaliana (	0.693	0.531	0.587	6e-172
TAIR|locus:2134766	784	AT4G19130 [Arabidopsis thalian	0.957	0.797	0.483	1.2e-161
UNIPROTKB|Q65XV7	951	P0016H04.11 "Os05g0111000 prot	0.830	0.569	0.450	3.3e-147
ZFIN|ZDB-GENE-030912-3	601	rpa1 "replication protein A1"	0.655	0.712	0.373	4.3e-92
UNIPROTKB|P27694	616	RPA1 "Replication protein A 70	0.670	0.711	0.371	8.9e-92
MGI|MGI:1915525	623	Rpa1 "replication protein A1"	0.656	0.688	0.366	1.7e-90
UNIPROTKB|Q0VCV0	616	RPA1 "Replication protein A1,	0.646	0.685	0.365	9e-90
UNIPROTKB|I3LHB2	625	RPA1 "Uncharacterized protein"	0.656	0.686	0.359	6.3e-89

TAIR|locus:2054577 RPA1A "replication protein A 1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 2289 (810.8 bits), Expect = 2.0e-237, P = 2.0e-237
 Identities = 444/655 (67%), Positives = 534/655 (81%)

Query:     1 MPVNLTPNSISLINGGDVNSKPLVQVMDIKLIGSTQER----YRFLISDSVSTQHAMLAT 56
             MPV+LTPN+I+ I+ GDVN KPL+QV++IK+IG +QER    YRFLISD VS QHAM+A 
Sbjct:     1 MPVSLTPNAITAIHDGDVNLKPLLQVLEIKMIGRSQERSQERYRFLISDGVSAQHAMVAV 60

Query:    57 QLNDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELT 116
             QLNDRVK+GQ +KGS+VQLIDYICS V+ RK+IVVLNMETI+   E IGNP IF E++  
Sbjct:    61 QLNDRVKSGQFEKGSIVQLIDYICSDVKGRKLIVVLNMETIVQQSETIGNPTIFGETDTE 120

Query:   117 AQKTIP-SNNLPQPVRVNNYSAPN-SGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGS 174
             AQKT   + N+P P RV  ++ P    + N       N QN  + +TP+   FR P   S
Sbjct:   121 AQKTFSGTGNIPPPNRVV-FNEPMVQHSVNRAPPRGVNIQNQAN-NTPS---FR-P---S 171

Query:   175 IVRSFXXXXXXXXXXXXNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLR 234
             +  S+            ++RNHGPI+KNEAPAR+IPIAALNPYQGRWAIKARVTAKGD+R
Sbjct:   172 VQPSYQPPA--------SYRNHGPIMKNEAPARVIPIAALNPYQGRWAIKARVTAKGDIR 223

Query:   235 RYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNF 294
             RYNNA+GDGKVFSFDLLD DGGEIRVTCFNA+VDRFY++ EVG+VYLISKGSLKPAQKNF
Sbjct:   224 RYNNAKGDGKVFSFDLLDYDGGEIRVTCFNALVDRFYDVTEVGKVYLISKGSLKPAQKNF 283

Query:   295 NHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAEXXXXXXXXXXXXXXXP 354
             NHLKNEWEIFLE+TSTV+LC +ED SIPKQQFSFR IS+IE+AE               P
Sbjct:   284 NHLKNEWEIFLESTSTVELCPDEDGSIPKQQFSFRPISDIENAENNTILDVIGVVTSVNP 343

Query:   355 SVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG 414
             SVPILRKNGMET RRILNLKD SG++VE+TLWG+FCN++G++L+EMVD  F PVL++K+G
Sbjct:   344 SVPILRKNGMETHRRILNLKDESGKAVEVTLWGEFCNRDGRQLEEMVDSAFHPVLAIKAG 403

Query:   415 KVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGG-AKNEI 473
             KV+DFSGKS+GTI STQLFINPDF EAH+LR WFD GGK+ A+ SISR+   GG ++NEI
Sbjct:   404 KVSDFSGKSVGTISSTQLFINPDFPEAHKLRTWFDYGGKDTASFSISRDTMPGGVSRNEI 463

Query:   474 HKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NR 532
              K VSQIK EGLGRS+KPDW+TV+A I+FIK+DSFCYTACPLMIGD+QCNKKVT+SG NR
Sbjct:   464 RKNVSQIKEEGLGRSDKPDWITVKATISFIKTDSFCYTACPLMIGDKQCNKKVTRSGTNR 523

Query:   533 WQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDD 592
             W CDRCNQE DECDYRYLLQ QIQD TGLTW+TAFQE+GEEI+GCPAK+LY +KYEL+ +
Sbjct:   524 WLCDRCNQESDECDYRYLLQVQIQDHTGLTWITAFQETGEEIMGCPAKKLYAMKYELEKE 583

Query:   593 VRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLI 647
               F EI+R R+F+QY+ +LKIKEE YGDEQRVK+TV++ D+VNY+SES+Y+LDL+
Sbjct:   584 EEFAEIVRDRLFHQYMLKLKIKEESYGDEQRVKMTVVKVDKVNYTSESKYMLDLL 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)]

 Score = 1899 (673.5 bits), Expect = 4.3e-196, P = 4.3e-196
 Identities = 368/659 (55%), Positives = 480/659 (72%)

Query:     5 LTPNSISLINGGDVNSKPLVQVMDIKLI-----GSTQ-ERYRFLISDSVSTQHAMLATQL 58
             LTPN ++    GD N KP++Q+++++ +     G T+ ER+R ++SD  +   A+ A QL
Sbjct:     4 LTPNGVAAALAGDTNLKPVLQIVELRGVQVNGAGVTRGERFRAVVSDGTAASSALFAAQL 63

Query:    59 NDRVKTGQVKKGSVVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSESELTAQ 118
             +D  ++G +++GS+VQL +Y+ + V  R+IIV+LN+E ++ +CE IGNP   SE+     
Sbjct:    64 SDHARSGALRRGSIVQLSEYVINEVGPRRIIVILNLEVLVSECEIIGNPTALSET----- 118

Query:   119 KTIPSNNLPQPVRVNNYS-APNSGTF--NLQNSGTFNSQNPGSFSTP---NSGTFRAPNA 172
                  + +P P RV  ++ AP  G    N  N+ T  S N   F      NS  F A   
Sbjct:   119 ----GSPIPNPTRVEQFNGAPQYGLMAGNSSNTTTKPSDNVPLFQNSMAGNSSNF-ATRP 173

Query:   173 GSIVRSFXXXXXXXXXXXXNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGD 232
                V  F            N++NHG I+KNEAPARIIPI+ALNPYQGRWAIKARVTAKGD
Sbjct:   174 SDKVPVFQPTVQPSYRPAPNYKNHGAIMKNEAPARIIPISALNPYQGRWAIKARVTAKGD 233

Query:   233 LRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQK 292
             +RRY+NA+GDGKVFSFDLLDSDGGEIRVTCFNA++DRFYE++EVG+VY++S+G+L+PAQK
Sbjct:   234 IRRYHNAKGDGKVFSFDLLDSDGGEIRVTCFNALLDRFYEVVEVGKVYVVSRGNLRPAQK 293

Query:   293 NFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAEXXXXXXXXXXXXXX 352
             N+NHL NEWEI LE  STVDLC +E+ SIP Q+F FR I+EIE A+              
Sbjct:   294 NYNHLNNEWEILLENGSTVDLCPDENSSIPTQRFDFRPINEIEDAQNNAILDIIGVVTSV 353

Query:   353 XPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK 412
              P   I RKNGMETQ+R +NLKD SGRSVE+T+WGDFCN+EG +LQ MV+ G FPVL+VK
Sbjct:   354 NPCTTIQRKNGMETQKRTMNLKDMSGRSVEVTMWGDFCNREGSQLQGMVERGIFPVLAVK 413

Query:   413 SGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNE 472
             +GKV+DFSGKS+GTI STQ FINPD AEAH LR+WFDSGG++A T SISR+I  G ++NE
Sbjct:   414 AGKVSDFSGKSVGTISSTQFFINPDSAEAHSLRQWFDSGGRDAFTQSISRDITPGASRNE 473

Query:   473 IHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN- 531
             I KTV+QIK+EGLG  +KPDW+TV+A + F K++SF YTACP MIGDRQCNKKVT+S N 
Sbjct:   474 IRKTVAQIKDEGLGMGDKPDWITVKATVIFFKNESFFYTACPNMIGDRQCNKKVTKSTNG 533

Query:   532 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQD 591
              W CD+C++E +ECDYRYLLQ QIQD +G  WVTAFQE+G+E+LGC A EL  LK   ++
Sbjct:   534 NWTCDKCDREFEECDYRYLLQFQIQDHSGTAWVTAFQEAGQELLGCSATELNALKE--RE 591

Query:   592 DVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKS 650
             D RF + + + +F +YL RLK+KEE YGDE++VK T ++ ++V+ S ES++LLDLISKS
Sbjct:   592 DPRFADTMLNCLFQEYLLRLKVKEESYGDERKVKNTAVKVEKVDPSGESKFLLDLISKS 650

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2163553 RPA70C [Arabidopsis thaliana (taxid:3702)]

 Score = 1478 (525.3 bits), Expect = 6.0e-172, Sum P(2) = 6.0e-172
 Identities = 268/456 (58%), Positives = 354/456 (77%)

Query:   195 NHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSD 254
             N GP+ +NEAP RI PIAALNPYQGRW IK RVT+K DLRR+NN RG+GK+FSFDLLD+D
Sbjct:   286 NRGPVARNEAPPRINPIAALNPYQGRWTIKVRVTSKADLRRFNNPRGEGKLFSFDLLDAD 345

Query:   255 GGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC 314
             GGEIRVTCFN  VD+F++ I VG VYLIS+G+LKPAQKNFNHL N++EI L++ ST+  C
Sbjct:   346 GGEIRVTCFNDAVDQFFDKIVVGNVYLISRGNLKPAQKNFNHLPNDYEIHLDSASTIQPC 405

Query:   315 TEEDDSIPKQQFSFRHISEIESAEXXXXXXXXXXXXXXXPSVPILRKNGMETQRRILNLK 374
              E+D +IP+  F FR+I +IE+ E               P+V I+RKN  E Q+R L LK
Sbjct:   406 -EDDGTIPRYHFHFRNIGDIENMENNSTTDVIGIVSSISPTVAIMRKNLTEVQKRSLQLK 464

Query:   375 DTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFI 434
             D SGRSVE+T+WG+FCN EGQKLQ + D G FPVL++K+G++ +F+GK + TI ++Q FI
Sbjct:   465 DMSGRSVEVTMWGNFCNAEGQKLQNLCDSGVFPVLALKAGRIGEFNGKQVSTIGASQFFI 524

Query:   435 NPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWV 494
              PDF EA ELR+W++  G+NA   SISRE +  G + E+ K ++QIK+E LG SEKPDW+
Sbjct:   525 EPDFPEARELRQWYEREGRNAHFTSISREFSGVG-RQEVRKVIAQIKDEKLGTSEKPDWI 583

Query:   495 TVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLLQA 553
             TV A I+F+K ++FCYTACP+M GDR C+KKVT +G+  W+C++C++ +DECDYRY+LQ 
Sbjct:   584 TVCATISFMKVENFCYTACPIMNGDRPCSKKVTNNGDGTWRCEKCDKCVDECDYRYILQI 643

Query:   554 QIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKI 613
             Q+QD T LTW TAFQE+GEEI+G  AK+LY +KYE QD+ +F +IIRS  F +Y+F+LKI
Sbjct:   644 QLQDHTDLTWATAFQEAGEEIMGMSAKDLYYVKYENQDEEKFEDIIRSVAFTKYIFKLKI 703

Query:   614 KEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
             KEE Y DEQRVK TV++A+++NYSS +R++L+ I K
Sbjct:   704 KEETYSDEQRVKATVVKAEKLNYSSNTRFMLEAIDK 739

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:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2134766 AT4G19130 [Arabidopsis thaliana (taxid:3702)]

 Score = 1574 (559.1 bits), Expect = 1.2e-161, P = 1.2e-161
 Identities = 313/647 (48%), Positives = 439/647 (67%)

Query:    22 PLVQVMDIKLIGS----TQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLID 77
             P++QV D+K I +    T+ER+R ++SD       ML T LN+ VK G ++ GS+V+L  
Sbjct:    26 PVLQVTDLKQIMAQQDPTRERFRMVLSDGTYLHQGMLGTDLNNLVKEGTLQPGSIVRLTR 85

Query:    78 YICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSE--SELTAQKTIPSNNLPQP---VR- 131
             ++   ++ R+I++V  +E +    + IG+P    +   +  A   I  N   Q    +R 
Sbjct:    86 FVGDVIKGRRIVIVPQLEVLKQISDIIGHPVPGGKHNDQRGADSGIKFNTTEQQGSGIRQ 145

Query:   132 VNNYSAPNSGT-FNLQNSGTFNSQNPGSFSTPNSGTFRAPNAGSIV--RSFXXXXXXXXX 188
             VNN     S    + Q  GT  S  P S +TP++  +  P++G+ V  + +         
Sbjct:   146 VNNIEPGRSNAAISPQVGGT-GSSVPAS-TTPSTRAYSNPSSGNGVTRQDYARDPPTSYP 203

Query:   189 XXXN-----FRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDG 243
                      + N GP+ +NEAP +IIP+ AL+PY GRW IKARVT K  L++Y+N RG+G
Sbjct:   204 HQPQPPPPMYANRGPVARNEAPPKIIPVNALSPYSGRWTIKARVTNKAALKQYSNPRGEG 263

Query:   244 KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEI 303
             KVF+FDLLD+DGGEIRVTCFNAV D+FY+ I VG +YLIS+GSL+PAQKNFNHL+N++EI
Sbjct:   264 KVFNFDLLDADGGEIRVTCFNAVADQFYDQIVVGNLYLISRGSLRPAQKNFNHLRNDYEI 323

Query:   304 FLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAEXXXXXXXXXXXXXXXPSVPILRKNG 363
              L+  ST+  C EED +IP+ QF FR I +IES E               P+V I RKNG
Sbjct:   324 MLDNASTIKQCYEEDAAIPRHQFHFRTIGDIESMENNCIVDVIGIVSSISPTVTITRKNG 383

Query:   364 METQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKS 423
               T +R L LKD SGRSVE+T+WGDFCN EGQ+LQ + D G FPVL+VK+G++++F+GK+
Sbjct:   384 TATPKRSLQLKDMSGRSVEVTMWGDFCNAEGQRLQSLCDSGVFPVLAVKAGRISEFNGKT 443

Query:   424 IGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNE 483
             + TI S+QLFI+PDF EA +L+ WF+  GK+   +S+SRE +  G K ++ KT+SQIK+E
Sbjct:   444 VSTIGSSQLFIDPDFVEAEKLKNWFEREGKSVPCISLSREFSGSG-KVDVRKTISQIKDE 502

Query:   484 GLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEI 542
              LG SEKPDW+TV A I ++K D+FCYTACP+M GDR C+KKVT +G+  W+C++C++ +
Sbjct:   503 KLGTSEKPDWITVSATILYLKFDNFCYTACPIMNGDRPCSKKVTDNGDGTWRCEKCDKSV 562

Query:   543 DECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSR 602
             DECDYRY+LQ QIQD T LT VTAFQE+GEEI+G  AK+LY +K E +D+ +F +IIR  
Sbjct:   563 DECDYRYILQLQIQDHTDLTCVTAFQEAGEEIMGISAKDLYYVKNEHKDEEKFEDIIRKV 622

Query:   603 VFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
              F +Y F+LK+KEE + DEQRVK TV++ D++NYS+++R +L  + K
Sbjct:   623 AFTKYNFKLKVKEETFSDEQRVKATVVKVDKLNYSADTRTMLGAMDK 669

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006302 "double-strand break repair" evidence=RCA

GO:0010332 "response to gamma radiation" evidence=RCA

UNIPROTKB|Q65XV7 P0016H04.11 "Os05g0111000 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 1236 (440.2 bits), Expect = 3.3e-147, Sum P(2) = 3.3e-147
 Identities = 252/559 (45%), Positives = 351/559 (62%)

Query:   103 PIGNPKIFSESELTAQKTIPSNNLPQPVRVN----NYSAPNSGTFNLQNSGTFNSQNPGS 158
             P     + S   ++AQ T  +N +    ++N    N   P S   N  N+ T    +  S
Sbjct:   193 PANVSAVGSYGAISAQNTTNANMMQPTSQLNIMNANTMQPTS-QLNTMNANTMQPTSQLS 251

Query:   159 FSTPNSGT-FRAPNAGSIVRSFXXXXXXXXXXXXN-----FRNHGPILKNEAPARIIPIA 212
                PN    F AP +G +                      + N GP  +N++  RIIPI 
Sbjct:   252 SLNPNQNQRFAAPASGGVFGPPGNAYGQPSRPSYQQPPPVYMNRGPASRNDSATRIIPIT 311

Query:   213 ALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYE 272
             ALNPYQ +W IKARVTAK D+R ++NAR  G VFSFDLLD+ GGEIR  C+    D+F+ 
Sbjct:   312 ALNPYQPKWTIKARVTAKSDIRHWSNARSSGTVFSFDLLDAQGGEIRAQCWKESADKFFG 371

Query:   273 IIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLE-ATSTVDLCTEEDDSIPKQQFSFRHI 331
              IEVGRVYLIS+GSLKPAQK +N L +++EI L+   STV++C+++D+SIP+ Q++FR I
Sbjct:   372 QIEVGRVYLISRGSLKPAQKKYNTLNHDYEITLDIGLSTVEVCSDDDNSIPRLQYNFRQI 431

Query:   332 SEIESAEXXXXXXXXXXXXXXXPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCN 391
             SE+E+                 PS  I+RK G ET++R + LKD SGRS+E+TLWG+FC+
Sbjct:   432 SELENMANETIVDLLGVVTSVSPSATIMRKIGTETRKRSIQLKDLSGRSIEVTLWGNFCD 491

Query:   392 KEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSG 451
              EGQ+LQ   D G  P+++ K  +V DF+GKS+ TI STQL INPDF E   LR+W+ + 
Sbjct:   492 AEGQQLQLQCDSGSNPIIAFKGARVGDFNGKSVSTIGSTQLIINPDFPEVERLRQWYMTE 551

Query:   452 GKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYT 511
             GK A  +S+SRE+   G + +  KT++QIK+E LGR EKPDW+TV+A I+ + ++SFCY 
Sbjct:   552 GKTAPCISLSREMLNMG-RTDARKTIAQIKDENLGRLEKPDWITVKAAISHVTTESFCYP 610

Query:   512 ACP--LMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQ 568
             ACP  L +G RQCNKK   +G+  W CDRC++     +YRY+L+ QIQD TG T+ +AF 
Sbjct:   611 ACPKLLPVG-RQCNKKAINNGDGMWHCDRCDESFQNPEYRYMLRFQIQDHTGSTYASAFD 669

Query:   569 ESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITV 628
             E+GE+I G  A EL+ ++   QDD +F EII    ++ YLF+LK+KEE Y DEQ +K T 
Sbjct:   670 EAGEQIFGRKAGELFSIRNVDQDDAQFAEIIEGVRWHLYLFKLKVKEETYNDEQSLKCTA 729

Query:   629 IRADQVNYSSESRYLLDLI 647
             ++ ++++ S ES  LL  I
Sbjct:   730 VKVEKLDPSKESNVLLGAI 748

GO:0005515 "protein binding" evidence=IPI

ZFIN|ZDB-GENE-030912-3 rpa1 "replication protein A1" [Danio rerio (taxid:7955)]

 Score = 792 (283.9 bits), Expect = 4.3e-92, Sum P(2) = 4.3e-92
 Identities = 166/445 (37%), Positives = 261/445 (58%)

Query:   206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
             ++++PIA+LNPYQ +W I+ARVT K  +R ++N+RGDGK+FS +L+D + GEIR T FN 
Sbjct:   169 SKVVPIASLNPYQSKWTIRARVTNKSAIRTWSNSRGDGKLFSMELVD-ESGEIRATGFNN 227

Query:   266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
              VD+F+ +IE G+V+ ISKG+LK A K F+ LKN++E+ L   +++  C + +D +P  Q
Sbjct:   228 EVDKFFSLIEQGKVFYISKGTLKIANKQFSSLKNDYEMTLNGETSIIPCEDSND-VPMLQ 286

Query:   326 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPILRKNGMETQRRILNLKDTSGRSVELTL 385
               F  I+++ES E                   I+ KN  E  +R + L D SGR ++LT+
Sbjct:   287 CDFVSIADLESREKDTILDVIGVCKNAEDVARIMTKNSREVSKRNIQLIDMSGRVIQLTM 346

Query:   386 WGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELR 445
             WG           E  D    P+L++K  +++DF G+S+ T+ S+ + INPD  EA++LR
Sbjct:   347 WGSDA--------ETFDGSGQPILAIKGARLSDFGGRSLSTLYSSTVMINPDIPEAYKLR 398

Query:   446 EWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKS 505
              W+D  G      S++     GG  N   KT++++KNE LG  +K D+ +  A I +I+ 
Sbjct:   399 GWYDKEGHALDGQSMTELRGPGGGGNTNWKTLAEVKNEHLGHGDKADYFSCIATIVYIRK 458

Query:   506 DSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWV 564
             ++  Y ACP     + CNKKV  Q    ++C++C++E  +  YR +L A I D     WV
Sbjct:   459 ENCLYQACP----SKDCNKKVVDQQNGMFRCEKCDKEFPDFKYRLMLSANIADFGDNQWV 514

Query:   565 TAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRV 624
             T FQ++ E +LG  +  L  LK    ++  F E+ +   FN ++FR ++K E Y DE R+
Sbjct:   515 TCFQDTAETLLGQNSSYLGQLKDT--NEAAFDEVFQHANFNTFVFRNRVKLETYNDESRI 572

Query:   625 KITVIRADQVNYSSESRYLLDLISK 649
             K+TV+ A  V++   S+ L+  I K
Sbjct:   573 KVTVVDAKPVDHREYSKRLIINIRK 597

GO:0003677 "DNA binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007507 "heart development" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|P27694 RPA1 "Replication protein A 70 kDa DNA-binding subunit" [Homo sapiens (taxid:9606)]

 Score = 774 (277.5 bits), Expect = 8.9e-92, Sum P(2) = 8.9e-92
 Identities = 171/460 (37%), Positives = 262/460 (56%)

Query:   197 GPILKNEA---PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS 253
             GP L + +    ++++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D 
Sbjct:   170 GPSLSHTSGGTQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD- 228

Query:   254 DGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDL 313
             + GEIR T FN  VD+F+ +IEV +VY  SKG+LK A K F  +KN++E+     ++V  
Sbjct:   229 ESGEIRATAFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMP 288

Query:   314 CTEEDDSIPKQQFSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILN 372
             C E+D  +P  QF F  I ++E+                  +  I +R N  E  +R + 
Sbjct:   289 C-EDDHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIY 347

Query:   373 LKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQL 432
             L DTSG+ V  TLWG+  +K     Q        PVL++K  +V+DF G+S+  + S+ +
Sbjct:   348 LMDTSGKVVTATLWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTI 399

Query:   433 FINPDFAEAHELREWFDSGGKNAATVSISREIAAG-GAKNEIHKTVSQIKNEGLGRSEKP 491
               NPD  EA++LR WFD+ G+    VSIS   + G G  N   KT+ ++K+E LG+ +KP
Sbjct:   400 IANPDIPEAYKLRGWFDAEGQALDGVSISDLKSGGVGGSNTNWKTLYEVKSENLGQGDKP 459

Query:   492 DWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYL 550
             D+ +  A + +++ ++  Y ACP     + CNKKV  Q    ++C++C+ E     YR +
Sbjct:   460 DYFSSVATVVYLRKENCMYQACPT----QDCNKKVIDQQNGLYRCEKCDTEFPNFKYRMI 515

Query:   551 LQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFR 610
             L   I D     WVT FQES E ILG  A  L  LK +  ++  F E+ ++  F  ++FR
Sbjct:   516 LSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKDK--NEQAFEEVFQNANFRSFIFR 573

Query:   611 LKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKS 650
             +++K E Y DE R+K TV+    V+Y    R L+  I +S
Sbjct:   574 VRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMSIRRS 613

GO:0046872 "metal ion binding" evidence=IEA

GO:0000800 "lateral element" evidence=IEA

GO:0001673 "male germ cell nucleus" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0007126 "meiosis" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0030097 "hemopoiesis" evidence=IEA

GO:0048873 "homeostasis of number of cells within a tissue" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0006261 "DNA-dependent DNA replication" evidence=TAS

GO:0006310 "DNA recombination" evidence=TAS

GO:0005662 "DNA replication factor A complex" evidence=IPI

GO:0016605 "PML body" evidence=IDA

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0000718 "nucleotide-excision repair, DNA damage removal" evidence=TAS

GO:0000722 "telomere maintenance via recombination" evidence=TAS

GO:0000723 "telomere maintenance" evidence=TAS

GO:0000724 "double-strand break repair via homologous recombination" evidence=TAS

GO:0000730 "DNA recombinase assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006260 "DNA replication" evidence=TAS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006297 "nucleotide-excision repair, DNA gap filling" evidence=TAS

GO:0006302 "double-strand break repair" evidence=TAS

GO:0032201 "telomere maintenance via semi-conservative replication" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0015629 "actin cytoskeleton" evidence=IDA

MGI|MGI:1915525 Rpa1 "replication protein A1" [Mus musculus (taxid:10090)]

 Score = 765 (274.4 bits), Expect = 1.7e-90, Sum P(2) = 1.7e-90
 Identities = 164/448 (36%), Positives = 258/448 (57%)

Query:   206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
             ++++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D + GEIR T FN 
Sbjct:   191 SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNE 249

Query:   266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
              VD+F+ +IEV +VY  SKG+LK A K F+ +KN++E+     ++V  C E+   +P  Q
Sbjct:   250 QVDKFFPLIEVNKVYYFSKGALKIANKQFSAVKNDYEMTFNNETSVLPC-EDGHHLPTVQ 308

Query:   326 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 384
             F F  I ++ES                  S+ I ++ N  E  +R + L D SG+ V  T
Sbjct:   309 FDFTGIGDLESKAKDALVDIIGICKSYEDSIKITVKSNNREVAKRNIYLMDMSGKVVTTT 368

Query:   385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
             LWG+  +K     Q        PV+++K  +V+DF G+S+  + S+ + +NPD  EA++L
Sbjct:   369 LWGEDADKFDGSRQ--------PVMAIKGARVSDFGGRSLSVLSSSTVIVNPDIPEAYKL 420

Query:   445 REWFDSGGKNAATVSISREIAAG-GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFI 503
             R WFDS G+    VSIS   + G G  N   KT+ + K+E LG+ +K D+ +  A + F+
Sbjct:   421 RGWFDSEGQALDGVSISDHRSGGAGGGNTNWKTLHEAKSENLGQGDKADYFSTVAAVVFL 480

Query:   504 KSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLT 562
             + ++  Y ACP     + CNKKV  Q    ++C++C++E     YR +L A I D     
Sbjct:   481 RKENCMYQACPT----QDCNKKVIDQQNGLYRCEKCDREFPNFKYRMILSANIADFQENQ 536

Query:   563 WVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQ 622
             WVT FQES E ILG     +Y+ + + +++  F E+ ++  F  + FR+++K E Y DE 
Sbjct:   537 WVTCFQESAEAILG--QNTMYLGELKEKNEQAFEEVFQNANFRSFTFRIRVKLETYNDES 594

Query:   623 RVKITVIRADQVNYSSESRYLLDLISKS 650
             R+K TV+    V++    R L+  I K+
Sbjct:   595 RIKATVMDVKPVDFRDYGRRLIANIRKN 622

GO:0000724 "double-strand break repair via homologous recombination" evidence=IMP

GO:0000793 "condensed chromosome" evidence=IDA

GO:0000794 "condensed nuclear chromosome" evidence=IDA

GO:0000800 "lateral element" evidence=IDA

GO:0001673 "male germ cell nucleus" evidence=IDA

GO:0001701 "in utero embryonic development" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005662 "DNA replication factor A complex" evidence=ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0007126 "meiosis" evidence=IDA

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0016605 "PML body" evidence=ISO

GO:0030097 "hemopoiesis" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0048873 "homeostasis of number of cells within a tissue" evidence=IMP

GO:0051276 "chromosome organization" evidence=IMP

UNIPROTKB|Q0VCV0 RPA1 "Replication protein A1, 70kDa" [Bos taurus (taxid:9913)]

 Score = 761 (272.9 bits), Expect = 9.0e-90, Sum P(2) = 9.0e-90
 Identities = 162/443 (36%), Positives = 253/443 (57%)

Query:   206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
             A+++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D + GEIR T FN 
Sbjct:   182 AKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSIELVD-ESGEIRATAFNE 240

Query:   266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
               D+F+ +I+V +VY  SKG+LK A K F  +KN++E+     ++V  C E+   +P  Q
Sbjct:   241 QADKFFPLIDVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDGHHLPTVQ 299

Query:   326 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPILRK-NGMETQRRILNLKDTSGRSVELT 384
             F F  I ++ES                     I+ K N  E  +R + L D SG+ V  T
Sbjct:   300 FDFTGIGDLESKSKDSLVDIIGICKNYEDVTKIIVKSNNREVSKRNIYLMDMSGKVVNAT 359

Query:   385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
             LWGD  +K     Q        PV+++K  +V+DF G+S+  + S+ + +NPD  EA++L
Sbjct:   360 LWGDDADKFDGSRQ--------PVMAIKGARVSDFGGRSLSVLSSSTIIVNPDIPEAYKL 411

Query:   445 REWFDSGGKNAATVSISREIAAGGA--KNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITF 502
             R WFDS G+    +SIS ++ +GGA   N   KT+ ++K+E LG+ +KPD+ +  A + +
Sbjct:   412 RGWFDSEGQALDGISIS-DLKSGGAGGSNTNWKTLYEVKSENLGQGDKPDYFSSVATVVY 470

Query:   503 IKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGL 561
             ++ ++  Y ACP     + CNKKV  Q    ++C++C+ E     YR +L   I D    
Sbjct:   471 LRKENCMYQACPT----QDCNKKVIDQQNGLYRCEKCDSEFPNFKYRMILSVNIADFQEN 526

Query:   562 TWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDE 621
              WVT FQES E ILG      Y+ + + +++  F E+ ++  F  + FR+++K E Y DE
Sbjct:   527 QWVTCFQESAEAILG--QSTAYLGELKEKNEQAFEEVFQNANFRSFTFRIRVKLETYNDE 584

Query:   622 QRVKITVIRADQVNYSSESRYLL 644
              R+K TV+    V+Y    R L+
Sbjct:   585 SRIKATVVDVKPVDYREYGRRLV 607

GO:0051276 "chromosome organization" evidence=IEA

GO:0048873 "homeostasis of number of cells within a tissue" evidence=IEA

GO:0030097 "hemopoiesis" evidence=IEA

GO:0016605 "PML body" evidence=IEA

GO:0015629 "actin cytoskeleton" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0007126 "meiosis" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0001673 "male germ cell nucleus" evidence=IEA

GO:0000800 "lateral element" evidence=IEA

GO:0000724 "double-strand break repair via homologous recombination" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|I3LHB2 RPA1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 750 (269.1 bits), Expect = 6.3e-89, Sum P(2) = 6.3e-89
 Identities = 161/448 (35%), Positives = 254/448 (56%)

Query:   206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
             A+++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D + GEIR T FN 
Sbjct:   191 AKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSIELVD-ESGEIRATAFNE 249

Query:   266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
              VD+F+ +I+V +VY  SKG+LK A K F  +KN++E+     ++V  C E+   +P  Q
Sbjct:   250 QVDKFFPLIDVNKVYYFSKGTLKIANKQFTAVKNDYEMTFSNETSVMPC-EDGHHLPTVQ 308

Query:   326 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 384
             F F  I+++E+                     I ++    E  +R + L D SG+ V  T
Sbjct:   309 FDFTGIADLENKSKDSLVDIIGICKNYEDVTKITVKSTNREVSKRNIYLMDMSGKVVNAT 368

Query:   385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
             LWG+  +K     Q        PV+++K  +V+DF G+S+  + S+ + +NPD  EA++L
Sbjct:   369 LWGEDADKFDGSRQ--------PVMAIKGARVSDFGGRSLSILSSSTVIVNPDIPEAYKL 420

Query:   445 REWFDSGGKNAATVSISREIAAG-GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFI 503
             R WFDS G+    VSIS   + G G  N   KT+ ++K+E LG+ +KPD+ +  A + ++
Sbjct:   421 RGWFDSEGQALDGVSISDLKSGGIGGSNTNWKTLYEVKSENLGQGDKPDYFSAVATVVYL 480

Query:   504 KSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLT 562
             + ++  Y ACP     + CNKKV  Q    ++C++C+ E     YR +L   I D     
Sbjct:   481 RKENCMYQACPT----QDCNKKVIDQQNGLYRCEKCDSEFPNFKYRMILSVNIADFQENQ 536

Query:   563 WVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQ 622
             WVT FQES E ILG      Y+ + + +++  F E+ ++  F  + FR+++K E Y DE 
Sbjct:   537 WVTCFQESAEAILG--QSTAYLGELKEKNEQAFEEVFQNANFRSFTFRIRVKLETYNDES 594

Query:   623 RVKITVIRADQVNYSSESRYLLDLISKS 650
             R+K TV+    V+Y    R L+  I K+
Sbjct:   595 RIKGTVMDVKPVDYKEYGRRLIMSIRKN 622

GO:0006260 "DNA replication" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5ZJJ2	RFA1_CHICK	No assigned EC number	0.3373	0.9173	0.9755	yes	no
Q5FW17	RFA1_XENTR	No assigned EC number	0.3399	0.9050	0.9704	yes	no
Q92372	RFA1_SCHPO	No assigned EC number	0.3027	0.9096	0.9753	yes	no
P22336	RFA1_YEAST	No assigned EC number	0.3078	0.8483	0.8921	yes	no
Q5R7Q4	RFA1_PONAB	No assigned EC number	0.3496	0.8989	0.9529	yes	no
P27694	RFA1_HUMAN	No assigned EC number	0.3486	0.9050	0.9594	yes	no
Q24492	RFA1_DROME	No assigned EC number	0.3185	0.8774	0.9502	yes	no
Q6NY74	RFA1_DANRE	No assigned EC number	0.3399	0.8989	0.9767	yes	no
Q8VEE4	RFA1_MOUSE	No assigned EC number	0.3359	0.8943	0.9373	yes	no

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	653
TIGR00617	608	TIGR00617, rpa1, replication factor-a protein 1 (r	0.0
pfam08646	146	pfam08646, Rep_fac-A_C, Replication factor-A C ter	7e-67
cd04476	166	cd04476, RPA1_DBD_C, RPA1_DBD_C: A subfamily of OB	2e-59
cd04474	104	cd04474, RPA1_DBD_A, RPA1_DBD_A: A subfamily of OB	4e-48
pfam04057	99	pfam04057, Rep-A_N, Replication factor-A protein 1	2e-32
cd04475	101	cd04475, RPA1_DBD_B, RPA1_DBD_B: A subfamily of OB	1e-31
cd04477	97	cd04477, RPA1N, RPA1N: A subfamily of OB folds cor	2e-29
COG1599	407	COG1599, RFA1, Single-stranded DNA-binding replica	1e-13
PRK12366	637	PRK12366, PRK12366, replication factor A; Reviewed	6e-13
cd04481	106	cd04481, RPA1_DBD_B_like, RPA1_DBD_B_like: A subgr	2e-08
pfam01336	75	pfam01336, tRNA_anti, OB-fold nucleic acid binding	3e-05
PRK12366	637	PRK12366, PRK12366, replication factor A; Reviewed	7e-05
cd03524	75	cd03524, RPA2_OBF_family, RPA2_OBF_family: A famil	1e-04
PRK12366	637	PRK12366, PRK12366, replication factor A; Reviewed	2e-04
PRK07211	485	PRK07211, PRK07211, replication factor A; Reviewed	7e-04

>gnl|CDD|233055 TIGR00617, rpa1, replication factor-a protein 1 (rpa1)

 Score =  593 bits (1531), Expect = 0.0
 Identities = 256/661 (38%), Positives = 381/661 (57%), Gaps = 68/661 (10%)

Query: 3   VNLTPNSISLING-GDVNS---KPLVQVMDIKLIGSTQ--ERYRFLISDSVSTQHAMLAT 56
           V+L+  +I+LI   G+ N     P++QV+D+K I   Q   RYR +ISD +    AMLAT
Sbjct: 2   VSLSNGAIALIMTNGEANGYPPDPVLQVLDLKPINGAQDPRRYRIVISDGIYYSKAMLAT 61

Query: 57  QLNDRVKTGQVKKGSVVQLIDYICSTV--QNRKIIVVLNMETIILDCEP---IGNPKIFS 111
           QLN  V+ G++++G++++L  +  +T+    RK+++V  +E +  + +    IGNP  + 
Sbjct: 62  QLNPLVREGELQEGTIIRLTKFEVNTIGKDGRKVLIVYELEVVKPELKVRDKIGNPVTYE 121

Query: 112 ESELTAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSGTFNSQNPGSFSTPNSGTFRAPN 171
           +   +  +        +P                      N  NP +   P +      N
Sbjct: 122 KYLDSWHE--EQVLASKP--------------------ATNPANPPNAKAPKNEVASYNN 159

Query: 172 AGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTAKG 231
           A +  R            PP   +           R++PIA+L+PYQ +W IKARVT K 
Sbjct: 160 AANPERGN---------APPAPNSGSTR-------RVMPIASLSPYQNKWTIKARVTNKS 203

Query: 232 DLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQ 291
           ++R ++NARG+GK+F+ +LLD + GEIR T FN   D+FY+II+ G+VY ISKGSLKPA 
Sbjct: 204 EIRTWSNARGEGKLFNVELLD-ESGEIRATAFNEQADKFYDIIQEGKVYYISKGSLKPAN 262

Query: 292 KNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVIS 351
           K F +L N++E+ L+  + ++ C E++ +IPK QF+F  I +I   E NS+VDVIGIV S
Sbjct: 263 KQFTNLGNDYEMTLDRDTVIEEC-EDETAIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQS 321

Query: 352 VNPSVPIL-RKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLS 410
           V+P+  I  RKN  E  +R + L D SG+SV +TLWGD   K         DV   PV++
Sbjct: 322 VSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATK--------FDVSVQPVIA 373

Query: 411 VKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAG-GA 469
           +K  +V+DF GKS+ T  S+ + +NPD  EA +L+ W+D+ GK     SIS  ++   G 
Sbjct: 374 IKGVRVSDFGGKSLSTGGSSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRVGG 433

Query: 470 KNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQS 529
            N   KT+++I+ E LG+S+KPD+ +V+A I+++K D+  Y ACP       CNKKV   
Sbjct: 434 SNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSE----DCNKKVVDQ 489

Query: 530 GN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYE 588
           G+  ++C++CN+   E  YRY+LQ  I D+TG  WVTAF +  E+ILG  A EL  LK E
Sbjct: 490 GDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELKEE 549

Query: 589 LQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLIS 648
             D   F  I +   F  Y+FRL++K++ Y DE R K TV+  D VNY +E++YLL  I 
Sbjct: 550 --DPDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVDPVNYRAEAKYLLQEIE 607

Query: 649 K 649
           K
Sbjct: 608 K 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

 Score =  215 bits (549), Expect = 7e-67
 Identities = 72/152 (47%), Positives = 97/152 (63%), Gaps = 7/152 (4%)

Query: 493 WVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLL 551
           + +V+A I FIK D+F Y ACP       CNKKVT+ G+  W+C++C++E  E  YRY+L
Sbjct: 1   YFSVKATIVFIKQDNFWYPACPSE----DCNKKVTEQGDGTWRCEKCDKEFPEPKYRYIL 56

Query: 552 QAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRL 611
              I D TG  WVT F E+ EEILG  A+EL  LK E  DD  F +I +  +F +Y+FRL
Sbjct: 57  SINISDHTGQIWVTLFNEAAEEILGMSAEELMELKEE--DDNEFEKIFQKALFREYVFRL 114

Query: 612 KIKEELYGDEQRVKITVIRADQVNYSSESRYL 643
           ++KEE Y DE RV+ TV+    V+Y  ES+ L
Sbjct: 115 RVKEETYNDESRVRYTVVSVAPVDYKKESKRL 146

This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA. Length = 146

>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)

 Score =  196 bits (501), Expect = 2e-59
 Identities = 74/174 (42%), Positives = 106/174 (60%), Gaps = 9/174 (5%)

Query: 477 VSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQC 535
           +++IK E LG  EKPD+ TV+A I FIK D++ Y ACP       CNKKV + GN  ++C
Sbjct: 1   IAEIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP------GCNKKVVEEGNGTYRC 54

Query: 536 DRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRF 595
           ++CN+ +   +YRY+L   + D TG  W+T F E  E+I G  A+EL  LK E  D   F
Sbjct: 55  EKCNKSVPNPEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEE--DPDAF 112

Query: 596 GEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
            + I+  V   +LFR+ +KEE Y DE R++ TV++   V+Y  ES+ L+  I K
Sbjct: 113 PDAIQDLVGKTFLFRVSVKEETYNDEGRIRYTVVKVAPVDYKKESKRLIQSIEK 166

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding. Length = 166

>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)

 Score =  163 bits (415), Expect = 4e-48
 Identities = 63/104 (60%), Positives = 82/104 (78%)

Query: 210 PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDR 269
           PI++LNPYQ +W IKARVT K D+R ++NARG+GK+FSFDLLD DGGEIR T FN  VD+
Sbjct: 1   PISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDK 60

Query: 270 FYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDL 313
           FY+++EVG+VY ISKGS+K A K FN LKN++EI     +++  
Sbjct: 61  FYDLLEVGKVYYISKGSVKVANKKFNTLKNDYEITFNRDTSIIE 104

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can. Length = 104

>gnl|CDD|202872 pfam04057, Rep-A_N, Replication factor-A protein 1, N-terminal domain

 Score =  120 bits (302), Expect = 2e-32
 Identities = 42/97 (43%), Positives = 68/97 (70%), Gaps = 4/97 (4%)

Query: 5  LTPNSISLING-GDVNSKPLVQVMDIKLIGS--TQERYRFLISDSVSTQHAMLATQLNDR 61
          LTP +I+ I   GD + KP++QV+D+K I S  + ERYRFL+SD  +   AMLATQLN  
Sbjct: 1  LTPGAIAAILATGDTSDKPVLQVVDLKPINSGNSPERYRFLLSDGKNKSSAMLATQLNPL 60

Query: 62 VKTGQVKKGSVVQLIDYICSTVQN-RKIIVVLNMETI 97
          V +G+++ GS+VQL  Y  + +++ R+++++L +E +
Sbjct: 61 VISGKLQNGSIVQLTRYTVNDIKDGRRVLIILELEVL 97

Length = 99

>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)

 Score =  118 bits (298), Expect = 1e-31
 Identities = 49/109 (44%), Positives = 65/109 (59%), Gaps = 9/109 (8%)

Query: 342 IVDVIGIVISVNPSVPILRKN-GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEM 400
           IVDVIG+V SV P   I  K+ G E  +R + L D SG SVELTLWG+            
Sbjct: 1   IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSEN-- 58

Query: 401 VDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFD 449
                 PV+++K  KV++F+GKS+ T  S+ + INPD  EAH+LR W+D
Sbjct: 59  ------PVIAIKGVKVSEFNGKSLSTGSSSTIIINPDIPEAHKLRGWYD 101

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can. Length = 101

>gnl|CDD|239923 cd04477, RPA1N, RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 (also called RPA70)

 Score =  111 bits (280), Expect = 2e-29
 Identities = 38/93 (40%), Positives = 66/93 (70%), Gaps = 5/93 (5%)

Query: 11 SLINGGD--VNSKPLVQVMDIKLIGS---TQERYRFLISDSVSTQHAMLATQLNDRVKTG 65
          ++ NG D     KP++QV++IK I S   + ERYR L+SD V    AMLATQLN  V++G
Sbjct: 5  AIFNGEDRSNVIKPVLQVLNIKKIDSSNGSSERYRILLSDGVYYVQAMLATQLNPLVESG 64

Query: 66 QVKKGSVVQLIDYICSTVQNRKIIVVLNMETII 98
          Q+++GS+++L  +IC+ ++ ++I+++L++E + 
Sbjct: 65 QLQRGSIIRLKRFICNVIKGKRILIILDLEVVQ 97

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C. Length = 97

>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]

 Score = 72.9 bits (179), Expect = 1e-13
 Identities = 68/300 (22%), Positives = 106/300 (35%), Gaps = 62/300 (20%)

Query: 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV 267
           I   + L+PYQ     KARV    +++ ++N  G+ KVFS +L D    E  V  F    
Sbjct: 162 IGEESLLSPYQ-----KARVVVGSEIKTFDNQGGESKVFSNELED---EERGVIVFTDWD 213

Query: 268 DRFYEIIEVGRVYLISKGSLKPAQKNF-NHLKNEWEIFLEATSTVDLCTEEDDSIPKQQF 326
                  + G VY I    +K   K    +L  E  + +E    ++              
Sbjct: 214 P-----SQDGDVYRIEGARVKTKNKQPEENLAEELVLRVEVRVAIEKAE----------- 257

Query: 327 SFRHISEIESAENNSIVDVIGIVISV--NPSVPILRKNGMETQRRILNLKDTSGRSVELT 384
             R     E  E+ S+V+  G V+ V   P    + + G           D     + +T
Sbjct: 258 --REEFVDEVKESVSLVEADGAVVDVTRVPECERVVRKGGCKGHGKDIGLDDLTGKIRVT 315

Query: 385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
           LWGD         + +++     V ++K   V D SG ++               EA  L
Sbjct: 316 LWGD-------ATEVLINEE--SVEALKGINVEDASGIALSA----------LDTEAVAL 356

Query: 445 REWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIK 504
             W+D  GK    + ++ +        E            L  S   D V VRA I  +K
Sbjct: 357 EIWYDILGKY---LRVTGDAREDRYLIEN-----------LVESSTWDDVDVRAEIEALK 402

Length = 407

>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed

 Score = 71.6 bits (176), Expect = 6e-13
 Identities = 85/410 (20%), Positives = 152/410 (37%), Gaps = 75/410 (18%)

Query: 195 NHGPILKN----EAPARIIPIAALNPYQ-GRWA-IKARVTAKGDLRRYNNARGDGKVFSF 248
           N+  IL+     E    I+ I  L  ++ G    +K R+ A  D R         +V   
Sbjct: 262 NNIEILEKLEKEEKELEIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDI 321

Query: 249 DLLDSDG-GEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEA 307
           +L  +DG G +RV+ +         + E G    I    ++     +   + E  + L A
Sbjct: 322 EL--ADGTGRVRVSFWGEKAKILENLKE-GDAVKIENCKVR----TYYDNEGEKRVDLNA 374

Query: 308 TSTVDLCTEEDDSIPKQQFSFRHISEIES-AENNSIVDVIGIVISVNPSVPILRKNGMET 366
             + ++  +E  S  + +     I +I +  E+++ + VI  V+   P     R +G + 
Sbjct: 375 GYSSEIIKDESISFEEIEEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERSDGSKG 434

Query: 367 QRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKV---NDFSGKS 423
           + R + L D +G S+ LTLW D    E       +  G    + +    V    D+   S
Sbjct: 435 KVRNIELADGTG-SIRLTLWDDDAEIE-------IKEG--DAIKILHPYVKENGDYLDLS 484

Query: 424 IGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNE 483
           IG     ++ INP                +     S  + IA      ++          
Sbjct: 485 IGR--YGRIEINP----------------EGEIIKSNRKFIA------DL---------- 510

Query: 484 GLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEID 543
                E+ D V +R  +  I+        CP       C K+V +    + C+ C     
Sbjct: 511 -----EEDDTVEIRGTVVDIRKQKIILYLCP------NCRKRVEEVDGEYICEFCG--EV 557

Query: 544 ECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDV 593
           E +   +L   + D TG      + ++ E++LG   +EL  L  E  +D+
Sbjct: 558 EPNELLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELNLEALEDL 607

Length = 637

>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)

 Score = 52.3 bits (126), Expect = 2e-08
 Identities = 28/105 (26%), Positives = 58/105 (55%), Gaps = 6/105 (5%)

Query: 344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDV 403
           DVIG+++ V P +  L      +++    ++D S   ++ TLWG++  +   K Q   + 
Sbjct: 1   DVIGVIVDVGP-LEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNG 59

Query: 404 GFFPVLSV-KSGKVNDFSG-KSI-GTIPSTQLFINPDFAEAHELR 445
              PV++V +  K+ ++ G KS+  +  +++++INPD  E  E++
Sbjct: 60  E--PVVAVLRFWKIKEYKGPKSLSNSFGASKVYINPDIPEVPEIK 102

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Length = 106

>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 21/84 (25%), Positives = 32/84 (38%), Gaps = 11/84 (13%)

Query: 221 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVY 280
             +  RVT+          R  GKV    L D   G I+V  F    ++  + ++ G V 
Sbjct: 1   VTVAGRVTSVR--------RSGGKVAFLTLRD-GTGSIQVVLFKEEAEKLAKKLKEGDVV 51

Query: 281 LISKGSLKPAQKNFNHLK-NEWEI 303
           L+  G +K        L   E E+
Sbjct: 52  LV-TGKVKKRPGGELELVVEEIEV 74

This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. Length = 75

>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed

 Score = 45.4 bits (108), Expect = 7e-05
 Identities = 43/174 (24%), Positives = 75/174 (43%), Gaps = 21/174 (12%)

Query: 222 AIKARVTAKGDLRRYNNARGD-GKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVY 280
            I+  VT    ++ +    G  GK+ SF L D D G IRVT +N + D     IEV +  
Sbjct: 188 TIEGEVTKAYPIKEFTRKDGSEGKLKSFILKD-DTGSIRVTLWNDLTD-----IEVNKGD 241

Query: 281 LIS-KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAEN 339
           ++  KG +K         +   EI       ++   +E+  +         I E+   E+
Sbjct: 242 IVRVKGYVKQG------YRTGLEISANNIEILEKLEKEEKELEIVN-----IEELTEFED 290

Query: 340 NSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE 393
              VDV G +I+++    + R +    + + + L D +GR V ++ WG+     
Sbjct: 291 GEEVDVKGRIIAISDKREVERDDR-TAEVQDIELADGTGR-VRVSFWGEKAKIL 342

Length = 637

>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)

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 240 RGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFN 295
           R +GKV  F L D  GG IRVT F  + +    +++ G+V  I KG +K  +    
Sbjct: 13  RTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYI-KGKVKKFRGRLQ 67

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1). Length = 75

>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 45/197 (22%), Positives = 78/197 (39%), Gaps = 28/197 (14%)

Query: 200 LKNEAPARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEI 258
              E       I+ +   Q    I  R+    +++ +    G  GK+ +  + D + G I
Sbjct: 55  YGQEEEEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIAD-NTGTI 113

Query: 259 RVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEE- 317
           R+T +N       + ++ G V  I     +           +W   +E  S  +   ++ 
Sbjct: 114 RLTLWNDNAK-LLKGLKEGDVIKIENARSR-----------KWNNDVELNSGSETRIDKL 161

Query: 318 ---DDS---IPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRIL 371
              D+S   I K+ +    I E+E   N S   + G V    P     RK+G E + +  
Sbjct: 162 EKYDESRYPIIKENYD---IPELE--PNLSAT-IEGEVTKAYPIKEFTRKDGSEGKLKSF 215

Query: 372 NLKDTSGRSVELTLWGD 388
            LKD +G S+ +TLW D
Sbjct: 216 ILKDDTG-SIRVTLWND 231

Length = 637

>gnl|CDD|180887 PRK07211, PRK07211, replication factor A; Reviewed

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 39/172 (22%), Positives = 76/172 (44%), Gaps = 18/172 (10%)

Query: 223 IKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYL 281
           +   V     +R ++   G +G+V +  + D  G  +RVT ++   D   E+ + G    
Sbjct: 176 LVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETG-RVRVTLWDDRADLAEEL-DAGESVE 233

Query: 282 ISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNS 341
           I  G ++    +        E+ +     V+   E+ + +P         + IES E + 
Sbjct: 234 IVDGYVRERDGSL-------ELHVGDRGAVEEVDEDVEYVPDT-------TPIESLEIDE 279

Query: 342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE 393
            VD+ G+V S +P     R +G E Q R + ++D +G  + + LWG+  + +
Sbjct: 280 TVDIAGVVRSADPKRTFDRDDGSEGQVRNVRIQDDTG-DIRVALWGEKADLD 330

Length = 485

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	653
TIGR00617	608	rpa1 replication factor-a protein 1 (rpa1). This f	100.0
PRK12366	637	replication factor A; Reviewed	100.0
PRK08402	355	replication factor A; Reviewed	100.0
cd04476	166	RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor	100.0
PF08646	146	Rep_fac-A_C: Replication factor-A C terminal domai	100.0
PRK07218	423	replication factor A; Provisional	100.0
PRK12366	637	replication factor A; Reviewed	100.0
PRK07211	485	replication factor A; Reviewed	100.0
PRK06386	358	replication factor A; Reviewed	100.0
PRK07211	485	replication factor A; Reviewed	99.98
PRK15491	374	replication factor A; Provisional	99.97
PRK15491	374	replication factor A; Provisional	99.96
PRK14699	484	replication factor A; Provisional	99.96
cd04474	104	RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor	99.96
PRK14699	484	replication factor A; Provisional	99.94
PF04057	101	Rep-A_N: Replication factor-A protein 1, N-termina	99.93
cd04477	97	RPA1N RPA1N: A subfamily of OB folds corresponding	99.9
cd04475	101	RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor	99.87
cd04481	106	RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc	99.83
cd04480	86	RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of unc	99.78
PF02721	95	DUF223: Domain of unknown function DUF223; InterPr	99.68
PRK08402	355	replication factor A; Reviewed	99.59
PRK07217	311	replication factor A; Reviewed	99.56
KOG0851	246	consensus Single-stranded DNA-binding replication	99.26
COG1599	407	RFA1 Single-stranded DNA-binding replication prote	99.25
cd04497	138	hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f	99.11
PRK07218	423	replication factor A; Provisional	99.08
PRK06386	358	replication factor A; Reviewed	99.06
cd04491	82	SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil	98.86
cd04491	82	SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil	98.86
PRK06461	129	single-stranded DNA-binding protein; Reviewed	98.79
PRK06461	129	single-stranded DNA-binding protein; Reviewed	98.76
PRK07217	311	replication factor A; Reviewed	98.31
COG1599	407	RFA1 Single-stranded DNA-binding replication prote	98.21
TIGR00617	608	rpa1 replication factor-a protein 1 (rpa1). This f	98.05
cd04474	104	RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor	97.84
PF01336	75	tRNA_anti-codon: OB-fold nucleic acid binding doma	97.82
PF02765	146	POT1: Telomeric single stranded DNA binding POT1/C	97.67
cd04475	101	RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor	97.25
cd03524	75	RPA2_OBF_family RPA2_OBF_family: A family of oligo	96.74
KOG3416	134	consensus Predicted nucleic acid binding protein [	96.2
KOG3416	134	consensus Predicted nucleic acid binding protein [	96.1
PF06075	579	DUF936: Plant protein of unknown function (DUF936)	95.97
cd04483	92	hOBFC1_like hOBFC1_like: A subfamily of OB folds s	95.1
cd04481	106	RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc	95.06
cd04497	138	hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f	95.02
cd03524	75	RPA2_OBF_family RPA2_OBF_family: A family of oligo	95.01
PF15489	1144	CTC1: CST, telomere maintenance, complex subunit C	94.99
PF01336	75	tRNA_anti-codon: OB-fold nucleic acid binding doma	94.91
cd04488	75	RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f	94.64
cd04485	84	DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp	94.63
PF09103	118	BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide	94.34
cd04490	79	PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds	94.29
PTZ00401	550	aspartyl-tRNA synthetase; Provisional	92.82
cd04490	79	PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds	92.46
cd04489	78	ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol	92.09
cd04485	84	DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp	91.51
KOG0851	246	consensus Single-stranded DNA-binding replication	91.42
PF11325	84	DUF3127: Domain of unknown function (DUF3127); Int	91.25
cd04320	102	AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r	91.11
PF14951	389	DUF4503: Domain of unknown function (DUF4503)	90.63
cd04322	108	LysRS_N LysRS_N: N-terminal, anticodon recognition	90.61
cd04492	83	YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol	90.05
PLN02850	530	aspartate-tRNA ligase	90.04
PF15072	86	DUF4539: Domain of unknown function (DUF4539)	89.84
cd04478	95	RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor	89.6
PF10341	106	TPP1: Shelterin complex subunit, TPP1/ACD; InterPr	88.96
cd04323	84	AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, a	88.7
cd04100	85	Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant	88.44
PRK07373	449	DNA polymerase III subunit alpha; Reviewed	87.63
PRK02801	101	primosomal replication protein N; Provisional	87.39
COG5235	258	RFA2 Single-stranded DNA-binding replication prote	87.23
cd04495	100	BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds	87.14
PRK13480	314	3'-5' exoribonuclease YhaM; Provisional	86.33
cd04316	108	ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a	86.31
PRK05733	172	single-stranded DNA-binding protein; Provisional	85.91
PRK06751	173	single-stranded DNA-binding protein; Provisional	85.71
PRK07459	121	single-stranded DNA-binding protein; Provisional	85.01
PF09104	143	BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide	84.88
PRK13732	175	single-stranded DNA-binding protein; Provisional	84.67
cd04489	78	ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol	84.6
PRK08763	164	single-stranded DNA-binding protein; Provisional	84.07
PRK05159	437	aspC aspartyl-tRNA synthetase; Provisional	84.03
cd04478	95	RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor	83.79
PF02721	95	DUF223: Domain of unknown function DUF223; InterPr	83.5
PLN02502	553	lysyl-tRNA synthetase	83.02
cd04484	82	polC_OBF polC_OBF: A subfamily of OB folds corresp	82.92
PRK07275	162	single-stranded DNA-binding protein; Provisional	82.77
cd04496	100	SSB_OBF SSB_OBF: A subfamily of OB folds similar t	82.76
PRK05813	219	single-stranded DNA-binding protein; Provisional	82.75
cd04492	83	YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol	82.64
PF02765	146	POT1: Telomeric single stranded DNA binding POT1/C	82.33
PRK09010	177	single-stranded DNA-binding protein; Provisional	82.21
cd04317	135	EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod	81.77
PRK07772	186	single-stranded DNA-binding protein; Provisional	81.19
PRK06293	161	single-stranded DNA-binding protein; Provisional	81.14
cd04480	86	RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of unc	81.05
cd04493	100	BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds	81.03
PRK13480	314	3'-5' exoribonuclease YhaM; Provisional	80.59
PTZ00417	585	lysine-tRNA ligase; Provisional	80.11

>TIGR00617 rpa1 replication factor-a protein 1 (rpa1)

Probab=100.00  E-value=9.9e-125  Score=1061.18  Aligned_cols=593  Identities=42%  Similarity=0.743  Sum_probs=507.4

Q ss_pred             CCCCCHHHHHHHhC-CCC---CCCCeEEEEEEEEcC--CCCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEE
Q 006263            2 PVNLTPNSISLING-GDV---NSKPLVQVMDIKLIG--STQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQL   75 (653)
Q Consensus         2 ~~~Lt~Gai~~i~~-~~~---~~~pvvQVl~ik~~~--~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl   75 (653)
                      +.+||+|||.+|+. ++.   ...||||||++|++.  .+..|||++||||.|+++|||+||||+++++|+|++|+||||
T Consensus         1 ~~~lt~ga~~~i~~~~~~~~~~~~pv~Qv~~~k~~~~~~~~~ryr~~lsDg~~~~~~ml~t~~n~~~~~~~l~~~~iv~l   80 (608)
T TIGR00617         1 AVSLSNGAIALIMTNGEANGYPPDPVLQVLDLKPINGAQDPRRYRIVISDGIYYSKAMLATQLNPLVREGELQEGTIIRL   80 (608)
T ss_pred             CCccChhHHHHHhccccccCCCCCcEEEEEeeEEcCCCCCCceEEEEEECchHHHHHHHHHHHHHHHHhCCccCCCEEEE
Confidence            35899999999998 333   368999999999995  245899999999999999999999999999999999999999


Q ss_pred             eeeEeeee-c-CeEEEEEEeeeEeecC---CcccCCCcccccccc-ccccCCCCCCCCCCccccccCCCCCCCccccCCC
Q 006263           76 IDYICSTV-Q-NRKIIVVLNMETIILD---CEPIGNPKIFSESEL-TAQKTIPSNNLPQPVRVNNYSAPNSGTFNLQNSG  149 (653)
Q Consensus        76 ~~y~~~~~-~-~k~~iii~~~evl~~~---~~~iG~P~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~  149 (653)
                      ++|.++.+ + +|++|||+++|||.+.   .++||+|++++.... +++.+. ..+.|.  .+      +        +.
T Consensus        81 ~~~~~~~~~~~~~~~lii~~~ev~~~~~~~~~~ig~p~~~~~~~~~~~~~~~-~~~~~~--~~------~--------~~  143 (608)
T TIGR00617        81 TKFEVNTIGKDGRKVLIVYELEVVKPELKVRDKIGNPVTYEKYLDSWHEEQV-LASKPA--TN------P--------AN  143 (608)
T ss_pred             eEEEEeEEccCCcEEEEEEeeEEeecccccccccCCCccccccccccCcccc-cccccc--cc------C--------CC
Confidence            99999999 5 6899999999999975   357999998875421 111000 000000  00      0        00


Q ss_pred             CCCCCCCCCCCCCCCCCcCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCccCCCCCCcceeccccCCCCCceEEEEEEEe
Q 006263          150 TFNSQNPGSFSTPNSGTFRAPNAGSIVRSFQPTVQPPYQPPPNFRNHGPILKNEAPARIIPIAALNPYQGRWAIKARVTA  229 (653)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pI~~L~p~~~~w~I~~RV~~  229 (653)
                      .+... .|             ++.  .+++.++++|      .+.+.++.......++++||++|+||+++|+|+|||++
T Consensus       144 ~~~~~-~~-------------~~~--~~~~~~~~~~------~~~~~~~~~~~~~~~~~~pI~~L~py~~~wtIkaRV~~  201 (608)
T TIGR00617       144 PPNAK-AP-------------KNE--VASYNNAANP------ERGNAPPAPNSGSTRRVMPIASLSPYQNKWTIKARVTN  201 (608)
T ss_pred             CCCcc-CC-------------Ccc--cccccCCCCc------ccCCCCCCccccCCcceEEHHHCCCCCCceEEEEEEEe
Confidence            00000 00             000  0001001111      11111111111234579999999999999999999999


Q ss_pred             eccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceEEEecccc
Q 006263          230 KGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATS  309 (653)
Q Consensus       230 k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T  309 (653)
                      ||++|+|++++|+|++|+|+|+| +||+|+||+|++.+++|+++|++|+||+|++|+|++|+++|++++|+|||+|+.+|
T Consensus       202 Ks~ir~~~~~~gegkvfsv~L~D-egg~Irat~f~~~~dkf~~~l~eG~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T  280 (608)
T TIGR00617       202 KSEIRTWSNARGEGKLFNVELLD-ESGEIRATAFNEQADKFYDIIQEGKVYYISKGSLKPANKQFTNLGNDYEMTLDRDT  280 (608)
T ss_pred             ccccceecCCCCCceeeEEEEec-CCCeEEEEECchHHHHHhhhcccCCEEEECceEEEEccccccCCCCCEEEEECCCe
Confidence            99999999999999999999999 99999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec-CCceeeEEEEEEEeCCCCEEEEEEccc
Q 006263          310 TVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK-NGMETQRRILNLKDTSGRSVELTLWGD  388 (653)
Q Consensus       310 ~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k-~g~~~~kr~i~l~D~s~~~i~vtLWg~  388 (653)
                      .|++|.| ...||.+.|+|++|+||.+.+.+.+|||||+|++|+++.+|++| +|++..||+|+|+|+||.+|+|||||+
T Consensus       281 ~I~~~~d-~~~iP~~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~  359 (608)
T TIGR00617       281 VIEECED-ETAIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGD  359 (608)
T ss_pred             EEEECCC-cccCCcccccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhh
Confidence            9999964 44699999999999999998888899999999999999999966 789999999999999999999999999


Q ss_pred             hhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccc-cC
Q 006263          389 FCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIA-AG  467 (653)
Q Consensus       389 ~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~-~~  467 (653)
                      +|..|        +...+|||+|+++||++|+|++||++++|+|++|||+||+++|+.||+++|....+.+++...+ ..
T Consensus       360 ~A~~~--------~~~~~~Vva~kg~~V~~f~g~sLs~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~s~~~~~~~~~  431 (608)
T TIGR00617       360 DATKF--------DVSVQPVIAIKGVRVSDFGGKSLSTGGSSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRV  431 (608)
T ss_pred             hhhhc--------CCCCCCEEEEEeEEEEecCCceEeccCCceEEECCCcHHHHHHHHHHHhcCCCccceeehhcccccc
Confidence            98764        4457899999999999999999999999999999999999999999999998776666654332 12


Q ss_pred             CCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecC-ceeecccCccccCCce
Q 006263          468 GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECD  546 (653)
Q Consensus       468 ~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~~~~~~  546 (653)
                      ++....++||+||+++++|.+++++||+|+|||++|+.|+|||+|||++    .|+|||.+++ +.|+|++|++++++|.
T Consensus       432 ~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y~ACp~~----~CnKKV~~~~~g~~~CekC~~~~~~~~  507 (608)
T TIGR00617       432 GGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALYRACPSE----DCNKKVVDQGDGTYRCEKCNKNFAEFK  507 (608)
T ss_pred             CCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEeccCChh----hCCCccccCCCCCEECCCCCCCCCCcc
Confidence            3446789999999999999999999999999999999999999999954    5999998876 4899999999999999


Q ss_pred             EEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEE
Q 006263          547 YRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKI  626 (653)
Q Consensus       547 ~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~  626 (653)
                      |||+|++.|+|+||++|+++||+.|++|||++|+||++|+  ++|+++|+++|.++.|++|.|+|++++++||||.|+||
T Consensus       508 ~RYil~~~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~--~~~~~~~~~i~~~~~~~~~~f~~~~k~e~yn~e~r~~~  585 (608)
T TIGR00617       508 YRYILQISISDETGQLWVTAFNDQAEQILGKSAAELGELK--EEDPDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKY  585 (608)
T ss_pred             EEEEEEEEEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHH--hcCHHHHHHHHHHhhCcEEEEEEEEEEcccCCEeeEEE
Confidence            9999999999999999999999999999999999999999  67889999999999999999999999999999999999


Q ss_pred             EEEEeecCChHHHHHHHHHHHHh
Q 006263          627 TVIRADQVNYSSESRYLLDLISK  649 (653)
Q Consensus       627 ~v~~~~~vd~~~e~~~ll~~i~~  649 (653)
                      +|++++|+||++|+++||++|++
T Consensus       586 ~v~~~~~vd~~~e~~~L~~~i~~  608 (608)
T TIGR00617       586 TVMSVDPVNYRAEAKYLLQEIEK  608 (608)
T ss_pred             EEEEeeeCCHHHHHHHHHHHhcC
Confidence            99999999999999999999974

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK12366 replication factor A; Reviewed

Probab=100.00  E-value=6.2e-66  Score=586.37  Aligned_cols=356  Identities=21%  Similarity=0.334  Sum_probs=319.8

Q ss_pred             cceeccccCCC-CC-ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          207 RIIPIAALNPY-QG-RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       207 ~~~pI~~L~p~-~~-~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      .++||++|+|| .+ +|+|+|||+.|+++|+|++.+|+|++|+++|.| ++|+||+|+|++.+++|++ |++|+||+|++
T Consensus       278 ~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D-~tG~IR~t~w~~~~d~~~~-l~~G~vy~is~  355 (637)
T PRK12366        278 EIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELAD-GTGRVRVSFWGEKAKILEN-LKEGDAVKIEN  355 (637)
T ss_pred             CceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEc-CCCeEEEEEeCchhhhhcc-cCCCCEEEEec
Confidence            46799999999 65 899999999999999999999999999999999 5679999999999999998 59999999999


Q ss_pred             eEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcc-cCccccEEEEEEEecCceeEEecCC
Q 006263          285 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAE-NNSIVDVIGIVISVNPSVPILRKNG  363 (653)
Q Consensus       285 ~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~-~~~~vDVIGvV~~v~~~~~i~~k~g  363 (653)
                      ++|+..+.  +...+.|||+|+..|.|.+  +++..+|...|+|++|.+|.+++ .+..|||+|+|++++++.+|++++|
T Consensus       356 ~~vk~y~~--~~~~~~~El~~~~~s~I~~--d~~~~~p~~~~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~~i~~k~G  431 (637)
T PRK12366        356 CKVRTYYD--NEGEKRVDLNAGYSSEIIK--DESISFEEIEEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERSDG  431 (637)
T ss_pred             CEEeeccc--cCCCcCEEEEcCCceEEEe--ccCCcccceeeccccHHHhhcccCCCcEEEEEEEEEEccCceEEEecCC
Confidence            99984332  1345789999999999998  34556999999999999999875 6889999999999999999998899


Q ss_pred             ceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEEEEcCChHHHH
Q 006263          364 METQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAH  442 (653)
Q Consensus       364 ~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i~inPdipe~~  442 (653)
                      ++..+|+++|.|+|| +|++||||+.|..         +...+++|+|++++|++|+|+ +||++++|+|.+||+.|+  
T Consensus       432 ~~~~~r~i~l~D~TG-~I~vtlWg~~a~~---------~~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~~e--  499 (637)
T PRK12366        432 SKGKVRNIELADGTG-SIRLTLWDDDAEI---------EIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGEI--  499 (637)
T ss_pred             CEeEEEEEEEEeCCC-EEEEEEecccccc---------CCCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCCcc--
Confidence            999999999999999 9999999999853         234689999999999999995 999999999999999887  


Q ss_pred             HHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccc
Q 006263          443 ELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQC  522 (653)
Q Consensus       443 ~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C  522 (653)
                       |+                          ..+++|++|++.        ++|.++|+|++|+.+++||+|||      .|
T Consensus       500 -l~--------------------------~~~~~I~~i~~~--------~~~~v~g~i~~i~~~~~~y~aCp------~C  538 (637)
T PRK12366        500 -IK--------------------------SNRKFIADLEED--------DTVEIRGTVVDIRKQKIILYLCP------NC  538 (637)
T ss_pred             -cc--------------------------ccccCHHHcccC--------CeEEEEEEEEEEeCCCEEEeccc------cc
Confidence             22                          036889999763        35999999999999999999999      89


Q ss_pred             cceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHh
Q 006263          523 NKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSR  602 (653)
Q Consensus       523 ~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~  602 (653)
                      ||||....+.|+|++|++.  .|.|||+|++.|+|+||++|+++|++.|++||||+|+||.+|.  +       +.|+++
T Consensus       539 nkKv~~~~g~~~C~~c~~~--~p~~~~~l~~~i~D~TG~~~~t~f~e~ae~l~G~sa~el~~l~--~-------~~l~~~  607 (637)
T PRK12366        539 RKRVEEVDGEYICEFCGEV--EPNELLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELN--L-------EALEDL  607 (637)
T ss_pred             CeEeEcCCCcEECCCCCCC--CCcEEEEEEEEEEcCCCCEEEEEEhHHhHHHhCCCHHHHHHHH--H-------HHHHHh
Confidence            9999876669999999997  8999999999999999999999999999999999999999988  2       567789


Q ss_pred             cCceEEEEEEEeeeccCceeeEEEEEEEeecCCh
Q 006263          603 VFNQYLFRLKIKEELYGDEQRVKITVIRADQVNY  636 (653)
Q Consensus       603 ~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd~  636 (653)
                      +|++|.|+++++.+  |++  +||+|.++.|+|+
T Consensus       608 ~g~~~~~~~~~k~~--~~~--~r~~v~~v~~~d~  637 (637)
T PRK12366        608 LGEEVVFYGNVSFR--NEE--LRFNVRRVNNVDV  637 (637)
T ss_pred             cCcEEEEEEEEeec--Cce--eEEEEEEeecccC
Confidence            99999999999988  654  5599999999985

>PRK08402 replication factor A; Reviewed

Probab=100.00  E-value=2.9e-45  Score=386.43  Aligned_cols=279  Identities=22%  Similarity=0.327  Sum_probs=238.5

Q ss_pred             eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhc-cCC
Q 006263          327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVD-VGF  405 (653)
Q Consensus       327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~-~~~  405 (653)
                      ..++|.||..  ....|.+.|.|+++++..++++++|.....++++|.|+|| .+++||||+.|..+       +. ...
T Consensus        61 ~~~kI~dl~~--g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG-~ir~TlW~~~a~~~-------~~~l~~  130 (355)
T PRK08402         61 PLMHISDLVP--GMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTG-RARVVLWDAKVAKY-------YNKINV  130 (355)
T ss_pred             CccCHHHccC--CCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCC-eEEEEEechhhhhh-------cccCCC
Confidence            3567777753  3468999999999999999999999888899999999999 67999999998652       22 247


Q ss_pred             CcEEEEEeeEeec-CCCc-eeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhc
Q 006263          406 FPVLSVKSGKVND-FSGK-SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNE  483 (653)
Q Consensus       406 ~~Vvaik~~rV~~-f~G~-sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~  483 (653)
                      ++||+|++++|++ |+|+ +||++++|+|.+|||+|+++.+             .+++...    +....+++|++|.+ 
T Consensus       131 Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd~~ea~~i-------------~~~~~~~----~~~~~~k~I~ei~~-  192 (355)
T PRK08402        131 GDVIKVIDAQVRESLSGLPELHINFRARIILNPDDPRVEEI-------------PPLEEVR----SYNYTRKKIGELEG-  192 (355)
T ss_pred             CCEEEEECCEEeecCCCcEEEEECCCceEEeCCCccccccc-------------ccccccc----cccccccCHHHccc-
Confidence            8999999999998 5999 9999999999999999999763             2222111    12466899999965 


Q ss_pred             CCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceee-ecCc-eeecccCccccCCceEEEEEEEEEEeCCCe
Q 006263          484 GLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGL  561 (653)
Q Consensus       484 ~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~-~~~~-~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~  561 (653)
                        |  +  +||.++|+|++|+. +++|+|||      .|||||. ++++ .|+|+.|++.  .|.|||+|++.|+|+||+
T Consensus       193 --g--d--~~v~v~g~Iv~i~~-~~~y~aCp------~CnKkv~~~~~~~~~~Ce~~~~v--~p~~ryil~~~l~D~TG~  257 (355)
T PRK08402        193 --G--E--RFVEVRGTIAKVYR-VLVYDACP------ECRRKVDYDPATDTWICPEHGEV--EPIKITILDFGLDDGTGY  257 (355)
T ss_pred             --C--C--cEEEEEEEEEEEec-CeeEecCC------CCCeEEEEecCCCCEeCCCCCCc--CcceeEEEEEEEEcCCCc
Confidence              1  2  78999999999998 77999999      8999998 4444 8999999973  799999999999999999


Q ss_pred             EEEEEechhhhhhhCCCHHHHHHH-h---hccCCh-----hHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEEEee
Q 006263          562 TWVTAFQESGEEILGCPAKELYML-K---YELQDD-----VRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRAD  632 (653)
Q Consensus       562 ~~~~~F~~~ae~llG~sA~el~~~-~---~e~~d~-----~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~  632 (653)
                      +|+++|++.|++|||++|+||.++ +   .+.-+.     ..|...+..++|++|.||++++.+.|+|+.   |+|.++.
T Consensus       258 ~~vt~f~e~ae~llG~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~~~---~~v~~~~  334 (355)
T PRK08402        258 IRVTLFGDDAAELLGVEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLGLI---LKASSWD  334 (355)
T ss_pred             EEEEEecHHHHHHhCCCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCCeE---EEEEEcc
Confidence            999999999999999999999988 4   211133     678889999999999999999999999965   9999999


Q ss_pred             cCChHHHHHHHHHHHHhhh
Q 006263          633 QVNYSSESRYLLDLISKSF  651 (653)
Q Consensus       633 ~vd~~~e~~~ll~~i~~~~  651 (653)
                      |+||++|+++|+++|.++.
T Consensus       335 ~vd~~~e~~~l~~~i~~~~  353 (355)
T PRK08402        335 EVDYKREIERVRAELEELG  353 (355)
T ss_pred             cCCHHHHHHHHHHHHHHhh
Confidence            9999999999999998875

>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)

Probab=100.00  E-value=8.6e-37  Score=293.68  Aligned_cols=165  Identities=44%  Similarity=0.828  Sum_probs=155.2

Q ss_pred             HHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecC-ceeecccCccccCCceEEEEEEEEE
Q 006263          477 VSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSG-NRWQCDRCNQEIDECDYRYLLQAQI  555 (653)
Q Consensus       477 i~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~-~~~~C~kC~~~~~~~~~rY~l~~~i  555 (653)
                      +++|++++++..+++++|.|+|+|..|+.++|||+|||      .|+|||.+.+ +.|+|++|++.+++|.|||+|++.|
T Consensus         1 i~~i~~~~~~~~~~~~~~~v~a~I~~I~~~~~~Y~aC~------~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i   74 (166)
T cd04476           1 IAEIKEENLGEGEKPDYFTVKATIVFIKPDNWWYPACP------GCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNV   74 (166)
T ss_pred             CchhhcccCCCCCCCCEEEEEEEEEEEcCCCeEEcccc------ccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEE
Confidence            35777777777678999999999999999999999999      9999999887 5999999999999999999999999


Q ss_pred             EeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEEEeecCC
Q 006263          556 QDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVN  635 (653)
Q Consensus       556 ~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd  635 (653)
                      +|+||++|+++||+.|++|||++|+||.++.  +++++.+++.|.++.|++|.|+++++.++|++|.|++|+|.+++|++
T Consensus        75 ~D~Tg~~~~~~F~~~ae~l~G~sa~el~~~~--~~~~~~~~~~i~~~~gk~~~f~v~~~~~~y~~e~~~~~~v~~i~~~~  152 (166)
T cd04476          75 ADHTGEAWLTLFDEVAEQIFGKSAEELLELK--EEDPDAFPDAIQDLVGKTFLFRVSVKEETYNDEGRIRYTVVKVAPVD  152 (166)
T ss_pred             EeCCCCEEEEEehHHHHHHhCCCHHHHHHHh--hcCHHHHHHHHHHhhCceEEEEEEEEehhcCCcceEEEEEEEcccCC
Confidence            9999999999999999999999999999998  45578899999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHh
Q 006263          636 YSSESRYLLDLISK  649 (653)
Q Consensus       636 ~~~e~~~ll~~i~~  649 (653)
                      +++|+++|++.|++
T Consensus       153 ~~~~~~~l~~~i~~  166 (166)
T cd04476         153 YKKESKRLIQSIEK  166 (166)
T ss_pred             HHHHHHHHHHHhhC
Confidence            99999999999864

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun

>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

Probab=100.00  E-value=7.8e-37  Score=287.69  Aligned_cols=145  Identities=46%  Similarity=0.820  Sum_probs=124.4

Q ss_pred             EEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCc-eeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhh
Q 006263          493 WVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESG  571 (653)
Q Consensus       493 ~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~a  571 (653)
                      ||+|+|+|..|+.++|||+|||++    .|+|||...++ .|+|++|++.+++|.|||+|++.|+|+||++|+++||++|
T Consensus         1 ~~~v~a~I~~I~~~~~~Y~aC~~~----~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~~~~~F~~~a   76 (146)
T PF08646_consen    1 YFTVRATIVEIKSDNWYYPACPNE----KCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSIWVTLFDEEA   76 (146)
T ss_dssp             EEEEEEEEEEEETTTTEEEE-TST----TTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEEEEEEEHHHH
T ss_pred             CEEEEEEEEEEECCCcEECCCCCc----cCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeEEEEEEhHHH
Confidence            799999999999999999999988    99999998854 9999999999999999999999999999999999999999


Q ss_pred             hhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEEEeecCChHHHHHHH
Q 006263          572 EEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYL  643 (653)
Q Consensus       572 e~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd~~~e~~~l  643 (653)
                      ++|||++|+||.++.  ++++..++.++.+++|++|.|+|+++.++|+++.|++++|++++|+||++|+++|
T Consensus        77 ~~l~G~~a~el~~~~--~~~~~~~~~~~~~~~~~~~~f~v~~~~~~y~~e~r~~~~v~~i~~vd~~~e~~~l  146 (146)
T PF08646_consen   77 EQLLGMSADELKELK--EEDPEEFPKIIKKLLGKEFVFRVRVKKESYNDESRVKYTVVRIEPVDYAEESKRL  146 (146)
T ss_dssp             HHHHCCHHCCCHHHC--CC-HHHHHHHHHCTTT-EEEEEEEEEE--------EEEEEEEEEE--HHHHHHHH
T ss_pred             HHHhCCCHHHHHHHH--hhchhHHHHHHHHhhCcEEEEEEEEEEhhhCCceEEEEEEEEeEeCCHHHHhhcC
Confidence            999999999999988  6788999999999999999999999999999999999999999999999999987

It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.

>PRK07218 replication factor A; Provisional

Probab=100.00  E-value=1.5e-33  Score=303.16  Aligned_cols=360  Identities=18%  Similarity=0.195  Sum_probs=288.7

Q ss_pred             CcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      ++...|++|.|...+-+|+|||+.+|+ |+|...+++|.+.+++|.| ++|.|+.|+|++.      -|++|++|.|.|+
T Consensus        56 ~~~~kI~Di~~~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~igD-eTG~Ir~tlW~~~------~l~~Gdvv~I~na  127 (423)
T PRK07218         56 PSSKDIKELSTDDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGILAD-ETGTISYTAWKDF------GLSPGDTVTIGNA  127 (423)
T ss_pred             CCCccHhhCCCCCceeEEEEEEEEecc-eeEecCCCceEEEEEEEEC-CCCeEEEEEECCC------CCCCCCEEEEecc
Confidence            456799999999988999999999999 9998766788999999999 8999999999965      2999999999999


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcc-cCccccEEEEEEEecCceeEEecCCc
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAE-NNSIVDVIGIVISVNPSVPILRKNGM  364 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~-~~~~vDVIGvV~~v~~~~~i~~k~g~  364 (653)
                      .++.-+.       ..++.+++.|.|.... +....|..   .....+|.++. ...-|+|.|.|.++.+ .+|++++|.
T Consensus       128 ~vre~~g-------~~el~ig~~t~I~~~d-e~~~~~~~---~~~~~kI~DL~~g~~~V~v~g~Vl~~~~-r~f~~~dg~  195 (423)
T PRK07218        128 GVREWDG-------RPELNIGESTTVSLLD-DSSLPPYS---IGGDKKLIDLGPGDRGVNVEARVLELEH-REIDGRDGE  195 (423)
T ss_pred             EeeccCC-------ceEEeccCcceEEEcC-cccccCcc---ccCccchhhccCCCCceEEEEEEEEecc-eeEEcCCCC
Confidence            9876543       3899999999999874 33333322   33344444443 3456999999999966 688877775


Q ss_pred             eeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEEEEcCChHHHHH
Q 006263          365 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHE  443 (653)
Q Consensus       365 ~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i~inPdipe~~~  443 (653)
                       ...++..|.|+|| +|++|||++.+.         +  ..+.+|-|.++.+++|+|+ +|+....|.|..+|+..++  
T Consensus       196 -~~v~~giigDeTG-~Ir~tlW~~~~~---------l--~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~v--  260 (423)
T PRK07218        196 -TTILSGVLADETG-RLPFTDWDPLPE---------I--EIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVSV--  260 (423)
T ss_pred             -eEEEEEEEECCCc-eEEEEEeccccc---------C--CCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCccc--
Confidence             4689999999999 899999998752         2  3689999999999999997 8999999999988853211  


Q ss_pred             HHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcE-EEEEEEEEEEeCCceEEecCCCCcCcccc
Q 006263          444 LREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDW-VTVRAFITFIKSDSFCYTACPLMIGDRQC  522 (653)
Q Consensus       444 l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~-~~v~atI~~i~~d~~~Y~aC~~~~~~~~C  522 (653)
                                               .....++.|.++.+.      ...| ..+.|+|+.|...+-.|..||      .|
T Consensus       261 -------------------------~~~~~~~~I~e~~~~------~g~~~Vev~G~Iv~i~~gsgli~rCP------~C  303 (423)
T PRK07218        261 -------------------------SKDPPRLKIREAVER------GGIFDVELVGNIISVRDGSGLIERCP------EC  303 (423)
T ss_pred             -------------------------cCCccccchhhhhcc------CCcceEEEEEEEEEeccCCcceecCc------Cc
Confidence                                     012346778888763      2234 689999999999988999999      99


Q ss_pred             cceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHH-HHHHHH
Q 006263          523 NKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRF-GEIIRS  601 (653)
Q Consensus       523 ~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~-~~~~~~  601 (653)
                      +|+|.    .|.|+.|++.  .|.+-.++.+.+.|+||++.+++|++.+++|.|++.++..+|..+.-|.... ..+-..
T Consensus       304 ~r~v~----~~~C~~hG~v--e~~~dlrik~vLDDGtg~~~~~~~~e~~e~l~G~~~e~a~~~~~~~~d~~~v~~~i~~~  377 (423)
T PRK07218        304 GRVIQ----KGQCRSHGAV--EGEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRER  377 (423)
T ss_pred             ccccc----CCcCCCCCCc--CCeeeeEEEEEEECCCCeEEEEEChhhhHhHhCCCHHHHHHHHHhhhcchhhHHHHHHh
Confidence            99995    4899999976  7899999999999999999999999999999999999998877433344444 444467


Q ss_pred             hcCceEEEEEEEeeeccCceeeEEEEEEEeecCC--hHHHHHHHHHHH
Q 006263          602 RVFNQYLFRLKIKEELYGDEQRVKITVIRADQVN--YSSESRYLLDLI  647 (653)
Q Consensus       602 ~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd--~~~e~~~ll~~i  647 (653)
                      ++|+.|.|+..+..+.|.    ..+.+.++..+|  .+.-++.||.++
T Consensus       378 llG~~~~v~G~~~~~~~g----~~~~a~~~~~~~~~~~~r~~~~l~~~  421 (423)
T PRK07218        378 LVGREYRVRGNLSVDEYG----ANLVAESFWVPDDDPAKRAVALLAEV  421 (423)
T ss_pred             hcCcEEEEEeccccccCC----cEEEEeEccccCCCHHHHHHHHHHhh
Confidence            999999999998877773    577778887775  445555666543

>PRK12366 replication factor A; Reviewed

Probab=100.00  E-value=5.7e-32  Score=308.45  Aligned_cols=282  Identities=20%  Similarity=0.273  Sum_probs=226.2

Q ss_pred             CCcceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          205 PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       205 ~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      ..+++||++|+||+.+|+|+|||+.+|++|+|++.+| +|++|+++|.| ++|+|++|+|++.++. ++.|++|+||+|+
T Consensus        60 ~~~~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~D-etG~Ir~t~W~~~~~~-~~~le~G~v~~i~  137 (637)
T PRK12366         60 EEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIAD-NTGTIRLTLWNDNAKL-LKGLKEGDVIKIE  137 (637)
T ss_pred             ccceeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEc-CCCEEEEEEEchhhhh-hccCCCCCEEEEe
Confidence            3468899999999999999999999999999999877 89999999999 6779999999999885 6899999999999


Q ss_pred             ceEEecCCCcccCCCCceEEEeccccEEEeccC-CCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecC
Q 006263          284 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTE-EDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKN  362 (653)
Q Consensus       284 ~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d-~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~  362 (653)
                      ++.++.       .+++|+|.++..|.|.++.+ ++..+|...++| +|.+|   ..+..|||+|+|++++++.++++|+
T Consensus       138 ~~~v~~-------~~~~~el~~~~~t~I~~~~~~d~~~i~~~~~~~-~I~el---~~g~~v~v~G~V~~~~~~~~f~rkd  206 (637)
T PRK12366        138 NARSRK-------WNNDVELNSGSETRIDKLEKYDESRYPIIKENY-DIPEL---EPNLSATIEGEVTKAYPIKEFTRKD  206 (637)
T ss_pred             ccEecc-------cCCceEEEcCCcceEEEccccccccCCcccccc-ccccc---CCCCeEEEEEEEEEccCcEEEEEcC
Confidence            999876       34779999999999999963 355789887776 55555   4677999999999999999999999


Q ss_pred             CceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecC-CCceeccccceEEEEcCChHHH
Q 006263          363 GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDF-SGKSIGTIPSTQLFINPDFAEA  441 (653)
Q Consensus       363 g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f-~G~sLs~~~~S~i~inPdipe~  441 (653)
                      |++..+|++.|.|+|| +|++||||+.|..         ....+++|+|++.++..| +|..|+.+..+.|-...+    
T Consensus       207 g~~~~~r~~~l~D~TG-~irvTlW~~~a~~---------~~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~~~----  272 (637)
T PRK12366        207 GSEGKLKSFILKDDTG-SIRVTLWNDLTDI---------EVNKGDIVRVKGYVKQGYRTGLEISANNIEILEKLEK----  272 (637)
T ss_pred             CCeeEEEEEEEEcCCC-cEEEEEEChhhcc---------cCCCCCEEEEEeEEecCcCCceEEEeCCceeeccccc----
Confidence            9999999999999999 8999999999843         234789999999888889 556888866665532110    


Q ss_pred             HHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCC-ceEEecCCCCcCcc
Q 006263          442 HELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSD-SFCYTACPLMIGDR  520 (653)
Q Consensus       442 ~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d-~~~Y~aC~~~~~~~  520 (653)
                               .                 ........|++|.+-     +....++++|.|+.+..- .|-.          
T Consensus       273 ---------~-----------------~~~~~~~pI~~L~~~-----~~g~~~~I~grV~~~~~~R~f~~----------  311 (637)
T PRK12366        273 ---------E-----------------EKELEIVNIEELTEF-----EDGEEVDVKGRIIAISDKREVER----------  311 (637)
T ss_pred             ---------c-----------------ccccCceeHHHCCcc-----cCCCEEEEEEEEEecCCceEEEc----------
Confidence                     0                 001134578888642     123468899999887531 1110          


Q ss_pred             cccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCC
Q 006263          521 QCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGC  577 (653)
Q Consensus       521 ~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~  577 (653)
                             .               .-. -...++.+.|.||++++++|++.|.++.++
T Consensus       312 -------~---------------~g~-gkv~s~~l~D~tG~IR~t~w~~~~d~~~~l  345 (637)
T PRK12366        312 -------D---------------DRT-AEVQDIELADGTGRVRVSFWGEKAKILENL  345 (637)
T ss_pred             -------C---------------CCc-EEEEEEEEEcCCCeEEEEEeCchhhhhccc
Confidence                   0               011 356789999999999999999999877664

>PRK07211 replication factor A; Reviewed

Probab=100.00  E-value=9.7e-32  Score=291.28  Aligned_cols=274  Identities=20%  Similarity=0.276  Sum_probs=218.0

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccC--CCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNA--RGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~--~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      .+.+|++|+||+++|+|+|||+.|+++|+|++.  +++|++|+++|.| ++|+|++|+|++.+++|++.|++|+||+|.+
T Consensus        52 e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~D-eTG~Ir~TlW~d~ad~~~~~Le~GdV~~I~~  130 (485)
T PRK07211         52 EVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVAD-ETGSVRVAFWDEQAVAAEEELEVGQVLRIKG  130 (485)
T ss_pred             ccccHhhCCCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEc-CCCeEEEEEechHhHhhhcccCCCCEEEEec
Confidence            467999999999999999999999999999987  4589999999999 8999999999999999999999999999965


Q ss_pred             eEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCc
Q 006263          285 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGM  364 (653)
Q Consensus       285 ~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~  364 (653)
                       .++   +.|+.+    ||+|+   .|++|++.  .+|....+|.+|.+|..  ....+||+|+|+.+++++++.+++|+
T Consensus       131 -~~~---~~ys~~----El~i~---~ve~~~d~--~i~~~~~~~~~I~dL~~--~~~~v~I~grV~~v~~iRtf~r~dGs  195 (485)
T PRK07211        131 -RPK---DGYNGL----EVSVD---KVEPDPDA--EIDVQIGDTYTVEDLSL--GLSDVTLVGVVLDTDSVRTFDRDDGS  195 (485)
T ss_pred             -eEe---ccccce----EEEEe---eEEEcccc--cccccccCCccHHHcCC--CCCceEEEEEEEEcCCCeEEECCCCC
Confidence             443   667763    99998   48888543  35555669999999974  46789999999999999999988998


Q ss_pred             eeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCC-ceeccccceEEEEcCChHHHHH
Q 006263          365 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG-KSIGTIPSTQLFINPDFAEAHE  443 (653)
Q Consensus       365 ~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G-~sLs~~~~S~i~inPdipe~~~  443 (653)
                      +...|++.|.|+|| +|++|||++.|..|     +.+  ..++||.|++++|++|+| .+|+....|.|..-++.  +. 
T Consensus       196 eGkv~sv~L~DeTG-~IR~TlW~d~Ad~~-----~~l--e~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~de--v~-  264 (485)
T PRK07211        196 EGRVSNLTVGDETG-RVRVTLWDDRADLA-----EEL--DAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDED--VE-  264 (485)
T ss_pred             eeEEEEEEEEcCCC-eEEEEEechhhhhh-----ccC--CCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcc--cc-
Confidence            99999999999999 69999999998774     112  468999999999999966 59999888888865541  10 


Q ss_pred             HHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCccccc
Q 006263          444 LREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCN  523 (653)
Q Consensus       444 l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~  523 (653)
                                   +  +.           ....|.+|.        ..+.+.+.|.|..+..-.-+-             
T Consensus       265 -------------~--vp-----------~~~~I~dl~--------~g~~vdV~GvV~~v~~~rtf~-------------  297 (485)
T PRK07211        265 -------------Y--VP-----------DTTPIESLE--------IDETVDIAGVVRSADPKRTFD-------------  297 (485)
T ss_pred             -------------c--cc-----------ccccHhhcC--------CCCceeEEEEEEEccCcEEEE-------------
Confidence                         0  00           013345443        223577888888776421111             


Q ss_pred             ceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhh
Q 006263          524 KKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGE  572 (653)
Q Consensus       524 KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae  572 (653)
                                  .+++      ....+.++.|.|.||++++++|++.|+
T Consensus       298 ------------r~dG------~~~~vr~l~l~D~TG~IrvTLWg~~A~  328 (485)
T PRK07211        298 ------------RDDG------SEGQVRNVRIQDDTGDIRVALWGEKAD  328 (485)
T ss_pred             ------------cCCC------CEeEEEEEEEEcCCCcEEEEEeCcccc
Confidence                        0122      234667899999999999999999994

>PRK06386 replication factor A; Reviewed

Probab=100.00  E-value=1.1e-29  Score=266.69  Aligned_cols=350  Identities=17%  Similarity=0.189  Sum_probs=278.4

Q ss_pred             eeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEe
Q 006263          209 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK  288 (653)
Q Consensus       209 ~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~  288 (653)
                      +.|++|+|...+-+|+|||+..| .|+|...+|+..+.+-+|.| ++|.|+.|+|+.     .+.|++|++|.|.|+.++
T Consensus         3 ~kI~DI~~~~~~V~v~akVl~~~-~r~i~~~~g~~~~~~gllgD-eTG~I~fT~W~~-----~~~l~~Gd~v~i~na~v~   75 (358)
T PRK06386          3 SKISDINAARQNVDLKVKVLSLN-KRTIKNDRGETIYYYGIIGD-ETGTVPFTAWEF-----PDAVKSGDVIEIKYCYSK   75 (358)
T ss_pred             cchhhcCCCCCcEEEEEEEEEcc-ceEEecCCCCeEEEEEEEEC-CcceEEEEecCC-----cccCCCCCEEEEEeEEEe
Confidence            57999999999999999999999 69998888776778888999 899999999995     257999999999999987


Q ss_pred             cCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeE
Q 006263          289 PAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQR  368 (653)
Q Consensus       289 ~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~k  368 (653)
                      .-+.       .++|.++..|.|.+..|.+..++ ..+..++|.||..  ...-|+|.|.|.++.+ .++. ++|.....
T Consensus        76 ~~~G-------~~~Lnv~~~t~v~~~~d~~iev~-~~~~~~KI~DL~~--g~~~v~V~akVle~~e-~e~~-~~g~~~~v  143 (358)
T PRK06386         76 EYNG-------KIRIYFDSRSEVMLKPDENIEVK-RTYKLVKIRDLSL--VTPYVSVIGKITGITK-KEYD-SDGTSKIV  143 (358)
T ss_pred             eECC-------EEEEEEcCceEEEecCccccccc-cccCccEeEeccC--CCCceEEEEEEEEccC-ceEe-cCCCccEE
Confidence            6443       58899999999976643322222 2246778888843  4567999999999977 5776 55666778


Q ss_pred             EEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEEEEcCChHHHHHHHHH
Q 006263          369 RILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHELREW  447 (653)
Q Consensus       369 r~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i~inPdipe~~~l~~w  447 (653)
                      +++.|.|+|| +|++|||++..             ..+.+|-|.++.+.+|+|+ +|+.+..|+|...|+.-+       
T Consensus       144 ~sg~lgDeTG-rIr~TlW~~~l-------------~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~ie-------  202 (358)
T PRK06386        144 YQGYIEDDTA-RVRISSFGKPL-------------EDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDIN-------  202 (358)
T ss_pred             EEEEEEcCCC-eEEEEEccccc-------------cCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCcc-------
Confidence            9999999999 89999999731             2589999999999999997 899999999887653211       


Q ss_pred             HhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceee
Q 006263          448 FDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT  527 (653)
Q Consensus       448 ~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~  527 (653)
                                  +          ...++.|.+|.+.. |      -..+.|+|+.|....-.|..||      .|+|+|.
T Consensus       203 ------------v----------~~~~~~I~di~~~~-g------~v~i~G~iv~i~~gsgli~rCP------~C~R~l~  247 (358)
T PRK06386        203 ------------L----------ESRNIFIFEIKSPV-G------GITIMGFIVSVGQGSRIFTKCS------VCNKIIE  247 (358)
T ss_pred             ------------c----------CccccchhhhhccC-C------eEEEEEEEEEEcCCcEeEecCc------CCCeEcc
Confidence                        0          02367889998632 1      2678899999999889999999      9999997


Q ss_pred             ecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceE
Q 006263          528 QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQY  607 (653)
Q Consensus       528 ~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~  607 (653)
                      .    +.|+.|++.  .+.+-.++.+.+.|+||.+.+++|++.+++|+|++-+|+.++.- +-+.  ...+=..++|+.|
T Consensus       248 ~----g~C~~HG~v--~~~~dlr~k~vLDDGtg~~~~~l~~e~~e~l~G~~lee~~~~a~-~~~~--~~~i~~~llGr~~  318 (358)
T PRK06386        248 D----GVCKDHPDA--PVYLDIFGYFTISDGTGFVTCYANKDSFLPYININENEFARKAS-SMNP--NMLIKKNLLGKCF  318 (358)
T ss_pred             C----CcCCCCCCC--CCeeEEEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHhh-ccCH--HHHhhhhhcccEE
Confidence            4    699999973  67788888889999999999999999999999999999987552 2222  2222267999999


Q ss_pred             EEEEEEeeeccCceeeEEEEEEEeecCChHHHHHHHHHHH
Q 006263          608 LFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLI  647 (653)
Q Consensus       608 ~f~v~~k~~~y~~e~r~~~~v~~~~~vd~~~e~~~ll~~i  647 (653)
                      .|+..+..+.|.    +.+.|.++..+|- .+.+..-..|
T Consensus       319 ~v~G~~~~~~~~----~~~~~~~~~~~~~-~~~~~~~~~~  353 (358)
T PRK06386        319 SVTGDLRKKDDE----IDMNVISAKSITA-DEIKIIEVEI  353 (358)
T ss_pred             EEEcceEeccCC----eEEEEEEeeeccc-hhhhHHHHHH
Confidence            999999877764    7889999998886 3444444333

>PRK07211 replication factor A; Reviewed

Probab=99.98  E-value=1.6e-31  Score=289.53  Aligned_cols=209  Identities=22%  Similarity=0.351  Sum_probs=182.8

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      +++||++|+|++..|+|+|||+.++++|+|.+.+| +|++++++|.| ++|+|++|+|++.+++| +.|++|+||+|+++
T Consensus       160 ~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~D-eTG~IR~TlW~d~Ad~~-~~le~G~Vv~I~~a  237 (485)
T PRK07211        160 DTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGD-ETGRVRVTLWDDRADLA-EELDAGESVEIVDG  237 (485)
T ss_pred             CCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEc-CCCeEEEEEechhhhhh-ccCCCCCEEEEEee
Confidence            57899999999999999999999999999998887 89999999999 67799999999999999 78999999999999


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCce
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGME  365 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~  365 (653)
                      +|+..+       +.|||+|+..|.|++|.++...+|.    +   .+|.+++.+..|||+|+|++++++.+|++++|++
T Consensus       238 ~Vre~~-------g~~ELsl~~~s~I~~~~dev~~vp~----~---~~I~dl~~g~~vdV~GvV~~v~~~rtf~r~dG~~  303 (485)
T PRK07211        238 YVRERD-------GSLELHVGDRGAVEEVDEDVEYVPD----T---TPIESLEIDETVDIAGVVRSADPKRTFDRDDGSE  303 (485)
T ss_pred             EEEecC-------CcEEEEECCCceEEECCcccccccc----c---ccHhhcCCCCceeEEEEEEEccCcEEEEcCCCCE
Confidence            998753       7899999999999999543233553    2   4455555777999999999999999999888999


Q ss_pred             eeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecC--CCceeccccceEEEEcCChHHH
Q 006263          366 TQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDF--SGKSIGTIPSTQLFINPDFAEA  441 (653)
Q Consensus       366 ~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f--~G~sLs~~~~S~i~inPdipe~  441 (653)
                      ..+|+++|.|+|| +|++||||+.|..         +...+++|+|++++|++|  +|++||+.++|.|.+-.+-|++
T Consensus       304 ~~vr~l~l~D~TG-~IrvTLWg~~A~~---------~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~~~~~  371 (485)
T PRK07211        304 GQVRNVRIQDDTG-DIRVALWGEKADL---------DIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDDGADA  371 (485)
T ss_pred             eEEEEEEEEcCCC-cEEEEEeCccccC---------CCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEccccccc
Confidence            9999999999999 8999999999832         345789999999999998  6899999988888775554443

>PRK15491 replication factor A; Provisional

Probab=99.97  E-value=2.5e-29  Score=269.01  Aligned_cols=277  Identities=19%  Similarity=0.287  Sum_probs=217.7

Q ss_pred             CcceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHH-hhcccCcEEEEe
Q 006263          206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFY-EIIEVGRVYLIS  283 (653)
Q Consensus       206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~-~~l~eG~vy~is  283 (653)
                      .++++|++|+|++++|+|+|||+.++++|+|++.+| +|++++++|.| ++|+|++|+|++.+++|+ +.|++|+||+|+
T Consensus        55 ~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~D-eTG~ir~tlW~~~a~~~~~~~le~G~v~~I~  133 (374)
T PRK15491         55 VDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVAD-ETGSIRLTLWDDLADLIKTGDIEVGKSLNIS  133 (374)
T ss_pred             cccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEc-CCCeEEEEEECchhhhhccCCcCCCCEEEEe
Confidence            468899999999999999999999999999999888 89999999999 888999999999999999 799999999998


Q ss_pred             ceEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCC
Q 006263          284 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNG  363 (653)
Q Consensus       284 ~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g  363 (653)
                      ++    +++.|+.    .||+|++.|.|.++.+ .  + ...|+|++|+||..  .+..|||.|.|+.++++.++++++|
T Consensus       134 ~~----~~~~y~g----~Ei~i~~~~~i~~~~~-~--~-~~~~~~~~I~dl~~--~~~~V~I~g~V~~~~~~r~~~~~~G  199 (374)
T PRK15491        134 GY----AKEGYSG----IEVNIGRYGGISESDE-N--V-KASINSQKISDIKD--GDSDINIVGKVLDISDVRTFQKKDG  199 (374)
T ss_pred             ee----eccCccc----EEEEeCCCceeeeccc-c--c-ccccCcccHHHcCC--CCccEEEEEEEEEccCceEEEecCC
Confidence            76    5667754    6999999999999843 2  2 34679999999975  3446999999999999999999899


Q ss_pred             ceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee--EeecCCCc-eeccccceEEEEcCChHH
Q 006263          364 METQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG--KVNDFSGK-SIGTIPSTQLFINPDFAE  440 (653)
Q Consensus       364 ~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~--rV~~f~G~-sLs~~~~S~i~inPdipe  440 (653)
                      ++...|++.|.|+|| .|++||||+.|..+     +.+  ..+.+|-+.++  |...|+|. .|+....|.|....+.++
T Consensus       200 ~~~~v~~~~l~DetG-~Ir~t~W~~~a~~~-----~~l--~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~~~e  271 (374)
T PRK15491        200 SQGRVRNITIGDETG-KIRVTLWDGKTDLA-----DKL--ENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDRNVE  271 (374)
T ss_pred             CeEEEEEEEEECCCC-eEEEEEecchhccc-----ccC--CCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCcccc
Confidence            988999999999999 69999999998763     112  35788888776  45578776 788877788765332111


Q ss_pred             HHHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcc
Q 006263          441 AHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDR  520 (653)
Q Consensus       441 ~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~  520 (653)
                      +                             ......|++|...        +.+.+.|.|..+.+-. -+..        
T Consensus       272 ~-----------------------------~~~f~~I~dl~~~--------~~~dv~G~V~~v~~~~-~~~~--------  305 (374)
T PRK15491        272 Y-----------------------------EEDFTPIADIIPG--------QPYSIKGAVSGLGDLK-EFTK--------  305 (374)
T ss_pred             c-----------------------------CCCccCHHHcCCC--------CceeEEEEEEEcCCcE-EEEc--------
Confidence            0                             0123457777531        2367888777774310 0000        


Q ss_pred             cccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhh
Q 006263          521 QCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEE  573 (653)
Q Consensus       521 ~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~  573 (653)
                                      +      +-....+-++.|.|.||.+.+++||+.|+.
T Consensus       306 ----------------~------~G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~  336 (374)
T PRK15491        306 ----------------S------DGSENKVSNIYVSDDTGRIRIALWGEKAEL  336 (374)
T ss_pred             ----------------c------CCCEeEEEeEEEEeCCCcEEEEEccccccc
Confidence                            0      122344567899999999999999999975

>PRK15491 replication factor A; Provisional

Probab=99.96  E-value=2.8e-27  Score=253.17  Aligned_cols=205  Identities=17%  Similarity=0.296  Sum_probs=175.0

Q ss_pred             ceeccccCCCCCceEEEEEEEeeccccccccCCCC-ceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGD-GKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       208 ~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~-gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      +.+|++|.++...+.|+|||+.++++|+|.+.+|+ |+++++.|.| ++|+|++|+|++.|++| +.|++|++|+|.++.
T Consensus       166 ~~~I~dl~~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D-etG~Ir~t~W~~~a~~~-~~l~~Gd~V~i~~~~  243 (374)
T PRK15491        166 SQKISDIKDGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGD-ETGKIRVTLWDGKTDLA-DKLENGDSVEIINGY  243 (374)
T ss_pred             cccHHHcCCCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEEC-CCCeEEEEEecchhccc-ccCCCCCEEEEEece
Confidence            56899999998899999999999999999988775 8999999999 67799999999999998 779999999999998


Q ss_pred             EecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCcee
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMET  366 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~  366 (653)
                      ++.     +..+|+|||+|+.+|.|.+|. +.   +.+.|+|++|+||..   +..+||+|+|++++++.+|++++|++.
T Consensus       244 ~r~-----~~~~g~~El~~~~~s~I~~~~-~~---~e~~~~f~~I~dl~~---~~~~dv~G~V~~v~~~~~~~~~~G~~~  311 (374)
T PRK15491        244 ART-----NNYSQEVEIQIGNHGSLRKTD-RN---VEYEEDFTPIADIIP---GQPYSIKGAVSGLGDLKEFTKSDGSEN  311 (374)
T ss_pred             EEE-----eccCCCEEEEeCCCceEEECC-cc---cccCCCccCHHHcCC---CCceeEEEEEEEcCCcEEEEccCCCEe
Confidence            753     345789999999999999994 33   355689999999974   567899999999999999999999999


Q ss_pred             eEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeec-CCC-ceeccccceEEEE
Q 006263          367 QRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVND-FSG-KSIGTIPSTQLFI  434 (653)
Q Consensus       367 ~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~-f~G-~sLs~~~~S~i~i  434 (653)
                      .+|+|+|.|+|| +|++||||+.|...     ..  ...+..|.+-++.+++ |+| ..||.+..|+|.+
T Consensus       312 ~~r~i~l~D~Tg-~Ir~tlWg~~a~~~-----~~--~~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~~  373 (374)
T PRK15491        312 KVSNIYVSDDTG-RIRIALWGEKAELV-----DK--LDIDTPIKIIDAFSKSGYNEDVELSAGNRSRVVV  373 (374)
T ss_pred             EEEeEEEEeCCC-cEEEEEcccccccc-----cc--cCCCCeEEEEEEEEeecCCCcEEEEeCCcceEEe
Confidence            999999999999 59999999998641     11  1234556677777764 655 6899999999875

>PRK14699 replication factor A; Provisional

Probab=99.96  E-value=3.9e-28  Score=266.53  Aligned_cols=206  Identities=21%  Similarity=0.300  Sum_probs=179.2

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      +++||++|+|++++|+|+|||+.++++|+|.+.+| +|+++++.|.| ++|+|++|+|++.+ +|++.|++|++..+.++
T Consensus       275 ~~~~I~~L~~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~D-eTG~Ir~T~W~~~a-~~~~~i~~Gd~v~i~~~  352 (484)
T PRK14699        275 EFTPIEDIKADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGD-STGKIRLTLWDEKT-NFLDEIDFDETVEVLNA  352 (484)
T ss_pred             cccCHHHcCCCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEEC-CCCeEEEEEeCccc-ccccccCCCceEEEEeE
Confidence            57899999999999999999999999999999887 89999999999 67799999999999 88888999999888887


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCce
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGME  365 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~  365 (653)
                      .+     +|+..+++|||+|+..|.|+++.+ .   ..+.++|++|++|.   .+..|||+|+|++++++.+|++++|++
T Consensus       353 y~-----~~~~~~~~~eL~~~~~t~I~~~~~-~---~e~~~~~~~I~die---~~~~vdV~G~V~~v~~~~~~~~~~g~~  420 (484)
T PRK14699        353 YS-----RENTFSQQVELNLGARGIIQKSEK-K---VEYREKFTDIADII---PGESYSVQGKVSEIGELREFEREDGTE  420 (484)
T ss_pred             EE-----EeccCCccEEEEecCceeEeecCC-c---ceeeeccccHHHcc---CCCeeEEEEEEEEcCCcceEEecCCCE
Confidence            75     466778899999999999999843 2   25678999999994   677999999999999999999999999


Q ss_pred             eeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeec-CCC-ceeccccceEEEE
Q 006263          366 TQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVND-FSG-KSIGTIPSTQLFI  434 (653)
Q Consensus       366 ~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~-f~G-~sLs~~~~S~i~i  434 (653)
                      ..+|+++|.|.|| +|+|||||+.|..|     +.+  ..+.-|.+-++.++. |+| ..||.+.+|+|.+
T Consensus       421 ~~vr~i~l~D~TG-~Ir~tlWg~~A~~~-----~~~--~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~  483 (484)
T PRK14699        421 NVVANLQLKDETG-SIRLTLWGEQAYVI-----EDL--DIDSEIQIIDAYARYGLNEEIELSVGNRSRVII  483 (484)
T ss_pred             EEEEEEEEEcCCC-eEEEEEcchhhhhc-----ccc--CCCCeEEEechhhhhcccccEEEEecCceEEEe
Confidence            9999999999999 99999999998763     112  346677777777764 666 4899999998864

>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)

Probab=99.96  E-value=1.4e-28  Score=217.62  Aligned_cols=104  Identities=61%  Similarity=1.062  Sum_probs=101.1

Q ss_pred             eccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263          210 PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP  289 (653)
Q Consensus       210 pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~  289 (653)
                      ||++|+|++.+|+|+|||++||++|.|.+.+++|++|+|+|+|++|++|+|++|++.+++|++.|+||+||+|++|+|++
T Consensus         1 pI~~L~p~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~   80 (104)
T cd04474           1 PISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKV   80 (104)
T ss_pred             ChhHccCCCCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEeccEEee
Confidence            79999999999999999999999999999888999999999998899999999999999999999999999999999999


Q ss_pred             CCCcccCCCCceEEEeccccEEEe
Q 006263          290 AQKNFNHLKNEWEIFLEATSTVDL  313 (653)
Q Consensus       290 a~~~f~~~~~~yei~f~~~T~I~~  313 (653)
                      |+++|++++|+|||.|+.+|.|++
T Consensus        81 a~~~y~~~~~~yeI~f~~~t~~~~  104 (104)
T cd04474          81 ANKKFNTLKNDYEITFNRDTSIIE  104 (104)
T ss_pred             ccccCCCCCCcEEEEECCCcEEeC
Confidence            999999999999999999998864

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct

>PRK14699 replication factor A; Provisional

Probab=99.94  E-value=1.5e-23  Score=230.44  Aligned_cols=277  Identities=19%  Similarity=0.266  Sum_probs=215.5

Q ss_pred             eeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEE
Q 006263          209 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL  287 (653)
Q Consensus       209 ~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V  287 (653)
                      ..|++|.|....-+|+|||+.++++|+|...+| +|++++++|.| ++|+|++|+|++.++ +++.|++|++|.|.++.+
T Consensus       167 ~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igD-eTG~ir~tlW~~~a~-~~~~l~~Gd~v~I~~a~v  244 (484)
T PRK14699        167 QKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGD-ETGTLRVTLWDDKTD-FLNQIEYGDTVELINAYA  244 (484)
T ss_pred             cchhhcCCCCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEc-CCceEEEEEECcccc-cccccCCCCEEEEecceE
Confidence            479999999887899999999999999998777 78999999999 899999999999886 888999999999999988


Q ss_pred             ecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceee
Q 006263          288 KPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQ  367 (653)
Q Consensus       288 ~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~  367 (653)
                      +..  .|+   +.++|+++..|.|.... +...++   .+|++|.+|..  ....++|.|.|++++++.++++++|++..
T Consensus       245 r~~--~~~---~~~el~~~~~s~i~~~~-~~~e~~---~~~~~I~~L~~--~~~~v~I~grV~~~~~~r~~~~~~Gseg~  313 (484)
T PRK14699        245 REN--AFT---QKVELQVGNRSIIRKSE-KKVEYE---EEFTPIEDIKA--DMNNINISGRVLDISEVRTFEKKDGSPGR  313 (484)
T ss_pred             eec--ccC---CceEEEecCceEeeccc-cccccc---ccccCHHHcCC--CCceeEEEEEEEEcCCCeEEEcCCCCeeE
Confidence            763  332   68999999999988873 332332   36788888863  45789999999999999999988898999


Q ss_pred             EEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEee--cCCCc-eeccccceEEEEcCChHHHHHH
Q 006263          368 RRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVN--DFSGK-SIGTIPSTQLFINPDFAEAHEL  444 (653)
Q Consensus       368 kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~--~f~G~-sLs~~~~S~i~inPdipe~~~l  444 (653)
                      .+++.|.|+|| .|++||||+.|..+     +.+  ..++++-+.++.++  .|++. .|+....|.|...++-.++   
T Consensus       314 v~~~~l~DeTG-~Ir~T~W~~~a~~~-----~~i--~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~e~---  382 (484)
T PRK14699        314 VGNLLLGDSTG-KIRLTLWDEKTNFL-----DEI--DFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKVEY---  382 (484)
T ss_pred             EEEEEEECCCC-eEEEEEeCcccccc-----ccc--CCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCccee---
Confidence            99999999999 79999999998431     112  24677888888776  45564 7888888877655543211   


Q ss_pred             HHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccc
Q 006263          445 REWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNK  524 (653)
Q Consensus       445 ~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~K  524 (653)
                                                ...+..|++|..        ...+.|.|+|..+..-.                .
T Consensus       383 --------------------------~~~~~~I~die~--------~~~vdV~G~V~~v~~~~----------------~  412 (484)
T PRK14699        383 --------------------------REKFTDIADIIP--------GESYSVQGKVSEIGELR----------------E  412 (484)
T ss_pred             --------------------------eeccccHHHccC--------CCeeEEEEEEEEcCCcc----------------e
Confidence                                      013456888832        23578999999886421                0


Q ss_pred             eeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhh
Q 006263          525 KVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEI  574 (653)
Q Consensus       525 Kv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~l  574 (653)
                      -...               .-.....-++.|.|.||++++++||+.|+++
T Consensus       413 ~~~~---------------~g~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~  447 (484)
T PRK14699        413 FERE---------------DGTENVVANLQLKDETGSIRLTLWGEQAYVI  447 (484)
T ss_pred             EEec---------------CCCEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence            0000               1134566789999999999999999999864

>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair

Probab=99.93  E-value=8.2e-26  Score=197.81  Aligned_cols=95  Identities=47%  Similarity=0.822  Sum_probs=83.2

Q ss_pred             CCHHHHHHHhC-CCCCCCCeEEEEEEEEcCC----CCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEEeeeE
Q 006263            5 LTPNSISLING-GDVNSKPLVQVMDIKLIGS----TQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYI   79 (653)
Q Consensus         5 Lt~Gai~~i~~-~~~~~~pvvQVl~ik~~~~----~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl~~y~   79 (653)
                      ||+|||++|++ ++...+|||||+++|+++.    +.+|||++||||.|+++|||+||||+++++|+|++||||||++|.
T Consensus         1 LT~Gai~~I~~~~~~~~~pvlQVl~~k~i~~~~~~~~~RyR~~lSDG~~~~~amLatqln~lv~~g~l~~~siirl~~y~   80 (101)
T PF04057_consen    1 LTPGAIEAIFSSGDVNDNPVLQVLNIKKINSKQGGGSDRYRLVLSDGVHSIQAMLATQLNHLVESGELQKGSIIRLKQYT   80 (101)
T ss_dssp             S-TTHHHHHHHHTSSS--TEEEEEEEEEE----TTS--EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-EEEEEEEE
T ss_pred             CChHHHHHHHhCCCCCCCcEEEEEeeEEccCCCCCCCceEEEEEEChHHHHHHHhHHHhHHHHhcCCcccCCEEEEeEEE
Confidence            89999999999 6667899999999999953    579999999999999999999999999999999999999999999


Q ss_pred             eeeec-CeEEEEEEeeeEeec
Q 006263           80 CSTVQ-NRKIIVVLNMETIIL   99 (653)
Q Consensus        80 ~~~~~-~k~~iii~~~evl~~   99 (653)
                      |+.++ +|+++||+++||+.+
T Consensus        81 ~n~v~~~k~iiiil~leVv~~  101 (101)
T PF04057_consen   81 CNTVKNGKKIIIILDLEVVQS  101 (101)
T ss_dssp             EEESTTSSEEEEEEEEEEEE-
T ss_pred             EeeccCCCEEEEEEeeEEEeC
Confidence            99999 999999999999863

The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.

>cd04477 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 (also called RPA70)

Probab=99.90  E-value=2.9e-24  Score=186.14  Aligned_cols=91  Identities=41%  Similarity=0.744  Sum_probs=85.5

Q ss_pred             HHHHHHhCCCC---CCCCeEEEEEEEEcCC---CCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEEeeeEee
Q 006263            8 NSISLINGGDV---NSKPLVQVMDIKLIGS---TQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICS   81 (653)
Q Consensus         8 Gai~~i~~~~~---~~~pvvQVl~ik~~~~---~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl~~y~~~   81 (653)
                      |||++|++++.   ...|||||+++|++..   +.+|||++||||.|+++|||+||||+++++|+|++||||||++|.|+
T Consensus         1 Gai~~i~~~~~~~~~~~PvlQv~~ik~i~~~~~~~~RyRi~lSDG~~~~~amLatqln~~v~~g~l~~~sIirl~~y~~~   80 (97)
T cd04477           1 GALAAIFNGEDRSNVIKPVLQVLNIKKIDSSNGSSERYRILLSDGVYYVQAMLATQLNPLVESGQLQRGSIIRLKRFICN   80 (97)
T ss_pred             ChHHHhhcCCCcCCCCCCEEEEEEEEEccCCCCCcceEEEEEEChhHHHHHHHhhhhhhHHhcCCccCCcEEEECeEEEE
Confidence            89999999876   5789999999999962   56899999999999999999999999999999999999999999999


Q ss_pred             eecCeEEEEEEeeeEee
Q 006263           82 TVQNRKIIVVLNMETII   98 (653)
Q Consensus        82 ~~~~k~~iii~~~evl~   98 (653)
                      .+++|+++||+|+||+.
T Consensus        81 ~i~~k~viiIldlevl~   97 (97)
T cd04477          81 VIKGKRILIILDLEVVQ   97 (97)
T ss_pred             EecCcEEEEEEeeEEeC
Confidence            99999999999999974

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C.

>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)

Probab=99.87  E-value=7.3e-22  Score=174.08  Aligned_cols=100  Identities=50%  Similarity=0.790  Sum_probs=92.9

Q ss_pred             cccEEEEEEEecCceeEEecC-CceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC
Q 006263          342 IVDVIGIVISVNPSVPILRKN-GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS  420 (653)
Q Consensus       342 ~vDVIGvV~~v~~~~~i~~k~-g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~  420 (653)
                      +|||+|+|++++++++|++|+ |++..+|+|+|.|+|+.++.|||||+.|..+        ....++||+|+++||++|+
T Consensus         1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~--------~~~~~~vv~~~~~~i~~~~   72 (101)
T cd04475           1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELF--------DGSENPVIAIKGVKVSEFN   72 (101)
T ss_pred             CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhc--------ccCCCCEEEEEeeEEEecC
Confidence            589999999999999999997 9999999999999999999999999998774        2223899999999999999


Q ss_pred             CceeccccceEEEEcCChHHHHHHHHHHh
Q 006263          421 GKSIGTIPSTQLFINPDFAEAHELREWFD  449 (653)
Q Consensus       421 G~sLs~~~~S~i~inPdipe~~~l~~w~~  449 (653)
                      |++|+++.+|+|++||++||+.+|+.||.
T Consensus        73 ~~~l~~~~~s~i~~np~~~e~~~l~~w~~  101 (101)
T cd04475          73 GKSLSTGSSSTIIINPDIPEAHKLRGWYD  101 (101)
T ss_pred             CeEEeecCceeEEECCCcHHHHHHHHhhC
Confidence            99999999999999999999999999984

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona

>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)

Probab=99.83  E-value=4.9e-20  Score=163.85  Aligned_cols=101  Identities=27%  Similarity=0.500  Sum_probs=91.0

Q ss_pred             cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEE-eeEeecCCC-
Q 006263          344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVK-SGKVNDFSG-  421 (653)
Q Consensus       344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik-~~rV~~f~G-  421 (653)
                      ||||+|++|++++++..+ |++..||+|+|+|.++.++.|||||++|.+|...+..  ....+||||+. ++||++|+| 
T Consensus         1 DviG~i~~v~~~~~~~~~-~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~--~~~~~~VVav~~~~rV~~~~g~   77 (106)
T cd04481           1 DVIGVIVDVGPLEELPPV-NKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQS--AGNGEPVVAVLRFWKIKEYKGP   77 (106)
T ss_pred             CeeEEEEEecceEecccC-CccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHH--hCCCCcEEEEEEeEEEEEEcCC
Confidence            899999999999999988 8899999999999999999999999999998766543  24578999975 599999997 


Q ss_pred             ceeccc-cceEEEEcCChHHHHHHHHH
Q 006263          422 KSIGTI-PSTQLFINPDFAEAHELREW  447 (653)
Q Consensus       422 ~sLs~~-~~S~i~inPdipe~~~l~~w  447 (653)
                      ++||+. ++|++++||++||+.+|+..
T Consensus        78 ~~ls~~~~~s~v~inp~ipe~~~~~~~  104 (106)
T cd04481          78 KSLSNSFGASKVYINPDIPEVPEIKMS  104 (106)
T ss_pred             cEEEcCCCceEEEECCCcHHHHHHHhh
Confidence            799988 99999999999999999864

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.

>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)

Probab=99.78  E-value=5.8e-19  Score=150.85  Aligned_cols=86  Identities=21%  Similarity=0.340  Sum_probs=80.6

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCce
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEW  301 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~y  301 (653)
                      +|+|||+|+|+.+...    +|+.++|+|+|++|++|+|++|++.+++|+++|+||+||+|++|.|.+++++|+.++|+|
T Consensus         1 ~I~Vrv~r~W~~~~~~----~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~y~~~~~~y   76 (86)
T cd04480           1 KICVRVLRLWDVYNNA----SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHPY   76 (86)
T ss_pred             CEEEEEEEEEcCcCCC----CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCcccccCCcE
Confidence            4899999999976532    689999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccccEE
Q 006263          302 EIFLEATSTV  311 (653)
Q Consensus       302 ei~f~~~T~I  311 (653)
                      +|.|..+|+|
T Consensus        77 ~I~f~~~T~V   86 (86)
T cd04480          77 KIKFMSDTVV   86 (86)
T ss_pred             EEEeecCcCC
Confidence            9999998865

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.

>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

Probab=99.68  E-value=1.8e-16  Score=138.03  Aligned_cols=87  Identities=23%  Similarity=0.391  Sum_probs=80.6

Q ss_pred             EEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccc
Q 006263          247 SFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQF  326 (653)
Q Consensus       247 ~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f  326 (653)
                      +|+|+|++|+.|+|+++++.+++|.+.|+||+||.|++|.|.++.+.|++++|+|+|.|..+|.|+++. .....+  .|
T Consensus         1 emvL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~-~~~~~~--~~   77 (95)
T PF02721_consen    1 EMVLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEID-PPSDPP--FF   77 (95)
T ss_pred             CEEEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECC-CCCCCc--eE
Confidence            489999999999999999999999999999999999999999999999999999999999999999994 333333  89


Q ss_pred             eecchhhhhh
Q 006263          327 SFRHISEIES  336 (653)
Q Consensus       327 ~f~~i~~i~~  336 (653)
                      +|++|++|.+
T Consensus        78 ~f~~F~~I~~   87 (95)
T PF02721_consen   78 NFTPFDEILE   87 (95)
T ss_pred             eecCHHHHhc
Confidence            9999999986

>PRK08402 replication factor A; Reviewed

Probab=99.59  E-value=4.6e-14  Score=149.84  Aligned_cols=177  Identities=25%  Similarity=0.393  Sum_probs=141.3

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      ++.+|++|.|+...|++.|||+.+++.|+|....| .|++.+++|.| ++|+|+.|+|++.++++++.|++|+|+.|.++
T Consensus        61 ~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~D-eTG~ir~TlW~~~a~~~~~~l~~Gdvi~I~~a  139 (355)
T PRK08402         61 PLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYD-DTGRARVVLWDAKVAKYYNKINVGDVIKVIDA  139 (355)
T ss_pred             CccCHHHccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEc-CCCeEEEEEechhhhhhcccCCCCCEEEEECC
Confidence            57899999999999999999999999999987655 57899999999 89999999999999999999999999999999


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEeccCCC--CCCCcc------cceecchhhhhhcccCccccEEEEEEEecCcee
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEED--DSIPKQ------QFSFRHISEIESAENNSIVDVIGIVISVNPSVP  357 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~--~~iP~~------~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~  357 (653)
                      .|+...      ...++|.+...|+|...++.+  ..+|.+      .+.+.+|++|..  .+..+.|.|.|+++.+-.-
T Consensus       140 ~V~e~~------~G~~eLsvg~~s~i~~~pd~~ea~~i~~~~~~~~~~~~~k~I~ei~~--gd~~v~v~g~Iv~i~~~~~  211 (355)
T PRK08402        140 QVRESL------SGLPELHINFRARIILNPDDPRVEEIPPLEEVRSYNYTRKKIGELEG--GERFVEVRGTIAKVYRVLV  211 (355)
T ss_pred             EEeecC------CCcEEEEECCCceEEeCCCcccccccccccccccccccccCHHHccc--CCcEEEEEEEEEEEecCee
Confidence            997642      234799999999999886533  234543      367888888865  3456999999999998211


Q ss_pred             ----------EEec----------CCc-e---eeEEEEEEEeCCCCEEEEEEccchhhhh
Q 006263          358 ----------ILRK----------NGM-E---TQRRILNLKDTSGRSVELTLWGDFCNKE  393 (653)
Q Consensus       358 ----------i~~k----------~g~-~---~~kr~i~l~D~s~~~i~vtLWg~~A~~~  393 (653)
                                +...          -|. +   .-...+.|.|.|| .++||||++.|...
T Consensus       212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG-~~~vt~f~e~ae~l  270 (355)
T PRK08402        212 YDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTG-YIRVTLFGDDAAEL  270 (355)
T ss_pred             EecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCC-cEEEEEecHHHHHH
Confidence                      1100          021 1   1233678899999 89999999999774

>PRK07217 replication factor A; Reviewed

Probab=99.56  E-value=4.1e-13  Score=137.59  Aligned_cols=222  Identities=16%  Similarity=0.197  Sum_probs=164.0

Q ss_pred             ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCc
Q 006263          328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP  407 (653)
Q Consensus       328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~  407 (653)
                      .++|.||..  .+.-|+|.|.|..+.+..     .+..  .+.=.|.|+|| +|++|+|++....         .-..+.
T Consensus        72 ~~kI~Di~~--~~~~VsV~aKVl~l~e~~-----~~si--~qvGllgDETG-~IkfT~W~~s~~~---------~leeGd  132 (311)
T PRK07217         72 LVNIADIDE--PEQWVDVTAKVVQLWEPS-----SDSI--AQVGLLGDETG-TIKFTKWAKSDLP---------ELEEGK  132 (311)
T ss_pred             ceeeeecCC--CCCcEEEEEEEEEecCCC-----CCce--EEEEEEEcCCc-eEEEEEccCCCCC---------cccCCC
Confidence            455666643  466899999999999853     2222  22236999999 8999999974211         113689


Q ss_pred             EEEEEeeEeecCCCc-eeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCC
Q 006263          408 VLSVKSGKVNDFSGK-SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLG  486 (653)
Q Consensus       408 Vvaik~~rV~~f~G~-sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg  486 (653)
                      ++-|.++.+++|+|+ +|+.+..|+|...++.=+                                       +.+    
T Consensus       133 ~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~Ie---------------------------------------V~~----  169 (311)
T PRK07217        133 SYLLKNVVTDEYQGRFSVKLNRTTSIEELDEDIE---------------------------------------VGD----  169 (311)
T ss_pred             EEEEEeEEEeeECCEEEEEeCCceEEEeCCCCcc---------------------------------------ccC----
Confidence            999999999999997 899888888876553100                                       000    


Q ss_pred             CCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEE
Q 006263          487 RSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTA  566 (653)
Q Consensus       487 ~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~  566 (653)
                           +-..+.|.|+.|...+-...-||.+    .|+|.+.    .+.|+.|++.  .+.+-.++.+.+.|+||.+.+.+
T Consensus       170 -----~~vei~G~lVdi~~GsglI~rCP~~----~C~Rvl~----~g~C~~HG~v--e~~~DLrik~vlDDGt~~~~~~~  234 (311)
T PRK07217        170 -----DEVEVEGALVDIQSGSGLIKRCPEE----DCTRVLQ----NGRCSEHGKV--EGEFDLRIKGVLDDGEEVQEVIF  234 (311)
T ss_pred             -----ccccceeEEEEEeCCCCCeecCCcc----ccCcccc----CCCCCCCCCc--CCceeeEEEEEEECCCCeEEEEE
Confidence                 0134788999999888788899954    5999994    4799999975  67888999999999999999999


Q ss_pred             echhhhhhhCCCHHHHHHHhhccCChhHHHH-HHHHhcCceEEEEEEEeeeccCceeeEEEEEEEeecC
Q 006263          567 FQESGEEILGCPAKELYMLKYELQDDVRFGE-IIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQV  634 (653)
Q Consensus       567 F~~~ae~llG~sA~el~~~~~e~~d~~~~~~-~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~v  634 (653)
                      -.+..++|.|++-+|+.+|..+--|.....+ +=+.++|+.|.|+...    | |   ..+-+..+++.
T Consensus       235 ~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~----~-g---~~l~~~~~~~~  295 (311)
T PRK07217        235 NREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT----L-G---RYLLADSVEPL  295 (311)
T ss_pred             ChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc----C-C---cEEEeeEeecc
Confidence            9999999999999999998742233333333 3357999999998854    2 2   24455555554

>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]

Probab=99.26  E-value=7.9e-11  Score=120.32  Aligned_cols=213  Identities=16%  Similarity=0.200  Sum_probs=160.1

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      .+++|.+|+|+.+.|+|+++|++.|+..  .+..  |..+.|.|.|+.|.+|+|++......+|.+.|.+|+|+.|..|.
T Consensus         3 ~~~~l~~l~~~~t~w~i~~~vl~v~~~~--~~~~--~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~~~~w~~i~~f~   78 (246)
T KOG0851|consen    3 GFHRLRDLSPSITGWRIQVKVLRVWKKY--SNPN--GEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKIITTFG   78 (246)
T ss_pred             cccchhhcCcCceeeEEEEEEEEEEEec--CCCC--ccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEeeeee
Confidence            4678999999999999999999998743  3332  67899999999999999999999999999999999999999999


Q ss_pred             EecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcc-cceecchhhhhh--cccCccccEEE-EEEEecCceeEEecC
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQ-QFSFRHISEIES--AENNSIVDVIG-IVISVNPSVPILRKN  362 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~-~f~f~~i~~i~~--~~~~~~vDVIG-vV~~v~~~~~i~~k~  362 (653)
                      |.++...++.+.|+|++.|...+.+.....   ..|-. ..+|.++..+.+  .....++|++| .|..|+.+.. +...
T Consensus        79 v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~~~~~v~~~~~-~~~~  154 (246)
T KOG0851|consen   79 VNPNSGQVRATTHSFKINFMDFTVVTSSDT---RLPCTPWGKFTPFDSIVEDKSDKRVLVDLIGVAVYDVSQLTV-TPAI  154 (246)
T ss_pred             ecccccceeeeeeEEEEEeccceeeccCCC---CccceeccccchhhhhhccccCCcEEEEeeceeEEEeeeeEe-cccc
Confidence            999999999999999999988887776522   23322 457777755554  34677999999 6666665532 1124


Q ss_pred             CceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHHH
Q 006263          363 GMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAH  442 (653)
Q Consensus       363 g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~~  442 (653)
                      +.....+.+...+.++       |+.             .. .-.+.+.++..+.+| +++ ...+.+.+..+|+   +.
T Consensus       155 ~~~~~~~~~~~~~~~~-------~~~-------------~~-~~~~c~~~~~~~~~~-~~~-~~l~~~~~~~~~~---l~  208 (246)
T KOG0851|consen  155 DTDVDGFYLTFKICNK-------SKF-------------SK-PVLWCEACGEQATDF-GRK-RSLGGGVIVIAPE---LL  208 (246)
T ss_pred             cCCcceEEEEEeeccc-------ccc-------------cC-ceEEehhhcchHHhh-hhh-eEecCCcEEccch---he
Confidence            5667788888888776       111             11 113334567777778 556 7777788888887   55


Q ss_pred             HHHHHHhcCCC
Q 006263          443 ELREWFDSGGK  453 (653)
Q Consensus       443 ~l~~w~~~~g~  453 (653)
                      .++.|....|.
T Consensus       209 ~~~~~~~~~G~  219 (246)
T KOG0851|consen  209 FWKIWRYFDGK  219 (246)
T ss_pred             eecccccccCC
Confidence            66666666653

>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]

Probab=99.25  E-value=4.5e-11  Score=131.09  Aligned_cols=245  Identities=28%  Similarity=0.380  Sum_probs=177.4

Q ss_pred             CCCcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          204 APARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       204 ~~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      ....+.++..+.||.     ++||+.+.++|+|.+.+|++++|+..|.|++.+.+..+.|.+.        ++|++|.+.
T Consensus       158 ~~~~i~~~~~~~~~~-----~~~v~~g~~ik~~~~~~ge~~~~~~~~~d~~~~~~~~~~~~~~--------~~g~~~~ie  224 (407)
T COG1599         158 DAREIGEESLLSPYQ-----KARVVVGSEIKTFDNQGGESKVFSNELEDEERGVIVFTDWDPS--------QDGDVYRIE  224 (407)
T ss_pred             cccccccccccCccc-----eEEEEecccceeEecCCCccceEeeeecccceeEEEeccCccc--------ccceeeeec
Confidence            445677889999988     9999999999999999999999999999966344444444442        999999999


Q ss_pred             ceEEecCCCcccCCCCceEEEeccc--cEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec
Q 006263          284 KGSLKPAQKNFNHLKNEWEIFLEAT--STVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK  361 (653)
Q Consensus       284 ~~~V~~a~~~f~~~~~~yei~f~~~--T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k  361 (653)
                      +.+|+..++++... +.+++.+...  +.|..+. ....+|...+. ++..++    .+..+|    |+.+.+...+..+
T Consensus       225 ~~~v~~~~~~~~~~-~~~e~~~~~~~~~~i~~~~-~~~~~~~~~~~-~~~~~~----~~~~v~----v~~~~~c~~~~~~  293 (407)
T COG1599         225 GARVKTKNKQPEEN-LAEELVLRVEVRVAIEKAE-REEFVDEVKES-VSLVEA----DGAVVD----VTRVPECERVVRK  293 (407)
T ss_pred             CcEEEEeccccccc-ccceEEEeecceeeccCCC-Cccccceeecc-ccccee----ccceEE----EEECCCceEEEeC
Confidence            99999999998887 9999999887  5555553 22334433332 332222    223333    7778777777666


Q ss_pred             CCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHH
Q 006263          362 NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEA  441 (653)
Q Consensus       362 ~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~  441 (653)
                      .+.....+++.|.|.+| .++|+|||+-+..       .+  +.+++.++++.++.++.|+.+++          .++++
T Consensus       294 ~~~~~~~~~~~l~D~~g-~~rv~~~~~~~e~-------~~--~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~  353 (407)
T COG1599         294 GGCKGHGKDIGLDDLTG-KIRVTLWGDATEV-------LI--NEESVEALKGINVEDASGIALSA----------LDTEA  353 (407)
T ss_pred             CCcccccccceEecCce-EEEEecCCCceEE-------Ee--cccchhheeeeeeeeccchhhhh----------hhhhh
Confidence            66667889999999988 8999999974322       12  35788889999999999987765          57888


Q ss_pred             HHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCC
Q 006263          442 HELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSD  506 (653)
Q Consensus       442 ~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d  506 (653)
                      ..+..||...|+...+...         ....+. +.    +.+..+.+.+++.+.+.|..++.+
T Consensus       354 ~a~~~~~~~~Gk~~~v~g~---------~~~~~~-~~----~~~~~~~~~~~~~~~~~i~~~~~~  404 (407)
T COG1599         354 VALEIWYDILGKYLRVTGD---------AREDRY-LI----ENLVESSTWDDVDVRAEIEALKEE  404 (407)
T ss_pred             hhhhcchhcccceEEeecc---------ccchhh-hh----hhhccccccCccchhheeeeeccc
Confidence            9999999998887655321         011121 11    122334566778888888887754

>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)

Probab=99.11  E-value=4.3e-10  Score=104.74  Aligned_cols=88  Identities=22%  Similarity=0.366  Sum_probs=74.1

Q ss_pred             ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCC---CEEEEEEccchhhhhhhhHHHhhc
Q 006263          326 FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSG---RSVELTLWGDFCNKEGQKLQEMVD  402 (653)
Q Consensus       326 f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~---~~i~vtLWg~~A~~~~~~l~~~~~  402 (653)
                      |+|++|++|.+ ..+..|||||+|+++++...   ..|+. .++.|+|.|.|+   ..|.|+||++.++.+    ..   
T Consensus         1 ~~f~~i~~~~~-~~~~~v~vigVV~~~~~p~~---s~g~d-~~~tl~i~D~S~~~~~~l~v~~F~~~~~~L----P~---   68 (138)
T cd04497           1 YKYTPLSSALK-ESGGSVNVIGVVVDAGPPVR---SKGTD-YCCTLTITDPSLANSDGLTVKLFRPNEESL----PI---   68 (138)
T ss_pred             CceEeHHHHHh-ccCCeEEEEEEEeecCCCcc---cCCCc-EEEEEEEECCCCCCCCcEEEEEECCChhhC----CC---
Confidence            57999999987 57899999999999999754   23554 899999999998   899999999997663    21   


Q ss_pred             cCCCcEEEEEeeEeecCCCceec
Q 006263          403 VGFFPVLSVKSGKVNDFSGKSIG  425 (653)
Q Consensus       403 ~~~~~Vvaik~~rV~~f~G~sLs  425 (653)
                      ...|+||+|++++|..|+|+.+.
T Consensus        69 v~~GDVIll~~~kv~~~~g~~~~   91 (138)
T cd04497          69 VKVGDIILLRRVKIQSYNGKPQG   91 (138)
T ss_pred             CCCCCEEEEEEEEEEEECCceEE
Confidence            24789999999999999998654

POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB

>PRK07218 replication factor A; Provisional

Probab=99.08  E-value=3.7e-09  Score=114.87  Aligned_cols=169  Identities=21%  Similarity=0.237  Sum_probs=132.8

Q ss_pred             ceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEE
Q 006263          208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL  287 (653)
Q Consensus       208 ~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V  287 (653)
                      ..+|.+|.|....-+|.|||+..|+ |+|...+|++.+.+..|-| ++|.|+.|.|++..     .|++|++|.|.++.+
T Consensus       162 ~~kI~DL~~g~~~V~v~g~Vl~~~~-r~f~~~dg~~~v~~giigD-eTG~Ir~tlW~~~~-----~l~~Gd~v~I~na~v  234 (423)
T PRK07218        162 DKKLIDLGPGDRGVNVEARVLELEH-REIDGRDGETTILSGVLAD-ETGRLPFTDWDPLP-----EIEIGASIRIEDAYV  234 (423)
T ss_pred             ccchhhccCCCCceEEEEEEEEecc-eeEEcCCCCeEEEEEEEEC-CCceEEEEEecccc-----cCCCCCEEEEeeeEE
Confidence            4579999999887899999999986 8999888888899999999 89999999999853     489999999999999


Q ss_pred             ecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec------
Q 006263          288 KPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK------  361 (653)
Q Consensus       288 ~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k------  361 (653)
                      +..+       ..++|.+++.|.|+..+ ++..++. .+.-++|.++.+-.....|.|.|.|++|.+-.-+..+      
T Consensus       235 ~e~~-------G~~elnv~~~t~I~~~d-~~i~v~~-~~~~~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~rCP~C~r  305 (423)
T PRK07218        235 REFR-------GVPSVNVSEFTTVEALD-REVSVSK-DPPRLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGR  305 (423)
T ss_pred             eccC-------CeEEEEECCceEEEECC-CCccccC-CccccchhhhhccCCcceEEEEEEEEEeccCCcceecCcCccc
Confidence            7643       35899999999999984 3333433 2455778887764333348999999999987432211      


Q ss_pred             -------------CCceeeEEEEEEEeCCCCEEEEEEccchhhhh
Q 006263          362 -------------NGMETQRRILNLKDTSGRSVELTLWGDFCNKE  393 (653)
Q Consensus       362 -------------~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~  393 (653)
                                   .+....+..+.|-|.+| ++.|+|.++.+...
T Consensus       306 ~v~~~~C~~hG~ve~~~dlrik~vLDDGtg-~~~~~~~~e~~e~l  349 (423)
T PRK07218        306 VIQKGQCRSHGAVEGEDDLRIKAILDDGTG-SVTVILDRELTEIV  349 (423)
T ss_pred             cccCCcCCCCCCcCCeeeeEEEEEEECCCC-eEEEEEChhhhHhH
Confidence                         23334566788888888 89999999988763

>PRK06386 replication factor A; Reviewed

Probab=99.06  E-value=8e-09  Score=109.56  Aligned_cols=163  Identities=18%  Similarity=0.191  Sum_probs=123.8

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      +.++|++|.|....-+|.|||+..|. |.|....+.|++.++.|-| ++|+|+.|.|++       .|++|++|.|.|+.
T Consensus       106 ~~~KI~DL~~g~~~v~V~akVle~~e-~e~~~~g~~~~v~sg~lgD-eTGrIr~TlW~~-------~l~eGd~v~i~na~  176 (358)
T PRK06386        106 KLVKIRDLSLVTPYVSVIGKITGITK-KEYDSDGTSKIVYQGYIED-DTARVRISSFGK-------PLEDNRFVRIENAR  176 (358)
T ss_pred             CccEeEeccCCCCceEEEEEEEEccC-ceEecCCCccEEEEEEEEc-CCCeEEEEEccc-------cccCCCEEEEeeeE
Confidence            35699999999866689999999988 7888555568999999999 899999999986       38999999999998


Q ss_pred             EecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecC-ceeEEe-----
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNP-SVPILR-----  360 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~-~~~i~~-----  360 (653)
                      +...+       ..++|.++..|.|++.+ ++  |. ..-.+.+|.||.+.  +..+-+.|.|++|.+ ..-|.+     
T Consensus       177 v~e~~-------G~~el~v~~~t~I~~~~-~~--ie-v~~~~~~I~di~~~--~g~v~i~G~iv~i~~gsgli~rCP~C~  243 (358)
T PRK06386        177 VSQYN-------GYIEISVGNKSVIKEVE-SD--IN-LESRNIFIFEIKSP--VGGITIMGFIVSVGQGSRIFTKCSVCN  243 (358)
T ss_pred             EEccC-------CeEEEEeCCeEEEEECC-CC--cc-cCccccchhhhhcc--CCeEEEEEEEEEEcCCcEeEecCcCCC
Confidence            76653       35899999999999984 32  33 33357888888763  234888899999886 222221     


Q ss_pred             ----c---------CCceeeEEEEEEEeCCCCEEEEEEccchhhh
Q 006263          361 ----K---------NGMETQRRILNLKDTSGRSVELTLWGDFCNK  392 (653)
Q Consensus       361 ----k---------~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~  392 (653)
                          +         .+....+-.+.|-|.+| .++|+|.++.+.+
T Consensus       244 R~l~~g~C~~HG~v~~~~dlr~k~vLDDGtg-~~~~~l~~e~~e~  287 (358)
T PRK06386        244 KIIEDGVCKDHPDAPVYLDIFGYFTISDGTG-FVTCYANKDSFLP  287 (358)
T ss_pred             eEccCCcCCCCCCCCCeeEEEEEEEEECCCC-eEEEEEChHHhHH
Confidence                1         11222333367777777 8999999999876

>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)

Probab=98.86  E-value=1.5e-08  Score=85.64  Aligned_cols=81  Identities=21%  Similarity=0.312  Sum_probs=70.5

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCce
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEW  301 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~y  301 (653)
                      +|.|||+.+++.|+|.+.+++++++++.|.| ++|.|++++|++.+   .+.|++|++|.|.++.++..+       +.+
T Consensus         1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D-~TG~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~~-------g~~   69 (82)
T cd04491           1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGD-ETGTIRFTLWDEKA---ADDLEPGDVVRIENAYVREFN-------GRL   69 (82)
T ss_pred             CEEEEEEEccCCeEeccCCCeeEEEEEEEEC-CCCEEEEEEECchh---cccCCCCCEEEEEeEEEEecC-------CcE
Confidence            4899999999999998444578999999999 67799999999876   788999999999999987654       569


Q ss_pred             EEEeccccEEEe
Q 006263          302 EIFLEATSTVDL  313 (653)
Q Consensus       302 ei~f~~~T~I~~  313 (653)
                      +|.++..|.|+.
T Consensus        70 ql~i~~~~~i~~   81 (82)
T cd04491          70 ELSVGKNSEIEK   81 (82)
T ss_pred             EEEeCCceEEEE
Confidence            999999998875

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

>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)

Probab=98.86  E-value=2.8e-08  Score=84.01  Aligned_cols=80  Identities=19%  Similarity=0.337  Sum_probs=69.3

Q ss_pred             cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-
Q 006263          344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-  422 (653)
Q Consensus       344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-  422 (653)
                      +|+|.|+++++..+++ ++|++...+++.|.|+|| +|++++|++.+..       .+  ..+.+|.++++++++|+|. 
T Consensus         1 ~v~~~V~~~~~~~~~~-~~g~~~~~~~~~l~D~TG-~i~~~~W~~~~~~-------~~--~~G~vv~i~~~~v~~~~g~~   69 (82)
T cd04491           1 SVEGKVLSISEPREFT-RDGSEGKVQSGLVGDETG-TIRFTLWDEKAAD-------DL--EPGDVVRIENAYVREFNGRL   69 (82)
T ss_pred             CEEEEEEEccCCeEec-cCCCeeEEEEEEEECCCC-EEEEEEECchhcc-------cC--CCCCEEEEEeEEEEecCCcE
Confidence            4899999999999998 889999999999999999 8999999998621       12  4678999999999999985 


Q ss_pred             eeccccceEEEE
Q 006263          423 SIGTIPSTQLFI  434 (653)
Q Consensus       423 sLs~~~~S~i~i  434 (653)
                      .|+....|.|..
T Consensus        70 ql~i~~~~~i~~   81 (82)
T cd04491          70 ELSVGKNSEIEK   81 (82)
T ss_pred             EEEeCCceEEEE
Confidence            888888887764

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

>PRK06461 single-stranded DNA-binding protein; Reviewed

Probab=98.79  E-value=3.7e-08  Score=90.61  Aligned_cols=95  Identities=20%  Similarity=0.261  Sum_probs=77.8

Q ss_pred             ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCc
Q 006263          328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP  407 (653)
Q Consensus       328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~  407 (653)
                      +++|.||..  ....|+++|+|.++++...+.+|.+ ....++++|.|+|| +|++|||++.|..        +  ..+.
T Consensus         4 ~~kI~dL~~--g~~~v~~~~~V~~i~~~~~~~~k~~-~~~v~~~~l~D~TG-~I~~tlW~~~a~~--------l--~~Gd   69 (129)
T PRK06461          4 ITKIKDLKP--GMERVNVTVRVLEVGEPKVIQTKGG-PRTISEAVVGDETG-RVKLTLWGEQAGS--------L--KEGE   69 (129)
T ss_pred             ceEHHHcCC--CCCceEEEEEEEEcCCceEEEeCCC-ceEEEEEEEECCCC-EEEEEEeCCcccc--------C--CCCC
Confidence            566777752  2268999999999999988888844 45688999999999 7999999997644        3  3589


Q ss_pred             EEEEEeeEeecCCCc-eeccccceEEEEcC
Q 006263          408 VLSVKSGKVNDFSGK-SIGTIPSTQLFINP  436 (653)
Q Consensus       408 Vvaik~~rV~~f~G~-sLs~~~~S~i~inP  436 (653)
                      ||.|++++|++|+|+ +|+....|.|..-+
T Consensus        70 vV~I~na~v~~f~G~lqL~i~~~~~i~~~~   99 (129)
T PRK06461         70 VVEIENAWTTLYRGKVQLNVGKYGSISESD   99 (129)
T ss_pred             EEEEECcEEeeeCCEEEEEECCCEEEEECC
Confidence            999999999999997 89988888887533

>PRK06461 single-stranded DNA-binding protein; Reviewed

Probab=98.76  E-value=6e-08  Score=89.18  Aligned_cols=97  Identities=15%  Similarity=0.198  Sum_probs=83.5

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      .+++|++|.|....-.+.++|+.++..|.+....+.+++.++.|.| ++|.|++++|++.++    .|++|+|+.|.++.
T Consensus         3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D-~TG~I~~tlW~~~a~----~l~~GdvV~I~na~   77 (129)
T PRK06461          3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGD-ETGRVKLTLWGEQAG----SLKEGEVVEIENAW   77 (129)
T ss_pred             CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEEC-CCCEEEEEEeCCccc----cCCCCCEEEEECcE
Confidence            4679999999988999999999999999887766667899999999 788999999998654    58899999999998


Q ss_pred             EecCCCcccCCCCceEEEeccccEEEecc
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVDLCT  315 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~  315 (653)
                      +..-+       ...+|.+..++.|..+.
T Consensus        78 v~~f~-------G~lqL~i~~~~~i~~~~   99 (129)
T PRK06461         78 TTLYR-------GKVQLNVGKYGSISESD   99 (129)
T ss_pred             EeeeC-------CEEEEEECCCEEEEECC
Confidence            86532       34899999999999984

>PRK07217 replication factor A; Reviewed

Probab=98.31  E-value=2.7e-05  Score=80.65  Aligned_cols=93  Identities=18%  Similarity=0.204  Sum_probs=75.6

Q ss_pred             CcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      ...++|++|+|...+-+|+|||+..|+.+.      +.....-.|.| ++|+|+.|.|.+.   =.+.|++|++|.|.|+
T Consensus        70 ~~~~kI~Di~~~~~~VsV~aKVl~l~e~~~------~si~qvGllgD-ETG~IkfT~W~~s---~~~~leeGd~~rI~na  139 (311)
T PRK07217         70 SELVNIADIDEPEQWVDVTAKVVQLWEPSS------DSIAQVGLLGD-ETGTIKFTKWAKS---DLPELEEGKSYLLKNV  139 (311)
T ss_pred             CCceeeeecCCCCCcEEEEEEEEEecCCCC------CceEEEEEEEc-CCceEEEEEccCC---CCCcccCCCEEEEEeE
Confidence            357899999999999999999999998553      12223345778 8999999999963   1466999999999999


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEecc
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCT  315 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~  315 (653)
                      .+..-+.       .++|.+++.|+|++..
T Consensus       140 ~v~ey~G-------~~~lnlg~~t~I~~~d  162 (311)
T PRK07217        140 VTDEYQG-------RFSVKLNRTTSIEELD  162 (311)
T ss_pred             EEeeECC-------EEEEEeCCceEEEeCC
Confidence            9876654       4899999999999984

>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]

Probab=98.21  E-value=3.2e-05  Score=85.17  Aligned_cols=188  Identities=19%  Similarity=0.192  Sum_probs=135.7

Q ss_pred             CCCcceeccccCCCCCceEEEEEEEeeccccccccCCCC-ceeEEEEEEeCCCCeEEE-EEchhHHHHHHhhcccCcEEE
Q 006263          204 APARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGD-GKVFSFDLLDSDGGEIRV-TCFNAVVDRFYEIIEVGRVYL  281 (653)
Q Consensus       204 ~~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~-gk~f~~~L~D~~g~~I~a-t~f~~~~~kf~~~l~eG~vy~  281 (653)
                      +...+.+|+++.+.+.+-.+.+||...+..+.|....|. +++.+..+.| +.|.++. +.|+..+.   ..++.|+++.
T Consensus        45 ~~~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~D-etg~v~~~~~~~~~a~---~~~e~Gdv~~  120 (407)
T COG1599          45 AMESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGD-ETGSVKTVTLWNIAAL---EKLEPGDVIR  120 (407)
T ss_pred             chhhcccccccchhhccccEEEEECccccceeeecccccccceEEEEEec-CCCCEEEEeecccccc---ccCCccceEE
Confidence            445678999999999999999999999998888877775 8899999999 8899998 78887543   4689999999


Q ss_pred             EeceEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec
Q 006263          282 ISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK  361 (653)
Q Consensus       282 is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k  361 (653)
                      |.++.+....       ...++.++..+.+...++.. ..+...+.-..+.++..+   ...+ .+.|..-+++.++...
T Consensus       121 i~~~~~~~~~-------~~~~~~~~~~~~v~~~~~~~-~~~~~~~~~~~i~~~~~~---~~~~-~~~v~~g~~ik~~~~~  188 (407)
T COG1599         121 IRNAYTSLYR-------GGKRLSVGRVGSVADVDDEE-DEARESEDAREIGEESLL---SPYQ-KARVVVGSEIKTFDNQ  188 (407)
T ss_pred             ecCccccccc-------CceeeecccccccccCchhh-cccccccccccccccccc---Cccc-eEEEEecccceeEecC
Confidence            9998764432       34788888888888874321 222222233333333322   2223 6677777777777643


Q ss_pred             CCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263          362 NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       362 ~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                       +.+...+...|.|++-..+.+++|....              .+++.-+-+++|.-|.+.
T Consensus       189 -~ge~~~~~~~~~d~~~~~~~~~~~~~~~--------------~g~~~~ie~~~v~~~~~~  234 (407)
T COG1599         189 -GGESKVFSNELEDEERGVIVFTDWDPSQ--------------DGDVYRIEGARVKTKNKQ  234 (407)
T ss_pred             -CCccceEeeeecccceeEEEeccCcccc--------------cceeeeecCcEEEEeccc
Confidence             4445677888889884489999998861              357777888888887764

>TIGR00617 rpa1 replication factor-a protein 1 (rpa1)

Probab=98.05  E-value=0.00068  Score=78.15  Aligned_cols=177  Identities=13%  Similarity=0.064  Sum_probs=116.4

Q ss_pred             eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263          327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF  406 (653)
Q Consensus       327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~  406 (653)
                      .|++|++|....  .-.-|.|.|+..+++..+..++| +....+|.|.|++| .|++|+|++.|..|...|      ..|
T Consensus       179 ~~~pI~~L~py~--~~wtIkaRV~~Ks~ir~~~~~~g-egkvfsv~L~Degg-~Irat~f~~~~dkf~~~l------~eG  248 (608)
T TIGR00617       179 RVMPIASLSPYQ--NKWTIKARVTNKSEIRTWSNARG-EGKLFNVELLDESG-EIRATAFNEQADKFYDII------QEG  248 (608)
T ss_pred             ceEEHHHCCCCC--CceEEEEEEEeccccceecCCCC-CceeeEEEEecCCC-eEEEEECchHHHHHhhhc------ccC
Confidence            588888887643  24788999999999998876554 23566899999655 999999999998864433      258


Q ss_pred             cEEEEEeeEeecCCCc--------eeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHH
Q 006263          407 PVLSVKSGKVNDFSGK--------SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVS  478 (653)
Q Consensus       407 ~Vvaik~~rV~~f~G~--------sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~  478 (653)
                      .|+.|.+++|+..+++        .|.....|.|..-+|.+.                   +.       .......+|+
T Consensus       249 ~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~-------------------iP-------~~~~~f~~i~  302 (608)
T TIGR00617       249 KVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETA-------------------IP-------KIQFNFVKID  302 (608)
T ss_pred             CEEEECceEEEEccccccCCCCCEEEEECCCeEEEECCCccc-------------------CC-------cccccceEHH
Confidence            9999999999765442        234444555554332110                   00       0112345788


Q ss_pred             hhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEEEEEEeC
Q 006263          479 QIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQ  558 (653)
Q Consensus       479 ~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~  558 (653)
                      +|....     ...+..|.|.|..+..-.- .....                             +-....+.++.|.|.
T Consensus       303 dI~~~~-----~~~~VDVIGvV~~v~~~~~-i~~k~-----------------------------~g~~~~kR~i~L~D~  347 (608)
T TIGR00617       303 DIGGYE-----GNSLVDVIGIVQSVSPTQT-ITSRK-----------------------------NNKEFPKRDITLVDD  347 (608)
T ss_pred             Hhhhhc-----CCCCccEEEEEeEecCceE-EEEcC-----------------------------CCCeeeeEEEEEEeC
Confidence            887532     2236778888888864210 00000                             112245678999999


Q ss_pred             CC-eEEEEEechhhhhh
Q 006263          559 TG-LTWVTAFQESGEEI  574 (653)
Q Consensus       559 Tg-~~~~~~F~~~ae~l  574 (653)
                      || ++.+++||+.|+.+
T Consensus       348 sg~sI~vTLWG~~A~~~  364 (608)
T TIGR00617       348 SGKSVRVTLWGDDATKF  364 (608)
T ss_pred             CCCEEEEEEEhhhhhhc
Confidence            99 58999999999764

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>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)

Probab=97.84  E-value=0.00012  Score=64.81  Aligned_cols=97  Identities=16%  Similarity=0.095  Sum_probs=70.8

Q ss_pred             hhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEE
Q 006263          331 ISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLS  410 (653)
Q Consensus       331 i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vva  410 (653)
                      |++|..  .....-+.|.|+..+++..++.++ .+....+|.|.|+.|.+|++|+|++.|..|...|.      .|.|+.
T Consensus         2 I~~L~p--~~~~~~I~~rV~~k~~~~~f~~~~-~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~------eG~vy~   72 (104)
T cd04474           2 ISSLNP--YQNKWTIKARVTNKSDIRTWSNAR-GEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLE------VGKVYY   72 (104)
T ss_pred             hhHccC--CCCcEEEEEEEeeccccccccCCC-CCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccc------cccEEE
Confidence            455543  223578999999999999887654 23445689999997779999999999888644432      589999


Q ss_pred             EEeeEeecCCCceeccccceEEEEcC
Q 006263          411 VKSGKVNDFSGKSIGTIPSTQLFINP  436 (653)
Q Consensus       411 ik~~rV~~f~G~sLs~~~~S~i~inP  436 (653)
                      |.+++|+.-+++.-.+...-.|.++.
T Consensus        73 i~~~~V~~a~~~y~~~~~~yeI~f~~   98 (104)
T cd04474          73 ISKGSVKVANKKFNTLKNDYEITFNR   98 (104)
T ss_pred             EeccEEeeccccCCCCCCcEEEEECC
Confidence            99999987766544444445555554

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct

>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

Probab=97.82  E-value=6e-05  Score=61.85  Aligned_cols=70  Identities=31%  Similarity=0.509  Sum_probs=56.2

Q ss_pred             eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCc
Q 006263          221 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNE  300 (653)
Q Consensus       221 w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~  300 (653)
                      ++|.|+|+++.  +      +.++++.++|.| .+|.|++.+|++...++.+.|++|+++.+. |.++..+..      +
T Consensus         1 V~v~G~V~~~~--~------~~~~~~~~~l~D-~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~------~   64 (75)
T PF01336_consen    1 VTVEGRVTSIR--R------SGGKIVFFTLED-GTGSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNGG------E   64 (75)
T ss_dssp             EEEEEEEEEEE--E------EETTEEEEEEEE-TTEEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETTS------S
T ss_pred             CEEEEEEEEEE--c------CCCCEEEEEEEE-CCccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECCc------c
Confidence            57999999986  2      235789999999 679999999999999999999999999999 888766432      3


Q ss_pred             eEEEec
Q 006263          301 WEIFLE  306 (653)
Q Consensus       301 yei~f~  306 (653)
                      ++|...
T Consensus        65 ~~l~~~   70 (75)
T PF01336_consen   65 LELIVP   70 (75)
T ss_dssp             EEEEEE
T ss_pred             EEEEEC
Confidence            555554

The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....

>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 []

Probab=97.67  E-value=0.00046  Score=64.97  Aligned_cols=86  Identities=20%  Similarity=0.359  Sum_probs=63.5

Q ss_pred             ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCC-------CEEEEEEccchhhhhhhhHHHh
Q 006263          328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSG-------RSVELTLWGDFCNKEGQKLQEM  400 (653)
Q Consensus       328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~-------~~i~vtLWg~~A~~~~~~l~~~  400 (653)
                      |+++++.. ...+..|||||+|++..+.....+| |+ --+..|+|.|.|.       ..|.|.++-...+.+    .. 
T Consensus         1 ~~~l~~~~-~~~~~~vnvigVV~~~~~p~~~~t~-g~-D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~L----P~-   72 (146)
T PF02765_consen    1 YTPLSTAK-EKFGKFVNVIGVVVDFSPPNPKKTR-GT-DYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESL----PN-   72 (146)
T ss_dssp             BCCGGGSC-TTSSEEEEEEEEEEEEEEECTEEES-SS-CEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHS----CT-
T ss_pred             Cccchhhh-hcCCCEEEEEEEEEEccCCcceEcC-CC-cEEEEEEEECCCCCccccccCCEEEEEECCCHHHC----CC-
Confidence            44555222 3467899999999999998544454 43 3578999999985       689999998775542    21 


Q ss_pred             hccCCCcEEEEEeeEeecCCCc
Q 006263          401 VDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       401 ~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                      . ...|+||.++.++|..|+|+
T Consensus        73 v-~~~GDii~l~r~kv~~~~~~   93 (146)
T PF02765_consen   73 V-KSVGDIIRLRRVKVQSYNGK   93 (146)
T ss_dssp             T-CSTTHEEEEEEEEEEEETTE
T ss_pred             C-CCCCCEEEEEEEEEEEECCE
Confidence            1 12489999999999999997

It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....

>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)

Probab=97.25  E-value=0.0019  Score=56.71  Aligned_cols=84  Identities=14%  Similarity=0.152  Sum_probs=66.9

Q ss_pred             EEEEEEEeeccccccccCC-C-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCC
Q 006263          222 AIKARVTAKGDLRRYNNAR-G-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKN  299 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~-g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~  299 (653)
                      -|.|.|+..++++++.... | ++...++.|.|+.+..|.+|+|++.++.|....  |.|+.|.++++..-+        
T Consensus         3 Dvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~--~~vv~~~~~~i~~~~--------   72 (101)
T cd04475           3 DVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSE--NPVIAIKGVKVSEFN--------   72 (101)
T ss_pred             eEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCC--CCEEEEEeeEEEecC--------
Confidence            3789999999999987654 3 567889999997667999999999999998765  999999999885433        


Q ss_pred             ceEEEeccccEEEecc
Q 006263          300 EWEIFLEATSTVDLCT  315 (653)
Q Consensus       300 ~yei~f~~~T~I~~~~  315 (653)
                      ...+.....|.|..-+
T Consensus        73 ~~~l~~~~~s~i~~np   88 (101)
T cd04475          73 GKSLSTGSSSTIIINP   88 (101)
T ss_pred             CeEEeecCceeEEECC
Confidence            1456666678877653

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona

>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)

Probab=96.74  E-value=0.0076  Score=48.24  Aligned_cols=60  Identities=37%  Similarity=0.614  Sum_probs=49.6

Q ss_pred             EEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263          223 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP  289 (653)
Q Consensus       223 I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~  289 (653)
                      |.|+|+.....++     | +..+.+.|.|..|+.|.+++|.+..+++...+++|+++.+. +.|..
T Consensus         2 v~g~v~~~~~~~~-----~-~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~   61 (75)
T cd03524           2 IVGIVVAVEEIRT-----E-GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKK   61 (75)
T ss_pred             eEEEEEeeccccc-----C-CeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEe
Confidence            6788887766544     1 35788999996559999999999999999999999999999 88854

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco

>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]

Probab=96.20  E-value=0.011  Score=52.73  Aligned_cols=70  Identities=21%  Similarity=0.320  Sum_probs=56.8

Q ss_pred             ceeccccCCCCCceEEEEEEEeeccccccccCCCCc-eeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       208 ~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~g-k~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      ..+|++|.|+.++.++..-|+.-...+.-+    +| ++-++-+.| ++|.|++.+|+|    +-..|+.|+++.++++-
T Consensus         4 ~i~ikdi~P~~kN~~v~fIvl~~g~~tkTk----dg~~v~~~kVaD-~TgsI~isvW~e----~~~~~~PGDIirLt~Gy   74 (134)
T KOG3416|consen    4 MIFIKDIKPGLKNINVTFIVLEYGRATKTK----DGHEVRSCKVAD-ETGSINISVWDE----EGCLIQPGDIIRLTGGY   74 (134)
T ss_pred             chhHhhcChhhhcceEEEEEEeeceeeecc----CCCEEEEEEEec-ccceEEEEEecC----cCcccCCccEEEecccc
Confidence            468999999999998888887766554432    35 688889999 899999999996    45688999999999863

>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]

Probab=96.10  E-value=0.027  Score=50.30  Aligned_cols=83  Identities=19%  Similarity=0.310  Sum_probs=59.6

Q ss_pred             chhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEE
Q 006263          330 HISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVL  409 (653)
Q Consensus       330 ~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vv  409 (653)
                      +|.||...-+  .+.|+=+|.+.+..+.  +|+|++  .|...+.|+|| +|.+.+|++....        |  ..++||
T Consensus         6 ~ikdi~P~~k--N~~v~fIvl~~g~~tk--Tkdg~~--v~~~kVaD~Tg-sI~isvW~e~~~~--------~--~PGDIi   68 (134)
T KOG3416|consen    6 FIKDIKPGLK--NINVTFIVLEYGRATK--TKDGHE--VRSCKVADETG-SINISVWDEEGCL--------I--QPGDII   68 (134)
T ss_pred             hHhhcChhhh--cceEEEEEEeeceeee--ccCCCE--EEEEEEecccc-eEEEEEecCcCcc--------c--CCccEE
Confidence            3555554222  3456667777776643  567874  58899999999 8999999987544        3  368999


Q ss_pred             EEEeeEeecCCCc-eeccccc
Q 006263          410 SVKSGKVNDFSGK-SIGTIPS  429 (653)
Q Consensus       410 aik~~rV~~f~G~-sLs~~~~  429 (653)
                      -+++.-.+-|+|. .|.++.+
T Consensus        69 rLt~Gy~Si~qg~LtL~~GK~   89 (134)
T KOG3416|consen   69 RLTGGYASIFQGCLTLYVGKG   89 (134)
T ss_pred             EecccchhhhcCceEEEecCC
Confidence            9999999889874 6766544

>PF06075 DUF936: Plant protein of unknown function (DUF936); InterPro: IPR010341 This family consists of several hypothetical proteins from plants

Probab=95.97  E-value=0.014  Score=66.43  Aligned_cols=105  Identities=16%  Similarity=0.193  Sum_probs=84.3

Q ss_pred             CCHHHHHHHhCCCC--------CCCCeEEEEEEEEcCC-----CCceEEEEEecccceeeeeecccchhhcccCCcccCc
Q 006263            5 LTPNSISLINGGDV--------NSKPLVQVMDIKLIGS-----TQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGS   71 (653)
Q Consensus         5 Lt~Gai~~i~~~~~--------~~~pvvQVl~ik~~~~-----~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~s   71 (653)
                      ||||.|.+++++-.        .-.+.|||++|-+.-.     .+.=|.|-|||+.|....-|...=++||.++.|+.|.
T Consensus         1 L~pGvL~klL~~mn~~~k~~gehRs~lLQV~~IvPaL~~~~l~p~~gF~lkvSDsshs~Yvsl~~~~~dlils~klqlGq   80 (579)
T PF06075_consen    1 LTPGVLLKLLQHMNSDVKVTGEHRSSLLQVTSIVPALAGSDLWPNQGFYLKVSDSSHSTYVSLPDEDDDLILSNKLQLGQ   80 (579)
T ss_pred             CCchHHHHHHHhcCCCCccCCcccccceeeeeeeecccccccCcCCceEEEecccccceeeecChhcccceecCCccccc
Confidence            89999999998532        2347999999998821     1234999999999999988998889999999999999


Q ss_pred             EEEEeeeEeeeecCeEEEEEEeeeEeecCCcccCCCcccccc
Q 006263           72 VVQLIDYICSTVQNRKIIVVLNMETIILDCEPIGNPKIFSES  113 (653)
Q Consensus        72 IIkl~~y~~~~~~~k~~iii~~~evl~~~~~~iG~P~~~~~~  113 (653)
                      +|-+.++..    +..+=++..+..|..-..-+|+|.++-..
T Consensus        81 fi~vdrle~----~~PvP~l~g~rp~pgR~pcvg~P~dl~~~  118 (579)
T PF06075_consen   81 FIYVDRLEA----ASPVPVLRGVRPVPGRHPCVGNPEDLVAT  118 (579)
T ss_pred             eEEEccccc----CCCCceeecCccCCCCCCCCCCChhhhhc
Confidence            998887653    45777888888888655569999887643

The function of this family is unknown.

>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1)

Probab=95.10  E-value=0.086  Score=45.51  Aligned_cols=68  Identities=22%  Similarity=0.434  Sum_probs=44.6

Q ss_pred             cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhh--h--------------hhHHHhhccCCCc
Q 006263          344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE--G--------------QKLQEMVDVGFFP  407 (653)
Q Consensus       344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~--~--------------~~l~~~~~~~~~~  407 (653)
                      |++|+|+++.+-.          .+..++|.|.|| .|+|.+|.......  .              ....+.+  ..+.
T Consensus         1 ~ivG~V~sv~~~~----------~~~~~tLdDgTG-~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i--~~G~   67 (92)
T cd04483           1 DILGTVVSRRERE----------TFYSFGVDDGTG-VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVL--EIGD   67 (92)
T ss_pred             CeEEEEEEEEecC----------CeEEEEEecCCc-eEEEEEEcCcCccccccccccccccccccccccccccc--CCCC
Confidence            6899999886532          357899999999 79999998753110  0              0001112  2456


Q ss_pred             EEEEEeeEeecCCCc-eec
Q 006263          408 VLSVKSGKVNDFSGK-SIG  425 (653)
Q Consensus       408 Vvaik~~rV~~f~G~-sLs  425 (653)
                      +|-++ ++|+.|+|+ .|.
T Consensus        68 vvrV~-G~i~~frg~~ql~   85 (92)
T cd04483          68 LLRVR-GSIRTYRGEREIN   85 (92)
T ss_pred             EEEEE-EEEeccCCeeEEE
Confidence            66666 678899985 554

Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.

>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)

Probab=95.06  E-value=0.28  Score=43.39  Aligned_cols=68  Identities=12%  Similarity=0.195  Sum_probs=52.2

Q ss_pred             EEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhc----ccCcEEEEec-eEEecCC
Q 006263          224 KARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEII----EVGRVYLISK-GSLKPAQ  291 (653)
Q Consensus       224 ~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l----~eG~vy~is~-~~V~~a~  291 (653)
                      .|-|+.-+++.+......+.....+.|.|..+..+++|+|++.|..|...+    ..+-|+.+-. .+|+.-+
T Consensus         3 iG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~   75 (106)
T cd04481           3 IGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYK   75 (106)
T ss_pred             eEEEEEecceEecccCCccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEc
Confidence            455666666666554334556789999998889999999999999999887    4677887766 7887655

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.

>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)

Probab=95.02  E-value=0.11  Score=48.42  Aligned_cols=83  Identities=14%  Similarity=0.257  Sum_probs=65.6

Q ss_pred             cceeccccC-CCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC---CeEEEEEchhHHHHHHhhcccCcEEEE
Q 006263          207 RIIPIAALN-PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG---GEIRVTCFNAVVDRFYEIIEVGRVYLI  282 (653)
Q Consensus       207 ~~~pI~~L~-p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g---~~I~at~f~~~~~kf~~~l~eG~vy~i  282 (653)
                      .++||++|. .....-.|.|-|+...+.+.   .+|.....+|.|+|..+   ..+++++|.+..+.|-.. .+|+|+.+
T Consensus         2 ~f~~i~~~~~~~~~~v~vigVV~~~~~p~~---s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v-~~GDVIll   77 (138)
T cd04497           2 KYTPLSSALKESGGSVNVIGVVVDAGPPVR---SKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIV-KVGDIILL   77 (138)
T ss_pred             ceEeHHHHHhccCCeEEEEEEEeecCCCcc---cCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCC-CCCCEEEE
Confidence            367888887 33356789999998888664   23444678899999766   779999999998887665 99999999


Q ss_pred             eceEEecCCCc
Q 006263          283 SKGSLKPAQKN  293 (653)
Q Consensus       283 s~~~V~~a~~~  293 (653)
                      ++++|+.-+.+
T Consensus        78 ~~~kv~~~~g~   88 (138)
T cd04497          78 RRVKIQSYNGK   88 (138)
T ss_pred             EEEEEEEECCc
Confidence            99999887755

POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB

>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)

Probab=95.01  E-value=0.15  Score=40.58  Aligned_cols=65  Identities=28%  Similarity=0.520  Sum_probs=46.6

Q ss_pred             cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263          344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                      +|.|+|.++.+..+     |+  ....++|.|.+|..++|++|.+....+.    ..  ...+.++.+. +++..++|+
T Consensus         1 ~v~g~v~~~~~~~~-----~~--~~~~~~l~D~~~~~i~~~~~~~~~~~~~----~~--~~~g~~v~v~-g~v~~~~~~   65 (75)
T cd03524           1 TIVGIVVAVEEIRT-----EG--KVLIFTLTDGTGGTIRVTLFGELAEELE----NL--LKEGQVVYIK-GKVKKFRGR   65 (75)
T ss_pred             CeEEEEEeeccccc-----CC--eEEEEEEEcCCCCEEEEEEEchHHHHHH----hh--ccCCCEEEEE-EEEEecCCe
Confidence            57899998877643     33  3578999999966999999998765431    11  2356788887 888877653

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco

>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1

Probab=94.99  E-value=5.3  Score=48.57  Aligned_cols=314  Identities=16%  Similarity=0.170  Sum_probs=165.5

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC-CeEEEEEchhHHHHHHhhcccCcEEEEece-----EEecCC
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-GEIRVTCFNAVVDRFYEIIEVGRVYLISKG-----SLKPAQ  291 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g-~~I~at~f~~~~~kf~~~l~eG~vy~is~~-----~V~~a~  291 (653)
                      ...+.+.|..++.+.... +...+.|+ . -..-|+.. .++-..|++. .-+|++.|+.|.||.+---     .|-.+.
T Consensus       704 ~~tlsF~~~g~wlGg~q~-~eg~~~~~-~-e~~~~~~~~~kVlLlF~G~-svrWF~fLhpg~vYRLva~~~~~p~l~~~s  779 (1144)
T PF15489_consen  704 KPTLSFQVSGSWLGGTQR-KEGTGWGP-P-EPLEDENKDQKVLLLFLGS-SVRWFPFLHPGQVYRLVAPNSPDPMLFGSS  779 (1144)
T ss_pred             CCceEEEEEEEEecceEe-ccCcccCC-C-CcCcccCCCceEEEEEecC-ceeeEeEecCCcEEEEecCCCCCceeecCC
Confidence            457889999888887654 21112222 1 11233333 4554444454 5699999999999987431     121000


Q ss_pred             --Ccc--cCCCCceEEEeccccEEEeccCCCCCCCcc-----cceecchhhhhhc-ccCccccEEEEEEEecCceeEE--
Q 006263          292 --KNF--NHLKNEWEIFLEATSTVDLCTEEDDSIPKQ-----QFSFRHISEIESA-ENNSIVDVIGIVISVNPSVPIL--  359 (653)
Q Consensus       292 --~~f--~~~~~~yei~f~~~T~I~~~~d~~~~iP~~-----~f~f~~i~~i~~~-~~~~~vDVIGvV~~v~~~~~i~--  359 (653)
                        ...  -...-.-.+++-.+=+++...  ..++|..     .+--.++.|+..- ..+.+|.+-|+|.+-.-.+...  
T Consensus       780 ~~s~r~l~~~~~~scl~vq~~W~le~~~--~~d~~~~l~~~~~~~~ssl~~lls~s~s~sLVSFs~~I~srt~ce~~~~~  857 (1144)
T PF15489_consen  780 CVSQRPLELAGCPSCLTVQDDWTLELES--SQDIPPVLRISKLLPESSLSELLSSSSSDSLVSFSAEILSRTLCEPLNAR  857 (1144)
T ss_pred             CcccccccccCCCccEEeCCCceecccc--cccchhhhhhcccCccccHHHHhccCCCCceEEEEEEEEEeeeccCCccc
Confidence              000  001111223333332333221  1234432     1224567777663 4688999999998874433211  


Q ss_pred             --ecCCce-----eeE--EEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee--EeecCCCceecccc
Q 006263          360 --RKNGME-----TQR--RILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG--KVNDFSGKSIGTIP  428 (653)
Q Consensus       360 --~k~g~~-----~~k--r~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~--rV~~f~G~sLs~~~  428 (653)
                        ++.|..     ..+  .-++..|-.+... +...-+..--     .--+.-..|.+|.|.+.  ||+-+++.++....
T Consensus       858 ~~~~~~~~~~~~~~vkltv~L~v~D~~~p~~-ldVYi~~~h~-----p~plGLLPGA~V~f~~lerkVSRs~nVYC~~~p  931 (1144)
T PF15489_consen  858 RWSKPGNAIASRGCVKLTVALTVADCESPPH-LDVYIEDPHL-----PYPLGLLPGARVLFSQLERKVSRSHNVYCCFLP  931 (1144)
T ss_pred             cccCCCCCcccccccceEEEEEEecCCCCCe-EEEEecCCCC-----CCcccccCCceeeeehhhhhhhccCcEEEEEcC
Confidence              121111     122  3455566665211 3333222111     00011135667777765  66666667776666


Q ss_pred             ceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCce
Q 006263          429 STQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSF  508 (653)
Q Consensus       429 ~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~  508 (653)
                      .|.|.+....++.                         +.........+.++....    ..+-...+.+.|+.|..=.+
T Consensus       932 sS~VtVlS~p~~t-------------------------~~~~~~P~~~L~~~~~~~----~~~~~a~~~chVV~V~~l~L  982 (1144)
T PF15489_consen  932 SSSVTVLSFPPET-------------------------NVSPPLPHIYLAELLQGS----QSPFQARVSCHVVSVLSLQL  982 (1144)
T ss_pred             CceEEEEecCccc-------------------------CCCCCCCeEEehhhhCCC----CCCceEEEEEEEEEEEEEEe
Confidence            6766654321111                         011122344555554321    22235667888887765333


Q ss_pred             EEecCCCCcCcccccceeeecCceeeccc----CccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHH
Q 006263          509 CYTACPLMIGDRQCNKKVTQSGNRWQCDR----CNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYM  584 (653)
Q Consensus       509 ~Y~aC~~~~~~~~C~KKv~~~~~~~~C~k----C~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~  584 (653)
                      .+ .|.      .|..-.. ++   +|..    |-..  ....+=..++.+.|+||++.+++-|+....+||.+..|...
T Consensus       983 ~W-vCa------~C~si~~-qg---~Csr~~p~C~s~--~sV~qA~ar~~vEDGTaeA~v~~~~~~V~~lLgL~~~eW~~ 1049 (1144)
T PF15489_consen  983 QW-VCA------HCGSICP-QG---RCSRQSPPCPSQ--TSVFQASARLLVEDGTAEAVVWCRGHHVAALLGLSPSEWES 1049 (1144)
T ss_pred             ee-hhh------hccCccc-CC---cCCCCCCCCCCC--cceeeEEEEEEEecCCeeEEEEECCcHHHHHhCCCHHHHHH
Confidence            22 677      6663222 11   3532    4332  45778888999999999999999999999999999987654


Q ss_pred             H
Q 006263          585 L  585 (653)
Q Consensus       585 ~  585 (653)
                      +
T Consensus      1050 L 1050 (1144)
T PF15489_consen 1050 L 1050 (1144)
T ss_pred             H
Confidence            3

>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

Probab=94.91  E-value=0.096  Score=42.51  Aligned_cols=63  Identities=25%  Similarity=0.447  Sum_probs=44.2

Q ss_pred             ccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263          343 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       343 vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                      |.|.|.|+++.       +.++  ....++|.|.|| .|.|++|++.+..+    .+.+  ..+.+|.++ ++++.|++.
T Consensus         1 V~v~G~V~~~~-------~~~~--~~~~~~l~D~tg-~i~~~~~~~~~~~~----~~~l--~~g~~v~v~-G~v~~~~~~   63 (75)
T PF01336_consen    1 VTVEGRVTSIR-------RSGG--KIVFFTLEDGTG-SIQVVFFNEEYERF----REKL--KEGDIVRVR-GKVKRYNGG   63 (75)
T ss_dssp             EEEEEEEEEEE-------EEET--TEEEEEEEETTE-EEEEEEETHHHHHH----HHTS---TTSEEEEE-EEEEEETTS
T ss_pred             CEEEEEEEEEE-------cCCC--CEEEEEEEECCc-cEEEEEccHHhhHH----hhcC--CCCeEEEEE-EEEEEECCc
Confidence            46789998877       1111  356899999998 99999999554443    2223  368899888 788877654

The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....

>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

Probab=94.64  E-value=0.19  Score=40.50  Aligned_cols=60  Identities=17%  Similarity=0.221  Sum_probs=41.9

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP  289 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~  289 (653)
                      +|+|+|+.....+ .   + .++.+.+.|.| +++.|.+++|+.. ......|++|+.|.+.+ ++..
T Consensus         1 ~i~~~V~~~~~~~-~---~-~~~~~~~~~~D-~~g~i~~~~F~~~-~~~~~~~~~G~~~~v~G-kv~~   60 (75)
T cd04488           1 TVEGTVVSVEVVP-R---R-GRRRLKVTLSD-GTGTLTLVFFNFQ-PYLKKQLPPGTRVRVSG-KVKR   60 (75)
T ss_pred             CEEEEEEEEEecc-C---C-CccEEEEEEEc-CCCEEEEEEECCC-HHHHhcCCCCCEEEEEE-EEee
Confidence            3678887763222 1   1 24689999999 6999999999831 23367899999998874 4433

RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha

>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)

Probab=94.63  E-value=0.16  Score=41.83  Aligned_cols=43  Identities=16%  Similarity=0.363  Sum_probs=37.1

Q ss_pred             eeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEe
Q 006263          244 KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK  288 (653)
Q Consensus       244 k~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~  288 (653)
                      +.+.+.|.| .+|.|.+++|++..+++.+.|++|.+|.+.+ .+.
T Consensus        19 ~~~~~~l~D-~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G-~v~   61 (84)
T cd04485          19 RMAFVTLED-LTGSIEVVVFPETYEKYRDLLKEDALLLVEG-KVE   61 (84)
T ss_pred             EEEEEEEEe-CCCeEEEEECHHHHHHHHHHhcCCCEEEEEE-EEE
Confidence            578899999 7889999999988788999999999998874 443

The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.

>PF09103 BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; InterPro: IPR015187 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

Probab=94.34  E-value=0.085  Score=47.67  Aligned_cols=67  Identities=22%  Similarity=0.334  Sum_probs=38.7

Q ss_pred             HHHHHhCCCCC-CCC-eEEEEEEEEcC-CCCceEEEEEecccceeeeeecccchhhcccCCcccCcEEEE
Q 006263            9 SISLINGGDVN-SKP-LVQVMDIKLIG-STQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQL   75 (653)
Q Consensus         9 ai~~i~~~~~~-~~p-vvQVl~ik~~~-~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl   75 (653)
                      ||.+|++++.. ..| ||=|.+|..-. .......+.|+||=|.++|.+...|..++..|.|..|.=+.+
T Consensus         2 aLrrI~E~D~~~~~~mVL~Vs~i~~~~~~~~~~~~lelTDGWY~Ika~lD~~L~~~l~~gki~vG~KL~v   71 (118)
T PF09103_consen    2 ALRRILEGDDSASKPMVLCVSSISSSDNDSPESAILELTDGWYSIKAQLDPPLTRLLRKGKIRVGQKLRV   71 (118)
T ss_dssp             HHHHHHTTSSTTB-SEEEEEEE-------------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-EEEE
T ss_pred             HhHHHhhCCCCcCCcEEEEEEEEccCCCCCCccCEEEEecCCEEEEEEeCHHHHHHHHhCCccCCccEEE
Confidence            68999999863 345 55566552222 345789999999999999999999999999999999987764

OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0000724 double-strand break repair via homologous recombination; PDB: 1IYJ_D 1MIU_A.

>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

Probab=94.29  E-value=0.19  Score=42.08  Aligned_cols=54  Identities=31%  Similarity=0.427  Sum_probs=39.1

Q ss_pred             cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhh--hhhhhHHHhhccCCCcEEEEEe
Q 006263          344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCN--KEGQKLQEMVDVGFFPVLSVKS  413 (653)
Q Consensus       344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~--~~~~~l~~~~~~~~~~Vvaik~  413 (653)
                      =++|+|.++.     .+|+|+.    -++|.|.+| ++++++|.+...  .+...    +  ..+.+|.+++
T Consensus         3 ~i~GiI~~v~-----~TK~g~~----~~~leD~~G-~~Ev~~F~~~~~~~~~~~~----l--~~d~~v~v~g   58 (79)
T cd04490           3 SIIGMVNDVR-----STKNGHR----IVELEDTTG-RITVLLTKDKEELFEEAED----I--LPDEVIGVSG   58 (79)
T ss_pred             EEEEEEeEEE-----EcCCCCE----EEEEECCCC-EEEEEEeCchhhhhhhhhh----c--cCCCEEEEEE
Confidence            4689999988     3566764    889999999 899999999876  54222    2  2355666655

PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.

>PTZ00401 aspartyl-tRNA synthetase; Provisional

Probab=92.82  E-value=0.96  Score=51.71  Aligned_cols=99  Identities=20%  Similarity=0.212  Sum_probs=72.4

Q ss_pred             CcceeccccCCCC---CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEc-----hhHHHHHHhhcccC
Q 006263          206 ARIIPIAALNPYQ---GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCF-----NAVVDRFYEIIEVG  277 (653)
Q Consensus       206 ~~~~pI~~L~p~~---~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f-----~~~~~kf~~~l~eG  277 (653)
                      +.++.|++|++..   ..-+|+|||.++   |.      .|++.-++|.| .++.|++++-     .+.+-+|-..|..|
T Consensus        63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~~---R~------~Gk~~Fl~LRd-~~~~iQ~v~~~~~~~~~~~~~~~~~l~~e  132 (550)
T PTZ00401         63 RTFIPVAVLSKPELVDKTVLIRARVSTT---RK------KGKMAFMVLRD-GSDSVQAMAAVEGDVPKEMIDFIGQIPTE  132 (550)
T ss_pred             CceEEHHHCCccccCCCEEEEEEEEEEE---ec------CCCeEEEEEEe-CCcCEEEEEECCCccCHHHHHHHhcCCCC
Confidence            5689999998765   457899999764   33      35777788999 7789999983     23445677789999


Q ss_pred             cEEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263          278 RVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       278 ~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                      +++.+.+.-+++....-+....++||....-..+.++
T Consensus       133 siV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~a  169 (550)
T PTZ00401        133 SIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTES  169 (550)
T ss_pred             CEEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeCC
Confidence            9999999666544332234567899999886666655

>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

Probab=92.46  E-value=0.56  Score=39.22  Aligned_cols=55  Identities=22%  Similarity=0.119  Sum_probs=43.0

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHH--HHHhhcccCcEEEEece
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKG  285 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~--kf~~~l~eG~vy~is~~  285 (653)
                      .+.|.|+...     .+.+  |+. .+.|-| ..|.+.+++|.+..+  ++.+.|++|.++.+..-
T Consensus         3 ~i~GiI~~v~-----~TK~--g~~-~~~leD-~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~   59 (79)
T cd04490           3 SIIGMVNDVR-----STKN--GHR-IVELED-TTGRITVLLTKDKEELFEEAEDILPDEVIGVSGT   59 (79)
T ss_pred             EEEEEEeEEE-----EcCC--CCE-EEEEEC-CCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEE
Confidence            4566666643     2233  334 778888 899999999999999  99999999999999873

PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.

>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

Probab=92.09  E-value=0.51  Score=38.81  Aligned_cols=54  Identities=22%  Similarity=0.359  Sum_probs=42.6

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      .|.|-|+.   +|. . .+  | ..-++|.| .+++|.+++|.+..+++.+.|++|+.+.+..
T Consensus         3 ~v~g~v~~---i~~-t-k~--g-~~~~~L~D-~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~g   56 (78)
T cd04489           3 WVEGEISN---LKR-P-SS--G-HLYFTLKD-EDASIRCVMWRSNARRLGFPLEEGMEVLVRG   56 (78)
T ss_pred             EEEEEEec---CEE-C-CC--c-EEEEEEEe-CCeEEEEEEEcchhhhCCCCCCCCCEEEEEE
Confidence            35666664   343 2 22  4 77889999 7899999999999999999999999888876

E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.

>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)

Probab=91.51  E-value=1.4  Score=36.07  Aligned_cols=64  Identities=28%  Similarity=0.414  Sum_probs=41.1

Q ss_pred             EEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCC
Q 006263          345 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG  421 (653)
Q Consensus       345 VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G  421 (653)
                      ++|+|.++..   ..+|.|+.  ...++|.|.+| .+++++|.+....+    ...+.  .+.++.+.| ++..|+|
T Consensus         2 i~g~v~~~~~---~~~k~g~~--~~~~~l~D~tg-~~~~~~f~~~~~~~----~~~l~--~g~~v~v~G-~v~~~~~   65 (84)
T cd04485           2 VAGLVTSVRR---RRTKKGKR--MAFVTLEDLTG-SIEVVVFPETYEKY----RDLLK--EDALLLVEG-KVERRDG   65 (84)
T ss_pred             EEEEEEEeEE---EEcCCCCE--EEEEEEEeCCC-eEEEEECHHHHHHH----HHHhc--CCCEEEEEE-EEEecCC
Confidence            5677776544   33456653  47789999999 79999998653332    22232  456666654 6777766

The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.

>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]

Probab=91.42  E-value=1  Score=45.58  Aligned_cols=68  Identities=15%  Similarity=0.131  Sum_probs=52.7

Q ss_pred             ceEEecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHH
Q 006263          507 SFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYM  584 (653)
Q Consensus       507 ~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~  584 (653)
                      .|+|..|+      .|+| -........|+.|+....+...+|.+.....+.++.   ..|...+..+.|.++..+..
T Consensus       159 ~~~~~~~~------~~~~-~~~~~~~~~c~~~~~~~~~~~~~~~l~~~~~~~~~~---l~~~~~~~~~~G~~~~~~~~  226 (246)
T KOG0851|consen  159 DGFYLTFK------ICNK-SKFSKPVLWCEACGEQATDFGRKRSLGGGVIVIAPE---LLFWKIWRYFDGKNVRIVLA  226 (246)
T ss_pred             ceEEEEEe------eccc-ccccCceEEehhhcchHHhhhhheEecCCcEEccch---heeecccccccCCchheeec
Confidence            69999999      8998 111112689999998877777778898888888887   88888888888877765543

>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function

Probab=91.25  E-value=1.3  Score=37.48  Aligned_cols=71  Identities=20%  Similarity=0.301  Sum_probs=51.3

Q ss_pred             EEEEEEEecCceeEEecCCceeeEEEEEEEeCCC--CEEEEEEccchhhhhhhhHHHhhccCCCcEEEE-EeeEeecCCC
Q 006263          345 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSG--RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSV-KSGKVNDFSG  421 (653)
Q Consensus       345 VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~--~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvai-k~~rV~~f~G  421 (653)
                      +-|.|..+-+..+-.+++|  ..||++.|.-...  ..|.+.+||+.+..+       +.-..|..|.+ -+.+-++|+|
T Consensus         2 i~Gkii~~l~~~~g~s~~G--w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l-------~~~~~Gd~V~Vsf~i~~RE~~g   72 (84)
T PF11325_consen    2 ITGKIIKVLPEQQGVSKNG--WKKREFVLETEEQYPQKICFEFWGDKIDLL-------DNFQVGDEVKVSFNIEGREWNG   72 (84)
T ss_pred             cccEEEEEecCcccCcCCC--cEEEEEEEeCCCcCCceEEEEEEcchhhhh-------ccCCCCCEEEEEEEeeccEecc
Confidence            4578767776665556677  9999999985554  589999999987652       22345677765 4778889998


Q ss_pred             cee
Q 006263          422 KSI  424 (653)
Q Consensus       422 ~sL  424 (653)
                      +.-
T Consensus        73 r~f   75 (84)
T PF11325_consen   73 RWF   75 (84)
T ss_pred             eEe
Confidence            754

>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)

Probab=91.11  E-value=4.1  Score=35.50  Aligned_cols=83  Identities=18%  Similarity=0.209  Sum_probs=55.2

Q ss_pred             eEEEEEEEeeccccccccCCCCc-eeEEEEEEeCCCCeEEEEEchh------HHHHHHhhcccCcEEEEeceEEecCCCc
Q 006263          221 WAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNA------VVDRFYEIIEVGRVYLISKGSLKPAQKN  293 (653)
Q Consensus       221 w~I~~RV~~k~~ir~~~~~~g~g-k~f~~~L~D~~g~~I~at~f~~------~~~kf~~~l~eG~vy~is~~~V~~a~~~  293 (653)
                      .+|+|||.++   |.      .| ++.-++|.| .++.|++.+-.+      ..-++...|..|+++.+.+--.+. .+.
T Consensus         2 V~i~Gwv~~~---R~------~g~k~~Fi~LrD-~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~-~~~   70 (102)
T cd04320           2 VLIRARVHTS---RA------QGAKLAFLVLRQ-QGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKP-EEP   70 (102)
T ss_pred             EEEEEEEEEe---ec------CCCceEEEEEec-CCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECC-CCc
Confidence            5788999774   33      25 666678999 678999999743      223344568999999999964432 221


Q ss_pred             ccC-CCCceEEEeccccEEEec
Q 006263          294 FNH-LKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       294 f~~-~~~~yei~f~~~T~I~~~  314 (653)
                      .+. ....|||....-..+..+
T Consensus        71 ~~~~~~~~~El~~~~i~il~~~   92 (102)
T cd04320          71 IKSCTQQDVELHIEKIYVVSEA   92 (102)
T ss_pred             ccCCCcCcEEEEEEEEEEEecC
Confidence            111 336799998776555554

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.

>PF14951 DUF4503: Domain of unknown function (DUF4503)

Probab=90.63  E-value=0.61  Score=49.24  Aligned_cols=82  Identities=16%  Similarity=0.346  Sum_probs=66.5

Q ss_pred             EEEEEEEEEEEeCC-ceEEecCCCCcCcccccc-eee---ecCceeecccCccccCCceEEEEEEEEEEeCC---CeEEE
Q 006263          493 WVTVRAFITFIKSD-SFCYTACPLMIGDRQCNK-KVT---QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQT---GLTWV  564 (653)
Q Consensus       493 ~~~v~atI~~i~~d-~~~Y~aC~~~~~~~~C~K-Kv~---~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~T---g~~~~  564 (653)
                      ...|.|+|+.++.+ .|.+|.|.      .|+. |+.   ++++.++|..|.+.+..|.-|.-|.+-+.=.+   .++.+
T Consensus       256 iCsvqG~VvgVdE~TAfSWPvCd------~CGn~rLe~~pe~rg~~~C~~Cs~~V~sP~~r~~LeVfl~Cps~p~ctvKV  329 (389)
T PF14951_consen  256 ICSVQGTVVGVDESTAFSWPVCD------RCGNGRLEQSPEDRGAFSCGDCSRVVTSPVLRMHLEVFLDCPSRPQCTVKV  329 (389)
T ss_pred             eEEEeeEEEEecCcccccCcccc------ccCCccceeCccCCCceeccchhhhccCcceeeeEEEEEeCCCCCCceEEE
Confidence            68899999999987 69999999      8854 666   33448999999999999999999998887333   56788


Q ss_pred             EEechhhhhhhCCCHH
Q 006263          565 TAFQESGEEILGCPAK  580 (653)
Q Consensus       565 ~~F~~~ae~llG~sA~  580 (653)
                      -+..+.-..||.-.|.
T Consensus       330 KL~q~sIsslL~~aa~  345 (389)
T PF14951_consen  330 KLLQRSISSLLMSAAS  345 (389)
T ss_pred             EEhHHHHHHHHhhhhc
Confidence            8888888878766664

>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS)

Probab=90.61  E-value=3.3  Score=36.54  Aligned_cols=76  Identities=22%  Similarity=0.420  Sum_probs=52.5

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh-----HHHHHHhhcccCcEEEEeceEEecCCCcccC
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-----VVDRFYEIIEVGRVYLISKGSLKPAQKNFNH  296 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~-----~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~  296 (653)
                      +|+|||.+.   |.      .|++.-++|.| .++.+++++...     ...+|...|..|+++.+.+.-++...     
T Consensus         3 ~v~GwV~~~---R~------~g~~~Fi~lrd-~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~-----   67 (108)
T cd04322           3 SVAGRIMSK---RG------SGKLSFADLQD-ESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKT-----   67 (108)
T ss_pred             EEEEEEEEE---ec------CCCeEEEEEEE-CCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCC-----
Confidence            688888763   33      35677788999 678999988643     23455556999999999875443322     


Q ss_pred             CCCceEEEeccccEEEec
Q 006263          297 LKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       297 ~~~~yei~f~~~T~I~~~  314 (653)
                        ..+||....-..+.++
T Consensus        68 --g~~El~~~~~~ils~~   83 (108)
T cd04322          68 --GELSIFVKEFTLLSKS   83 (108)
T ss_pred             --CCEEEEeCEeEEeecc
Confidence              4589977665555554

These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein

>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)

Probab=90.05  E-value=1.1  Score=36.95  Aligned_cols=43  Identities=21%  Similarity=0.328  Sum_probs=35.7

Q ss_pred             eeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263          244 KVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP  289 (653)
Q Consensus       244 k~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~  289 (653)
                      +.+.+.|-| .+|.|.+++|++.. .+...|++|.++.+. +.|..
T Consensus        19 ~~~~~~l~D-~tg~i~~~~f~~~~-~~~~~l~~g~~v~v~-G~v~~   61 (83)
T cd04492          19 PYLALTLQD-KTGEIEAKLWDASE-EDEEKFKPGDIVHVK-GRVEE   61 (83)
T ss_pred             cEEEEEEEc-CCCeEEEEEcCCCh-hhHhhCCCCCEEEEE-EEEEE
Confidence            578899999 78899999999664 457899999999998 66643

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

>PLN02850 aspartate-tRNA ligase

Probab=90.04  E-value=2.6  Score=48.16  Aligned_cols=98  Identities=15%  Similarity=0.130  Sum_probs=70.8

Q ss_pred             CcceeccccCCCC--CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh------HHHHHHhhcccC
Q 006263          206 ARIIPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA------VVDRFYEIIEVG  277 (653)
Q Consensus       206 ~~~~pI~~L~p~~--~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~------~~~kf~~~l~eG  277 (653)
                      +.++.|.+|++..  ...+|+|||.+.   |.      .|++.-++|.| .++.|++++...      ..-+|...|..|
T Consensus        67 ~~~~~i~~l~~~~~g~~V~v~Grv~~~---R~------~gk~~Fl~Lrd-~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~e  136 (530)
T PLN02850         67 REWTDVSDLGEELAGSEVLIRGRVHTI---RG------KGKSAFLVLRQ-SGFTVQCVVFVSEVTVSKGMVKYAKQLSRE  136 (530)
T ss_pred             ceEeEhhhcchhhCCCEEEEEEEEEEE---cc------CCCeEEEEEEe-CCcCEEEEEECCccccCHHHHHHHhCCCCC
Confidence            4678999998754  468899999763   32      46776678899 788999998543      345677889999


Q ss_pred             cEEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263          278 RVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       278 ~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                      +++.+.+--+++... -+....++||....-..+..+
T Consensus       137 s~V~V~G~v~~~~~~-~~~~t~~~El~~~~i~vls~a  172 (530)
T PLN02850        137 SVVDVEGVVSVPKKP-VKGTTQQVEIQVRKIYCVSKA  172 (530)
T ss_pred             CEEEEEEEEEccCcC-CCCCCccEEEEEeEEEEEeCC
Confidence            999998865544322 223344899999887666665

>PF15072 DUF4539: Domain of unknown function (DUF4539)

Probab=89.84  E-value=1.5  Score=37.36  Aligned_cols=60  Identities=20%  Similarity=0.201  Sum_probs=46.8

Q ss_pred             EEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceEEEeccccEEE
Q 006263          246 FSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVD  312 (653)
Q Consensus       246 f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~  312 (653)
                      ..+.|.| -+|+|+|++-.+..+.|.+.|..|.|..+.+..|-.      +....+-|.......+.
T Consensus        21 ~~v~l~D-pTG~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~------ps~~~~yLnIt~~Nlv~   80 (86)
T PF15072_consen   21 AFVVLKD-PTGEIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFS------PSPRSHYLNITLNNLVR   80 (86)
T ss_pred             eEEEEEC-CCCcEEEEEeHHHHhhcCCccccCEEEEEeeeeEEe------cCCCccEEEEehhHeee
Confidence            5788999 788999999999999999999999999999988743      33434555554444443

>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)

Probab=89.60  E-value=1.5  Score=37.64  Aligned_cols=68  Identities=26%  Similarity=0.391  Sum_probs=44.0

Q ss_pred             ccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263          343 VDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       343 vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                      |.++|+|+++....          .+..++|.|.|| +|++.+|......- ....+.+  ..+.+|.+ .++++.|+|+
T Consensus         2 v~~vG~V~~~~~~~----------~~~~~tL~D~TG-~I~~~~W~~~~~~~-~~~~~~~--~~g~~v~v-~G~v~~~~g~   66 (95)
T cd04478           2 VTLVGVVRNVEEQS----------TNITYTIDDGTG-TIEVRQWLDDDNDD-SSEVEPI--EEGTYVRV-FGNLKSFQGK   66 (95)
T ss_pred             EEEEEEEEeeeEcc----------cEEEEEEECCCC-cEEEEEeCCCCCcc-ccccccc--ccCCEEEE-EEEEcccCCe
Confidence            67889998876542          467899999999 79999998653210 0001122  23455544 4567889885


Q ss_pred             -eec
Q 006263          423 -SIG  425 (653)
Q Consensus       423 -sLs  425 (653)
                       .|.
T Consensus        67 ~ql~   70 (95)
T cd04478          67 KSIM   70 (95)
T ss_pred             eEEE
Confidence             565

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam

>PF10341 TPP1: Shelterin complex subunit, TPP1/ACD; InterPro: IPR019437 EST3 is a component of the telomerase holoenzyme, involved in telomere replication

Probab=88.96  E-value=1.4  Score=38.98  Aligned_cols=60  Identities=15%  Similarity=0.266  Sum_probs=35.0

Q ss_pred             eEEEEEEEEcCCCCceEEEEEecccceeeeeecccchhhcccCC------cccCcEEEEeeeEeeee
Q 006263           23 LVQVMDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQ------VKKGSVVQLIDYICSTV   83 (653)
Q Consensus        23 vvQVl~ik~~~~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~------l~~~sIIkl~~y~~~~~   83 (653)
                      ++||+..-. ........++||||.|++.|.|+.+.-...+...      --+|++|.|++|.+...
T Consensus        28 ~~ri~~~~~-~~~~~~i~a~lsDs~~~I~a~ft~eai~~fe~~~~~~~t~~t~g~li~I~~~~l~~~   93 (106)
T PF10341_consen   28 LLRILKFAK-STSDGAITALLSDSTHQILAIFTREAIENFEREEKKRITSSTKGCLILIKDFNLVFQ   93 (106)
T ss_dssp             EEEEEE-S----TTS-EEEEEE-SS-EEEEEE-HHHHHTS--TTS-SSSTT-TTEEEEEEEEEEEEE
T ss_pred             EEEEEEEec-CCCCCcEEEEEEcCCeEEEEEECHHHHHHHHHhccCcccccCCceEEEEEEEEEEEE
Confidence            566665500 2335689999999999999999854443333211      12789999999988765

It has been demonstrated that Est3 dimerises and binds to DNA and RNA. Furthermore, Est3 stimulates the dissociation of RNA/DNA hetero-duplexes [, ]. ; GO: 0042162 telomeric DNA binding, 0007004 telomere maintenance via telomerase, 0032508 DNA duplex unwinding, 0000781 chromosome, telomeric region, 0005697 telomerase holoenzyme complex; PDB: 2I46_B.

>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

Probab=88.70  E-value=3.8  Score=34.34  Aligned_cols=74  Identities=12%  Similarity=0.096  Sum_probs=48.2

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHH--HHHhhcccCcEEEEeceEEecCCCcccCCCC
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKGSLKPAQKNFNHLKN  299 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~--kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~  299 (653)
                      +|+|||.++   |.      .|++.-++|.| .++.+++.+..+...  ++...|..|+++.+.+- +....+.- ...+
T Consensus         3 ~v~Gwv~~~---R~------~g~~~Fi~LrD-~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~-v~~~~~~~-~~~~   70 (84)
T cd04323           3 KVFGWVHRL---RS------QKKLMFLVLRD-GTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGE-VKEDPRAK-QAPG   70 (84)
T ss_pred             EEEEEEEEE---ec------CCCcEEEEEEc-CCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEE-EEECCccc-CCCC
Confidence            678888664   22      25666678899 677899988654322  23356889999999774 44333221 3456


Q ss_pred             ceEEEecc
Q 006263          300 EWEIFLEA  307 (653)
Q Consensus       300 ~yei~f~~  307 (653)
                      +|||...+
T Consensus        71 ~~Ei~~~~   78 (84)
T cd04323          71 GYELQVDY   78 (84)
T ss_pred             CEEEEEEE
Confidence            79988744

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with

>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs)

Probab=88.44  E-value=3.7  Score=34.47  Aligned_cols=74  Identities=20%  Similarity=0.219  Sum_probs=49.0

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHH---HHHHhhcccCcEEEEeceEEecCCCcccCCC
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV---DRFYEIIEVGRVYLISKGSLKPAQKNFNHLK  298 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~---~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~  298 (653)
                      +|+|||.++   |.      .|++.-++|.| .++.+++.+-.+..   .++...|..|+++.+.+.-.....+.  ...
T Consensus         3 ~i~Gwv~~~---R~------~g~~~Fi~Lrd-~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~--~~~   70 (85)
T cd04100           3 TLAGWVHSR---RD------HGGLIFIDLRD-GSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGN--LAT   70 (85)
T ss_pred             EEEEEEehh---cc------CCCEEEEEEEe-CCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCC--CCC
Confidence            678888553   33      35666678889 67899998865432   23456799999999988644432221  234


Q ss_pred             CceEEEecc
Q 006263          299 NEWEIFLEA  307 (653)
Q Consensus       299 ~~yei~f~~  307 (653)
                      .++||..+.
T Consensus        71 ~~~El~~~~   79 (85)
T cd04100          71 GEIELQAEE   79 (85)
T ss_pred             CCEEEEEeE
Confidence            678887643

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A

>PRK07373 DNA polymerase III subunit alpha; Reviewed

Probab=87.63  E-value=1.8  Score=48.36  Aligned_cols=71  Identities=17%  Similarity=0.252  Sum_probs=52.5

Q ss_pred             eeccccC--CCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          209 IPIAALN--PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       209 ~pI~~L~--p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      .++++|.  +.....+|-|.|+..-.++   .++|+ .+.-+.|-| ..|.|.+++|.+..+++.+.|++|.++.|.+
T Consensus       269 ~~~~~l~~~~~~~~v~vaG~I~~ik~~~---TKkG~-~maf~~leD-~tG~ie~vvFp~~y~~~~~~l~~~~~v~v~G  341 (449)
T PRK07373        269 INLSELEEQKEKTKVSAVVMLNEVKKIV---TKKGD-PMAFLQLED-LSGQSEAVVFPKSYERISELLQVDARLIIWG  341 (449)
T ss_pred             cCHHHHhcccCCCEEEEEEEEEEeEecc---cCCCC-EEEEEEEEE-CCCCEEEEECHHHHHHHHHHhccCCEEEEEE
Confidence            3566664  2234567888888754433   34443 455567888 8999999999999999999999999999965

>PRK02801 primosomal replication protein N; Provisional

Probab=87.39  E-value=2.9  Score=36.66  Aligned_cols=68  Identities=15%  Similarity=0.077  Sum_probs=53.1

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEEeC----C-CC------eEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDS----D-GG------EIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~----~-g~------~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      +|+-.+.||+++.-++|...+  | -.+.+|.|.=.    + +.      .|.|++|++.++.+...|..|+.+.|.++.
T Consensus         2 mN~v~L~Grl~~dpelr~Tp~--G-~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V~G~L   78 (101)
T PRK02801          2 TNRLVLSGTVCRTPKRKVSPS--G-IPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQGFI   78 (101)
T ss_pred             ccEEEEEEEECcCcceEECCC--C-CeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEEEEE
Confidence            467889999999999997532  2 25667766421    2 22      299999999999999999999999999986


Q ss_pred             Ee
Q 006263          287 LK  288 (653)
Q Consensus       287 V~  288 (653)
                      -.
T Consensus        79 ~~   80 (101)
T PRK02801         79 SC   80 (101)
T ss_pred             EE
Confidence            43

>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]

Probab=87.23  E-value=2.2  Score=41.77  Aligned_cols=53  Identities=25%  Similarity=0.421  Sum_probs=33.5

Q ss_pred             EEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhcc-CCCcEEEEEeeEeecCCCc-eecccc
Q 006263          369 RILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDV-GFFPVLSVKSGKVNDFSGK-SIGTIP  428 (653)
Q Consensus       369 r~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~-~~~~Vvaik~~rV~~f~G~-sLs~~~  428 (653)
                      ..++|.|.+| .|+|+.|-..+.+.     +.... ..+--|- -+.-++.|+|| +++...
T Consensus        85 ~~~~iEDGTG-~Ievr~W~~~~~~~-----e~~~d~~~~~yvk-V~G~lk~F~GK~~I~~~~  139 (258)
T COG5235          85 SMFVIEDGTG-SIEVRFWPGNSYEE-----EQCKDLEEQNYVK-VNGSLKTFNGKRSISASH  139 (258)
T ss_pred             eEEEEecCCc-eEEEEecCCCchHH-----HhccccccccEEE-EecceeeeCCeeEEehhh
Confidence            4678999999 89999999887652     22221 1122222 24456789996 776443

>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

Probab=87.14  E-value=4.4  Score=35.15  Aligned_cols=81  Identities=20%  Similarity=0.253  Sum_probs=55.4

Q ss_pred             cEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC--C
Q 006263          344 DVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS--G  421 (653)
Q Consensus       344 DVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~--G  421 (653)
                      |++|+|++|+...+     |   ..-.+.|.|+.-.-+-+.+|........+   +..  .++..||+.+...+-..  |
T Consensus         1 D~VGvVvsV~~~~~-----g---~~~~vYLaDe~~nll~vkfw~~l~~~~~E---Dvv--k~~~lia~SNLQwR~~s~~~   67 (100)
T cd04495           1 DTVGVVISVGKPIE-----G---KFPAVYLADECLNLLCVKFWSSLEQYAYE---DVV--KRRVLLAASNLQWRTESTSG   67 (100)
T ss_pred             CceEEEEEEccccc-----C---ccceEEEecCCcCEEEEEEecchHHhhhh---hhc--ccceEEEEecceEeccccCC
Confidence            89999999998751     2   23468999999999999999976543211   111  34567888888776543  3


Q ss_pred             c-eeccccceEEEEcCC
Q 006263          422 K-SIGTIPSTQLFINPD  437 (653)
Q Consensus       422 ~-sLs~~~~S~i~inPd  437 (653)
                      . +|-.+.-|.+..||.
T Consensus        68 iPtl~Age~t~FS~nPK   84 (100)
T cd04495          68 VPTLFAGEYSTFSANPK   84 (100)
T ss_pred             CceeeeecceeecCCcc
Confidence            3 444566677777773

BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).

>PRK13480 3'-5' exoribonuclease YhaM; Provisional

Probab=86.33  E-value=2.2  Score=45.40  Aligned_cols=70  Identities=11%  Similarity=0.065  Sum_probs=49.2

Q ss_pred             eccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          210 PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       210 pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      .|++|.++. .......|..+ .+|+-+|  | ...++++|.| .+|+|.|.+|+.. +.....+++|+++.+.+-.
T Consensus         4 ~i~~l~~g~-~v~~~~lv~~~-~~~~~kn--G-~~yl~l~l~D-~tG~I~ak~W~~~-~~~~~~~~~g~vv~v~G~v   73 (314)
T PRK13480          4 GIEELEVGE-QVDHFLLIKSA-TKGVASN--G-KPFLTLILQD-KSGDIEAKLWDVS-PEDEATYVPETIVHVKGDI   73 (314)
T ss_pred             hHhhcCCCC-EeeEEEEEEEc-eeeecCC--C-CeEEEEEEEc-CCcEEEEEeCCCC-hhhHhhcCCCCEEEEEEEE
Confidence            578888765 33434444443 3343221  1 2589999999 8999999999864 5668889999999888754

>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS)

Probab=86.31  E-value=12  Score=32.88  Aligned_cols=81  Identities=16%  Similarity=0.078  Sum_probs=54.7

Q ss_pred             CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH----HHHHHhhcccCcEEEEeceEEecCCCcc
Q 006263          219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV----VDRFYEIIEVGRVYLISKGSLKPAQKNF  294 (653)
Q Consensus       219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~----~~kf~~~l~eG~vy~is~~~V~~a~~~f  294 (653)
                      ...+|+|||.++   |.      .|++.-++|.| .++.|++.+-.+.    +-++-..|..|+++.+.+--.+...   
T Consensus        13 ~~V~v~Gwv~~~---R~------~g~~~Fi~LrD-~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~---   79 (108)
T cd04316          13 EEVTVAGWVHEI---RD------LGGIKFVILRD-REGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPK---   79 (108)
T ss_pred             CEEEEEEEEEee---ec------cCCeEEEEEec-CCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCC---
Confidence            358899999764   33      24666677888 5779999887542    2233356899999999996443322   


Q ss_pred             cCCCCceEEEeccccEEEec
Q 006263          295 NHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       295 ~~~~~~yei~f~~~T~I~~~  314 (653)
                        ...+|||....-..+..+
T Consensus        80 --~~~~~Ei~~~~i~il~~~   97 (108)
T cd04316          80 --APNGVEIIPEEIEVLSEA   97 (108)
T ss_pred             --CCCCEEEEEeEEEEEeCC
Confidence              135799998775555554

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.

>PRK05733 single-stranded DNA-binding protein; Provisional

Probab=85.91  E-value=3  Score=40.27  Aligned_cols=65  Identities=22%  Similarity=0.246  Sum_probs=50.5

Q ss_pred             CCCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC-------eEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG-------EIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       217 ~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~-------~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      .+++-+|.|||.+--.+|.+.+  | ..+.+|.|.      |+++|       -+.+++|+..++.+...|+.|+.++|.
T Consensus         4 ~mNkV~LiGrlg~DPElr~t~n--G-~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~Ve   80 (172)
T PRK05733          4 GVNKVILVGTCGQDPEVRYLPN--G-NAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIE   80 (172)
T ss_pred             cceEEEEEEEecCCCEEEECCC--C-CEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEE
Confidence            3578899999999888887654  2 256666654      22223       399999999999999999999999998


Q ss_pred             c
Q 006263          284 K  284 (653)
Q Consensus       284 ~  284 (653)
                      +
T Consensus        81 G   81 (172)
T PRK05733         81 G   81 (172)
T ss_pred             E
Confidence            6

>PRK06751 single-stranded DNA-binding protein; Provisional

Probab=85.71  E-value=2.8  Score=40.55  Aligned_cols=64  Identities=22%  Similarity=0.296  Sum_probs=50.2

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCC----CeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDG----GEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g----~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      +++..|.|||++--++|...+  | ..+.+|.|+      ++.|    .-|.+++|+..++.+...|+.|+-+.|.+
T Consensus         2 mN~V~LiGrL~~DpelR~t~s--G-~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeG   75 (173)
T PRK06751          2 MNRVILVGRLTKDPDLRYTPN--G-VAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDG   75 (173)
T ss_pred             ceEEEEEEEECCCCcEEECCC--C-CEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEE
Confidence            467899999999999986532  2 257677764      2222    46899999999999999999999998876

>PRK07459 single-stranded DNA-binding protein; Provisional

Probab=85.01  E-value=3.6  Score=37.36  Aligned_cols=64  Identities=13%  Similarity=0.222  Sum_probs=52.1

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      .+.-.|.||+.+--.+|...+  | ..+.+|.|+      |++.+=+.+++|+..++.+...|+.|+-+.+.+
T Consensus         3 ~N~v~LiGrL~~DPelr~t~~--G-~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G   72 (121)
T PRK07459          3 LNSVTLVGRAGRDPEVRYFES--G-SVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITG   72 (121)
T ss_pred             ccEEEEEEEccCCCEEEEcCC--C-CEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEE
Confidence            367889999999888887543  2 257777776      235778999999999999999999999999886

>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

Probab=84.88  E-value=4.7  Score=37.53  Aligned_cols=107  Identities=18%  Similarity=0.341  Sum_probs=57.4

Q ss_pred             cchhhhhh---cccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCC
Q 006263          329 RHISEIES---AENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGF  405 (653)
Q Consensus       329 ~~i~~i~~---~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~  405 (653)
                      +.|++|.+   .+.=.-||++|+|+.|..      +.|-   .--+.|.|....-+.|-.|++...--   +.+.  -.+
T Consensus         4 ~~f~~l~~p~f~pp~~EvD~VG~VvsV~~------~~~f---~~~vYLsD~~~Nll~Ikfw~~l~~~~---~eDi--lk~   69 (143)
T PF09104_consen    4 THFSDLQDPDFQPPYGEVDTVGFVVSVSK------KQGF---QPLVYLSDECHNLLAIKFWTGLNQYG---YEDI--LKP   69 (143)
T ss_dssp             --CGGGGSTT--TCCCEEEEEEEEEEEE--------TTS-----EEEEE-TTS-EEEEEESS----------SS-----T
T ss_pred             echhhhcCcccCCCccccceEEEEEEEEe------cCCC---ceeEEeecCCccEEEEEeccCccccc---hhhh--cCc
Confidence            34566655   234568999999999921      1221   12378889999899999999986321   0011  146


Q ss_pred             CcEEEEEeeEee-cC-CCc-eeccccceEEEEcCC---hHH-HHHHHHHHh
Q 006263          406 FPVLSVKSGKVN-DF-SGK-SIGTIPSTQLFINPD---FAE-AHELREWFD  449 (653)
Q Consensus       406 ~~Vvaik~~rV~-~f-~G~-sLs~~~~S~i~inPd---ipe-~~~l~~w~~  449 (653)
                      +.+||+.+..-+ +. .|. .+-.+.-|.+.-||.   ..| ...|+.-+.
T Consensus        70 ~~liA~SNLqwR~~s~s~iP~~~A~d~S~FS~nPK~~hLqe~~~~Lk~~i~  120 (143)
T PF09104_consen   70 GSLIAASNLQWRPESTSGIPTLFATDLSVFSANPKESHLQEAFNKLKNTIE  120 (143)
T ss_dssp             T-EEEEEEEEE-S-TTSSS-EEEEECCEEEESS-SSCCCHHHHHHHCHHHH
T ss_pred             ceEEEEeeeEeecccccCCCeeEeccceeeecCccHHHHHHHHHHHHHHhh
Confidence            889999987664 22 333 455677788888883   333 345555444

OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.

>PRK13732 single-stranded DNA-binding protein; Provisional

Probab=84.67  E-value=3.9  Score=39.62  Aligned_cols=65  Identities=22%  Similarity=0.272  Sum_probs=51.5

Q ss_pred             CCCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC-------eEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG-------EIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       217 ~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~-------~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      .++..+|.||+.+--++|.+.+  | ..+.+|.|+      |.++|       -+++++|+..++.+...|+.|+.+++.
T Consensus         5 ~mN~V~LiGrLg~DPElR~t~n--G-~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~V~Ve   81 (175)
T PRK13732          5 GINKVILVGRLGKDPEVRYIPN--G-GAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIE   81 (175)
T ss_pred             CceEEEEEEEecCCCEEEEcCC--C-CEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence            3578999999999888888654  2 367777765      22223       468999999999999999999999988


Q ss_pred             c
Q 006263          284 K  284 (653)
Q Consensus       284 ~  284 (653)
                      +
T Consensus        82 G   82 (175)
T PRK13732         82 G   82 (175)
T ss_pred             E
Confidence            7

>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

Probab=84.60  E-value=2.8  Score=34.32  Aligned_cols=39  Identities=21%  Similarity=0.399  Sum_probs=29.5

Q ss_pred             EEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhh
Q 006263          345 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE  393 (653)
Q Consensus       345 VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~  393 (653)
                      |.|.|.++..     +|.|    .--++|.|.++ .+++++|.+....+
T Consensus         4 v~g~v~~i~~-----tk~g----~~~~~L~D~~~-~i~~~~f~~~~~~~   42 (78)
T cd04489           4 VEGEISNLKR-----PSSG----HLYFTLKDEDA-SIRCVMWRSNARRL   42 (78)
T ss_pred             EEEEEecCEE-----CCCc----EEEEEEEeCCe-EEEEEEEcchhhhC
Confidence            5677776553     3445    67899999998 89999999976553

E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.

>PRK08763 single-stranded DNA-binding protein; Provisional

Probab=84.07  E-value=4.4  Score=38.87  Aligned_cols=64  Identities=17%  Similarity=0.220  Sum_probs=50.6

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC------eEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG------EIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~------~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      .++..|.+|+.+--.+|...+  | ..+.+|.|+      |++|.      -+++++|+..++.....|+.|+-++|.+
T Consensus         5 ~Nkv~LiGrLg~DPelr~t~~--G-~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeG   80 (164)
T PRK08763          5 INKVILVGNLGNDPDIKYTQS--G-MTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEG   80 (164)
T ss_pred             ceEEEEEEEecCCCeEEEcCC--C-CeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEEE
Confidence            678999999999888886543  2 357677665      43443      3899999999999999999999999886

>PRK05159 aspC aspartyl-tRNA synthetase; Provisional

Probab=84.03  E-value=6.6  Score=43.84  Aligned_cols=92  Identities=15%  Similarity=0.099  Sum_probs=65.4

Q ss_pred             eeccccCCCC--CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH---HHHHHhhcccCcEEEEe
Q 006263          209 IPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV---VDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       209 ~pI~~L~p~~--~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~---~~kf~~~l~eG~vy~is  283 (653)
                      +.|.+|++..  ..-+|+|||.++   |.      .|++.-++|.| .+|.|++++-.+.   ..++-..|..|+++.+.
T Consensus         5 ~~~~~l~~~~~g~~V~i~GrV~~~---R~------~gk~~Fl~LrD-~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~   74 (437)
T PRK05159          5 HLTSELTPELDGEEVTLAGWVHEI---RD------LGGIAFLILRD-RSGIIQVVVKKKVDEELFETIKKLKRESVVSVT   74 (437)
T ss_pred             eEhhhCChhhCCCEEEEEEEeEee---ec------CCCeEEEEEEc-CCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEE
Confidence            4678888776  468899999875   33      35777788999 6779999986432   23344668999999999


Q ss_pred             ceEEecCCCcccCCCCceEEEeccccEEEecc
Q 006263          284 KGSLKPAQKNFNHLKNEWEIFLEATSTVDLCT  315 (653)
Q Consensus       284 ~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~  315 (653)
                      +.-++...     ....+||....-+.+..+.
T Consensus        75 G~v~~~~~-----~~~~~el~~~~i~vls~a~  101 (437)
T PRK05159         75 GTVKANPK-----APGGVEVIPEEIEVLNKAE  101 (437)
T ss_pred             EEEEcCCC-----CCCCEEEEEeEEEEEeCCC
Confidence            96554321     2356999997777776663

>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)

Probab=83.79  E-value=2  Score=36.85  Aligned_cols=53  Identities=17%  Similarity=0.151  Sum_probs=38.2

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHH---HHHhhcccCcEEEEec
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD---RFYEIIEVGRVYLISK  284 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~---kf~~~l~eG~vy~is~  284 (653)
                      ++.|+|.++..         .+..+.+.|.| .+|.|.|.+|...-+   .-.+.+++|+++.+.+
T Consensus         3 ~~vG~V~~~~~---------~~~~~~~tL~D-~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G   58 (95)
T cd04478           3 TLVGVVRNVEE---------QSTNITYTIDD-GTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFG   58 (95)
T ss_pred             EEEEEEEeeeE---------cccEEEEEEEC-CCCcEEEEEeCCCCCcccccccccccCCEEEEEE
Confidence            45666666432         13568999999 788999999986532   3467799999776654

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam

>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

Probab=83.50  E-value=4.6  Score=34.83  Aligned_cols=47  Identities=19%  Similarity=0.174  Sum_probs=38.6

Q ss_pred             EEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263          370 ILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       370 ~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                      ++.|+|+.|..|..+++.+++..|...|.      +|.+..|.+..|..-.|.
T Consensus         1 emvL~De~G~~I~A~I~~~~~~~f~~~l~------Eg~~y~i~~F~V~~~~~~   47 (95)
T PF02721_consen    1 EMVLVDEKGDKIQATIPKELVDKFKDSLK------EGSWYTISNFTVSPNSGS   47 (95)
T ss_pred             CEEEEecCCCEEEEEECHHHHHHHHhhcc------cCCEEEeEeEEEEeCCCc
Confidence            47899999999999999999888654442      578999999999876664

>PLN02502 lysyl-tRNA synthetase

Probab=83.02  E-value=6.5  Score=45.12  Aligned_cols=79  Identities=25%  Similarity=0.403  Sum_probs=57.2

Q ss_pred             CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH-------HHHHHhhcccCcEEEEeceEEecCC
Q 006263          219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-------VDRFYEIIEVGRVYLISKGSLKPAQ  291 (653)
Q Consensus       219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~-------~~kf~~~l~eG~vy~is~~~V~~a~  291 (653)
                      ...+|.|||.++   |.      .|++.-++|.| .+|.|++.+-.+.       .+++...|..|+++.+.+.-.+.. 
T Consensus       109 ~~V~v~GrV~~~---R~------~Gk~~F~~LrD-~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~-  177 (553)
T PLN02502        109 VSVSVAGRIMAK---RA------FGKLAFYDLRD-DGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTK-  177 (553)
T ss_pred             CEEEEEEEEEEE---ec------CCCeEEEEEec-CCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecC-
Confidence            358899999875   32      36787889999 6889999886432       334445689999999998755432 


Q ss_pred             CcccCCCCceEEEeccccEEEec
Q 006263          292 KNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       292 ~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                            ...++|...+-+.+.+|
T Consensus       178 ------~gelel~~~~i~vLs~~  194 (553)
T PLN02502        178 ------KGELSIFPTSFEVLTKC  194 (553)
T ss_pred             ------CCCEEEEEeEEEEEecc
Confidence                  23688888777666666

>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)

Probab=82.92  E-value=6.2  Score=33.14  Aligned_cols=59  Identities=19%  Similarity=0.245  Sum_probs=43.5

Q ss_pred             eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEch-hHHHHHHhhcc-cCcEEEEece
Q 006263          221 WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFN-AVVDRFYEIIE-VGRVYLISKG  285 (653)
Q Consensus       221 w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~-~~~~kf~~~l~-eG~vy~is~~  285 (653)
                      -+|+|.|... +.|..++  | ..++++.|.| ..+.|.|..|. +..+.+ ..|+ +|+|+.+.+=
T Consensus         2 v~i~G~Vf~~-e~re~k~--g-~~i~~~~itD-~t~Si~~K~F~~~~~~~~-~~ik~~G~~v~v~G~   62 (82)
T cd04484           2 VVVEGEVFDL-EIRELKS--G-RKILTFKVTD-YTSSITVKKFLRKDEKDK-EELKSKGDWVRVRGK   62 (82)
T ss_pred             EEEEEEEEEE-EEEEecC--C-CEEEEEEEEc-CCCCEEEEEeccCChhHH-hhcccCCCEEEEEEE
Confidence            3678888765 4455543  2 4688999999 78999999998 344444 6689 9999988763

Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.

>PRK07275 single-stranded DNA-binding protein; Provisional

Probab=82.77  E-value=3.7  Score=39.27  Aligned_cols=64  Identities=14%  Similarity=0.191  Sum_probs=51.1

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eC----CCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS----DGGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~----~g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      +++..|.||+++--++|...+  | ..+.+|.|+      +.    +.+-|++++|+..++.+...|+.|+-+.|.+
T Consensus         2 ~N~v~LiGrL~~DPElr~t~s--G-~~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae~~~~~l~KG~~V~VeG   75 (162)
T PRK07275          2 INNVVLVGRMTRDAELRYTPS--N-VAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALIGVTG   75 (162)
T ss_pred             eeEEEEEEEECCCCeEEECCC--C-CEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHHHHHHcCCCCEEEEEE
Confidence            367889999999999987643  2 257777775      32    3467999999999999999999999988876

>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB)

Probab=82.76  E-value=5.1  Score=34.30  Aligned_cols=62  Identities=19%  Similarity=0.310  Sum_probs=46.4

Q ss_pred             EEEEEEEeeccccccccCCCCceeEEEEEE-----------eCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          222 AIKARVTAKGDLRRYNNARGDGKVFSFDLL-----------DSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       222 ~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~-----------D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      +|.|||...-.+|...+  | ..+.+|.|.           +....-+++++|++.++.+...++.|+.+.+.+..
T Consensus         2 ~l~G~l~~~p~~~~~~~--g-~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~l   74 (100)
T cd04496           2 ILIGRLGKDPELRYTPS--G-TPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRL   74 (100)
T ss_pred             EEEEEecCCCEEEECCC--C-CEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEEE
Confidence            46788888777776543  1 245455442           23567899999999999999999999999999853

SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart

>PRK05813 single-stranded DNA-binding protein; Provisional

Probab=82.75  E-value=56  Score=32.89  Aligned_cols=162  Identities=15%  Similarity=0.221  Sum_probs=98.7

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEE-----EeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec-eEEecCC
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDL-----LDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK-GSLKPAQ  291 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L-----~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~-~~V~~a~  291 (653)
                      .++-.+.||+++--++|+-  ..|++ +..|.|     .| ..+.|.+++|..+++...  |..|+-+.+.+ ++     
T Consensus         8 ~NkV~L~Grl~~d~e~~~~--~~G~~-~~~f~laV~R~s~-~~D~i~v~v~~rlae~~~--l~kG~~v~VeGqlr-----   76 (219)
T PRK05813          8 NNKVYLEGKVVSELEFSHE--MYGEG-FYNFKLEVPRLSD-SKDILPVTVSERLLAGMD--LKVGTLVIVEGQLR-----   76 (219)
T ss_pred             cCEEEEEEEEcCCceEEEE--eCCeE-EEEEEEEeeccCC-CccEEEEEEEhhhhhhhc--ccCCCEEEEEEEEE-----
Confidence            3678899999999998873  33554 344443     35 789999999999998777  99999888876 44     


Q ss_pred             Cccc---CCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeE
Q 006263          292 KNFN---HLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQR  368 (653)
Q Consensus       292 ~~f~---~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~k  368 (653)
                       .|+   ...+.|.+.+-.. .|+.+... .                ....-..|-++|.+..--.+.  .+.+|+.+  
T Consensus        77 -sy~~~~~G~~R~vl~V~a~-~i~~l~~~-~----------------~~~~~N~V~LiGrL~~DPelR--~t~~G~~v--  133 (219)
T PRK05813         77 -SYNKFIDGKNRLILTVFAR-NIEYCDER-S----------------DIKNPNEIFLDGYICKEPVYR--TTPFGREI--  133 (219)
T ss_pred             -EeccCCCCcEEEEEEEEEE-EEEEccCC-C----------------ccCCccEEEEEEEccCCCeEE--ECCCCCEE--
Confidence             232   2344555444321 23333111 0                011234677888887653333  23456644  


Q ss_pred             EEEEEEeCC----CCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee-EeecCC
Q 006263          369 RILNLKDTS----GRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG-KVNDFS  420 (653)
Q Consensus       369 r~i~l~D~s----~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~-rV~~f~  420 (653)
                      -.|.|.-..    ..-|.|++||..|...     ..+  ..|.-|++.|- +...|.
T Consensus       134 a~f~lAvnr~~~~td~i~~v~wg~~Ae~~-----~~l--~KG~~V~V~GrL~sr~y~  183 (219)
T PRK05813        134 ADLLLAVNRPYNKSDYIPCIAWGRNARFC-----KTL--EVGDNIRVWGRVQSREYQ  183 (219)
T ss_pred             EEEEEEEcCCCCCceEEEEEEEhHHhHHH-----hhC--CCCCEEEEEEEEEecceE
Confidence            445554321    2479999999998652     223  35777777644 445564

>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)

Probab=82.64  E-value=5.5  Score=32.66  Aligned_cols=63  Identities=27%  Similarity=0.387  Sum_probs=38.9

Q ss_pred             EEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCC
Q 006263          345 VIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG  421 (653)
Q Consensus       345 VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G  421 (653)
                      .+.+|.++..   ..+|.|+  ....++|.|.+| .+++++|++.-..     ...+  ..+.++.+. ++|..|+|
T Consensus         2 ~~~~v~~~~~---~~tk~g~--~~~~~~l~D~tg-~i~~~~f~~~~~~-----~~~l--~~g~~v~v~-G~v~~~~~   64 (83)
T cd04492           2 GFFLIKSKEL---RTAKNGK--PYLALTLQDKTG-EIEAKLWDASEED-----EEKF--KPGDIVHVK-GRVEEYRG   64 (83)
T ss_pred             cEEEEEEeee---ecccCCC--cEEEEEEEcCCC-eEEEEEcCCChhh-----HhhC--CCCCEEEEE-EEEEEeCC
Confidence            3445555443   2345565  357899999999 7999999965321     2223  245566555 66776766

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

>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 []

Probab=82.33  E-value=5.9  Score=37.13  Aligned_cols=84  Identities=11%  Similarity=0.154  Sum_probs=58.6

Q ss_pred             eeccccCCC-CCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC-------CeEEEEEchhHHHHHHhhcccCcEE
Q 006263          209 IPIAALNPY-QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-------GEIRVTCFNAVVDRFYEIIEVGRVY  280 (653)
Q Consensus       209 ~pI~~L~p~-~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g-------~~I~at~f~~~~~kf~~~l~eG~vy  280 (653)
                      +||+.+.-. ...-.|.|-|+.....+... .+|..-..+|.|.|...       ..|.+.+|....+.+-..-..|+|+
T Consensus         2 ~~l~~~~~~~~~~vnvigVV~~~~~p~~~~-t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii   80 (146)
T PF02765_consen    2 TPLSTAKEKFGKFVNVIGVVVDFSPPNPKK-TRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDII   80 (146)
T ss_dssp             CCGGGSCTTSSEEEEEEEEEEEEEEECTEE-ESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEE
T ss_pred             ccchhhhhcCCCEEEEEEEEEEccCCcceE-cCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEE
Confidence            455533323 23577888888877662222 23444678899999643       5799999988877775555559999


Q ss_pred             EEeceEEecCCCc
Q 006263          281 LISKGSLKPAQKN  293 (653)
Q Consensus       281 ~is~~~V~~a~~~  293 (653)
                      .+.+++|+.-+.+
T Consensus        81 ~l~r~kv~~~~~~   93 (146)
T PF02765_consen   81 RLRRVKVQSYNGK   93 (146)
T ss_dssp             EEEEEEEEEETTE
T ss_pred             EEEEEEEEEECCE
Confidence            9999999877754

It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....

>PRK09010 single-stranded DNA-binding protein; Provisional

Probab=82.21  E-value=10  Score=36.77  Aligned_cols=64  Identities=20%  Similarity=0.245  Sum_probs=51.0

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCC-------CCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSD-------GGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~-------g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      .++.+|.+||.+--.+|.+.+  | ..+.+|.|+      |.+       ..-+++++|+..++.+...|+.|+-++|..
T Consensus         6 ~N~V~LiGrLg~DPelR~t~n--G-~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L~KGs~V~VeG   82 (177)
T PRK09010          6 VNKVILVGNLGQDPEVRYMPN--G-GAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYIEG   82 (177)
T ss_pred             ceEEEEEEEeCCCceEEEcCC--C-CEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhcCCCCEEEEEE
Confidence            578999999999999998754  2 367777664      322       234699999999999999999999999887

>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS

Probab=81.77  E-value=12  Score=34.47  Aligned_cols=86  Identities=15%  Similarity=0.119  Sum_probs=55.9

Q ss_pred             CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHH--HHHhhcccCcEEEEeceEEecCC--Ccc
Q 006263          219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVD--RFYEIIEVGRVYLISKGSLKPAQ--KNF  294 (653)
Q Consensus       219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~--kf~~~l~eG~vy~is~~~V~~a~--~~f  294 (653)
                      ..-+|+|||.++   |.      .|++.-++|.| .++.+++++..+..+  ++...|..|+++.+.+--.....  +.-
T Consensus        15 ~~V~i~Gwv~~~---R~------~gk~~Fi~LrD-~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~   84 (135)
T cd04317          15 QEVTLCGWVQRR---RD------HGGLIFIDLRD-RYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNP   84 (135)
T ss_pred             CEEEEEEeEehh---cc------cCCEEEEEEec-CCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCC
Confidence            358899999663   33      35666678888 567899998654333  34456999999999996443221  111


Q ss_pred             cCCCCceEEEeccccEEEec
Q 006263          295 NHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       295 ~~~~~~yei~f~~~T~I~~~  314 (653)
                      .....++||....-..+.++
T Consensus        85 ~~~~~~~El~~~~i~vl~~~  104 (135)
T cd04317          85 KLPTGEIEVVASELEVLNKA  104 (135)
T ss_pred             CCCCCcEEEEEeEEEEEECC
Confidence            12345799998765555544

These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh

>PRK07772 single-stranded DNA-binding protein; Provisional

Probab=81.19  E-value=8.3  Score=37.78  Aligned_cols=64  Identities=17%  Similarity=0.271  Sum_probs=48.7

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eC--------CCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS--------DGGEIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~--------~g~~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      .+..+|.+|++.--.+|...+  | ..+.+|.|+      |.        +..-|++++|+.+++.+...|+.|+-+.+.
T Consensus         4 ~~~VtLiGrL~~DPElR~t~s--G-~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~   80 (186)
T PRK07772          4 DTTITVVGNLTADPELRFTPS--G-AAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVT   80 (186)
T ss_pred             cCEEEEEEEeCCCCeEEEcCC--C-CEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence            356789999999988887643  2 245566655      11        234679999999999999999999999888


Q ss_pred             c
Q 006263          284 K  284 (653)
Q Consensus       284 ~  284 (653)
                      .
T Consensus        81 G   81 (186)
T PRK07772         81 G   81 (186)
T ss_pred             E
Confidence            6

>PRK06293 single-stranded DNA-binding protein; Provisional

Probab=81.14  E-value=5.6  Score=38.00  Aligned_cols=64  Identities=16%  Similarity=0.125  Sum_probs=51.3

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEEe-------CCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD-------SDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D-------~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      ++..+|.+|+.+--.+|...+  | ..+.+|.|+=       ++..-|++++|+..++.....|+.|+-+.+.+
T Consensus         1 MN~V~LiGrLg~DPElR~t~s--G-~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeG   71 (161)
T PRK06293          1 MMFGYIVGRLGADPEERMTSK--G-KRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAG   71 (161)
T ss_pred             CeEEEEEEEecCCCeEEEcCC--C-CEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEE
Confidence            467889999999888887543  2 2577777762       24667999999999999999999999999886

>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)

Probab=81.05  E-value=5.9  Score=33.34  Aligned_cols=52  Identities=15%  Similarity=0.077  Sum_probs=41.4

Q ss_pred             eeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263          365 ETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       365 ~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                      .....++.|.|+.|..|..+.+.+.+..|...|.      +|-+..|.+.+|..-.+.
T Consensus        17 ~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~------eg~vy~is~f~v~~~~~~   68 (86)
T cd04480          17 SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLK------EGKWYTISNFEVAPNTGS   68 (86)
T ss_pred             CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhce------eCCEEEEeeEEEEcCCCc
Confidence            3456789999999999999999999888654443      478888999999876553

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.

>cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD

Probab=81.03  E-value=3.6  Score=35.96  Aligned_cols=39  Identities=18%  Similarity=0.295  Sum_probs=34.7

Q ss_pred             ceEEEEEecccceeeeeecccchhhcccCCcccCcEEEE
Q 006263           37 ERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQL   75 (653)
Q Consensus        37 ~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sIIkl   75 (653)
                      ..-.+.|+||=|.+++.+...|+.++++|.|..|.=+++
T Consensus        21 ~~~~lEltDGWYsi~a~lD~~L~~~l~~gkl~vGqKL~i   59 (100)
T cd04493          21 HMPIIELTDGWYSIRAQLDPPLTNLVRKGKLRVGQKLRI   59 (100)
T ss_pred             cccEEEEecCeEEEEEEeCHHHHHHHHcCCeecccEEEE
Confidence            456899999999999999999999999999998876655

BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly.

>PRK13480 3'-5' exoribonuclease YhaM; Provisional

Probab=80.59  E-value=8.2  Score=41.06  Aligned_cols=75  Identities=25%  Similarity=0.336  Sum_probs=51.6

Q ss_pred             hhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe
Q 006263          334 IESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS  413 (653)
Q Consensus       334 i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~  413 (653)
                      |.++..+..|+.+..|++..--   ++|+|+.  ...++|.|.|| +|+..+|+..-..     ...|.  .+.||-++|
T Consensus         5 i~~l~~g~~v~~~~lv~~~~~~---~~knG~~--yl~l~l~D~tG-~I~ak~W~~~~~~-----~~~~~--~g~vv~v~G   71 (314)
T PRK13480          5 IEELEVGEQVDHFLLIKSATKG---VASNGKP--FLTLILQDKSG-DIEAKLWDVSPED-----EATYV--PETIVHVKG   71 (314)
T ss_pred             HhhcCCCCEeeEEEEEEEceee---ecCCCCe--EEEEEEEcCCc-EEEEEeCCCChhh-----HhhcC--CCCEEEEEE
Confidence            3344457788888888876432   2467764  78999999999 8999999975322     23343  466776654


Q ss_pred             eEeecCCCc
Q 006263          414 GKVNDFSGK  422 (653)
Q Consensus       414 ~rV~~f~G~  422 (653)
                       +|.+|+|+
T Consensus        72 -~v~~y~g~   79 (314)
T PRK13480         72 -DIINYRGR   79 (314)
T ss_pred             -EEEEECCc
Confidence             55689985

>PTZ00417 lysine-tRNA ligase; Provisional

Probab=80.11  E-value=10  Score=43.82  Aligned_cols=78  Identities=28%  Similarity=0.349  Sum_probs=52.1

Q ss_pred             ceEEEEEEEeeccccccccCCCCc-eeEEEEEEeCCCCeEEEEEchhH-------HHHHHhhcccCcEEEEeceEEecCC
Q 006263          220 RWAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAV-------VDRFYEIIEVGRVYLISKGSLKPAQ  291 (653)
Q Consensus       220 ~w~I~~RV~~k~~ir~~~~~~g~g-k~f~~~L~D~~g~~I~at~f~~~-------~~kf~~~l~eG~vy~is~~~V~~a~  291 (653)
                      ..+|.|||.++   |.      .| ++.-++|.| +||.||+.+-.+.       .+.+...|..|+++.+.+.-.+   
T Consensus       134 ~v~v~Grv~~~---R~------~G~k~~F~~L~d-~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~---  200 (585)
T PTZ00417        134 ILNVTGRIMRV---SA------SGQKLRFFDLVG-DGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGK---  200 (585)
T ss_pred             eEEEEEEEEee---ec------CCCCCEEEEEEe-CCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcC---
Confidence            47899999874   43      25 566678889 7889999996431       2333456999999999997322   


Q ss_pred             CcccCCCCceEEEeccccEEEec
Q 006263          292 KNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       292 ~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                          +-...++|....-+.+.++
T Consensus       201 ----t~~gel~i~~~~i~llsk~  219 (585)
T PTZ00417        201 ----SKKGELSIFPKETIILSPC  219 (585)
T ss_pred             ----CCCceEEEEEEEEEEEecC
Confidence                1134566666655555544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	653
4gop_C	444	Structure And Conformational Change Of A Replicatio		1e-79
1fgu_A	252	Ssdna-Binding Domain Of The Large Subunit Of Replic		1e-48
1jmc_A	246	Single Stranded Dna-Binding Domain Of Human Replica		1e-47
1l1o_C	181	Structure Of The Human Replication Protein A (Rpa)		1e-24
1ynx_A	114	Solution Structure Of Dna Binding Domain A (Dbd-A)		3e-22
2b29_A	123	N-Terminal Domain Of The Rpa70 Subunit Of Human Rep		2e-09
1ewi_A	114	Human Replication Protein A: Global Fold Of The N-T		9e-09

>pdb|4GOP|C Chain C, Structure And Conformational Change Of A Replication Protein A Heterotrimer Bound To Ssdna Length = 444

Iteration: 1
 Score =  294 bits (753), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 166/450 (36%), Positives = 246/450 (54%), Gaps = 22/450 (4%)
Query: 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV 267
           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: 268 DRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFS 327
           DRFY +++   VYLISK  +  A+K F++L+NE+EI  E ++ ++ CT+  D +P+ ++ 
Sbjct: 62  DRFYPLLQENHVYLISKARVNIAKKQFSNLQNEYEITFENSTEIEECTDATD-VPEVKYE 120
Query: 328 FRHISEIESAEXXXXXXXXXXXXXXXPSVPILRKNGME-TQRRILNLKDTSGRSVELTLW 386
           F  I+E+ES E                   I+ K      Q+R L L D   RSV+LTLW
Sbjct: 121 FVRINELESVEANQQCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTLW 180
Query: 387 GDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELRE 446
           G    K  +       V   PVL+ K  KV DF G+S+    S+ + INPD  E+H LR 
Sbjct: 181 G----KTAETFPTNAGVDEKPVLAFKGVKVGDFGGRSLSMFSSSTMLINPDITESHVLRG 236
Query: 447 WFDSGGKNA--------ATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRA 498
           W+D+ G +A             +      GA     +T+ Q+K+E LG SEKPD+  VRA
Sbjct: 237 WYDNDGAHAQFQPYTNGGVGGGAMGGGGAGANMAERRTIVQVKDENLGMSEKPDYFNVRA 296
Query: 499 FITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQD 557
            + +IK ++  YTAC        CNKKV     N W+C++C++     +YRY+L   + D
Sbjct: 297 TVVYIKQENLYYTAC----ASEGCNKKVNLDHENNWRCEKCDRSYATPEYRYILSTNVAD 352
Query: 558 QTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEEL 617
            TG  W++ F E   +++G  A EL+ L+ E + +  F   +       Y+F  + K + 
Sbjct: 353 ATGQMWLSGFNEDATQLIGMSAGELHKLREESESE--FSAALHRAANRMYMFNCRAKMDT 410
Query: 618 YGDEQRVKITVIRADQVNYSSESRYLLDLI 647
           + 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

Iteration: 1
 Score =  191 bits (485), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 102/257 (39%), Positives = 153/257 (59%), Gaps = 11/257 (4%)
Query: 206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
           ++++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D + GEIR T FN 
Sbjct: 2   SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNE 60
Query: 266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
            VD+F+ +IEV +VY  SKG+LK A K F  +KN++E+     ++V  C E+D  +P  Q
Sbjct: 61  QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHLPTVQ 119
Query: 326 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 384
           F F  I ++E+                  +  I +R N  E  +R + L DTSG+ V  T
Sbjct: 120 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 179
Query: 385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
           LWG+  +K     Q        PVL++K  +V+DF G+S+  + S+ +  NPD  EA++L
Sbjct: 180 LWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKL 231
Query: 445 REWFDSGGKNAATVSIS 461
           R WFD+ G+    VSIS
Sbjct: 232 RGWFDAEGQALDGVSIS 248

>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

Iteration: 1
 Score =  187 bits (476), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/249 (39%), Positives = 149/249 (59%), Gaps = 11/249 (4%)
Query: 206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
           ++++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D + GEIR T FN 
Sbjct: 6   SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNE 64
Query: 266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
            VD+F+ +IEV +VY  SKG+LK A K F  +KN++E+     ++V  C E+D  +P  Q
Sbjct: 65  QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHLPTVQ 123
Query: 326 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 384
           F F  I ++E+                  +  I +R N  E  +R + L DTSG+ V  T
Sbjct: 124 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 183
Query: 385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
           LWG+  +K     Q        PVL++K  +V+DF G+S+  + S+ +  NPD  EA++L
Sbjct: 184 LWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKL 235
Query: 445 REWFDSGGK 453
           R WFD+ G+
Sbjct: 236 RGWFDAEGQ 244

>pdb|1L1O|C Chain C, Structure Of The Human Replication Protein A (Rpa) Trimerization Core Length = 181

Iteration: 1
 Score =  111 bits (277), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 65/184 (35%), Positives = 102/184 (55%), Gaps = 7/184 (3%)
Query: 468 GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT 527
           G  N   KT+ ++K+E LG+ +KPD+ +  A + +++ ++  Y ACP     + CNKKV 
Sbjct: 1   GGSNTNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPT----QDCNKKVI 56
Query: 528 -QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLK 586
            Q    ++C++C+ E     YR +L   I D     WVT FQES E ILG  A  L  LK
Sbjct: 57  DQQNGLYRCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK 116
Query: 587 YELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDL 646
              +++  F E+ ++  F  ++FR+++K E Y DE R+K TV+    V+Y    R L+  
Sbjct: 117 --DKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMS 174
Query: 647 ISKS 650
           I +S
Sbjct: 175 IRRS 178

>pdb|1YNX|A Chain A, Solution Structure Of Dna Binding Domain A (Dbd-A) Of S.Cerevisiae Replication Protein A (Rpa) Length = 114

Iteration: 1
 Score =  103 bits (257), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 47/112 (41%), Positives = 75/112 (66%), Gaps = 1/112 (0%)
Query: 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV 267
           I  I  L+PYQ  W IKARV+ KG+++ ++N RGDGK+F+ + LD+  GEIR T FN   
Sbjct: 4   IFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDT-SGEIRATAFNDFA 62
Query: 268 DRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDD 319
            +F EI++ G+VY +SK  L+PA+  F +L + +E+ L+  + ++ C +E +
Sbjct: 63  TKFNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDESN 114

>pdb|2B29|A Chain A, N-Terminal Domain Of The Rpa70 Subunit Of Human Replication Protein A. Length = 123

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 38/110 (34%), Positives = 71/110 (64%), Gaps = 9/110 (8%)
Query: 11  SLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQLNDRVKTGQV 67
           +++  GD N KP++QV++I+ I  G++  RYR L+SD ++T  + MLATQLN  V+  Q+
Sbjct: 15  AIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQL 74
Query: 68  KKGSVVQLIDYICSTVQN-RKIIVVLNMETIILDCEP----IGNPKIFSE 112
               V Q+  +I +T+++ R++++++ +E ++   E     IGNP  ++E
Sbjct: 75  SSNCVCQIHRFIVNTLKDGRRVVILMELE-VLKSAEAVGVKIGNPVPYNE 123

>pdb|1EWI|A Chain A, Human Replication Protein A: Global Fold Of The N-Terminal Rpa-70 Domain Reveals A Basic Cleft And Flexible C- Terminal Linker Length = 114

Iteration: 1
 Score = 58.9 bits (141), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 62/91 (68%), Gaps = 4/91 (4%)
Query: 11  SLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQLNDRVKTGQV 67
           +++  GD N KP++QV++I+ I  G++  RYR L+SD ++T  + MLATQLN  V+  Q+
Sbjct: 12  AIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQL 71
Query: 68  KKGSVVQLIDYICSTVQN-RKIIVVLNMETI 97
               V Q+  +I +T+++ R++++++ +E +
Sbjct: 72  SSNCVCQIHRFIVNTLKDGRRVVILMELEVL 102

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	653
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	3e-69
1l1o_C	181	Replication protein A 70 kDa DNA-binding subunit;	1e-63
3u50_C	172	Telomerase-associated protein 82; TEB1, processivi	1e-50
1ynx_A	114	Replication factor-A protein 1; canonical OB fold,	1e-39
2b29_A	123	Replication protein A 70 kDa DNA-binding subunit;	2e-31
2k50_A	115	Replication factor A related protein; uncharacteri	2e-13
2k50_A	115	Replication factor A related protein; uncharacteri	5e-09
1o7i_A	119	SSB, SSO2364, single stranded DNA binding protein;	3e-13
1o7i_A	119	SSB, SSO2364, single stranded DNA binding protein;	1e-06
3dm3_A	105	Replication factor A; probably plays AN essential	3e-06
3e0e_A	97	Replication protein A; structural genomics, PSI-2,	4e-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

 Score =  224 bits (572), Expect = 3e-69
 Identities = 103/250 (41%), Positives = 157/250 (62%), Gaps = 11/250 (4%)

Query: 206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
           ++++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D   GEIR T FN 
Sbjct: 6   SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDES-GEIRATAFNE 64

Query: 266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
            VD+F+ +IEV +VY  SKG+LK A K F  +KN++E+     ++V  C ++   +P  Q
Sbjct: 65  QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDDHH-LPTVQ 123

Query: 326 FSFRHISEIESAENNSIVDVIGIVISVNPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 384
           F F  I ++E+   +S+VD+IGI  S   +  I +R N  E  +R + L DTSG+ V  T
Sbjct: 124 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 183

Query: 385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
           LWG+  +K     Q        PVL++K  +V+DF G+S+  + S+ +  NPD  EA++L
Sbjct: 184 LWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKL 235

Query: 445 REWFDSGGKN 454
           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

 Score =  207 bits (527), Expect = 1e-63
 Identities = 64/183 (34%), Positives = 101/183 (55%), Gaps = 7/183 (3%)

Query: 468 GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT 527
           G  N   KT+ ++K+E LG+ +KPD+ +  A + +++ ++  Y ACP     + CNKKV 
Sbjct: 1   GGSNTNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACP----TQDCNKKVI 56

Query: 528 QSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLK 586
              N  ++C++C+ E     YR +L   I D     WVT FQES E ILG  A  L  LK
Sbjct: 57  DQQNGLYRCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK 116

Query: 587 YELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDL 646
            +  ++  F E+ ++  F  ++FR+++K E Y DE R+K TV+    V+Y    R L+  
Sbjct: 117 DK--NEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMS 174

Query: 647 ISK 649
           I +
Sbjct: 175 IRR 177

>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae} Length = 114

 Score =  140 bits (354), Expect = 1e-39
 Identities = 47/113 (41%), Positives = 74/113 (65%), Gaps = 1/113 (0%)

Query: 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV 266
            I  I  L+PYQ  W IKARV+ KG+++ ++N RGDGK+F+ + LD   GEIR T FN  
Sbjct: 3   PIFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLD-TSGEIRATAFNDF 61

Query: 267 VDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDD 319
             +F EI++ G+VY +SK  L+PA+  F +L + +E+ L+  + ++ C +E +
Sbjct: 62  ATKFNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDESN 114

>2b29_A Replication protein A 70 kDa DNA-binding subunit; 1.60A {Homo sapiens} SCOP: b.40.4.3 PDB: 2b3g_A 1ewi_A Length = 123

 Score =  117 bits (294), Expect = 2e-31
 Identities = 40/120 (33%), Positives = 71/120 (59%), Gaps = 8/120 (6%)

Query: 1   MPVNLTPNSISLI-NGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSV-STQHAMLAT 56
           M   L+  +I+ I   GD N KP++QV++I+ I  G++  RYR L+SD + +    MLAT
Sbjct: 4   MVGQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLAT 63

Query: 57  QLNDRVKTGQVKKGSVVQLIDYICSTVQN-RKIIVVLNMETIILDCEP---IGNPKIFSE 112
           QLN  V+  Q+    V Q+  +I +T+++ R++++++ +E +         IGNP  ++E
Sbjct: 64  QLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNE 123

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Length = 115

 Score = 66.1 bits (161), Expect = 2e-13
 Identities = 22/115 (19%), Positives = 40/115 (34%), Gaps = 10/115 (8%)

Query: 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGD-GKVFSFDLLDSDGGEIRVTCFNA 265
           R+  I+ L        +  RV      R +   +G  GK+ +  + D D GE+R   +  
Sbjct: 6   RMDTISKLEEGA-ETPVTGRVMKISSPRTFTTRKGREGKLANVIIAD-DTGELRAVFWTE 63

Query: 266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDS 320
            +    +    G V  I   +++             E  L   STV++    +  
Sbjct: 64  NIK-LLKKFREGDVIRIKDVNIRGG------FGGRKEAHLMPRSTVEVLDPLEHH 111

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Length = 115

 Score = 53.4 bits (128), Expect = 5e-09
 Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 10/115 (8%)

Query: 331 ISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFC 390
           +  I   E  +   V G V+ ++       + G E +   + + D +G  +    W +  
Sbjct: 7   MDTISKLEEGAETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGE-LRAVFWTENI 65

Query: 391 NKEGQKLQEMVDVGFFPVLSVKSGKVND-FSGK-SIGTIPSTQLFINPDFAEAHE 443
                KL +    G   V+ +K   +   F G+     +P + + +       H 
Sbjct: 66  -----KLLKKFREG--DVIRIKDVNIRGGFGGRKEAHLMPRSTVEVLDPLEHHHH 113

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Length = 119

 Score = 65.6 bits (160), Expect = 3e-13
 Identities = 18/135 (13%), Positives = 41/135 (30%), Gaps = 21/135 (15%)

Query: 211 IAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRF 270
           +  L P      +  RV    + R+     G   +    + D   G +++T +       
Sbjct: 5   VGNLKPNMESVNVTVRVLEASEARQIQTKNGVRTISEAIVGDET-GRVKLTLWGKHAGS- 62

Query: 271 YEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRH 330
              I+ G+V  I               K + ++   + + +      +D  P+       
Sbjct: 63  ---IKEGQVVKIENAW-------TTAFKGQVQLNAGSKTKIAEA--SEDGFPE------- 103

Query: 331 ISEIESAENNSIVDV 345
            S+I      +   +
Sbjct: 104 SSQIPENTPTAPQQM 118

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Length = 119

 Score = 46.8 bits (111), Expect = 1e-06
 Identities = 24/119 (20%), Positives = 48/119 (40%), Gaps = 17/119 (14%)

Query: 331 ISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFC 390
           +  ++    +  V+V   V+  + +  I  KNG         + D +GR V+LTLWG   
Sbjct: 5   VGNLKPNMES--VNVTVRVLEASEARQIQTKNG-VRTISEAIVGDETGR-VKLTLWGKHA 60

Query: 391 NKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPD--FAEAHELRE 446
                     +  G   V+ +++     F G+  +     T++    +  F E+ ++ E
Sbjct: 61  GS--------IKEG--QVVKIENAWTTAFKGQVQLNAGSKTKIAEASEDGFPESSQIPE 109

>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii} Length = 105

 Score = 45.4 bits (107), Expect = 3e-06
 Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 9/91 (9%)

Query: 330 HISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDF 389
           +I E+            G VIS  P     R +G   + +   ++D +G  + +TLW + 
Sbjct: 7   NIGELSPGMT---ATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGS-IRVTLWDNL 62

Query: 390 CN---KEGQ--KLQEMVDVGFFPVLSVKSGK 415
            +     G   +++  +  G++  L   +  
Sbjct: 63  TDIDVGRGDYVRVRGYIREGYYGGLECTANY 93

>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

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 334 IESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKE 393
           I     N    +   V++  P     RK+G + Q + L LKD +G  +  TLW +  + E
Sbjct: 5   ISELMPNLSGTINAEVVTAYPKKEFSRKDGTKGQLKSLFLKDDTGS-IRGTLWNELADFE 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	653
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	100.0
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	100.0
1l1o_C	181	Replication protein A 70 kDa DNA-binding subunit;	100.0
3u50_C	172	Telomerase-associated protein 82; TEB1, processivi	100.0
1ynx_A	114	Replication factor-A protein 1; canonical OB fold,	99.97
2b29_A	123	Replication protein A 70 kDa DNA-binding subunit;	99.96
3dm3_A	105	Replication factor A; probably plays AN essential	99.45
1o7i_A	119	SSB, SSO2364, single stranded DNA binding protein;	99.44
3e0e_A	97	Replication protein A; structural genomics, PSI-2,	99.38
2k50_A	115	Replication factor A related protein; uncharacteri	99.36
1o7i_A	119	SSB, SSO2364, single stranded DNA binding protein;	99.33
3dm3_A	105	Replication factor A; probably plays AN essential	99.27
2k50_A	115	Replication factor A related protein; uncharacteri	99.19
2k75_A	106	Uncharacterized protein TA0387; closed beta barrel	99.08
3e0e_A	97	Replication protein A; structural genomics, PSI-2,	98.97
1wjj_A	145	Hypothetical protein F20O9.120; DNA-binding protei	98.85
2k75_A	106	Uncharacterized protein TA0387; closed beta barrel	98.8
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	98.59
2kbn_A	109	Conserved protein; nucleic acid binding protein, b	98.59
1wjj_A	145	Hypothetical protein F20O9.120; DNA-binding protei	98.41
1xjv_A	294	Protection of telomeres 1; protein-DNA complex, si	98.4
2kbn_A	109	Conserved protein; nucleic acid binding protein, b	98.3
1jb7_A	495	Telomere-binding protein alpha subunit; DNA-protei	98.29
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	98.2
1ynx_A	114	Replication factor-A protein 1; canonical OB fold,	98.13
1xjv_A	294	Protection of telomeres 1; protein-DNA complex, si	97.96
1qzg_A	187	Protection of telomeres protein 1; protrein-DNA co	97.59
3u58_A	213	Tetrahymena TEB1 AB; tetrahymena, telomerase, TEB1	97.46
1miu_A	738	BRCA2, breast cancer type 2 susceptibility protein	97.36
3u4v_A	117	Telomerase-associated protein 82; TEB1, processivi	97.09
1jb7_A	495	Telomere-binding protein alpha subunit; DNA-protei	96.97
1se8_A	301	Single-strand binding protein; DNA binding protein	94.81
3mxn_A	157	RECQ-mediated genome instability protein 1; bloom	94.29
2fxq_A	264	Single-strand binding protein; strand beta-sheet e	93.86
3ebe_A	200	Protein MCM10 homolog; OB-fold, zinc finger, CCCH,	93.27
4hik_A	143	Protection of telomeres protein 1; specificity, pl	92.0
3u4z_A	109	Telomerase-associated protein 82; TEB1, processivi	91.9
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	91.52
3ebe_A	200	Protein MCM10 homolog; OB-fold, zinc finger, CCCH,	91.1
4gop_B	136	Putative uncharacterized protein; OB fold, ssDNA b	90.25
3i7f_A	548	Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-bi	89.27
1txy_A	104	Primosomal replication protein N; OB fold, dimer,	88.66
3en2_A	101	Probable primosomal replication protein N; PRIB RS	88.36
3kf6_A	159	Protein STN1; OB fold, chromosomal protein, DNA-bi	86.89
1eov_A	487	ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy	86.7
3eiv_A	199	Single-stranded DNA-binding protein 2; DNA damage,	86.32
4gop_B	136	Putative uncharacterized protein; OB fold, ssDNA b	86.06
3fhw_A	115	Primosomal replication protein N; PRIB BPR162 X-RA	85.78
2vw9_A	134	Single-stranded DNA binding protein; DNA replicati	85.1
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	85.07
3ulp_A	124	Single-strand binding protein; OB-fold, DNA bindin	84.13
3tqy_A	158	Single-stranded DNA-binding protein; DNA replicati	83.64
3k8a_A	103	Putative primosomal replication protein; beta-barr	83.5
3u58_A	213	Tetrahymena TEB1 AB; tetrahymena, telomerase, TEB1	83.06
3vdy_A	116	SSB, single-stranded DNA-binding protein SSBB; OB	82.72
3koj_A	108	Uncharacterized protein YCF41; single-strand bindi	82.49
1z9f_A	153	Single-strand binding protein; TM0604, single stra	82.32
3rn5_A	208	Interferon-inducible protein AIM2; OB fold, DNA bi	81.23
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	80.49
1v1q_A	134	Primosomal replication protein N; primosome, DNA r	80.22

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=100.00  E-value=1.9e-96  Score=812.51  Aligned_cols=433  Identities=39%  Similarity=0.704  Sum_probs=403.4

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      +++||++|+||+++|+|+|||++||++|+|++++|+|++|+|+|+|+.| +|+||+|++.+++|++.|++|+||+|++|.
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            5889999999999999999999999999999999999999999999655 999999999999999999999999999999


Q ss_pred             EecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec-CCce
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK-NGME  365 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k-~g~~  365 (653)
                      |++++++|++++|+|||.|+.+|+|++|++ +..||.+.|+|++|++|.+++.+.+|||||+|++|+++.+|++| +|++
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            999999999999999999999999999964 45799999999999999998889999999999999999999988 7999


Q ss_pred             eeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHHHHHH
Q 006263          366 TQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELR  445 (653)
Q Consensus       366 ~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~~~l~  445 (653)
                      ..+|+|+|.|+||.+|+|||||++|..|...   .+ ...+|||+|+++||++|+|++||+.++|+|++|||+||+++|+
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            9999999999999999999999999876421   11 3578999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCccceeeccccc-------c-cCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCc
Q 006263          446 EWFDSGGKNAATVSISREI-------A-AGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMI  517 (653)
Q Consensus       446 ~w~~~~g~~~~~~sls~~~-------~-~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~  517 (653)
                      +||+++|.+..+.+++...       . +++.....++||+||+++++|.+++|+||.|+|+|++|+.++|||+|||++ 
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            9999999988888877543       1 122355688999999999999999999999999999999999999999944 


Q ss_pred             CcccccceeeecCc-eeecccCccccCCceEEEEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHH
Q 006263          518 GDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFG  596 (653)
Q Consensus       518 ~~~~C~KKv~~~~~-~~~C~kC~~~~~~~~~rY~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~  596 (653)
                         .|+|||.+.++ .|+|++|++.+++|.|||+|++.|+|+||++|+++||+.|++|||++|+||.+++  ++|++.|+
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               59999987654 8999999999999999999999999999999999999999999999999999999  67899999


Q ss_pred             HHHHHhcCceEEEEEEEeeeccCceeeEEEEEEEeecCChHHHHHHHHHHHHhhh
Q 006263          597 EIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISKSF  651 (653)
Q Consensus       597 ~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~~~~vd~~~e~~~ll~~i~~~~  651 (653)
                      ++|+++.|++|.|+|++++++|+||.|+||+|++++|+||++|+++||++|++||
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            9999999999999999999999999999999999999999999999999999986

>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

Probab=100.00  E-value=3.4e-54  Score=439.59  Aligned_cols=240  Identities=43%  Similarity=0.796  Sum_probs=225.7

Q ss_pred             CCcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          205 PARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       205 ~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      ++.++||++|+||+++|+|+|||++||++|+|++++++|++|+|+|+|++| +|+|++|++.+++|++.|++|+||+|++
T Consensus         5 ~~~~~~I~~L~p~~~~w~I~~rV~~k~~~r~~~~~~~~g~~~~~~L~De~G-~I~at~~~~~~~~~~~~l~~G~vy~i~~   83 (246)
T 1jmc_A            5 QSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESG-EIRATAFNEQVDKFFPLIEVNKVYYFSK   83 (246)
T ss_dssp             --CBCCGGGCCTTCCCCEEEEEEEEECCCEEEECSSCEEEEEEEEEECSSC-EEEEEEEHHHHHHHGGGCCTTCEEEEEC
T ss_pred             ccceEEHHHCCCCCCceEEEEEEEEecccceeeCCCCCceEEEEEEECCCC-eEEEEEChHHHHHhhhhcccCCEEEECC
Confidence            346899999999999999999999999999999999999999999999777 9999999999999999999999999999


Q ss_pred             eEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEec-CC
Q 006263          285 GSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK-NG  363 (653)
Q Consensus       285 ~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k-~g  363 (653)
                      |.|++++++|++++|+|||.|+.+|+|++|++ ..++|.+.|+|++|++|.+++.+.+|||||+|++|+++.++++| +|
T Consensus        84 ~~v~~~~~~y~~~~~~~ei~~~~~T~I~~~~~-~~~iP~~~~~f~~i~~i~~~~~~~~vDViG~V~~v~~~~~~~~k~~g  162 (246)
T 1jmc_A           84 GTLKIANKQFTAVKNDYEMTFNNETSVMPCED-DHHLPTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNN  162 (246)
T ss_dssp             CEEEECCGGGCCCCCSEEEECCTTCEEEECCS-CSCCCCCCCCBCCGGGGGGSCTTCEEEEEEEEEEECCCEEEEETTTT
T ss_pred             CEEEEcccCcccCCCCEEEEEcCCcEEEEccC-cccCCcceeeeEEHHHHhcccCCCceeEEEEEEEecCeEEEEEecCC
Confidence            99999999999999999999999999999964 45799999999999999998888999999999999999999988 79


Q ss_pred             ceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHHHH
Q 006263          364 METQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHE  443 (653)
Q Consensus       364 ~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~~~  443 (653)
                      ++..+|+|+|.|+||.+|+|||||++|..|        +...++||+|+++||++|+|++|++.++|+|++|||+|||++
T Consensus       163 ~~~~~r~~~l~D~sg~~i~~tLWg~~a~~~--------~~~~~~vv~i~~~~v~~f~g~~ls~~~~s~i~inpd~pe~~~  234 (246)
T 1jmc_A          163 REVAKRNIYLMDTSGKVVTATLWGEDADKF--------DGSRQPVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYK  234 (246)
T ss_dssp             EEEEEEEEEEECTTCCEEEEEEEHHHHHHC--------CCTTCCEEEEEEEEEECTTSSEEECCSSCEEESSCCSHHHHH
T ss_pred             CccEEEEEEEECCCCCEEEEEEEchhhhhc--------ccCCCCEEEEEEEEEEecCCeEEEecCcceEEECCCCHHHHH
Confidence            999999999999999999999999998764        445789999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCc
Q 006263          444 LREWFDSGGKN  454 (653)
Q Consensus       444 l~~w~~~~g~~  454 (653)
                      |++||+++|.+
T Consensus       235 l~~w~~~~g~~  245 (246)
T 1jmc_A          235 LRGWFDAEGQA  245 (246)
T ss_dssp             HHHHHHHTTC-
T ss_pred             HHHHHHhcCCc
Confidence            99999998864

>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

Probab=100.00  E-value=4.3e-46  Score=360.62  Aligned_cols=177  Identities=36%  Similarity=0.655  Sum_probs=163.2

Q ss_pred             CcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCc-eeecccCccccCCceEE
Q 006263          470 KNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYR  548 (653)
Q Consensus       470 ~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~~~~r  548 (653)
                      +.+.++||+||+++++|.+++|+||+|+|||++|+.++|||+|||++    .|+|||++.++ .|+|++|++++++|.||
T Consensus         3 ~~~~~kti~qi~~~~lg~~~k~~~f~v~atI~~i~~d~~~Y~aC~~~----~CnKKv~~~~~g~~~CekC~~~~~~~~~r   78 (181)
T 1l1o_C            3 SNTNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPTQ----DCNKKVIDQQNGLYRCEKCDTEFPNFKYR   78 (181)
T ss_dssp             -CCCBCCHHHHHHHTTTSSSSCEEEEEEEEEEEECCSTTEEEBCCST----TCCCBCEEETTTEEEETTTTEEESSCCEE
T ss_pred             CccceEEHHHHhhhccCCCCCCcEEEEEEEEEEEeCCCEEECCCCch----hcCCccccCCCCeEECCCCCCcCCCceEE
Confidence            45679999999999999999999999999999999999999999954    59999997654 89999999999999999


Q ss_pred             EEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEE
Q 006263          549 YLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITV  628 (653)
Q Consensus       549 Y~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v  628 (653)
                      |+|++.|+|+||++|+++||+.|++|||+||+||.++.  ++++.+|+++|.++.|++|.|+|+++.++||++.|+||+|
T Consensus        79 y~l~~~i~D~Tg~~~~t~F~~~ae~ilG~sA~el~~l~--e~~~~~~~~~~~~~~~~~~~f~l~vk~e~yn~e~r~~~~v  156 (181)
T 1l1o_C           79 MILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK--DKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATV  156 (181)
T ss_dssp             EEEEEEEECSSCEEEEEEEHHHHHHHHSSCHHHHHHHT--TSCHHHHHHHHHHTTTCEEEEEEEEECCCC-----CEEEE
T ss_pred             EEEEEEEEeCCCCEEEEEEhHHHHHHhCCCHHHHHHHH--hhChHHHHHHHHHhcCceEEEEEEEEEeecCCEEEEEEEE
Confidence            99999999999999999999999999999999999998  6789999999999999999999999999999999999999


Q ss_pred             EEeecCChHHHHHHHHHHHHhhhc
Q 006263          629 IRADQVNYSSESRYLLDLISKSFR  652 (653)
Q Consensus       629 ~~~~~vd~~~e~~~ll~~i~~~~~  652 (653)
                      +++.|+||++|+++|++.|++|.+
T Consensus       157 ~~~~~vd~~~e~~~L~~~i~~~~~  180 (181)
T 1l1o_C          157 MDVKPVDYREYGRRLVMSIRRSAL  180 (181)
T ss_dssp             EEEEECCHHHHHHHHHHHHHHHHH
T ss_pred             EEeeeCCHHHHHHHHHHHHHHhhc
Confidence            999999999999999999998853

>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=99.97  E-value=3.9e-31  Score=236.75  Aligned_cols=110  Identities=42%  Similarity=0.846  Sum_probs=106.5

Q ss_pred             CcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      ++++||++|+||+++|+|+|||++||++|+|++++|+|++|+|+|+|++| +|+|++|++.+++|++.|+||+||+|++|
T Consensus         2 ~~~~~Is~L~p~~~~w~I~~rV~~k~~~r~~~~~~~~g~~~~~~L~De~G-~I~at~~~~~~~~f~~~l~eG~vy~Is~~   80 (114)
T 1ynx_A            2 RPIFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDTSG-EIRATAFNDFATKFNEILQEGKVYYVSKA   80 (114)
T ss_dssp             CCBCCGGGCCTTTCCCEEEEEEEEEEEEEEEECSSCEEEEEEEEEEETTE-EEEEEECHHHHHHHHHHSCSSSEEEEESC
T ss_pred             CceEEHHHCCCCCCceEEEEEEEEeccceEEecCCCCceEEEEEEECCCC-eEEEEECHHHHHHHHhhcccCcEEEECCc
Confidence            46899999999999999999999999999999999999999999999777 99999999999999999999999999999


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEeccC
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTE  316 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d  316 (653)
                      .|++|+++|++++|+|||.|+.+|+|++|.|
T Consensus        81 ~V~~a~~~y~~~~~~yei~f~~~T~I~~~~d  111 (114)
T 1ynx_A           81 KLQPAKPQFTNLTHPYELNLDRDTVIEECFD  111 (114)
T ss_dssp             EEEECCTTTSSSSSCEEEEECSSCEEEESCC
T ss_pred             EEEECCCCcccCCCCEEEEECCCCEEEECCC
Confidence            9999999999999999999999999999964

>2b29_A Replication protein A 70 kDa DNA-binding subunit; 1.60A {Homo sapiens} SCOP: b.40.4.3 PDB: 2b3g_A 1ewi_A

Probab=99.96  E-value=8.7e-29  Score=222.68  Aligned_cols=111  Identities=35%  Similarity=0.580  Sum_probs=101.9

Q ss_pred             CCCCCCHHHHHHHhC-CCCCCCCeEEEEEEEEcC--CCCceEEEEEecccceeee-eecccchhhcccCCcccCcEEEEe
Q 006263            1 MPVNLTPNSISLING-GDVNSKPLVQVMDIKLIG--STQERYRFLISDSVSTQHA-MLATQLNDRVKTGQVKKGSVVQLI   76 (653)
Q Consensus         1 m~~~Lt~Gai~~i~~-~~~~~~pvvQVl~ik~~~--~~~~ryr~~lSDG~~~~~~-ml~t~ln~~v~~~~l~~~sIIkl~   76 (653)
                      |+.+||+|||++|++ +....+|||||+++|+++  ++.+|||++||||.|++++ ||+||||+++++|+|++|+||||+
T Consensus         4 M~~~LT~Gai~~I~~~~~~~~~PvlQVl~~K~i~~~~~~~RyRl~lSDG~~~~~~~mLatqln~~v~~g~l~~~sIirl~   83 (123)
T 2b29_A            4 MVGQLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIH   83 (123)
T ss_dssp             --CCCCTTHHHHHHHHCCCSCCCEEEEEEEEEECCTTSCCEEEEEEECSSEEEEEEEECGGGHHHHHTTSSCTTCEEEEE
T ss_pred             hhhcCCHhHHHHHHhcCCCCCCceEEEEeeeecCCCCCCceEEEEEECcchheeeehhHHHHHHHHhcCCccCCCEEEEE
Confidence            777899999999998 666789999999999995  3468999999999999998 999999999999999999999999


Q ss_pred             eeEeeeec-CeEEEEEEeeeEeec---CCcccCCCcccc
Q 006263           77 DYICSTVQ-NRKIIVVLNMETIIL---DCEPIGNPKIFS  111 (653)
Q Consensus        77 ~y~~~~~~-~k~~iii~~~evl~~---~~~~iG~P~~~~  111 (653)
                      +|.++.++ +|+++||+++|||.+   .+++||+|++++
T Consensus        84 ~y~~~~v~~~k~vliIl~levl~~~e~~~~~iG~P~~~~  122 (123)
T 2b29_A           84 RFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYN  122 (123)
T ss_dssp             EEEEEECSSSCEEEEEEEEEEEECSTTSCSCCSCCEECC
T ss_pred             EEEEEEecCCcEEEEEEeeEEeecccccCCccCCCccCC
Confidence            99999999 999999999999998   588999999864

>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii}

Probab=99.45  E-value=2.5e-13  Score=118.91  Aligned_cols=97  Identities=21%  Similarity=0.264  Sum_probs=87.3

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      .++||++|.|+ .+|+|.|||+.++++|+|.+..| +|+++++.|.| ++|.|++|+|++.++.   .|++|++|.| ++
T Consensus         4 ~~~~I~dL~~~-~~v~v~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D-~TG~IrvtlW~~~a~~---~l~~Gdvv~i-~g   77 (105)
T 3dm3_A            4 DTYNIGELSPG-MTATFEGEVISALPIKEFKRADGSIGKLKSFIVRD-ETGSIRVTLWDNLTDI---DVGRGDYVRV-RG   77 (105)
T ss_dssp             CEECGGGCCSS-EEEEEEEEEEEEEEEEEEECTTSCEEEEEEEEEEE-TTEEEEEEEEGGGGGS---CCCTTCEEEE-EE
T ss_pred             cceEHHHCCCC-CeEEEEEEEEECCCceEEEcCCCCeeEEEEEEEEC-CCCcEEEEEECccccc---ccCCCCEEEE-EE
Confidence            57899999999 78999999999999999987666 58999999999 6779999999998876   8999999999 99


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEecc
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCT  315 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~  315 (653)
                      .|+...      .+.+||.+...|.|++|.
T Consensus        78 ~vk~~~------~g~~eL~~g~~~~i~~~~  101 (105)
T 3dm3_A           78 YIREGY------YGGLECTANYVEILKKGE  101 (105)
T ss_dssp             EEEECT------TSSEEEEEEEEEEEECCC
T ss_pred             EEEEcc------CCCEEEEeCCceEEEecc
Confidence            998874      347999999999999984

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3

Probab=99.44  E-value=5.8e-13  Score=119.61  Aligned_cols=109  Identities=17%  Similarity=0.207  Sum_probs=94.5

Q ss_pred             ceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEE
Q 006263          208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL  287 (653)
Q Consensus       208 ~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V  287 (653)
                      +++|++|.|+.+.|.+.++|..++++|+|.+.+|.++++++.|.| ++|+|++++|++.++    .|++|+||.|.++.|
T Consensus         2 f~~I~dL~~~~~~v~~~~~V~~~~~~~~~~~k~G~~~~~~~~l~D-~TG~I~~tlW~~~~~----~~~~G~vv~i~~g~v   76 (119)
T 1o7i_A            2 EEKVGNLKPNMESVNVTVRVLEASEARQIQTKNGVRTISEAIVGD-ETGRVKLTLWGKHAG----SIKEGQVVKIENAWT   76 (119)
T ss_dssp             BCCGGGCCTTCSSEEEEEEEEEECCCEEECCTTCCEEEEEEEEEE-TTEEEEEEEEGGGTT----CCCTTCEEEEEEEEE
T ss_pred             cEEHHHCcCCCCcEEEEEEEEECCCCeeEEecCCCEEEEEEEEEe-CCCEEEEEEECChhh----cCCCCCEEEEEeEEE
Confidence            568999999988999999999999999998777767899999999 788899999999874    589999999999998


Q ss_pred             ecCCCcccCCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhc
Q 006263          288 KPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESA  337 (653)
Q Consensus       288 ~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~  337 (653)
                      ...       .+.++|.+.+.+.|+.+++         ++|..+++|.+.
T Consensus        77 ~~~-------~g~~qL~i~~~~~i~~~~~---------~~~~~~~~l~~~  110 (119)
T 1o7i_A           77 TAF-------KGQVQLNAGSKTKIAEASE---------DGFPESSQIPEN  110 (119)
T ss_dssp             EEE-------TTEEEEEECTTCEEEECCC---------TTCCCGGGSCCC
T ss_pred             EEe-------CCEEEEEECCCEEEEEcCC---------cCCCcHHHhhhc
Confidence            764       3569999999999999842         457778888764

>3e0e_A Replication protein A; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.60A {Methanococcus maripaludis} PDB: 2k5v_A

Probab=99.38  E-value=1.1e-12  Score=113.36  Aligned_cols=93  Identities=25%  Similarity=0.330  Sum_probs=79.3

Q ss_pred             eeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEE
Q 006263          209 IPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSL  287 (653)
Q Consensus       209 ~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V  287 (653)
                      .||++|+|+ .+|+|.|||+.+.++|+|.+..| +++++++.|.| ++|.|++|+|++.++.   .|++|++|.| ++.|
T Consensus         3 ~kI~dl~~g-~~v~i~~~V~~~~~~r~~~~~~G~~~~v~~~~l~D-eTG~I~~tlW~~~~~~---~i~~Gdvv~i-~g~v   76 (97)
T 3e0e_A            3 YKISELMPN-LSGTINAEVVTAYPKKEFSRKDGTKGQLKSLFLKD-DTGSIRGTLWNELADF---EVKKGDIAEV-SGYV   76 (97)
T ss_dssp             ECGGGCCTT-EEEEEEEEEEEECCCEEEC----CCEEEEEEEEEE-TTEEEEEEEEGGGGGC---CCCTTCEEEE-EEEE
T ss_pred             eEHHHCCCC-CcEEEEEEEEECCCceEEEcCCCCeeEEEEEEEEC-CCCcEEEEEECCcccc---ccCCCCEEEE-EEEE
Confidence            489999999 79999999999999999987555 58999999999 7889999999998875   7999999999 8888


Q ss_pred             ecCCCcccCCCCceEEEeccccEEEec
Q 006263          288 KPAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       288 ~~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                      +...       ..+||.+++++.|+.+
T Consensus        77 ~~~~-------~~~el~~g~~~~i~k~   96 (97)
T 3e0e_A           77 KQGY-------SGLEISVDNIGIIEKS   96 (97)
T ss_dssp             EEC---------CEEEEEEEEEEEECC
T ss_pred             EEcC-------CeEEEEECCCcEEEEC
Confidence            5543       2699999999999875

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=99.36  E-value=3.2e-12  Score=114.06  Aligned_cols=106  Identities=15%  Similarity=0.281  Sum_probs=91.0

Q ss_pred             ccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhcc
Q 006263          324 QQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDV  403 (653)
Q Consensus       324 ~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~  403 (653)
                      ..|+|++|++|.   .+..+|++|+|++++++.++++|+|++..+++++|.|+|| +|++|||++.+..+     +.+  
T Consensus         3 ~~~~~~~I~~L~---~g~~v~i~~~V~~~~~~~~~~~k~G~~~~~~~~~l~D~TG-~I~~t~w~~~~~~~-----~~l--   71 (115)
T 2k50_A            3 PEHRMDTISKLE---EGAETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTG-ELRAVFWTENIKLL-----KKF--   71 (115)
T ss_dssp             CTTCCCCTTTCC---TTCEEEEEEEEEEECCCEECCCTTSSCCEEEEEEEEETTE-EEEEEEETTGGGGG-----GTC--
T ss_pred             cccceEEHHHCC---CCCEeEEEEEEEECCCceEEEcCCCCEEEEEEEEEEeCCC-eEEEEEeCchhhhh-----hcC--
Confidence            357889998886   4677899999999999998888888777899999999999 99999999987642     123  


Q ss_pred             CCCcEEEEEeeEeec-CCCc-eeccccceEEEEcCChHH
Q 006263          404 GFFPVLSVKSGKVND-FSGK-SIGTIPSTQLFINPDFAE  440 (653)
Q Consensus       404 ~~~~Vvaik~~rV~~-f~G~-sLs~~~~S~i~inPdipe  440 (653)
                      ..+++|+|++++|++ |+|+ +|+....|.+..+||+..
T Consensus        72 ~~G~vv~i~g~~v~~~f~g~~qL~~~~~~~i~~~~~~~~  110 (115)
T 2k50_A           72 REGDVIRIKDVNIRGGFGGRKEAHLMPRSTVEVLDPLEH  110 (115)
T ss_dssp             CTTSEEEEEEEEECCCSSSSCEEEECTTCCEEEESSCCC
T ss_pred             CCCCEEEEEeeEEccccCCeEEEEECCCceEEECCcccc
Confidence            468999999999987 9985 899999999999998754

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3

Probab=99.33  E-value=3e-12  Score=114.94  Aligned_cols=103  Identities=21%  Similarity=0.355  Sum_probs=87.0

Q ss_pred             ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCc
Q 006263          328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP  407 (653)
Q Consensus       328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~  407 (653)
                      |++|+||..  ....+|++|+|++++++..+++|+|+ ..+++++|.|+|| +|++|||++.|..        |  ..++
T Consensus         2 f~~I~dL~~--~~~~v~~~~~V~~~~~~~~~~~k~G~-~~~~~~~l~D~TG-~I~~tlW~~~~~~--------~--~~G~   67 (119)
T 1o7i_A            2 EEKVGNLKP--NMESVNVTVRVLEASEARQIQTKNGV-RTISEAIVGDETG-RVKLTLWGKHAGS--------I--KEGQ   67 (119)
T ss_dssp             BCCGGGCCT--TCSSEEEEEEEEEECCCEEECCTTCC-EEEEEEEEEETTE-EEEEEEEGGGTTC--------C--CTTC
T ss_pred             cEEHHHCcC--CCCcEEEEEEEEECCCCeeEEecCCC-EEEEEEEEEeCCC-EEEEEEECChhhc--------C--CCCC
Confidence            677888764  23479999999999999999888887 7899999999999 6999999999743        3  3589


Q ss_pred             EEEEEeeEeecCCCc-eeccccceEEEEcCC--hHHHHHH
Q 006263          408 VLSVKSGKVNDFSGK-SIGTIPSTQLFINPD--FAEAHEL  444 (653)
Q Consensus       408 Vvaik~~rV~~f~G~-sLs~~~~S~i~inPd--ipe~~~l  444 (653)
                      ||.|++++|++|+|+ +|+....|+|..+|+  +|++.+|
T Consensus        68 vv~i~~g~v~~~~g~~qL~i~~~~~i~~~~~~~~~~~~~l  107 (119)
T 1o7i_A           68 VVKIENAWTTAFKGQVQLNAGSKTKIAEASEDGFPESSQI  107 (119)
T ss_dssp             EEEEEEEEEEEETTEEEEEECTTCEEEECCCTTCCCGGGS
T ss_pred             EEEEEeEEEEEeCCEEEEEECCCEEEEEcCCcCCCcHHHh
Confidence            999999999999995 899999999999874  5665554

>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii}

Probab=99.27  E-value=2e-11  Score=106.77  Aligned_cols=93  Identities=24%  Similarity=0.305  Sum_probs=78.3

Q ss_pred             eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263          327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF  406 (653)
Q Consensus       327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~  406 (653)
                      +|++|+||..   +..+||+|+|++++++.++++++|++..+|+++|.|+|| +|++||||+.|..         ...++
T Consensus         4 ~~~~I~dL~~---~~~v~v~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D~TG-~IrvtlW~~~a~~---------~l~~G   70 (105)
T 3dm3_A            4 DTYNIGELSP---GMTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETG-SIRVTLWDNLTDI---------DVGRG   70 (105)
T ss_dssp             CEECGGGCCS---SEEEEEEEEEEEEEEEEEEECTTSCEEEEEEEEEEETTE-EEEEEEEGGGGGS---------CCCTT
T ss_pred             cceEHHHCCC---CCeEEEEEEEEECCCceEEEcCCCCeeEEEEEEEECCCC-cEEEEEECccccc---------ccCCC
Confidence            5788888875   378999999999999999998999999999999999999 8999999999863         12468


Q ss_pred             cEEEEEeeEeecC--CCceeccccceEEE
Q 006263          407 PVLSVKSGKVNDF--SGKSIGTIPSTQLF  433 (653)
Q Consensus       407 ~Vvaik~~rV~~f--~G~sLs~~~~S~i~  433 (653)
                      ++|.| .++|+.+  ++..|+....|.|.
T Consensus        71 dvv~i-~g~vk~~~~g~~eL~~g~~~~i~   98 (105)
T 3dm3_A           71 DYVRV-RGYIREGYYGGLECTANYVEILK   98 (105)
T ss_dssp             CEEEE-EEEEEECTTSSEEEEEEEEEEEE
T ss_pred             CEEEE-EEEEEEccCCCEEEEeCCceEEE
Confidence            99999 6777654  46789888777764

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=99.19  E-value=7.5e-11  Score=105.12  Aligned_cols=101  Identities=23%  Similarity=0.346  Sum_probs=86.8

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      ++++|++|.|+.. .+|.++|..++++|+|.+.+| +++++++.|.| ++|+|++++|++.++.+ +.|++|++|.|++.
T Consensus         6 ~~~~I~~L~~g~~-v~i~~~V~~~~~~~~~~~k~G~~~~~~~~~l~D-~TG~I~~t~w~~~~~~~-~~l~~G~vv~i~g~   82 (115)
T 2k50_A            6 RMDTISKLEEGAE-TPVTGRVMKISSPRTFTTRKGREGKLANVIIAD-DTGELRAVFWTENIKLL-KKFREGDVIRIKDV   82 (115)
T ss_dssp             CCCCTTTCCTTCE-EEEEEEEEEECCCEECCCTTSSCCEEEEEEEEE-TTEEEEEEEETTGGGGG-GTCCTTSEEEEEEE
T ss_pred             ceEEHHHCCCCCE-eEEEEEEEECCCceEEEcCCCCEEEEEEEEEEe-CCCeEEEEEeCchhhhh-hcCCCCCEEEEEee
Confidence            4678999999865 599999999999999877666 37899999999 67799999999987765 78999999999999


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEeccC
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTE  316 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d  316 (653)
                      .|+..   |+   ..++|.+...+.|++++|
T Consensus        83 ~v~~~---f~---g~~qL~~~~~~~i~~~~~  107 (115)
T 2k50_A           83 NIRGG---FG---GRKEAHLMPRSTVEVLDP  107 (115)
T ss_dssp             EECCC---SS---SSCEEEECTTCCEEEESS
T ss_pred             EEccc---cC---CeEEEEECCCceEEECCc
Confidence            88653   43   469999999999999853

>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum}

Probab=99.08  E-value=6.2e-10  Score=97.54  Aligned_cols=92  Identities=14%  Similarity=0.233  Sum_probs=79.0

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      ++++|++|.|+...+++.++|+.+++.| .. ..| ++++.++.|.| ++|+|++++|++.       |++|++|.|.|+
T Consensus         2 ~~~kI~dl~pg~~~v~v~~~V~~~~~~~-~~-k~G~~~~v~~~~l~D-eTG~I~~tlW~~~-------l~~Gdvv~i~ng   71 (106)
T 2k75_A            2 DLVKIRDVSLSTPYVSVIGKITGIHKKE-YE-SDGTTKSVYQGYIED-DTARIRISSFGKQ-------LQDSDVVRIDNA   71 (106)
T ss_dssp             CBCCSTTCCTTCSEEEEEEEEEEEEEEE-EE-ETTEEEEEEEEEEEC-SSCEEEEEEESSC-------CCTTEEEEEEEE
T ss_pred             CcEEHHHcCCCCceEEEEEEEEEccccc-cc-cCCCeeEEEEEEEEc-CCCeEEEEEEcCc-------cCCCCEEEEEee
Confidence            3678999999998899999999999988 32 233 34699999999 7889999999986       999999999999


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEecc
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCT  315 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~  315 (653)
                      .+..-       ...++|.+++.+.|+++.
T Consensus        72 ~v~~~-------~g~~~L~v~~~~~I~~~~   94 (106)
T 2k75_A           72 RVAQF-------NGYLSLSVGDSSRIESVN   94 (106)
T ss_dssp             EEEEE-------TTEEEEEECTTSEEEECC
T ss_pred             EEeEE-------CCEEEEEECCcEEEEECC
Confidence            88653       346999999999999984

>3e0e_A Replication protein A; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.60A {Methanococcus maripaludis} PDB: 2k5v_A

Probab=98.97  E-value=3.3e-09  Score=91.41  Aligned_cols=90  Identities=28%  Similarity=0.299  Sum_probs=69.7

Q ss_pred             chhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEE
Q 006263          330 HISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVL  409 (653)
Q Consensus       330 ~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vv  409 (653)
                      +|+||.   .+..++++|.|.+++++.++++++|.+...+++.|.|+|| +|++|||++.|..         .-..+++|
T Consensus         4 kI~dl~---~g~~v~i~~~V~~~~~~r~~~~~~G~~~~v~~~~l~DeTG-~I~~tlW~~~~~~---------~i~~Gdvv   70 (97)
T 3e0e_A            4 KISELM---PNLSGTINAEVVTAYPKKEFSRKDGTKGQLKSLFLKDDTG-SIRGTLWNELADF---------EVKKGDIA   70 (97)
T ss_dssp             CGGGCC---TTEEEEEEEEEEEECCCEEEC----CCEEEEEEEEEETTE-EEEEEEEGGGGGC---------CCCTTCEE
T ss_pred             EHHHCC---CCCcEEEEEEEEECCCceEEEcCCCCeeEEEEEEEECCCC-cEEEEEECCcccc---------ccCCCCEE
Confidence            556654   4578999999999999999988899888999999999999 9999999999753         12468999


Q ss_pred             EEEeeEeecCCCc-eeccccceEEE
Q 006263          410 SVKSGKVNDFSGK-SIGTIPSTQLF  433 (653)
Q Consensus       410 aik~~rV~~f~G~-sLs~~~~S~i~  433 (653)
                      .| .++|+.|.|. .|+....+.|.
T Consensus        71 ~i-~g~v~~~~~~~el~~g~~~~i~   94 (97)
T 3e0e_A           71 EV-SGYVKQGYSGLEISVDNIGIIE   94 (97)
T ss_dssp             EE-EEEEEEC--CEEEEEEEEEEEE
T ss_pred             EE-EEEEEEcCCeEEEEECCCcEEE
Confidence            99 6799887664 78877777664

>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

Probab=98.85  E-value=2.6e-08  Score=91.56  Aligned_cols=98  Identities=12%  Similarity=0.196  Sum_probs=83.3

Q ss_pred             CcceeccccCCCCCceEEEEEEEeecccc---ccccCCC-------CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcc
Q 006263          206 ARIIPIAALNPYQGRWAIKARVTAKGDLR---RYNNARG-------DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIE  275 (653)
Q Consensus       206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir---~~~~~~g-------~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~  275 (653)
                      ..+++|++|.|...+-++.|||+..+.++   ++....|       ++++.++.|.| ++|.|+.|+|++.++    .|+
T Consensus        14 p~~~kI~dL~pg~~~v~l~~kVl~~~~v~~~~~~~R~dG~~~~~~r~~~V~~~lVgD-eTG~I~ftlW~e~~~----~l~   88 (145)
T 1wjj_A           14 PVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGD-ETGCILFTARNDQVD----LMK   88 (145)
T ss_dssp             CSSCCSTTCCTTCCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEEC-SSCEEEEEECTTHHH----HTC
T ss_pred             ccceEHHHcCCCCCceEEEEEEEEcccccccccccccCCccccccCCceEEEEEEEc-CCcEEEEEEecCCcC----cCC
Confidence            35779999999998899999999999988   5543334       67899999999 899999999999775    588


Q ss_pred             cCcEEEEeceEEecCCCcccCCCCceEEEeccccEEEecc
Q 006263          276 VGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCT  315 (653)
Q Consensus       276 eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~  315 (653)
                      +|++|.|.|+.++.-+       ..++|.+++++.|+...
T Consensus        89 ~Gd~v~i~na~v~~~~-------G~~~L~vgk~g~Ie~~~  121 (145)
T 1wjj_A           89 PGATVILRNSRIDMFK-------GTMRLGVDKWGRIEATG  121 (145)
T ss_dssp             TTCEEEEEEEEEEEET-------TEEEEEECTTCCBCCCS
T ss_pred             CCCEEEEeccEEEeEC-------CEEEEEECCCEEEEECC
Confidence            9999999999986532       35999999999999873

>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum}

Probab=98.80  E-value=1.9e-08  Score=87.98  Aligned_cols=91  Identities=15%  Similarity=0.255  Sum_probs=76.8

Q ss_pred             ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCC
Q 006263          326 FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGF  405 (653)
Q Consensus       326 f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~  405 (653)
                      |+|++|+||..  ....|+++|.|.++++..  .+|+|++...+++.|.|+|| +|++|||++.   +          ..
T Consensus         1 ~~~~kI~dl~p--g~~~v~v~~~V~~~~~~~--~~k~G~~~~v~~~~l~DeTG-~I~~tlW~~~---l----------~~   62 (106)
T 2k75_A            1 SDLVKIRDVSL--STPYVSVIGKITGIHKKE--YESDGTTKSVYQGYIEDDTA-RIRISSFGKQ---L----------QD   62 (106)
T ss_dssp             CCBCCSTTCCT--TCSEEEEEEEEEEEEEEE--EEETTEEEEEEEEEEECSSC-EEEEEEESSC---C----------CT
T ss_pred             CCcEEHHHcCC--CCceEEEEEEEEEccccc--cccCCCeeEEEEEEEEcCCC-eEEEEEEcCc---c----------CC
Confidence            56888888864  234599999999999887  46788877889999999999 8999999997   1          25


Q ss_pred             CcEEEEEeeEeecCCCc-eeccccceEEEE
Q 006263          406 FPVLSVKSGKVNDFSGK-SIGTIPSTQLFI  434 (653)
Q Consensus       406 ~~Vvaik~~rV~~f~G~-sLs~~~~S~i~i  434 (653)
                      +.+|.|+++++..|+|+ .|+....|+|..
T Consensus        63 Gdvv~i~ng~v~~~~g~~~L~v~~~~~I~~   92 (106)
T 2k75_A           63 SDVVRIDNARVAQFNGYLSLSVGDSSRIES   92 (106)
T ss_dssp             TEEEEEEEEEEEEETTEEEEEECTTSEEEE
T ss_pred             CCEEEEEeeEEeEECCEEEEEECCcEEEEE
Confidence            89999999999999996 898888888764

>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

Probab=98.59  E-value=3.4e-06  Score=84.93  Aligned_cols=177  Identities=13%  Similarity=0.074  Sum_probs=121.3

Q ss_pred             eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263          327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF  406 (653)
Q Consensus       327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~  406 (653)
                      .+++|++|....  ....|.|.|...+++..+.... .+....++.|.|++| .|++|+|++.|..|...|      ..|
T Consensus         7 ~~~~I~~L~p~~--~~w~I~~rV~~k~~~r~~~~~~-~~g~~~~~~L~De~G-~I~at~~~~~~~~~~~~l------~~G   76 (246)
T 1jmc_A            7 KVVPIASLTPYQ--SKWTICARVTNKSQIRTWSNSR-GEGKLFSLELVDESG-EIRATAFNEQVDKFFPLI------EVN   76 (246)
T ss_dssp             CBCCGGGCCTTC--CCCEEEEEEEEECCCEEEECSS-CEEEEEEEEEECSSC-EEEEEEEHHHHHHHGGGC------CTT
T ss_pred             ceEEHHHCCCCC--CceEEEEEEEEecccceeeCCC-CCceEEEEEEECCCC-eEEEEEChHHHHHhhhhc------ccC
Confidence            578888886532  3578999999999999887544 345567899999999 999999999988764332      368


Q ss_pred             cEEEEEeeEeecCCC-------c-eeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHH
Q 006263          407 PVLSVKSGKVNDFSG-------K-SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVS  478 (653)
Q Consensus       407 ~Vvaik~~rV~~f~G-------~-sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~  478 (653)
                      .++.|.+++|+..++       . .|.....|.|..-++.+.                   +.       ........|+
T Consensus        77 ~vy~i~~~~v~~~~~~y~~~~~~~ei~~~~~T~I~~~~~~~~-------------------iP-------~~~~~f~~i~  130 (246)
T 1jmc_A           77 KVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDDHH-------------------LP-------TVQFDFTGID  130 (246)
T ss_dssp             CEEEEECCEEEECCGGGCCCCCSEEEECCTTCEEEECCSCSC-------------------CC-------CCCCCBCCGG
T ss_pred             CEEEECCCEEEEcccCcccCCCCEEEEEcCCcEEEEccCccc-------------------CC-------cceeeeEEHH
Confidence            999999999986533       1 455566677665543210                   10       0112346678


Q ss_pred             hhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEEEEEEeC
Q 006263          479 QIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQ  558 (653)
Q Consensus       479 ~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~  558 (653)
                      +|.+.     +...+..|.|.|..+..-. .+....                             +-....+..+.|.|.
T Consensus       131 ~i~~~-----~~~~~vDViG~V~~v~~~~-~~~~k~-----------------------------~g~~~~~r~~~l~D~  175 (246)
T 1jmc_A          131 DLENK-----SKDSLVDIIGICKSYEDAT-KITVRS-----------------------------NNREVAKRNIYLMDT  175 (246)
T ss_dssp             GGGGS-----CTTCEEEEEEEEEEECCCE-EEEETT-----------------------------TTEEEEEEEEEEECT
T ss_pred             HHhcc-----cCCCceeEEEEEEEecCeE-EEEEec-----------------------------CCCccEEEEEEEECC
Confidence            88762     2234788999998886411 010000                             112345788999999


Q ss_pred             CC-eEEEEEechhhhhh
Q 006263          559 TG-LTWVTAFQESGEEI  574 (653)
Q Consensus       559 Tg-~~~~~~F~~~ae~l  574 (653)
                      || ++.+++|++.|+.+
T Consensus       176 sg~~i~~tLWg~~a~~~  192 (246)
T 1jmc_A          176 SGKVVTATLWGEDADKF  192 (246)
T ss_dssp             TCCEEEEEEEHHHHHHC
T ss_pred             CCCEEEEEEEchhhhhc
Confidence            99 49999999999865

>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_A

Probab=98.59  E-value=5.4e-07  Score=79.18  Aligned_cols=92  Identities=15%  Similarity=0.190  Sum_probs=76.0

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      ++++|++|.|....-++.+||+.+|..|.      ......++|.| ++|.|++|+|++.   -.+.|++|++|.|.|+.
T Consensus         4 ~~~kI~dl~~~~~~v~v~~~V~~~~~~~~------~~~~~~~~l~D-eTG~I~~t~W~~~---~~~~~~~G~~V~i~n~~   73 (109)
T 2kbn_A            4 QLTKIVDIVENGQWANLKAKVIQLWENTH------ESISQVGLLGD-ETGIIKFTIWKNA---ELPLLEQGESYLLRSVV   73 (109)
T ss_dssp             CBCCTTTCCSTTCEEEEEEEEEEEEECCC------SSEEEEEEEEC-TTCCEEEEEEGGG---CCCCCCTTCEEEEEEEE
T ss_pred             CceEHHHCCCCCCcEEEEEEEEEeEcCCC------CeEEEEEEEEC-CCCeEEEEEECcc---cccccCCCCEEEEEEEE
Confidence            46689999998888899999999987442      23566789999 7899999999943   23589999999999999


Q ss_pred             EecCCCcccCCCCceEEEeccccEEEecc
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVDLCT  315 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~  315 (653)
                      +..-+       ...+|.+++.+.|+...
T Consensus        74 v~~~~-------G~~~L~v~~~~~I~~~~   95 (109)
T 2kbn_A           74 VGEYN-------DRFQVQVNKNSSIEKLS   95 (109)
T ss_dssp             EEEET-------TEEEEEECSSSEEEECS
T ss_pred             EEEEC-------CEEEEEECCceEEEECC
Confidence            87754       35999999999999874

>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

Probab=98.41  E-value=4.4e-07  Score=83.33  Aligned_cols=101  Identities=14%  Similarity=0.145  Sum_probs=79.1

Q ss_pred             cccceecchhhhhhcccCccccEEEEEEEecCce---eEEecCCc------eeeEEEEEEEeCCCCEEEEEEccchhhhh
Q 006263          323 KQQFSFRHISEIESAENNSIVDVIGIVISVNPSV---PILRKNGM------ETQRRILNLKDTSGRSVELTLWGDFCNKE  393 (653)
Q Consensus       323 ~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~---~i~~k~g~------~~~kr~i~l~D~s~~~i~vtLWg~~A~~~  393 (653)
                      ...-.|++|.||..-  ..-+++.|.|.+++++.   +..+++|.      +...+++.|.|+|| .|.+|||++++.. 
T Consensus        11 ~~kp~~~kI~dL~pg--~~~v~l~~kVl~~~~v~~~~~~~R~dG~~~~~~r~~~V~~~lVgDeTG-~I~ftlW~e~~~~-   86 (145)
T 1wjj_A           11 KRKPVFVKVEQLKPG--TTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETG-CILFTARNDQVDL-   86 (145)
T ss_dssp             CCCCSSCCSTTCCTT--CCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSC-EEEEEECTTHHHH-
T ss_pred             ccCccceEHHHcCCC--CCceEEEEEEEEcccccccccccccCCccccccCCceEEEEEEEcCCc-EEEEEEecCCcCc-
Confidence            445678999999752  34699999999999865   33223564      56778999999999 8999999998643 


Q ss_pred             hhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEEEEcC
Q 006263          394 GQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINP  436 (653)
Q Consensus       394 ~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i~inP  436 (653)
                             +  ..+.+|-|+++.++.|+|+ .|+....++|...+
T Consensus        87 -------l--~~Gd~v~i~na~v~~~~G~~~L~vgk~g~Ie~~~  121 (145)
T 1wjj_A           87 -------M--KPGATVILRNSRIDMFKGTMRLGVDKWGRIEATG  121 (145)
T ss_dssp             -------T--CTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCS
T ss_pred             -------C--CCCCEEEEeccEEEeECCEEEEEECCCEEEEECC
Confidence                   3  2689999999999999996 88888877776543

>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

Probab=98.40  E-value=1e-05  Score=83.65  Aligned_cols=226  Identities=10%  Similarity=0.077  Sum_probs=138.8

Q ss_pred             CcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       206 ~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      ..++||++|.. ...-.|.|.|+.....+.-   +|..-..+|.|.|..-..|++.+|.+..+.+=....+|+|+.++++
T Consensus         4 y~y~~l~~l~~-~~~vnvigVV~~~~~p~~s---~G~d~~~tl~I~D~S~~gl~v~iF~~~~~~LP~v~~~GDII~l~~v   79 (294)
T 1xjv_A            4 YIYTPLNQLKG-GTIVNVYGVVKFFKPPYLS---KGTDYCSVVTIVDQTNVKLTCLLFSGNYEALPIIYKNGDIVRFHRL   79 (294)
T ss_dssp             CCCCCGGGCCS-SEEEEEEEEEEEEEEEEEC---SSSSEEEEEEEECTTCCEEEEEEEESSGGGSCCCCSTTCEEEEEEE
T ss_pred             ceEEEHHHhhC-CCeeEEEEEEEEcCCCccC---CCCeEEEEEEEEcCCCCCEEEEEECCChHHCCCCCCCCCEEEEEEE
Confidence            45889999965 4568999999988776543   4556789999999777779999999766555555699999999999


Q ss_pred             EEecCCCcccCCCCceEEEeccccEEEeccCCC-CC-CCcc---cceec----------------------chhhhhhcc
Q 006263          286 SLKPAQKNFNHLKNEWEIFLEATSTVDLCTEED-DS-IPKQ---QFSFR----------------------HISEIESAE  338 (653)
Q Consensus       286 ~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~-~~-iP~~---~f~f~----------------------~i~~i~~~~  338 (653)
                      +|+.-+..       ..+..+....+-...... .. .|..   .|.|.                      ++..|.++.
T Consensus        80 ki~~~~g~-------~~~v~~~~~s~~~f~g~~~~~~~p~~~~~~~~~~~~e~~~~~~Lr~w~~~~~~~~~~~~~L~di~  152 (294)
T 1xjv_A           80 KIQVYKKE-------TQGITSSGFASLTFEGTLGAPIIPRTSSKYFNFTTEDHKMVEALRVWASTHMSPSWTLLKLCDVQ  152 (294)
T ss_dssp             EEEEETTE-------EEEEEEEEEEEEEECCSTTCCCCCBCSCSSCCCCHHHHHHHHHHHHHHHHHCC---CCCCGGGCC
T ss_pred             EEEEECCe-------EEEEccCCeEEEEECCCCCCCcCCcccCCCcCCCHHHHHHHHHHHHHHHhccCCCCceeEHHHcc
Confidence            99865433       222223322222221111 11 1211   12121                      222444455


Q ss_pred             cCccccEEEEEEEecCce--eEE--ecCCceeeEEEEEEEeC--------------CCCEEEEEEccchhhhhhhhHHHh
Q 006263          339 NNSIVDVIGIVISVNPSV--PIL--RKNGMETQRRILNLKDT--------------SGRSVELTLWGDFCNKEGQKLQEM  400 (653)
Q Consensus       339 ~~~~vDVIGvV~~v~~~~--~i~--~k~g~~~~kr~i~l~D~--------------s~~~i~vtLWg~~A~~~~~~l~~~  400 (653)
                      .+..+|+++.|+.+....  .+.  ..+|+......+...++              ...++.|++|++.|.-     +. 
T Consensus       153 ~~~f~DLv~qVv~v~~~~~~~~~LyVwDgT~~~~~~~~~~~~~~~~~gd~~~~~~~~~lt~~V~~~d~h~~~-----~~-  226 (294)
T 1xjv_A          153 PMQYFDLTCQLLGKAEVDGASFLLKVWDGTRTPFPSWRVLIQDLVLEGDLSHIHRLQNLTIDILVYDNHVHV-----AR-  226 (294)
T ss_dssp             SSCEEEEEEEEEEEEECSSSEEEEEEECSSCCSSCBCCCCCCSSCCEECHHHHHHHGGGSEEEEEETTHHHH-----HH-
T ss_pred             cCCeeeEEEEEEEEEecCCCeEEEEEECCCCCCCCccccccccccccCcccccccccCeeEEEEEEcchhHH-----Hh-
Confidence            678999999999886431  111  12443322111111111              1137999999999842     22 


Q ss_pred             hccCCCcEEEEEeeEeecC--------CCc---ee--ccccceEEEEcC-ChHHHHHHHHHHh
Q 006263          401 VDVGFFPVLSVKSGKVNDF--------SGK---SI--GTIPSTQLFINP-DFAEAHELREWFD  449 (653)
Q Consensus       401 ~~~~~~~Vvaik~~rV~~f--------~G~---sL--s~~~~S~i~inP-dipe~~~l~~w~~  449 (653)
                       ....+..|.|++++++.-        +|.   .|  .....++|.+-| +.+.+.++++++.
T Consensus       227 -~lk~Gd~V~l~Nv~~k~~~~~~~~~~~~~le~~lh~~~~~~~~i~~l~~~~~~~~~~~~~~~  288 (294)
T 1xjv_A          227 -SLKVGSFLRIYSLHTKLQSMNSENQTMLSLEFHLHGGTSYGRGIRVLPESNSDVDQLKKDLE  288 (294)
T ss_dssp             -HCCTTCEEEEEEEEEEEEEECTTSCEEEEEEEEECSSCGGGCEEEEECTTSHHHHHHHHHHH
T ss_pred             -cCCCCcEEEEeeeEEEecccccccCCCcceEEEEecCcccCcEeEEecCCCCCHHHHHHHHh
Confidence             235789999999988643        221   12  133457787777 6678888887765

>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_A

Probab=98.30  E-value=2.5e-06  Score=74.86  Aligned_cols=90  Identities=13%  Similarity=0.190  Sum_probs=68.8

Q ss_pred             ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCc
Q 006263          328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP  407 (653)
Q Consensus       328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~  407 (653)
                      |++|+||..  .+..|++.|.|.++++.     +.+.  ..+.+.|.|+|| +|++|||++.+..       .+  ..+.
T Consensus         5 ~~kI~dl~~--~~~~v~v~~~V~~~~~~-----~~~~--~~~~~~l~DeTG-~I~~t~W~~~~~~-------~~--~~G~   65 (109)
T 2kbn_A            5 LTKIVDIVE--NGQWANLKAKVIQLWEN-----THES--ISQVGLLGDETG-IIKFTIWKNAELP-------LL--EQGE   65 (109)
T ss_dssp             BCCTTTCCS--TTCEEEEEEEEEEEEEC-----CCSS--EEEEEEEECTTC-CEEEEEEGGGCCC-------CC--CTTC
T ss_pred             ceEHHHCCC--CCCcEEEEEEEEEeEcC-----CCCe--EEEEEEEECCCC-eEEEEEECccccc-------cc--CCCC
Confidence            556676653  25679999999999863     2333  457899999999 8999999944221       12  3689


Q ss_pred             EEEEEeeEeecCCCc-eeccccceEEEEcC
Q 006263          408 VLSVKSGKVNDFSGK-SIGTIPSTQLFINP  436 (653)
Q Consensus       408 Vvaik~~rV~~f~G~-sLs~~~~S~i~inP  436 (653)
                      +|-|+++++.+|+|+ +|+....+.|..-+
T Consensus        66 ~V~i~n~~v~~~~G~~~L~v~~~~~I~~~~   95 (109)
T 2kbn_A           66 SYLLRSVVVGEYNDRFQVQVNKNSSIEKLS   95 (109)
T ss_dssp             EEEEEEEEEEEETTEEEEEECSSSEEEECS
T ss_pred             EEEEEEEEEEEECCEEEEEECCceEEEECC
Confidence            999999999999995 89888888887543

>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

Probab=98.29  E-value=0.00025  Score=77.99  Aligned_cols=338  Identities=13%  Similarity=0.113  Sum_probs=193.6

Q ss_pred             CCCcceeccccCC-CCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCC-------eE-----EEEEchhHHHHH
Q 006263          204 APARIIPIAALNP-YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGG-------EI-----RVTCFNAVVDRF  270 (653)
Q Consensus       204 ~~~~~~pI~~L~p-~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~-------~I-----~at~f~~~~~kf  270 (653)
                      .+..+++|+++.- ....-.|.|-|+.....+.   .+|..-..+|.|.|..-.       .|     .+.+|.+..+.+
T Consensus        34 ~~y~y~~L~~a~~~~~~~VnviGVVvd~~~P~~---T~G~D~~~t~tI~D~S~~~~~~~~~Gl~~~~~~v~iF~~~~e~L  110 (495)
T 1jb7_A           34 HKYEYVELAKASLTSAQPQHFYAVVIDATFPYK---TNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDL  110 (495)
T ss_dssp             --CCBCCTTTSCSSCCSCEEEEEEEEEECCCEE---CSSSCEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSGGGS
T ss_pred             CCCccEEHHHHHhccCCeEEEEEEEeecCCcee---cCCCeEEEEEEEEeCCCCcccccccccccCceEEEEECCChHHC
Confidence            4457899997742 2446789999998877764   245556889999995333       47     999998754433


Q ss_pred             Hhhc-ccCcEEEEeceEEecCCCcccC-CCCce---EEEeccccEEE----eccC-CCCCCCc----ccceec-------
Q 006263          271 YEII-EVGRVYLISKGSLKPAQKNFNH-LKNEW---EIFLEATSTVD----LCTE-EDDSIPK----QQFSFR-------  329 (653)
Q Consensus       271 ~~~l-~eG~vy~is~~~V~~a~~~f~~-~~~~y---ei~f~~~T~I~----~~~d-~~~~iP~----~~f~f~-------  329 (653)
                       +.+ .+|+|+.+++++|+.-+....- ....+   =..|.......    ..+. .....|.    ..|.|.       
T Consensus       111 -P~V~~~GDII~LhrvkIq~~ng~~~~v~~~~~~SswavF~~~~~~~~~~i~~~~~~~~~~P~~~S~~~~~~~~~d~~~v  189 (495)
T 1jb7_A          111 -PIIHRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSKHATIEKNEISIL  189 (495)
T ss_dssp             -CCCCEETCEEEEEEEEEEEETTEEEEEEETTTTCEEEEECSSSSCHHHHHHTCCCSCTTSCSEESSSCCCCCTTHHHHH
T ss_pred             -CCCCCCCCEEEEEEEEEEEECCcEEEEecCCCceEEEEEeCCccccccccCCcccCcccCCccccCCCccCCHHHHHHH
Confidence             445 7999999999999876654321 11111   13343333000    0000 0111221    112221       


Q ss_pred             --------------------chhhhh-hcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccc
Q 006263          330 --------------------HISEIE-SAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGD  388 (653)
Q Consensus       330 --------------------~i~~i~-~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~  388 (653)
                                          ++..|. ++..+..+|++|.|+.+....      +   .+-.+.+-|.|+.. .++++..
T Consensus       190 ~~LR~W~~~~~~~~~~~~~~~f~~L~~di~~~~f~DLv~qVv~~~~~d------~---~~~~L~VwDgT~~~-~~~~~~~  259 (495)
T 1jb7_A          190 QNLRKWANQYFSSYSVISSDMYTALNKAQAQKGDFDVVAKILQVHELD------E---YTNELKLKDASGQV-FYTLSLK  259 (495)
T ss_dssp             HHHHHHHHHHHHHSCSSCGGGSCCGGGGGGCSSCEEEEEEEEEEEECS------S---SEEEEEEEETTCCE-EEEEEET
T ss_pred             HHHHHHHHhcccccccccccchhhhhhhhccCCceeEEEEEeEEeccC------C---CeEEEEEEeCCCCC-cceeecc
Confidence                                222333 445678999999999986541      1   34677888988843 3333332


Q ss_pred             hhhhhhhhHHHhhccCC--CcEEEEEeeEeecCCC----ceeccccceEEEEcCChHHHHHHHHHHhcCCCccceeeccc
Q 006263          389 FCNKEGQKLQEMVDVGF--FPVLSVKSGKVNDFSG----KSIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISR  462 (653)
Q Consensus       389 ~A~~~~~~l~~~~~~~~--~~Vvaik~~rV~~f~G----~sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~  462 (653)
                      .          .| ...  +.|+-|...+..+-.+    ..++-. .-...+.|.-....++++++.... ...-..+..
T Consensus       260 ~----------~f-P~~~~G~Vlri~~~~~de~~~~l~~~~~~~w-~ni~~~~~~sk~~ke~~~~~l~~~-~~~~~~~~~  326 (495)
T 1jb7_A          260 L----------KF-PHVRTGEVVRIRSATYDETSTQKKVLILSHY-SNIITFIQSSKLAKELRAKIQDDH-SVEVASLKK  326 (495)
T ss_dssp             T----------TC-TTCCTTCEEEEEEEEECTTCCSSCEEEEEEE-EEEEEECTTCHHHHHHHHHSCCCC-HHHHHHTTS
T ss_pred             c----------cC-CceeeEEEEEEecCccchhhhhhhhhccccc-cceeEEcccchhhhhhhhcccchh-hhhhhhccc
Confidence            2          12 123  7888888887765333    112222 112245555555567777755433 000000100


Q ss_pred             cc-------c--cCCCCcchhccHHhhhhcCCCCCCC-C-cEEEEEEEEEEEeC-C--ceEEecCCCCcCcccccceeee
Q 006263          463 EI-------A--AGGAKNEIHKTVSQIKNEGLGRSEK-P-DWVTVRAFITFIKS-D--SFCYTACPLMIGDRQCNKKVTQ  528 (653)
Q Consensus       463 ~~-------~--~~~~~~~~~kti~~i~~~~lg~~~~-~-~~~~v~atI~~i~~-d--~~~Y~aC~~~~~~~~C~KKv~~  528 (653)
                      ..       +  -..-......||.||....-...+- . ..|.|.+.|+.+-+ +  .|.=+-|+      .|.+. ..
T Consensus       327 ~~~~~~~~lT~~~~~~~~~p~ttL~dIL~~~~~~~~v~~K~~fr~~VRVV~~~P~~i~df~~~~~~------~~~~~-~s  399 (495)
T 1jb7_A          327 NVSLNAVVLTEVDKKHAALPSTSLQDLFHHADSDKELQAQDTFRTQFYVTKIEPSDVKEWVKGYDR------KTKKS-SS  399 (495)
T ss_dssp             SSCSSCEECEEECGGGTTSCBCCHHHHHHTTTTCHHHHTCSEEEEEEEEEEEESSSGGGGEEEEET------TTTEE-EC
T ss_pred             ccCCCCCcCCeecccCCCCCcEEHHHHhcCcccCccccccccEEEEEEEEEecCCCHHHhhhhhcc------ccccc-cc
Confidence            00       0  0000122346899997642100011 1 23888888887654 3  67766688      88876 22


Q ss_pred             cCceeecccCccccCCceEEEEEEEEEEeCC-------CeEEEEEechhhhhhhCCCHHHHHH
Q 006263          529 SGNRWQCDRCNQEIDECDYRYLLQAQIQDQT-------GLTWVTAFQESGEEILGCPAKELYM  584 (653)
Q Consensus       529 ~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~T-------g~~~~~~F~~~ae~llG~sA~el~~  584 (653)
                      .     +.+|.+.    .+.|++.+.|.|.|       +.+.+.++|+.|.++|+++|.+|..
T Consensus       400 ~-----~g~~~~~----~~~~~f~LlveD~t~~~~~~~~ri~l~v~g~~~a~Fl~l~a~nL~~  453 (495)
T 1jb7_A          400 L-----KGASGKG----DNIFQVQFLVKDASTQLNNNTYRVLLYTQDGLGANFFNVKADNLHK  453 (495)
T ss_dssp             S-----TTCGGGC----EEEEEEEEEEECGGGTTBSEEEEEEEECTTSTTTTTTSSCCCCTTT
T ss_pred             c-----ccccCCC----CceEEEEEEEecCCCCCCCcccEEEEEEeCcchheecCCChHhhhc
Confidence            1     1234442    46788999999999       9999999999999999999998844

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=98.20  E-value=2.2e-05  Score=85.90  Aligned_cols=177  Identities=15%  Similarity=0.057  Sum_probs=118.9

Q ss_pred             ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCc
Q 006263          328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP  407 (653)
Q Consensus       328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~  407 (653)
                      |++|++|...  ....-|.|.|+..+++..+...+| +....++.|.|++| .|++|+|++.+..|...|      ..|.
T Consensus         3 ~~~I~~L~p~--~~~w~I~~rV~~k~~ir~~~~~~~-~g~~~~~~L~De~G-~I~at~~~~~~~~f~~~l------~eG~   72 (444)
T 4gop_C            3 IYPIEGLSPY--QNRWTIKARVTSKSDIRHWSNQRG-EGKLFSVNLLDDSG-EIKATGFNDAVDRFYPLL------QENH   72 (444)
T ss_dssp             CCCSTTCCTT--CCSCEEEEECCEECCCEEEECSSC-EEEEEEEEEECSSC-EEEEEEETHHHHHHTTTC------CTTC
T ss_pred             ceeHHHCCCC--CcceEEEEEEEEccCcceecCCCC-CceEEEEEEEcCCC-EEEEEEeHHHHHHHHHhe------ecCC
Confidence            6777887643  246799999999999998875544 34567899999999 999999999988764332      3689


Q ss_pred             EEEEEeeEeecCCCc--------eeccccceEEEEcCChHHHHHHHHHHhcCCCccceeecccccccCCCCcchhccHHh
Q 006263          408 VLSVKSGKVNDFSGK--------SIGTIPSTQLFINPDFAEAHELREWFDSGGKNAATVSISREIAAGGAKNEIHKTVSQ  479 (653)
Q Consensus       408 Vvaik~~rV~~f~G~--------sLs~~~~S~i~inPdipe~~~l~~w~~~~g~~~~~~sls~~~~~~~~~~~~~kti~~  479 (653)
                      |+.|.+++|+..+++        .|.....|.|..-++.+              .     +..       ......+|++
T Consensus        73 vy~Is~~~V~~~~~~y~~~~~~~ei~~~~~T~V~~~~d~~--------------~-----iP~-------~~~~f~~i~~  126 (444)
T 4gop_C           73 VYLISKARVNIAKKQFSNLQNEYEITFENSTEIEECTDAT--------------D-----VPE-------VKYEFVRINE  126 (444)
T ss_dssp             EEEEESCEEEECCGGGCSCCCSEEEEECTTCEEEECSCCS--------------S-----SCC-------CCCCBCCGGG
T ss_pred             EEEEcCCEEEecCCccccCCCCEEEEEcCCcEEEEccCcc--------------c-----Ccc-------eeecccCHHH
Confidence            999999999865432        35555667776554321              0     000       1123466788


Q ss_pred             hhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCceeecccCccccCCceEEEEEEEEEEeCC
Q 006263          480 IKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGNRWQCDRCNQEIDECDYRYLLQAQIQDQT  559 (653)
Q Consensus       480 i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~~~~C~kC~~~~~~~~~rY~l~~~i~D~T  559 (653)
                      |.+.     +....+.|.|.|..+..-. .+                       ....      .-....+..+.|.|.|
T Consensus       127 i~~~-----~~~~~vDViG~V~~v~~~~-~i-----------------------~~k~------~g~~~~kr~i~L~D~s  171 (444)
T 4gop_C          127 LESV-----EANQQCDVIGILDSYGELS-EI-----------------------VSKA------SQRPVQKRELTLVDQG  171 (444)
T ss_dssp             GGGS-----CSSCCCBEEEEEEEECCCE-EE-----------------------CCTT------TCSCEEEEEEEEECTT
T ss_pred             Hhcc-----CCCCceEEEEEEEEcCCcE-EE-----------------------EEcc------CCceeeEEEEEEEeCC
Confidence            8752     2224566889888885311 00                       0000      0112346789999999


Q ss_pred             C-eEEEEEechhhhhhh
Q 006263          560 G-LTWVTAFQESGEEIL  575 (653)
Q Consensus       560 g-~~~~~~F~~~ae~ll  575 (653)
                      | .+.+++|++.|+.+-
T Consensus       172 g~~i~~tLWg~~A~~f~  188 (444)
T 4gop_C          172 NRSVKLTLWGKTAETFP  188 (444)
T ss_dssp             CBEEEEEEEHHHHHTST
T ss_pred             CCEEEEEEEhhhhhhhh
Confidence            9 799999999998653

>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.13  E-value=1.6e-05  Score=70.26  Aligned_cols=101  Identities=18%  Similarity=0.116  Sum_probs=76.2

Q ss_pred             eecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCC
Q 006263          327 SFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFF  406 (653)
Q Consensus       327 ~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~  406 (653)
                      ++++|++|....  .-.-+.|.|+..+++..+..++| +....++.|.|++| +|++|+|++.|..|...|      ..|
T Consensus         3 ~~~~Is~L~p~~--~~w~I~~rV~~k~~~r~~~~~~~-~g~~~~~~L~De~G-~I~at~~~~~~~~f~~~l------~eG   72 (114)
T 1ynx_A            3 PIFAIEQLSPYQ--NVWTIKARVSYKGEIKTWHNQRG-DGKLFNVNFLDTSG-EIRATAFNDFATKFNEIL------QEG   72 (114)
T ss_dssp             CBCCGGGCCTTT--CCCEEEEEEEEEEEEEEEECSSC-EEEEEEEEEEETTE-EEEEEECHHHHHHHHHHS------CSS
T ss_pred             ceEEHHHCCCCC--CceEEEEEEEEeccceEEecCCC-CceEEEEEEECCCC-eEEEEECHHHHHHHHhhc------ccC
Confidence            467888886432  34889999999999999886654 45677899999999 999999999998864433      368


Q ss_pred             cEEEEEeeEeecCCC--------ceeccccceEEEEcCC
Q 006263          407 PVLSVKSGKVNDFSG--------KSIGTIPSTQLFINPD  437 (653)
Q Consensus       407 ~Vvaik~~rV~~f~G--------~sLs~~~~S~i~inPd  437 (653)
                      .|+.|.+++|+.-++        -.|.....|.|..-+|
T Consensus        73 ~vy~Is~~~V~~a~~~y~~~~~~yei~f~~~T~I~~~~d  111 (114)
T 1ynx_A           73 KVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFD  111 (114)
T ss_dssp             SEEEEESCEEEECCTTTSSSSSCEEEEECSSCEEEESCC
T ss_pred             cEEEECCcEEEECCCCcccCCCCEEEEECCCCEEEECCC
Confidence            999999999975322        1455666677765554

>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

Probab=97.96  E-value=6.7e-05  Score=77.54  Aligned_cols=143  Identities=10%  Similarity=0.147  Sum_probs=96.1

Q ss_pred             cceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccC
Q 006263          325 QFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVG  404 (653)
Q Consensus       325 ~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~  404 (653)
                      .|.|++|++|.   .+..|+|||+|+++++...  + .|+ --...|+|.|.|...|.|.+|.+....+    .. + ..
T Consensus         3 ~y~y~~l~~l~---~~~~vnvigVV~~~~~p~~--s-~G~-d~~~tl~I~D~S~~gl~v~iF~~~~~~L----P~-v-~~   69 (294)
T 1xjv_A            3 NYIYTPLNQLK---GGTIVNVYGVVKFFKPPYL--S-KGT-DYCSVVTIVDQTNVKLTCLLFSGNYEAL----PI-I-YK   69 (294)
T ss_dssp             CCCCCCGGGCC---SSEEEEEEEEEEEEEEEEE--C-SSS-SEEEEEEEECTTCCEEEEEEEESSGGGS----CC-C-CS
T ss_pred             cceEEEHHHhh---CCCeeEEEEEEEEcCCCcc--C-CCC-eEEEEEEEEcCCCCCEEEEEECCChHHC----CC-C-CC
Confidence            47899999873   5788999999999987743  2 354 4578999999998889999998764442    21 1 14


Q ss_pred             CCcEEEEEeeEeecCCCc-ee-ccccceEEEEcCC--------------------hHHHHHHHHHHhcCCCccceeeccc
Q 006263          405 FFPVLSVKSGKVNDFSGK-SI-GTIPSTQLFINPD--------------------FAEAHELREWFDSGGKNAATVSISR  462 (653)
Q Consensus       405 ~~~Vvaik~~rV~~f~G~-sL-s~~~~S~i~inPd--------------------ipe~~~l~~w~~~~g~~~~~~sls~  462 (653)
                      .|.||.+++++|..|+|+ .+ +....+.+.+++.                    ..-+..||.|+.+..        +.
T Consensus        70 ~GDII~l~~vki~~~~g~~~~v~~~~~s~~~f~g~~~~~~~p~~~~~~~~~~~~e~~~~~~Lr~w~~~~~--------~~  141 (294)
T 1xjv_A           70 NGDIVRFHRLKIQVYKKETQGITSSGFASLTFEGTLGAPIIPRTSSKYFNFTTEDHKMVEALRVWASTHM--------SP  141 (294)
T ss_dssp             TTCEEEEEEEEEEEETTEEEEEEEEEEEEEEECCSTTCCCCCBCSCSSCCCCHHHHHHHHHHHHHHHHHC--------C-
T ss_pred             CCCEEEEEEEEEEEECCeEEEEccCCeEEEEECCCCCCCcCCcccCCCcCCCHHHHHHHHHHHHHHHhcc--------CC
Confidence            689999999999999996 33 2222222334431                    123567999986421        00


Q ss_pred             ccccCCCCcchhccHHhhhhcCCCCCCCCcEEEEEEEEEEEe
Q 006263          463 EIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIK  504 (653)
Q Consensus       463 ~~~~~~~~~~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~  504 (653)
                              ......|+||++.        .||.+.|.|..+-
T Consensus       142 --------~~~~~~L~di~~~--------~f~DLv~qVv~v~  167 (294)
T 1xjv_A          142 --------SWTLLKLCDVQPM--------QYFDLTCQLLGKA  167 (294)
T ss_dssp             ----------CCCCGGGCCSS--------CEEEEEEEEEEEE
T ss_pred             --------CCceeEHHHcccC--------CeeeEEEEEEEEE
Confidence                    0112356666542        4899999999764

>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

Probab=97.59  E-value=0.00025  Score=67.47  Aligned_cols=89  Identities=18%  Similarity=0.283  Sum_probs=70.2

Q ss_pred             ceecchhhhhh-cccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCC----CCEEEEEEccchhhhhhhhHHHh
Q 006263          326 FSFRHISEIES-AENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTS----GRSVELTLWGDFCNKEGQKLQEM  400 (653)
Q Consensus       326 f~f~~i~~i~~-~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s----~~~i~vtLWg~~A~~~~~~l~~~  400 (653)
                      +.|+++.++.+ +..+..|||||||+++++...  +..|+.--...|+|.|.|    +..|.|.++.+.....    .. 
T Consensus        27 ~~~~~~r~~l~~~~~g~~VNviGVVvd~~~P~~--S~rGtkD~~~TltI~D~S~~~~~~gL~v~iF~~~~e~L----P~-   99 (187)
T 1qzg_A           27 LTFQSIRSSQELQKKNTIVNLFGIVKDFTPSRQ--SLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGNDL----PV-   99 (187)
T ss_dssp             EEEECHHHHTSCCSSCEEEEEEEEEEEEEEEEE--CSSTTCCEEEEEEEECTTSCTTSCCEEEEEEESSSSCS----CC-
T ss_pred             eeEEEHHHHHhhccCCCEEEEEEEEEEccCcee--cCCCCccEEEEEEEEeCCCCCCCCceEEEEECCChhhC----CC-
Confidence            67899999876 567899999999999999853  213554567899999998    5689999998875442    21 


Q ss_pred             hccCCCcEEEEEeeEeecCCCc
Q 006263          401 VDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       401 ~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                      . ...|+||.+++++|..|+|.
T Consensus       100 V-~~~GDIIlL~rvkiq~~~g~  120 (187)
T 1qzg_A          100 I-KQVGQPLLLHQITLRSYRDR  120 (187)
T ss_dssp             C-CSTTCEEEEEEEEEEEETTE
T ss_pred             C-CCCCCEEEEEEEEEEEECCe
Confidence            1 14689999999999999996

>3u58_A Tetrahymena TEB1 AB; tetrahymena, telomerase, TEB1, processivity factor, DNA BIND protein-DNA complex; HET: DNA; 2.61A {Tetrahymena thermophila}

Probab=97.46  E-value=0.017  Score=51.05  Aligned_cols=158  Identities=23%  Similarity=0.354  Sum_probs=111.4

Q ss_pred             eeccccCCCCCc--eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          209 IPIAALNPYQGR--WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       209 ~pI~~L~p~~~~--w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      ..|+.|..+.++  +...+||+.|+.  +|.|.. +.+.|-+.-.|+..-+|...+|.. +|.-|..|++|+-|++-++.
T Consensus        12 llisqlqvgknrfsfkfegrvvykss--tfqnqq-dskyffitaqdannqeinlsfwqk-vdqsyqtlkvgqyyyfigge   87 (213)
T 3u58_A           12 LLISQLQVGKNRFSFKFEGRVVYKSS--TFQNQQ-DSKYFFITAQDANNQEINLSFWQK-VDQSYQTLKVGQYYYFIGGE   87 (213)
T ss_dssp             ECGGGCCTTSCTTSEEEEEEEEEECC--CBCCST-TCCBEEEEEECTTSCEEEEEECSS-HHHHHHHCCTTCEEEEESCE
T ss_pred             hhhhhhhhccceeeEEeeeEEEEeec--cccccc-cccEEEEEeecCCCceechHHHHH-hhhhhheeeeceEEEEEccc
Confidence            467888877764  668899999987  788764 568899999999999999999987 68888999999999999999


Q ss_pred             EecCCCcccCCCCceEEEeccc-cEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCce
Q 006263          287 LKPAQKNFNHLKNEWEIFLEAT-STVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGME  365 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~-T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~  365 (653)
                      |+.-.       +..|+.|.-. -.|.+-+.-.++    .=.-.-|+++... ......|++.|+++....       + 
T Consensus        88 vkqfk-------nnlelkfkfgdyqiipketlggs----ggstllisevlkt-skqylsvlaqvvdiqssd-------k-  147 (213)
T 3u58_A           88 VKQFK-------NNLELKFKFGDYQIIPKETLGGS----GGSTLLISEVLKT-SKQYLSVLAQVVDIQSSD-------K-  147 (213)
T ss_dssp             EEECS-------SSEEEEECSSCCEEEESTTTTCS----TTCCBCHHHHTTC-CCSEEEEEEEEEEEEECS-------S-
T ss_pred             Hhhhc-------cceEEEEecCceEEechhhcCCC----CCceeehHHHHHH-hHHHHHHHHHhhccccCC-------C-
Confidence            97532       3477776543 344443211110    0112235555442 345677888887765431       1 


Q ss_pred             eeEEEEEEEeCCC-CEEEEEEccchhhh
Q 006263          366 TQRRILNLKDTSG-RSVELTLWGDFCNK  392 (653)
Q Consensus       366 ~~kr~i~l~D~s~-~~i~vtLWg~~A~~  392 (653)
                        ...+.|.|.|. ..+.+.++-+.+-+
T Consensus       148 --nirlkicdnscnqelkvvifpdlcye  173 (213)
T 3u58_A          148 --NIRLKICDNSCNQELKVVIFPDLCYE  173 (213)
T ss_dssp             --CEEEEEECTTCSCCEEEEECTTTTGG
T ss_pred             --ceEEEeecccccceeEEEEchhHhhH
Confidence              23467889884 78999999998765

>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

Probab=97.36  E-value=0.0017  Score=73.42  Aligned_cols=172  Identities=13%  Similarity=0.172  Sum_probs=118.7

Q ss_pred             CeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceEEEeccccEEEeccCCCCCCCc-c-cceecchhh
Q 006263          256 GEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPK-Q-QFSFRHISE  333 (653)
Q Consensus       256 ~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~-~-~f~f~~i~~  333 (653)
                      ...-.++|+..-+ ..+.|+||++|.|.+.......  .+.-....+|+-.+.|.+.+.+..+..++. + .-..++|++
T Consensus       525 k~~iLSIW~P~ed-l~s~L~EG~~y~iy~L~~s~s~--~~~~~~~lqLtAtk~T~~~~L~~~~~~~~~~~~pR~~~~~~~  601 (738)
T 1miu_A          525 KSALLSIWRPSSD-LSSLLTEGKRYRIYHLAVSKSK--SKFERPSIQLTATKRTQYQQLPVSSETLLQVYQPRESLHFSR  601 (738)
T ss_dssp             CCEEEEEESCCHH-HHHHCCSSCEEEEEEECCCCCC--CSSSCCSCEEEEEEEEEEEEECCCHHHHTTTCCCCCBCCSGG
T ss_pred             ceEEEEEeCCChH-HHhhccCCcEEEEEEeeccCCC--ccCccceEEEeecccceeEECCcchhhhccccCCcceeeHHH
Confidence            4777899997644 7788999999999997654443  222334678999999999998532211111 1 113456777


Q ss_pred             hhh---cccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEE
Q 006263          334 IES---AENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLS  410 (653)
Q Consensus       334 i~~---~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vva  410 (653)
                      |.+   .+...-||++|+|+.|+...      |   ..-.+.|.|.+..-+-|.+|+...++          -..+.+||
T Consensus       602 l~~~~f~p~~~EvDivG~Vv~v~~~~------~---~~~~vylsD~~~nll~Ikf~~~l~eD----------~~~~~~va  662 (738)
T 1miu_A          602 LSDPAFQPPCSEVDVVGVVVSVVKPI------G---LAPLVYLSDECLNLLVVKFGIDLNED----------IKPRVLIA  662 (738)
T ss_dssp             GGSSSCCTTTTEEEEEEEEEEEECCT------T---SCCEEEEECSSSCEEEEEESSCCCSC----------CCSSCEEE
T ss_pred             hcCccccCCCCceeEEEEEEEEcccC------c---ccceEEEEcCCCcEEEEEEecCchhh----------CccccEEE
Confidence            776   56778999999999997642      2   12367789999889999999998632          24689999


Q ss_pred             EEeeEeecCC--Cc-eeccccceEEEEcCC---h-HHHHHHHHHHh
Q 006263          411 VKSGKVNDFS--GK-SIGTIPSTQLFINPD---F-AEAHELREWFD  449 (653)
Q Consensus       411 ik~~rV~~f~--G~-sLs~~~~S~i~inPd---i-pe~~~l~~w~~  449 (653)
                      +.+.......  |. .|-.+..|.+.-||.   . .+.+.|+.-..
T Consensus       663 ~sNL~~r~~~~~~ip~~~a~~~t~fs~~pk~~hl~~~~~~lk~~~~  708 (738)
T 1miu_A          663 ASNLQCQPESTSGVPTLFAGHFSIFSASPKEAYFQEKVNNLKHAIE  708 (738)
T ss_dssp             EEEEECCSCCSSSCCCEEECTTCEEESSCCCTTTHHHHHHHTHHHH
T ss_pred             EeeeEeeccccccCceEEeccceEEecCccHhHHHHHHHHHHHhhh
Confidence            9999886432  33 455677788888883   2 33455555443

>3u4v_A Telomerase-associated protein 82; TEB1, processivity factor, DNA BIND protein; 1.80A {Tetrahymena thermophila}

Probab=97.09  E-value=0.0053  Score=49.61  Aligned_cols=88  Identities=27%  Similarity=0.475  Sum_probs=71.8

Q ss_pred             eeccccCCCCCc--eEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          209 IPIAALNPYQGR--WAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       209 ~pI~~L~p~~~~--w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      ..|+.|..+.++  +...+||+.|+.  +|.|.. +.+.|-+.-.|+..-+|..++|.. +|.=|..|++|+.|++-++.
T Consensus        16 llisqlqvgknrfsfkfegrvvykss--tfqnqq-dskyffitaqdannqeinmsfwqk-vdqsyqtlkvgqyyyfigge   91 (117)
T 3u4v_A           16 LLISQLQVGKNRFSFKFEGRVVYKSS--TFQNQQ-DSKYFFITAQDANNQEINMSFWQK-VDQSYQTLKVGQYYYFIGGE   91 (117)
T ss_dssp             ECGGGCCTTCCTTSCEEEEEEEEECC--CEECTT-SCEEEEEEEECTTSCEEEEEEESS-THHHHTTCCTTCEEEEESCE
T ss_pred             eehhhhhcccceeeEEeeeEEEEeec--cccccc-cccEEEEEeecCCCceechHHHHH-hhhhhheEeeceEEEEEccc
Confidence            468888888764  678899999987  787764 568999999999999999999987 58888999999999999999


Q ss_pred             EecCCCcccCCCCceEEEecc
Q 006263          287 LKPAQKNFNHLKNEWEIFLEA  307 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~  307 (653)
                      |+.-       .+..|+.|.-
T Consensus        92 vkqf-------knnlelkfkf  105 (117)
T 3u4v_A           92 VKQF-------KNNLELKFKF  105 (117)
T ss_dssp             EEEE-------TTEEEEEEET
T ss_pred             hhhh-------ccceEEEEec
Confidence            9653       2346666643

>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

Probab=96.97  E-value=0.0044  Score=68.12  Aligned_cols=89  Identities=10%  Similarity=0.135  Sum_probs=65.6

Q ss_pred             cccceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCC-------EE-----EEEEccchh
Q 006263          323 KQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGR-------SV-----ELTLWGDFC  390 (653)
Q Consensus       323 ~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~-------~i-----~vtLWg~~A  390 (653)
                      ...|.|++|+++... .+..|||||||+++++...  ++ |+ --...|+|.|.|-.       .+     .|.++.+..
T Consensus        33 ~~~y~y~~L~~a~~~-~~~~VnviGVVvd~~~P~~--T~-G~-D~~~t~tI~D~S~~~~~~~~~Gl~~~~~~v~iF~~~~  107 (495)
T 1jb7_A           33 GHKYEYVELAKASLT-SAQPQHFYAVVIDATFPYK--TN-QE-RYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRF  107 (495)
T ss_dssp             ---CCBCCTTTSCSS-CCSCEEEEEEEEEECCCEE--CS-SS-CEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSG
T ss_pred             cCCCccEEHHHHHhc-cCCeEEEEEEEeecCCcee--cC-CC-eEEEEEEEEeCCCCcccccccccccCceEEEEECCCh
Confidence            456899999998753 5778999999999998852  32 44 35789999998754       37     999988764


Q ss_pred             hhhhhhHHHhhccCCCcEEEEEeeEeecCCCc
Q 006263          391 NKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       391 ~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~  422 (653)
                      ..    |.. . ...|+||.|++++|..|+|+
T Consensus       108 e~----LP~-V-~~~GDII~LhrvkIq~~ng~  133 (495)
T 1jb7_A          108 ED----LPI-I-HRAGDIIRVHRATLRLYNGQ  133 (495)
T ss_dssp             GG----SCC-C-CEETCEEEEEEEEEEEETTE
T ss_pred             HH----CCC-C-CCCCCEEEEEEEEEEEECCc
Confidence            33    121 1 02589999999999999996

>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3

Probab=94.81  E-value=0.82  Score=46.88  Aligned_cols=181  Identities=14%  Similarity=0.143  Sum_probs=96.8

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCC------CeEEEEEchhHHHHHHhh-cccCcEEEEec
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDG------GEIRVTCFNAVVDRFYEI-IEVGRVYLISK  284 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g------~~I~at~f~~~~~kf~~~-l~eG~vy~is~  284 (653)
                      +++.+|.+||.+.-.+|...+  | ..+.+|.|.      |++|      .-|++++|+..++.+... |+.|+-++|.+
T Consensus         5 mN~V~LiGrL~~dPelr~t~~--G-~~v~~f~LAv~r~~~~~~G~~~~~t~~i~vv~~g~~Ae~~~~~~l~KG~~V~VeG   81 (301)
T 1se8_A            5 MNHVYLIGALARDPELRYTGN--G-MAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAEWQAERNLKGGDAVVVEG   81 (301)
T ss_dssp             EEEEEEEEEESSCCEEEECTT--S-CEEEEEEEEEEEEC-------CEEEEEEEEEEESHHHHHHHHTCCCTTCEEEEEE
T ss_pred             eeEEEEEEEECCCceEEECCC--C-CEEEEEEEEEcCceECCCCCEecceEEEEEEEEcHHHHHHHhhCCCCCCEEEEEE
Confidence            467899999999999987643  2 256677663      2223      358999999999999999 99999999997


Q ss_pred             eEEecCCCcccC--CCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcc-cCccccEEEEEEEecCceeEEec
Q 006263          285 GSLKPAQKNFNH--LKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAE-NNSIVDVIGIVISVNPSVPILRK  361 (653)
Q Consensus       285 ~~V~~a~~~f~~--~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~-~~~~vDVIGvV~~v~~~~~i~~k  361 (653)
                      ..- .  +.|..  ....|.+.+.-+ .|+.+..... .-..     ....+ .+. .-..|-++|.|..--++.  .+.
T Consensus        82 ~L~-~--r~~~dkdG~~r~~~ev~a~-~i~~l~~~~~-~~~d-----~~gg~-rm~~mmN~V~L~GrL~~dPelr--~t~  148 (301)
T 1se8_A           82 TLE-Y--RQWEAPEGGKRSAVNVKAL-RMEQLGTQPE-LIQD-----AGGGV-RMSGAMNEVLVLGNVTRDPEIR--YTP  148 (301)
T ss_dssp             EEE-E--EEEC-----CEEEEEEEEE-EEEECSSCCC-EEEC-----TTSCE-EEETCEEEEEEEEEECSCCEEE--ECT
T ss_pred             EEE-e--eeEECCCCCEEEEEEEEEe-EEEEeecccc-cccc-----ccccc-chhcceeEEEEEEEECcCCEEE--ECC
Confidence            432 1  12211  112232222111 2333311000 0000     00000 000 112356778776533332  234


Q ss_pred             CCceeeEEEEEE----EeCCCC------EEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe-eEeecCCC
Q 006263          362 NGMETQRRILNL----KDTSGR------SVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS-GKVNDFSG  421 (653)
Q Consensus       362 ~g~~~~kr~i~l----~D~s~~------~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~-~rV~~f~G  421 (653)
                      +|+.+.+-.|-.    .|..|.      -+.|++||+.|+..    +. +  ..+..|.+.| .+...|.+
T Consensus       149 ~G~~v~~f~lAv~~~~~d~~Ge~~~~t~~i~vvawg~~Ae~~----~~-l--~KG~~V~V~GrL~~~~y~d  212 (301)
T 1se8_A          149 AGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLAENM----KE-L--RKGDPVMIMGRLVNEGWTD  212 (301)
T ss_dssp             TCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHHHH----TT-C--CTTCEEEEEEEEEEEECC-
T ss_pred             CCCEEEEEEEEEcCceEcCCCCcccccEEEEEEECCHHHHHH----Hh-c--CCCCEEEEEEEEeeeeEEC
Confidence            676543333322    233332      59999999998774    22 2  3567776664 46666753

>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

Probab=94.29  E-value=0.056  Score=49.53  Aligned_cols=89  Identities=20%  Similarity=0.231  Sum_probs=60.6

Q ss_pred             EEEEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhH---HHHHHHH----hcCceEEEEEEEeeeccCce
Q 006263          549 YLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVR---FGEIIRS----RVFNQYLFRLKIKEELYGDE  621 (653)
Q Consensus       549 Y~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~---~~~~~~~----~~~k~~~f~v~~k~~~y~~e  621 (653)
                      |.|.+.|+|+|+.+.+.+=+++-+.++|.|+.|+..++   .|+..   +.+.+.+    +.--.-.++|......    
T Consensus        60 W~l~a~IsDGS~~LdV~f~~~VLt~lIGfS~~E~~~lk---kdp~~~~~l~e~L~~~Q~~L~dl~clM~I~~~~~~----  132 (157)
T 3mxn_A           60 WSITAKVSDGTAYLDVDFVDEILTSLIGFSVPEMKQSK---KDPLQYQKFLEGLQKCQRDLIDLCCLMTISFNPSL----  132 (157)
T ss_dssp             CBCEEEEECSSCEEEEEECHHHHHHHHSCCHHHHHHHT---TSHHHHHHHHHHHHHHHHHHHHCEEEEEEEEETTT----
T ss_pred             EEEEEEEeCCceeEEEEeeHHHHHhhhCCCHHHHHHHh---hCHHHHHHHHHHHHHHHHHHHhhccEEEEEEcCCC----
Confidence            56889999999999999999999999999999999988   34433   3333433    3333445666443221    


Q ss_pred             eeEEEEEEEeecCChHHHHHHHHHHH
Q 006263          622 QRVKITVIRADQVNYSSESRYLLDLI  647 (653)
Q Consensus       622 ~r~~~~v~~~~~vd~~~e~~~ll~~i  647 (653)
                        -+-.|.++++++- +....|-+.|
T Consensus       133 --~~pVV~~l~d~s~-~~l~~L~kRl  155 (157)
T 3mxn_A          133 --SKAMVLALQDVNM-EHLENLKKRL  155 (157)
T ss_dssp             --TEEEEEEEECCCH-HHHHHHHHHT
T ss_pred             --CCCEEEEecCCCH-HHHHHHHHHh
Confidence              1557778887775 3444554444

>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

Probab=93.86  E-value=1.4  Score=44.23  Aligned_cols=178  Identities=14%  Similarity=0.184  Sum_probs=96.8

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC------eEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG------EIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~------~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      +++.+|.|||.+--.+|...+  | ..+.+|.|.      |++|.      -|++++|+..++.....|+.|+-++|.+.
T Consensus         5 ~N~v~L~G~l~~dpelr~t~~--G-~~v~~f~lA~~~~~~~~~G~~~~~t~~~~v~~~g~~Ae~~~~~l~KG~~V~V~G~   81 (264)
T 2fxq_A            5 LNQVFLIGTLTARPDMRYTPG--G-LAILDLNLAGQDAFTDESGQEREVPWYHRVRLLGRQAEMWGDLLEKGQLIFVEGR   81 (264)
T ss_dssp             EEEEEEEEEESSCCCCEECTT--C-CEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHHHHTTTCCTTCEEEEEEE
T ss_pred             eeEEEEEEEeccCCeEEECCC--C-CEEEEEEEEECCcEECCCCCEecccEEEEEEEEchHHHHHHHhCCCCCEEEEEEE
Confidence            468999999999999987643  2 256666653      43442      48999999999999999999999999964


Q ss_pred             EEecCCCccc-CC--CCceEEEeccccEEEeccCCCC-CCCcccceecchhhhhhcc-cCccccEEEEEEEecCceeEEe
Q 006263          286 SLKPAQKNFN-HL--KNEWEIFLEATSTVDLCTEEDD-SIPKQQFSFRHISEIESAE-NNSIVDVIGIVISVNPSVPILR  360 (653)
Q Consensus       286 ~V~~a~~~f~-~~--~~~yei~f~~~T~I~~~~d~~~-~iP~~~f~f~~i~~i~~~~-~~~~vDVIGvV~~v~~~~~i~~  360 (653)
                      . +.  ..|. ..  ...++|..+   .|..+..... ......      .. ..+. .-..|-++|.|..--++.  .+
T Consensus        82 L-~~--~~~~~dG~~r~~~ev~a~---~i~~l~~~~~~~~~d~~------g~-~~m~~~~N~v~l~G~l~~dpe~r--~t  146 (264)
T 2fxq_A           82 L-EY--RQWEKDGEKKSEVQVRAE---FIDPLEGRGRETLEDAR------GQ-PRLRRALNQVILMGNLTRDPDLR--YT  146 (264)
T ss_dssp             E-EE--C---------CCEEEEEE---EEEECCCC---------------------CCCCEEEEEEEEESSCCCCE--EC
T ss_pred             E-Ee--eeEEeCCEEEEEEEEEEE---EEEECcCCccccccccc------cc-cccccceEEEEEEEEECCCCEEE--EC
Confidence            3 22  1222 11  122344433   2443311000 000000      00 0000 123466888877543333  23


Q ss_pred             cCCceeeEEEEEEEeC-------CCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEe-eEeecCC
Q 006263          361 KNGMETQRRILNLKDT-------SGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKS-GKVNDFS  420 (653)
Q Consensus       361 k~g~~~~kr~i~l~D~-------s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~-~rV~~f~  420 (653)
                      .+|+.+.+-.|-.-..       .-.-+.|++||+.|.... +    +  ..|..|.+.| .+...|.
T Consensus       147 ~~G~~v~~f~lAv~~~~~g~~~~~t~~~~v~~wg~~Ae~~~-~----l--~KG~~V~V~G~l~~~~~~  207 (264)
T 2fxq_A          147 PQGTAVVRLGLAVNERRRGQEEERTHFLEVQAWRELAEWAS-E----L--RKGDGLLVIGRLVNDSWT  207 (264)
T ss_dssp             TTCCEEEEEEEEEECCC-------EEEEEEEEEHHHHHHHT-T----C--CTTCEEEEEEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEcCCcCCCCccccEEEEEEEEChHHHHhh-h----c--CCCCEEEEEEEEEeeEEE
Confidence            4566543322222211       112699999999987642 2    2  3566666654 4566664

>3ebe_A Protein MCM10 homolog; OB-fold, zinc finger, CCCH, DNA replication, metal-binding, zinc-finger, replication; 2.30A {Xenopus laevis} PDB: 3h15_A

Probab=93.27  E-value=0.56  Score=45.07  Aligned_cols=83  Identities=22%  Similarity=0.266  Sum_probs=57.5

Q ss_pred             CCCcceeccccC-----CC--CCceEEEEEEEeeccccccccCCCCceeEE-EEEEeC--CCCeEEEEEchhHHHHHHhh
Q 006263          204 APARIIPIAALN-----PY--QGRWAIKARVTAKGDLRRYNNARGDGKVFS-FDLLDS--DGGEIRVTCFNAVVDRFYEI  273 (653)
Q Consensus       204 ~~~~~~pI~~L~-----p~--~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~-~~L~D~--~g~~I~at~f~~~~~kf~~~  273 (653)
                      ..+++..|++|-     |.  ..+|.+-|-|+.|++.|.-.+    |+-|. +.|.|=  ...++...+|+++.++++ .
T Consensus        34 ~~~k~~~l~~L~~~v~~~~~~e~dwv~~GVV~~Ks~pk~~~~----gk~y~~w~l~DL~~~~~~V~lfLFg~a~~~~~-k  108 (200)
T 3ebe_A           34 NGRKLIRLAQLQNKIATEKLEEEDWVTFGVIVKKITPQSSNN----GKTFSIWRLNDLKDLDKYISLFLFGDVHKEHW-K  108 (200)
T ss_dssp             TTCEECCGGGHHHHHHTTCSTTSCEEEEEEEEEEECC-----------CCEEEEEECSSSTTCCEEEEECHHHHHHHT-T
T ss_pred             cCCeEEeHHHHHhhccCCCCCcCCEEEEEEEEecCCccCcCC----CCeEEEEEEEecCCCCcEEEEEEechHHHHhc-C
Confidence            456778888772     21  258999999999999987432    44332 334442  336799999999999966 5


Q ss_pred             cccCcEEEEeceEEecCC
Q 006263          274 IEVGRVYLISKGSLKPAQ  291 (653)
Q Consensus       274 l~eG~vy~is~~~V~~a~  291 (653)
                      +++|.|+-|-|..+.+.+
T Consensus       109 ~~~G~ViaiLNP~i~~~~  126 (200)
T 3ebe_A          109 TDQGTVIGLLNANPMKPK  126 (200)
T ss_dssp             CCTTEEEEEESCEECCCC
T ss_pred             cCCceEEEEECCEEccCC
Confidence            899999999999876543

>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*

Probab=92.00  E-value=0.7  Score=41.91  Aligned_cols=111  Identities=11%  Similarity=-0.016  Sum_probs=62.0

Q ss_pred             hhhhhhcccCccccEEEEEEEecCc-eeEEec--CCceee-EEEEEE-EeC-------CCCEEEEEEccchhhhhhhhHH
Q 006263          331 ISEIESAENNSIVDVIGIVISVNPS-VPILRK--NGMETQ-RRILNL-KDT-------SGRSVELTLWGDFCNKEGQKLQ  398 (653)
Q Consensus       331 i~~i~~~~~~~~vDVIGvV~~v~~~-~~i~~k--~g~~~~-kr~i~l-~D~-------s~~~i~vtLWg~~A~~~~~~l~  398 (653)
                      |+-|.++..+.++|++|.|+.+-.- ..++-.  +..+-. -..... .|.       ...++.||||+..|.-     +
T Consensus         5 f~llkdv~~~~F~Dl~~qVv~~~~~~~~~~LyVTDYT~N~~~~~~~~~~~~~~W~Gp~G~~tlqVtlwd~ha~~-----a   79 (143)
T 4hik_A            5 FSLLSQITPHQRCSFYAQVIKTWYSDKNFTLYVTDYTENELFFPMSPYTSSSRWRGPFGRFSIRCILWDEHDFY-----C   79 (143)
T ss_dssp             CCCGGGCCSSCEEEEEEEEEEEEECSSCEEEEEECSCCCTTSCCBCTTCTTCSCCCCCBSCCEEEEECHHHHHH-----H
T ss_pred             hhhHHhCCCCCeEEEEEEEEEEEcCCCeEEEEEecCCCCCcccccccCCCCccccCCCCcEEEEEEEECcHHHH-----H
Confidence            4445566689999999999886532 122211  111100 000000 011       2248999999999865     2


Q ss_pred             HhhccCCCcEEEEEeeEeecC-CCc---eecccc----ce-EEEEcCChHHHHHHHHH
Q 006263          399 EMVDVGFFPVLSVKSGKVNDF-SGK---SIGTIP----ST-QLFINPDFAEAHELREW  447 (653)
Q Consensus       399 ~~~~~~~~~Vvaik~~rV~~f-~G~---sLs~~~----~S-~i~inPdipe~~~l~~w  447 (653)
                      .. +...|..|.|++++++.- +|.   .|....    .. ...++|+.|+.++|...
T Consensus        80 r~-~lk~Gd~v~L~Nv~iK~~~~g~LEG~l~~dr~~~~ki~v~~ld~~~~~lk~ll~R  136 (143)
T 4hik_A           80 RN-YIKEGDYVVMKNVRTKIDHLGYLECILHGDSAKRYNMSIEKVDSEEPELNEIKSR  136 (143)
T ss_dssp             TT-TCCTTCEEEEEEEEEEECTTSCEEEEECCCTTCCSCCEEEEECTTCGGGHHHHHH
T ss_pred             Hh-hCCCCCEEEEEeEEEeecCCceEEEEEcCCCCCCCcceEEEcCCCCHHHHHHHHH
Confidence            21 135689999999999743 452   232111    11 23467766888777654

>3u4z_A Telomerase-associated protein 82; TEB1, processivity factor, DNA BIND protein; 2.30A {Tetrahymena thermophila}

Probab=91.90  E-value=4  Score=32.52  Aligned_cols=84  Identities=12%  Similarity=0.170  Sum_probs=63.6

Q ss_pred             CCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC-CeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCc
Q 006263          215 NPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-GEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKN  293 (653)
Q Consensus       215 ~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g-~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~  293 (653)
                      .......++.|.|+....         ..+-+.+-++|... -+.++.+|.++|-.|.+.+..++||++..|--...|  
T Consensus         9 ktskqylsvlaqvvdiqs---------sdknirlkicdnscnqelkvvifpdlcyewrdkfsinkwyyfnefvrqiyn--   77 (109)
T 3u4z_A            9 KTSKQYLSVLAQVVDIQS---------SDKNIRLKICDNSCNQELKVVIFPDLCYEWRDKFSINKWYYFNEFVRQIYN--   77 (109)
T ss_dssp             TCCCSEEEEEEEEEEEEC---------CSSCEEEEEECSSCSSCEEEEECTTHHHHHTTTCCTTCEEEEEEEEEEESS--
T ss_pred             HHHHHHHHHHHHHhhhhc---------CCCceEEEeecccccceeEEEEchhHHHHHHhhcchhhhhhHHHHHHHHhh--
Confidence            334456778888876421         13567889999653 589999999999999999999999999998544333  


Q ss_pred             ccCCCCceEEEeccccEEEec
Q 006263          294 FNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       294 f~~~~~~yei~f~~~T~I~~~  314 (653)
                           .+..+.-+-++.|.+.
T Consensus        78 -----devqlknnihssikes   93 (109)
T 3u4z_A           78 -----DEVQLKNNIHSSIKES   93 (109)
T ss_dssp             -----SCEEEECCTTCEEEEC
T ss_pred             -----hHHhHhhhhhhhhhcc
Confidence                 2466666778999987

>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

Probab=91.52  E-value=0.47  Score=42.40  Aligned_cols=70  Identities=17%  Similarity=0.318  Sum_probs=45.3

Q ss_pred             ccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC
Q 006263          341 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS  420 (653)
Q Consensus       341 ~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~  420 (653)
                      ..|.++|+|.++.+-          .....++|.|.||..|++.+|.+...... . ...+  ..+..|-+.|. ++.|+
T Consensus        32 ~~V~iVG~V~~~~~~----------~~~~~~~ldD~TG~~I~~~~W~~~~~~~~-~-~~~~--~~g~yVrV~G~-l~~f~   96 (132)
T 3kdf_D           32 SQVTIVGIIRHAEKA----------PTNIVYKIDDMTAAPMDVRQWVDTDDTSS-E-NTVV--PPETYVKVAGH-LRSFQ   96 (132)
T ss_dssp             CEEEEEEEEEEEEEC----------SSEEEEEEECSSSSCEEEEEEC-----------CCC--CTTCEEEEEEE-EEEET
T ss_pred             EEEEEEEEEEEEEEc----------CCeEEEEEECCCCCEEEEEEEccCCCccc-c-cccc--cCCCEEEEEEE-EEeEC
Confidence            468999999988542          14678999999998899999987642210 0 1112  35677776655 78899


Q ss_pred             Cc-eec
Q 006263          421 GK-SIG  425 (653)
Q Consensus       421 G~-sLs  425 (653)
                      |+ .|.
T Consensus        97 g~~qi~  102 (132)
T 3kdf_D           97 NKKSLV  102 (132)
T ss_dssp             TEEEEE
T ss_pred             CEEEEE
Confidence            95 554

>3ebe_A Protein MCM10 homolog; OB-fold, zinc finger, CCCH, DNA replication, metal-binding, zinc-finger, replication; 2.30A {Xenopus laevis} PDB: 3h15_A

Probab=91.10  E-value=0.71  Score=44.33  Aligned_cols=81  Identities=15%  Similarity=0.269  Sum_probs=54.1

Q ss_pred             ceecchhhhhh-cccCccc--c--EEEEEEEecCceeEEecCCceeeEEEEEEEeCCC--CEEEEEEccchhhhhhhhHH
Q 006263          326 FSFRHISEIES-AENNSIV--D--VIGIVISVNPSVPILRKNGMETQRRILNLKDTSG--RSVELTLWGDFCNKEGQKLQ  398 (653)
Q Consensus       326 f~f~~i~~i~~-~~~~~~v--D--VIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~--~~i~vtLWg~~A~~~~~~l~  398 (653)
                      ..|++|++|.. +..+.+.  |  ++|+|.+-++...  +++|+...  -..|.|..+  .+|.|-|+|+-..+      
T Consensus        36 ~k~~~l~~L~~~v~~~~~~e~dwv~~GVV~~Ks~pk~--~~~gk~y~--~w~l~DL~~~~~~V~lfLFg~a~~~------  105 (200)
T 3ebe_A           36 RKLIRLAQLQNKIATEKLEEEDWVTFGVIVKKITPQS--SNNGKTFS--IWRLNDLKDLDKYISLFLFGDVHKE------  105 (200)
T ss_dssp             CEECCGGGHHHHHHTTCSTTSCEEEEEEEEEEECC---------CCE--EEEEECSSSTTCCEEEEECHHHHHH------
T ss_pred             CeEEeHHHHHhhccCCCCCcCCEEEEEEEEecCCccC--cCCCCeEE--EEEEEecCCCCcEEEEEEechHHHH------
Confidence            58999999976 3332222  3  6699999988754  34566543  467777665  67999999998644      


Q ss_pred             HhhccCCCcEEEEEeeEee
Q 006263          399 EMVDVGFFPVLSVKSGKVN  417 (653)
Q Consensus       399 ~~~~~~~~~Vvaik~~rV~  417 (653)
                       .|....|.||||-+..+-
T Consensus       106 -~~k~~~G~ViaiLNP~i~  123 (200)
T 3ebe_A          106 -HWKTDQGTVIGLLNANPM  123 (200)
T ss_dssp             -HTTCCTTEEEEEESCEEC
T ss_pred             -hcCcCCceEEEEECCEEc
Confidence             355578999999888774

>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=90.25  E-value=0.54  Score=42.21  Aligned_cols=71  Identities=15%  Similarity=0.318  Sum_probs=46.0

Q ss_pred             ccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC
Q 006263          341 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS  420 (653)
Q Consensus       341 ~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~  420 (653)
                      ..|.++|+|.++..-.          ....++|.|.|| .|++.+|.+........ .+.+  ..+.+|-+.|. ++.|+
T Consensus        37 ~~V~iVG~V~~~~~~~----------~~~~~~ldD~TG-~I~~~~W~~~~~~~~~~-~~~~--~~g~yVrV~G~-v~~f~  101 (136)
T 4gop_B           37 GQLTFVAVVRNISRNA----------TNVAYSVEDGTG-QIEVRQWLDSSSDDSSK-ASEI--RNNVYVRVLGT-LKSFQ  101 (136)
T ss_dssp             CEEEEEEEEEEEEECS----------SEEEEEEECSSC-EEEEEEECC---------CCSC--CTTCEEEEEEE-EEEET
T ss_pred             EEEEEEEEEEEEEecC----------CeEEEEEECCCC-CEEEEEecccCCccccc-cccc--CCCCEEEEEEE-EEEeC
Confidence            4689999999885421          367899999999 89999998754310000 1112  35777777665 78899


Q ss_pred             Cc-eecc
Q 006263          421 GK-SIGT  426 (653)
Q Consensus       421 G~-sLs~  426 (653)
                      |+ .|..
T Consensus       102 g~~qi~~  108 (136)
T 4gop_B          102 NRRSISS  108 (136)
T ss_dssp             TEEEEEE
T ss_pred             CEEEEEE
Confidence            95 5543

>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding, aminoacyl-tRNA synthetase, LI nucleotide-binding, protein biosynthesis; 2.80A {Entamoeba histolytica}

Probab=89.27  E-value=1.9  Score=47.80  Aligned_cols=99  Identities=18%  Similarity=0.141  Sum_probs=71.7

Q ss_pred             CcceeccccCCCC--CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEch-----hHHHHHHhhcccCc
Q 006263          206 ARIIPIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFN-----AVVDRFYEIIEVGR  278 (653)
Q Consensus       206 ~~~~pI~~L~p~~--~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~-----~~~~kf~~~l~eG~  278 (653)
                      +..+.|.+|++..  ...+|+|||.++   |.      .|++.-++|.| .++.||+++..     +..-+|...|..|+
T Consensus        48 ~~~~~i~~l~~~~~g~~V~v~Gwv~~~---R~------~gkl~Fi~LrD-~~g~iQ~v~~~~~~~~~~~~~~~~~l~~es  117 (548)
T 3i7f_A           48 LKYTEIEELVPAMAEKTVTIRARVQAV---RG------KGNMVFLFLRK-GIYTCQALVMKSETISKEFVQFCQKISAES  117 (548)
T ss_dssp             CCBCCGGGCSGGGTTCEEEEEEEEEEE---EE------CSSEEEEEEEE-TTEEEEEEEECSSSSCHHHHHHHHTCCTTE
T ss_pred             CceEEhhhcchhcCCCEEEEEEEEEEE---ec------CCCeEEEEEEE-CCeeEEEEEECCCccCHHHHHHHhCCCCCC
Confidence            4567888887432  468999999874   33      35777789999 67799999975     23445677899999


Q ss_pred             EEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263          279 VYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       279 vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                      ++.+.+.-++...+.-+.....+||...+-..+..+
T Consensus       118 ~V~V~G~v~~~~~~~~~~~~~~~El~~~~i~vls~a  153 (548)
T 3i7f_A          118 ICDITGIVKAVEKPIEKATQQDVEIHVTSIAVVSLA  153 (548)
T ss_dssp             EEEEEEEEEECSSCCTTSSSCSEEEEEEEEEEEECC
T ss_pred             EEEEEEEEEeCCcccccCCCCcEEEEEeEEEEEecC
Confidence            999997655543322123457899999887777766

>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

Probab=88.66  E-value=0.98  Score=38.55  Aligned_cols=66  Identities=15%  Similarity=0.059  Sum_probs=53.0

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEEe----CCCCe-------EEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD----SDGGE-------IRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D----~~g~~-------I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      +++..+.||+++--++|...+  | ..+.+|.|.=    .+.+-       |++++|+..++.....|..|+-+++.+..
T Consensus         2 ~N~v~L~G~l~~dpelR~t~~--G-~~v~~f~lA~~~~~~~~~~~r~~~~~~~vv~~g~~Ae~~~~~l~KG~~V~V~G~L   78 (104)
T 1txy_A            2 TNRLVLSGTVCRAPLRKVSPS--G-IPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFI   78 (104)
T ss_dssp             CEEEEEEEEEEEEEEEEECTT--S-CEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESSTTHHHHTTCCTTCEEEEEEEE
T ss_pred             cEEEEEEEEECCCceEEECCC--C-CEEEEEEEEEeCccccCCceeceeEEEEEEEEhHHHHHHHhhCCCCCEEEEEEEE
Confidence            467899999999999997543  2 2567776642    24567       99999999999999999999999999754

>3en2_A Probable primosomal replication protein N; PRIB RSR213C NESG X-RAY Q8XZT7 Q8XZT7_ralso, structural genomics, PSI-2; 2.30A {Ralstonia solanacearum}

Probab=88.36  E-value=2.6  Score=35.79  Aligned_cols=65  Identities=14%  Similarity=0.035  Sum_probs=49.4

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE-----eCCCCe------EEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL-----DSDGGE------IRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~-----D~~g~~------I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      +|+..+.||+++--++|.-.  .| -.+.+|.|.     ++.|++      |.|++|+..++.... +..|+-+.|.++.
T Consensus         2 MN~v~L~GrLt~dPelRyTp--sG-~~V~~f~LA~~s~~~e~g~~r~~~f~i~vv~wGk~AE~~~~-~~kGs~V~VeGrL   77 (101)
T 3en2_A            2 INRLQLVATLVEREVMRYTP--AG-VPIVNCLLSYSGQAMEAQAARQVEFSIEALGAGKMASVLDR-IAPGTVLECVGFL   77 (101)
T ss_dssp             CCCEEEEEEEEEECCCEECT--TC-CEEEEEEEEEEEEEECC--EEEEEEEEEEEEETHHHHHHTT-SCTTCEEEEEEEE
T ss_pred             cCEEEEEEEECcCccEEECC--CC-CEEEEEEEEEcceEecCCCcEeeeEEEEEEEEhHHHHHHhh-cCCCCEEEEEEEE
Confidence            57899999999999999643  23 256777664     234432      999999999998875 7899999999875

>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe}

Probab=86.89  E-value=6.1  Score=36.36  Aligned_cols=71  Identities=15%  Similarity=0.222  Sum_probs=47.3

Q ss_pred             ccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC
Q 006263          341 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS  420 (653)
Q Consensus       341 ~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~  420 (653)
                      ..|+|+|+|+++.+-      .    .+..++|-|.||..|+|.+|=+...... .+.  .....|.+|-++| +|+.|+
T Consensus        48 ~~V~IvGiVv~~~~~------~----~~~~ytIDD~TG~~I~cv~w~~~~~~~~-~~~--~~l~~G~~VrV~G-~v~~fr  113 (159)
T 3kf6_A           48 RWIQIVGYIAAIDIY------E----GKHVLTVDDCSGMVLRVVFIIQDDFSMS-KRA--ISMSPGNVVCVFG-KINSFR  113 (159)
T ss_dssp             CEEEEEEEEEEEEEE------T----TEEEEEEECSSSCEEEEEEEGGGCHHHH-HHH--TTCCTTCEEEEEE-EEECSS
T ss_pred             EEEEEEEEEEEEEEe------C----CEEEEEEecCCCCeEEEEEEccCCCCcc-ccc--ccCCCCCEEEEEE-EEEeeC
Confidence            368999999997632      1    3567888888998999999987622110 011  1124578887775 467788


Q ss_pred             C-ceec
Q 006263          421 G-KSIG  425 (653)
Q Consensus       421 G-~sLs  425 (653)
                      | +.|.
T Consensus       114 ~~rqI~  119 (159)
T 3kf6_A          114 SEVELI  119 (159)
T ss_dssp             SSCEEE
T ss_pred             CEEEEE
Confidence            8 4554

>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*

Probab=86.70  E-value=2.7  Score=46.02  Aligned_cols=97  Identities=13%  Similarity=0.106  Sum_probs=66.3

Q ss_pred             ceeccccCCC---CCceEEEEEEEeeccccccccCCCCcee-EEEEEEeCCCCeEEEEEchh-------HHHHHHhhccc
Q 006263          208 IIPIAALNPY---QGRWAIKARVTAKGDLRRYNNARGDGKV-FSFDLLDSDGGEIRVTCFNA-------VVDRFYEIIEV  276 (653)
Q Consensus       208 ~~pI~~L~p~---~~~w~I~~RV~~k~~ir~~~~~~g~gk~-f~~~L~D~~g~~I~at~f~~-------~~~kf~~~l~e  276 (653)
                      .+.|.+|...   ....+|+|||.++   |.      .|++ .-++|.| .+|.||+++-.+       ..-++...|..
T Consensus        23 ~~~~~~l~~~~~~g~~V~v~GwV~~~---R~------~g~~l~Fi~LrD-~~g~iQvv~~~~~~~~~~~~~~~~~~~l~~   92 (487)
T 1eov_A           23 RVKFVDLDEAKDSDKEVLFRARVHNT---RQ------QGATLAFLTLRQ-QASLIQGLVKANKEGTISKNMVKWAGSLNL   92 (487)
T ss_dssp             CCCGGGCCTTTTTTCEEEEEEEEEEE---EE------CSSSEEEEEEEE-TTEEEEEEEECCSSSSSCHHHHHHHTTCCT
T ss_pred             eeEHHHhcccccCCCEEEEEEEEEEe---ec------cCCccEEEEEEE-CCccEEEEEeccccccccHHHHHHHhcCCC
Confidence            4457777643   3468999999875   33      2565 6688999 678999998532       23345567999


Q ss_pred             CcEEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263          277 GRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       277 G~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                      |+++.+.+.-++...+.-+.....+||...+-..+..|
T Consensus        93 e~~V~V~G~v~~~~~~~~~~~~g~~El~~~~i~vl~~a  130 (487)
T 1eov_A           93 ESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISET  130 (487)
T ss_dssp             TCEEEEEEEEEECSSCCTTSSEEEEEEEEEEEEEEECC
T ss_pred             CCEEEEEEEEEeCCCCCcCCCCCcEEEEEEEEEEeecc
Confidence            99999998765554322122335799999877777766

>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor}

Probab=86.32  E-value=2.9  Score=40.04  Aligned_cols=65  Identities=11%  Similarity=0.185  Sum_probs=50.8

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEEe------C--------CCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD------S--------DGGEIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D------~--------~g~~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      .++.+|.+||++.-++|...+  | ..+.+|.|+=      .        +..-|++++|+.+++.+...|+.|+.++|.
T Consensus         4 ~N~V~LiGrL~~DPElR~T~~--G-~~Va~FsLAvn~R~~d~~~Ge~~d~~T~wi~VvawgklAE~v~~~L~KG~~V~Ve   80 (199)
T 3eiv_A            4 ETVITVVGNLVDDPELRFTPS--G-AAVAKFRVASTPRTFDRQTNEWKDGESLFLTCSVWRQAAENVAESLQRGMRVIVQ   80 (199)
T ss_dssp             CCEEEEEEEESSCCEEEECTT--C-CEEEEEEEEECC-----------CCCCEEEEEEEETHHHHHHHHHCCTTCEEEEE
T ss_pred             ccEEEEEEEECCCCeEEECCC--C-CEEEEEEEEEcCcccccCCCcEecCccEEEEEEEEhHHHHHHHHhcCCCCEEEEE
Confidence            467899999999999997643  2 2566766642      1        234599999999999999999999999998


Q ss_pred             ce
Q 006263          284 KG  285 (653)
Q Consensus       284 ~~  285 (653)
                      .-
T Consensus        81 Gr   82 (199)
T 3eiv_A           81 GR   82 (199)
T ss_dssp             EE
T ss_pred             EE
Confidence            63

>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=86.06  E-value=2  Score=38.34  Aligned_cols=77  Identities=14%  Similarity=0.159  Sum_probs=50.6

Q ss_pred             EEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEEE
Q 006263          551 LQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIR  630 (653)
Q Consensus       551 l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~  630 (653)
                      +.+.+.|.||.+.+..|++..+.    ++          .+...+      ..|.  .++|..+...|++.  ....+.+
T Consensus        55 ~~~~ldD~TG~I~~~~W~~~~~~----~~----------~~~~~~------~~g~--yVrV~G~v~~f~g~--~qi~~~~  110 (136)
T 4gop_B           55 VAYSVEDGTGQIEVRQWLDSSSD----DS----------SKASEI------RNNV--YVRVLGTLKSFQNR--RSISSGH  110 (136)
T ss_dssp             EEEEEECSSCEEEEEEECC----------------------CCSC------CTTC--EEEEEEEEEEETTE--EEEEESE
T ss_pred             EEEEEECCCCCEEEEEecccCCc----cc----------cccccc------CCCC--EEEEEEEEEEeCCE--EEEEEEE
Confidence            67888999999999999865321    00          000000      0122  66777777889974  4566777


Q ss_pred             eecC-ChHHHHHHHHHHHHhhh
Q 006263          631 ADQV-NYSSESRYLLDLISKSF  651 (653)
Q Consensus       631 ~~~v-d~~~e~~~ll~~i~~~~  651 (653)
                      +.|+ |+.+..-.+|+.|...+
T Consensus       111 ir~v~d~Nei~~H~Le~i~~hl  132 (136)
T 4gop_B          111 MRPVIDYNEVMFHRLEAVHAHL  132 (136)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHH
T ss_pred             EEECCCccHHHHHHHHHHHHHH
Confidence            7777 69999999999987543

>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

Probab=85.78  E-value=5.3  Score=34.71  Aligned_cols=67  Identities=15%  Similarity=0.143  Sum_probs=50.7

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEEe-----CCCCe------EEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD-----SDGGE------IRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D-----~~g~~------I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      +|+..+.||+++--++|...  .| -.+.+|.|.-     +.|.+      |.|++|+..++.. ..|..|+-+.|.++.
T Consensus         1 MNkviL~GrL~~dPelRyTp--sG-~~V~~f~LA~~~~~~~~g~~r~~~~~i~vv~~Gk~AE~~-~~l~kGs~V~VeGrL   76 (115)
T 3fhw_A            1 MNTLELSARVLECGAMRHTP--AG-LPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLL-ADTPLGTEMQVQGFL   76 (115)
T ss_dssp             CEEEEEEEEEEEECCCEECT--TS-CEEEEEEEEEEEECCCCC--CEEEEEEEEEEETHHHHHH-TTCCTTCEEEEEEEE
T ss_pred             CCEEEEEEEECcCcceEECC--CC-CEEEEEEEEEcceeecCCCeeeeeEEEEEEEEhHHHHhh-hccCCCCEEEEEEEE
Confidence            46789999999999999543  23 2577777652     23322      9999999999987 889999999999875


Q ss_pred             Ee
Q 006263          287 LK  288 (653)
Q Consensus       287 V~  288 (653)
                      -.
T Consensus        77 ~t   78 (115)
T 3fhw_A           77 AP   78 (115)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>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}

Probab=85.10  E-value=2.6  Score=37.68  Aligned_cols=65  Identities=18%  Similarity=0.243  Sum_probs=50.7

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC------eEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG------EIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~------~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      +++.+|.|||++--.+|...+  | ..+.+|.|+      |++|.      -|.+++|+..++.....|+.|+.+.|.+.
T Consensus         2 mN~V~L~GrL~~dPelr~t~~--G-~~v~~f~lA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~   78 (134)
T 2vw9_A            2 FNKVIMVGRLTRNVELKYLPS--G-SAAATIGLATSRRFKKQDGTLGEEVCFIDARLFGRTAEIANQYLSKGSSVLIEGR   78 (134)
T ss_dssp             CCCEEEEEEESSCCEEEECTT--S-CEEEEEEEEEEEEEECSSSCEEEEEEEEEEEEEHHHHHHHHHHCCTTCEEEEEEE
T ss_pred             eeEEEEEEEECCCCEEEECCC--C-CEEEEEEEEEeCCeECCCCCCccccEEEEEEEEcHHHHHHHHhCCCCCEEEEEEE
Confidence            467899999999988887543  2 256666653      33332      49999999999999999999999999974

>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

Probab=85.07  E-value=1.6  Score=44.02  Aligned_cols=70  Identities=16%  Similarity=0.319  Sum_probs=46.3

Q ss_pred             cccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCC
Q 006263          342 IVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSG  421 (653)
Q Consensus       342 ~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G  421 (653)
                      .|+++|+|+++..-          .....++|.|.||..|++.+|.+....- .. .+.|  ..+.+|-+.| +|+.|+|
T Consensus        73 ~V~ivG~V~~i~~~----------~~~~~~~L~D~TG~~I~~k~W~~~~~~~-~~-~~~~--~~G~yVrV~G-~v~~f~g  137 (270)
T 2pi2_A           73 QVTIVGIIRHAEKA----------PTNIVYKIDDMTAAPMDVRQWVDTDDTS-SE-NTVV--PPETYVKVAG-HLRSFQN  137 (270)
T ss_dssp             EEEEEEEEEEEEEC----------SSEEEEEEECSSSSCEEEEEECC---------CCCC--CTTCEEEEEE-EEEEETT
T ss_pred             EEEEEEEEEEEEec----------cceEEEEEECCCCCEEEEEEEcCcCccc-ch-hhcC--CCCCEEEEEE-EEEecCC
Confidence            58899999887432          1467899999999779999998753210 00 0112  3578887775 7888999


Q ss_pred             c-eecc
Q 006263          422 K-SIGT  426 (653)
Q Consensus       422 ~-sLs~  426 (653)
                      + .|..
T Consensus       138 ~~qi~i  143 (270)
T 2pi2_A          138 KKSLVA  143 (270)
T ss_dssp             EEEEEE
T ss_pred             eeEEEE
Confidence            5 5543

>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}

Probab=84.13  E-value=2.2  Score=37.56  Aligned_cols=65  Identities=23%  Similarity=0.393  Sum_probs=50.5

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCCC-------eEEEEEch-hHHHHHHhhcccCcEEEEe
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDGG-------EIRVTCFN-AVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g~-------~I~at~f~-~~~~kf~~~l~eG~vy~is  283 (653)
                      +++.+|.||+.+--.+|...+  | ..+.+|.|+      |.++|       -|++++|+ ..++.....|+.|+-++|.
T Consensus         6 ~N~v~l~Grl~~dpelr~t~~--G-~~v~~f~lA~~~~~~~~~~G~~~~~t~~~~v~~wg~~~Ae~~~~~l~KG~~V~V~   82 (124)
T 3ulp_A            6 LNKIMLIGRVGCEPDIKILNG--G-DKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQ   82 (124)
T ss_dssp             EEEEEEEEEECSCCEEEECTT--S-CEEEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCHHHHHHHHHHCCTTCEEEEE
T ss_pred             ceEEEEEEEECCCcEEEECCC--C-CEEEEEEEEEccceecccCCcEecccEEEEEEEEEchHHHHHHhhcCCCCEEEEE
Confidence            468999999999988887643  2 256666663      33323       39999999 7999999999999999998


Q ss_pred             ce
Q 006263          284 KG  285 (653)
Q Consensus       284 ~~  285 (653)
                      +-
T Consensus        83 G~   84 (124)
T 3ulp_A           83 GS   84 (124)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii}

Probab=83.64  E-value=2  Score=39.63  Aligned_cols=66  Identities=20%  Similarity=0.240  Sum_probs=51.2

Q ss_pred             CCCceEEEEEEEeeccccccccCCCCceeEEEEEE------eC-CC------CeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS-DG------GEIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       217 ~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~-~g------~~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      .+++.+|.+||++.-.+|...+  | ..+.+|.|.      |+ .|      .-|++++|+..++.+...|+.|+.++|.
T Consensus         7 ~mN~V~LiGrL~~dPelr~t~~--G-~~v~~f~lA~~~~~~d~~~Ge~~e~t~~i~vv~wg~~Ae~~~~~l~KG~~V~Ve   83 (158)
T 3tqy_A            7 GVNKVILIGNLGQDPEVRYTPN--G-NAVANVTLATSTTWRDKQTGELQERTEWHRIAFFNRLAEIVGEYLRKGSKIYIE   83 (158)
T ss_dssp             CEEEEEEEEEESSSCEEEECTT--C-CEEEEEEEEEEEEEECTTTCCEEEEEEEEEEEEETHHHHHHHHHCCTTCEEEEE
T ss_pred             ccCEEEEEEEECCCCEEEECCC--C-CEEEEEEEEEcCceeccCCCCEeeeeEEEEEEEEhHHHHHHHhhcCCCCEEEEE
Confidence            3578999999999999987643  2 256666553      43 22      3479999999999999999999999998


Q ss_pred             ce
Q 006263          284 KG  285 (653)
Q Consensus       284 ~~  285 (653)
                      +.
T Consensus        84 G~   85 (158)
T 3tqy_A           84 GS   85 (158)
T ss_dssp             EE
T ss_pred             EE
Confidence            85

>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold, DNA binding protein; 2.70A {Neisseria gonorrhoeae fa 1090}

Probab=83.50  E-value=7.3  Score=33.06  Aligned_cols=63  Identities=13%  Similarity=0.084  Sum_probs=49.0

Q ss_pred             CceEEEEEEEeeccccccccCCCCceeEEEEEE-----eCCCC-----e-EEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL-----DSDGG-----E-IRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~-----D~~g~-----~-I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      |+..+.||+++--++|...+  | ..+.+|.|.     ++.|.     . |++++|+..++ ... |..|+-++|.++.
T Consensus         8 Nkv~LiG~L~~dPelRytp~--G-~~v~~f~lA~~~~~~~~g~~~~~~~~i~vv~~gk~Ae-~~~-l~KG~~v~veGrL   81 (103)
T 3k8a_A            8 NLVSLAALIEKAFPIRYTPA--G-IPVLDIILKHESWQEENGQQCLVQLEIPARILGRQAE-EWQ-YRQGDCATVEGFL   81 (103)
T ss_dssp             EEEEEEEEEEEECCCEECTT--S-CEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEHHHHH-HST-TCTTCEEEEEEEE
T ss_pred             cEEEEEEEECCCCceEECCC--C-CEEEEEEEEEcccCccCCCEEEeeEEEEEEEEhHHhh-hhc-cCCCCEEEEEEEE
Confidence            78999999999999997542  2 257777765     22342     2 89999999999 555 9999999999875

>3u58_A Tetrahymena TEB1 AB; tetrahymena, telomerase, TEB1, processivity factor, DNA BIND protein-DNA complex; HET: DNA; 2.61A {Tetrahymena thermophila}

Probab=83.06  E-value=8.8  Score=33.85  Aligned_cols=85  Identities=13%  Similarity=0.183  Sum_probs=63.6

Q ss_pred             cCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCC-CeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCC
Q 006263          214 LNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDG-GEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQK  292 (653)
Q Consensus       214 L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g-~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~  292 (653)
                      |.......++.|.|+..-.         ..+-+.+-++|... -+.++++|.++|-.|.+.+..++||++..|--...| 
T Consensus       126 lktskqylsvlaqvvdiqs---------sdknirlkicdnscnqelkvvifpdlcyewrdkfsinkwyyfnefvrqiyn-  195 (213)
T 3u58_A          126 LKTSKQYLSVLAQVVDIQS---------SDKNIRLKICDNSCNQELKVVIFPDLCYEWRDKFSINKWYYFNEFVRQIYN-  195 (213)
T ss_dssp             TTCCCSEEEEEEEEEEEEE---------CSSCEEEEEECTTCSCCEEEEECTTTTGGGTTCCCTTCEEEEEEEEECCSS-
T ss_pred             HHHhHHHHHHHHHhhcccc---------CCCceEEEeecccccceeEEEEchhHhhHhhhhcchhhhhhHHHHHHHHhh-
Confidence            4555567889999987421         13557889999653 589999999999999999999999999998543332 


Q ss_pred             cccCCCCceEEEeccccEEEec
Q 006263          293 NFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       293 ~f~~~~~~yei~f~~~T~I~~~  314 (653)
                            .+..+.-+-++.|.+.
T Consensus       196 ------devqlknnihssikes  211 (213)
T 3u58_A          196 ------DEVQLKNNIHSSIKES  211 (213)
T ss_dssp             ------SSCEEECCTTCEEEEC
T ss_pred             ------hhhhhhhhhhhhhccc
Confidence                  2355666667788775

>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis}

Probab=82.72  E-value=3.4  Score=35.77  Aligned_cols=67  Identities=16%  Similarity=0.169  Sum_probs=51.8

Q ss_pred             CCCceEEEEEEEeeccccccccCCCCceeEEEEEE-e-----CC----CCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL-D-----SD----GGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       217 ~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~-D-----~~----g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      .+++.+|.|||++--.+|...+  | ..+.+|.|. +     ++    ..-|++++|+..++.....|+.|+.+.+.+..
T Consensus         4 mmN~v~l~G~l~~dpe~r~t~~--G-~~v~~f~la~~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l   80 (116)
T 3vdy_A            4 MFNQVMLVGRLTKDPDLRYTSA--G-AAVAHVTLAVNRSFKNASGEIEADYVNCTLWRKTAENTALYCQKGSLVGVSGRI   80 (116)
T ss_dssp             CCCCEEEEEEESSCCEEEECTT--S-CEEEEEEEEEECSSCCSSSCCCEEEEEEEEEHHHHHHHHHHCCTTCEEEEEEEE
T ss_pred             eEeEEEEEEEEccCcEEEECCC--C-CEEEEEEEEEeccccCCCCccccEEEEEEEECHHHHHHHHhCCCCCEEEEEEEE
Confidence            4578999999999988887543  2 256666664 2     11    23599999999999999999999999999753

>3koj_A Uncharacterized protein YCF41; single-strand binding protein family, PF00436, SNR59A, NESG, structural genomics, PSI-2; 1.90A {Synechococcus elongatus pcc 6301}

Probab=82.49  E-value=5.1  Score=34.36  Aligned_cols=67  Identities=12%  Similarity=0.131  Sum_probs=52.7

Q ss_pred             CCCceEEEEEEEeeccccccccCCCCceeEEEEEEe------CCCCeEEEEEchhHHHHHHhhcccCcEEEEece
Q 006263          217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD------SDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKG  285 (653)
Q Consensus       217 ~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D------~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~  285 (653)
                      .++.-.+.||+++--++|...+  |...+.+|.|+=      ++.+-|++++|+..++.....|..|+-+.|.+=
T Consensus        10 ~~~~v~LiGrL~~DPelR~t~~--g~~~va~f~lAv~~~~~~~~t~fi~vv~wgk~AE~~~~yl~KG~~V~VeGr   82 (108)
T 3koj_A           10 HMNSCILQATVVEAPQLRYAQD--NQTPVAEMVVQFPGLSSKDAPARLKVVGWGAVAQELQDRCRLNDEVVLEGR   82 (108)
T ss_dssp             SCEEEEEEEEEEEEEEEEECTT--SSSEEEEEEEEECC-----CCEEEEEEEETHHHHHHHHHCCTTCEEEEEEE
T ss_pred             ccceEEEEEEECCCCEEEEeCC--CCEEEEEEEEEECCcccCCCcEEEEEEEEhHHHHHHHHhCCCCCEEEEEEE
Confidence            3567889999999999997643  223677777652      245679999999999999999999999988863

>1z9f_A Single-strand binding protein; TM0604, single stranded DNA-binding protein, structural GENO joint center for structural genomics, JCSG; 2.30A {Thermotoga maritima}

Probab=82.32  E-value=2.4  Score=38.84  Aligned_cols=67  Identities=16%  Similarity=0.267  Sum_probs=51.7

Q ss_pred             CCCCceEEEEEEEeeccccccccCCCCceeEEEEEE-eC------C-----CCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          216 PYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL-DS------D-----GGEIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       216 p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~-D~------~-----g~~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      |..++.+|.|||++--.+|...+  | ..+.+|.|+ +.      +     ..-|++++|+..++.....|+.|+-++|.
T Consensus        14 ~~~N~V~LiGrL~~DPelr~t~~--G-~~va~f~lAv~~r~~~~~~Ge~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~Ve   90 (153)
T 1z9f_A           14 SFFNKIILIGRLVRDPEERYTLS--G-TPVTTFTIAVDRVPRKNAPDDAQTTDFFRIVTFGRLAEFARTYLTKGRLVLVE   90 (153)
T ss_dssp             SCCCCEEEEEEESSCCEEEECC-----CEEEEEEEEEEC-----------CEEEEEEEEEHHHHHHHHHHCCTTCEEEEE
T ss_pred             cceeEEEEEEEECCCCEEEECCC--C-CEEEEEEEEEcCCccccCCCCEeeeEEEEEEEECHHHHHHHhhCCCCCEEEEE
Confidence            45688999999999999987643  2 257777764 21      1     23489999999999999999999999998


Q ss_pred             ce
Q 006263          284 KG  285 (653)
Q Consensus       284 ~~  285 (653)
                      +-
T Consensus        91 Gr   92 (153)
T 1z9f_A           91 GE   92 (153)
T ss_dssp             EE
T ss_pred             EE
Confidence            63

>3rn5_A Interferon-inducible protein AIM2; OB fold, DNA binding, cytosolic, immune system-DNA complex; HET: DNA; 2.50A {Homo sapiens} PDB: 3rn2_A*

Probab=81.23  E-value=37  Score=32.01  Aligned_cols=175  Identities=13%  Similarity=0.104  Sum_probs=116.1

Q ss_pred             EEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEecCCCcccCCCCceE
Q 006263          223 IKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWE  302 (653)
Q Consensus       223 I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~a~~~f~~~~~~ye  302 (653)
                      ..|.|+.-.+.=+|....|+.++|.-+++- +..-.++-+|+-   .+.+.|..+++..||++.-           +.--
T Consensus        15 ~~VmVLkaTepF~Ye~~E~~~~MFHATVAT-etqfF~VKVfn~---~LKeKF~pk~iI~ISdY~~-----------~~gf   79 (208)
T 3rn5_A           15 LPVMVLKAKKPFTFETQEGKQEMFHATVAT-EKEFFFVKVFNT---LLKDKFIPKRIIIIARYYR-----------HSGF   79 (208)
T ss_dssp             EEEEEEEECCCEEEEETTEEEEEEEEEEEC-SSCEEEEEECCG---GGGGTCCTTCEEEEESBEE-----------CSSC
T ss_pred             eEEEEEeccCCeeeecccccceEEEEEEee-ccceEEEEEecc---hhhhhcCCCcEEEEEeccc-----------ccce
Confidence            356677766766777666555799999999 799999999997   4577899999999999742           2233


Q ss_pred             EEeccccEEEecc-CCCCCCCccc----ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCC
Q 006263          303 IFLEATSTVDLCT-EEDDSIPKQQ----FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTS  377 (653)
Q Consensus       303 i~f~~~T~I~~~~-d~~~~iP~~~----f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s  377 (653)
                      |..++.|.|.++. |..-.||...    -.=-+|++|.....+.+|+=+=.|....      .+  +  ...-..|.|.+
T Consensus        80 LEi~~~SsVse~~~dq~~eVp~~ii~~A~~TPKI~~L~~q~~Gt~V~G~F~v~KK~------v~--~--~~~~YeI~DnT  149 (208)
T 3rn5_A           80 LEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVT------EK--K--KNILFDLSDNT  149 (208)
T ss_dssp             EEECTTSEEEECCTTCCCCCCHHHHHHHHSCCCHHHHHTSCSSCEEEEEEEEEEEE------EC--S--SEEEEEEEETT
T ss_pred             EEEecccEEEEccCCceeecCHHHHHhcccCcchhhhhcCCCCCEEeEEEEEEEEE------ec--c--ceEEEEEecCC
Confidence            5667888998884 3334567532    1234588887777777766433333211      11  1  23456899999


Q ss_pred             CCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEE
Q 006263          378 GRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQL  432 (653)
Q Consensus       378 ~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i  432 (653)
                      | .++|...|.+...         ...+|+=+-+....++..+++ .|.+...|-|
T Consensus       150 G-~MeVvv~G~~~~i---------~CEeGDKLrL~cFeL~~~~~~~qL~s~~HSfi  195 (208)
T 3rn5_A          150 G-KMEVLGVRNEDTM---------KCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTI  195 (208)
T ss_dssp             E-EEEEEEECSTGGG---------SCCTTCEEEEEEEEEEECSSSEEEECCTTCEE
T ss_pred             C-cEEEEEeccCccc---------ccCCCCeeEEEEEEEeccCCeeeEEEecceeE
Confidence            9 7999999998643         234566666665666544443 5655555544

>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

Probab=80.49  E-value=7.4  Score=34.39  Aligned_cols=75  Identities=9%  Similarity=0.139  Sum_probs=48.9

Q ss_pred             EEEEEEeCCC-eEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEE
Q 006263          551 LQAQIQDQTG-LTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVI  629 (653)
Q Consensus       551 l~~~i~D~Tg-~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~  629 (653)
                      +.+.|.|+|| .+.+..|.+....-     .+    .      ..+      -.|.  .++|..+...|++.  ....+.
T Consensus        50 ~~~~ldD~TG~~I~~~~W~~~~~~~-----~~----~------~~~------~~g~--yVrV~G~l~~f~g~--~qi~~~  104 (132)
T 3kdf_D           50 IVYKIDDMTAAPMDVRQWVDTDDTS-----SE----N------TVV------PPET--YVKVAGHLRSFQNK--KSLVAF  104 (132)
T ss_dssp             EEEEEECSSSSCEEEEEEC------------------------CCC------CTTC--EEEEEEEEEEETTE--EEEEEE
T ss_pred             EEEEEECCCCCEEEEEEEccCCCcc-----cc----c------ccc------cCCC--EEEEEEEEEeECCE--EEEEEE
Confidence            6788999999 99999998754210     00    0      000      0122  56677777789975  456677


Q ss_pred             EeecC-ChHHHHHHHHHHHHhh
Q 006263          630 RADQV-NYSSESRYLLDLISKS  650 (653)
Q Consensus       630 ~~~~v-d~~~e~~~ll~~i~~~  650 (653)
                      ++.|+ |+.+..-.+|+.|...
T Consensus       105 ~ir~v~d~Nei~~H~Le~i~~h  126 (132)
T 3kdf_D          105 KIMPLEDMNEFTTHILEVINAH  126 (132)
T ss_dssp             EEEECSSTHHHHHHHHHHHHHH
T ss_pred             EEEEcCCccHHHHHHHHHHHHH
Confidence            77777 7899999999998754

>1v1q_A Primosomal replication protein N; primosome, DNA replication, DNA binding; 2.1A {Escherichia coli} SCOP: b.40.4.3 PDB: 2ccz_A

Probab=80.22  E-value=2.9  Score=37.39  Aligned_cols=65  Identities=15%  Similarity=0.056  Sum_probs=51.8

Q ss_pred             CceEEEEEEEeeccccccccCCCCceeEEEEEE-----eCCCC------eEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL-----DSDGG------EIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~-----D~~g~------~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      ++..+.||+++--++|...+  | ..+.+|.|.     ++.|.      .|++++|+..++.....|..|+-++|.++.
T Consensus        20 NkViLiGrL~~DPElRyTps--G-~~Va~ftLA~~~~~~~~G~~~~~~~~i~vv~wGk~AE~~~~yl~KGs~V~VeGrL   95 (134)
T 1v1q_A           20 NRLVLSGTVCRAPLRKVSPS--G-IPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFI   95 (134)
T ss_dssp             EEEEEEEEEEEEEEEEECTT--C-CEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESTGGGGGGTTCCTTCEEEEEEEE
T ss_pred             eEEEEEEEECcCCceEECCC--C-CEEEEEEEEEeCcCcCCCCEecceEEEEEEEEhHHHHHHHHhcCCCCEEEEEEEE
Confidence            78999999999999997542  3 257777664     32331      399999999999999999999999999764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	653
d1l1oc_	178	b.40.4.3 (C:) Replication protein A 70 KDa subunit	2e-64
d1jmca2	122	b.40.4.3 (A:299-420) Replication protein A 70 KDa	4e-38
d1jmca1	116	b.40.4.3 (A:183-298) Replication protein A 70 KDa	5e-37
d2b3ga1	112	b.40.4.3 (A:3-114) Replication protein A 70 KDa su	1e-29
d1o7ia_	115	b.40.4.3 (A:) Archaeal ssDNA-binding protein {Arch	2e-15

>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Length = 178

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 = 2e-64
 Identities = 62/176 (35%), Positives = 99/176 (56%), Gaps = 7/176 (3%)

Query: 475 KTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RW 533
           KT+ ++K+E LG+ +KPD+ +  A + +++ ++  Y ACP     + CNKKV    N  +
Sbjct: 5   KTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPT----QDCNKKVIDQQNGLY 60

Query: 534 QCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDV 593
           +C++C+ E     YR +L   I D     WVT FQES E ILG  A  L  LK   +++ 
Sbjct: 61  RCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK--DKNEQ 118

Query: 594 RFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDLISK 649
            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

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 =  135 bits (341), Expect = 4e-38
 Identities = 49/130 (37%), Positives = 75/130 (57%), Gaps = 9/130 (6%)

Query: 325 QFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK-NGMETQRRILNLKDTSGRSVEL 383
           QF F  I ++E+   +S+VD+IGI  S   +  I  + N  E  +R + L DTSG+ V  
Sbjct: 1   QFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTA 60

Query: 384 TLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHE 443
           TLWG+  +K         D    PVL++K  +V+DF G+S+  + S+ +  NPD  EA++
Sbjct: 61  TLWGEDADK--------FDGSRQPVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYK 112

Query: 444 LREWFDSGGK 453
           LR WFD+ G+
Sbjct: 113 LRGWFDAEGQ 122

>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Length = 116

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 =  131 bits (332), Expect = 5e-37
 Identities = 55/117 (47%), Positives = 82/117 (70%), Gaps = 2/117 (1%)

Query: 207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV 266
           +++PIA+L PYQ +W I ARVT K  +R ++N+RG+GK+FS +L+D + GEIR T FN  
Sbjct: 1   KVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNEQ 59

Query: 267 VDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPK 323
           VD+F+ +IEV +VY  SKG+LK A K F  +KN++E+     ++V  C E+D  +P 
Sbjct: 60  VDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHLPT 115

>d2b3ga1 b.40.4.3 (A:3-114) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Length = 112

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 =  110 bits (278), Expect = 1e-29
 Identities = 37/110 (33%), Positives = 66/110 (60%), Gaps = 8/110 (7%)

Query: 5   LTPNSISLI-NGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSV-STQHAMLATQLND 60
           L+  +I+ I   GD N KP++QV++I+ I  G++  RYR L+SD + +    MLATQLN 
Sbjct: 3   LSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNP 62

Query: 61  RVKTGQVKKGSVVQLIDYICSTVQN-RKIIVVLNMETIILDCEP---IGN 106
            V+  Q+    V Q+  +I +T+++ R++++++ +E +         IGN
Sbjct: 63  LVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGN 112

>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Length = 115

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Archaeal ssDNA-binding protein
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

 Score = 70.3 bits (172), Expect = 2e-15
 Identities = 15/108 (13%), Positives = 36/108 (33%), Gaps = 12/108 (11%)

Query: 211 IAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRF 270
           +  L P      +  RV    + R+     G   +    + D   G +++T +     + 
Sbjct: 5   VGNLKPNMESVNVTVRVLEASEARQIQTKNGVRTISEAIVGDET-GRVKLTLW----GKH 59

Query: 271 YEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEED 318
              I+ G+V  I               K + ++   + + +   +E+ 
Sbjct: 60  AGSIKEGQVVKIENAWT-------TAFKGQVQLNAGSKTKIAEASEDG 100

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	653
d1l1oc_	178	Replication protein A 70 KDa subunit (RPA70) {Huma	100.0
d1jmca2	122	Replication protein A 70 KDa subunit (RPA70) {Huma	99.96
d1jmca1	116	Replication protein A 70 KDa subunit (RPA70) {Huma	99.96
d2b3ga1	112	Replication protein A 70 KDa subunit (RPA70) {Huma	99.94
d1o7ia_	115	Archaeal ssDNA-binding protein {Archaeon Sulfolobu	99.49
d1o7ia_	115	Archaeal ssDNA-binding protein {Archaeon Sulfolobu	98.93
d1wjja_	145	Hypothetical protein At4g28440 (F20O9.120) {Thale	98.72
d1wjja_	145	Hypothetical protein At4g28440 (F20O9.120) {Thale	98.54
d1jmca1	116	Replication protein A 70 KDa subunit (RPA70) {Huma	98.33
d1xjva1	140	Protection of telomeres protein 1, Pot1 {Human (Ho	98.16
d1jmca2	122	Replication protein A 70 KDa subunit (RPA70) {Huma	97.57
d1jb7a1	169	Telomere end binding protein alpha subunit {Oxytri	97.4
d1qzga_	170	Protection of telomeres protein 1, Pot1 {Fission y	96.98
d1se8a_	231	ssDNA-binding protein {Deinococcus radiodurans [Ta	96.02
d1xjva1	140	Protection of telomeres protein 1, Pot1 {Human (Ho	92.59
d1eova1	134	Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S	92.04
d1xjva2	151	Protection of telomeres protein 1, Pot1 {Human (Ho	91.64
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	90.45
d1iyjb3	133	OB-fold domains of BRCA2 {Rat (Rattus norvegicus)	89.91
d1n9wa1	93	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	89.1
d1v1qa_	111	Primosomal replication protein N, PriB {Escherichi	88.51
d1jb7a1	169	Telomere end binding protein alpha subunit {Oxytri	88.42
d1gm5a2	180	RecG "wedge" domain {Thermotoga maritima [TaxId: 2	87.93
d1c0aa1	106	Aspartyl-tRNA synthetase (AspRS) {Escherichia coli	86.84
d1b8aa1	103	Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ	85.7
d2pi2a1	128	Replication protein A 32 KDa subunit (RPA32) fragm	83.98
d1l0wa1	104	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	83.69
d1qvca_	145	ssDNA-binding protein {Escherichia coli [TaxId: 56	82.77
d1ue1a_	118	ssDNA-binding protein {Mycobacterium tuberculosis	82.17

>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

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=3.3e-46  Score=356.92  Aligned_cols=175  Identities=36%  Similarity=0.655  Sum_probs=162.8

Q ss_pred             chhccHHhhhhcCCCCCCCCcEEEEEEEEEEEeCCceEEecCCCCcCcccccceeeecCc-eeecccCccccCCceEEEE
Q 006263          472 EIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVTQSGN-RWQCDRCNQEIDECDYRYL  550 (653)
Q Consensus       472 ~~~kti~~i~~~~lg~~~~~~~~~v~atI~~i~~d~~~Y~aC~~~~~~~~C~KKv~~~~~-~~~C~kC~~~~~~~~~rY~  550 (653)
                      .+||||+||+++++|.+++|+||+|+|+|..|+.++|||+|||++    .|+|||++.++ .|+|++|++.+++|.|||+
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            568999999999999999999999999999999999999999965    79999987654 8999999999999999999


Q ss_pred             EEEEEEeCCCeEEEEEechhhhhhhCCCHHHHHHHhhccCChhHHHHHHHHhcCceEEEEEEEeeeccCceeeEEEEEEE
Q 006263          551 LQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIR  630 (653)
Q Consensus       551 l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~e~~d~~~~~~~~~~~~~k~~~f~v~~k~~~y~~e~r~~~~v~~  630 (653)
                      |++.|+|+||++|+++||+.|++|||++|+||.++.  +++++.++++++++.|++|.|+++++.++||||.|+|++|++
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             eecCChHHHHHHHHHHHHhhhc
Q 006263          631 ADQVNYSSESRYLLDLISKSFR  652 (653)
Q Consensus       631 ~~~vd~~~e~~~ll~~i~~~~~  652 (653)
                      ++|+||++|+++|++.|++|.+
T Consensus       156 i~pvd~~~e~~~L~~~I~~~~~  177 (178)
T d1l1oc_         156 VKPVDYREYGRRLVMSIRRSAL  177 (178)
T ss_dssp             EEECCHHHHHHHHHHHHHHHHH
T ss_pred             eEeCCHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999864

>d1jmca2 b.40.4.3 (A:299-420) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

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=99.96  E-value=4.9e-30  Score=229.90  Aligned_cols=121  Identities=40%  Similarity=0.717  Sum_probs=113.5

Q ss_pred             cceecchhhhhhcccCccccEEEEEEEecCceeEEec-CCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhcc
Q 006263          325 QFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK-NGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDV  403 (653)
Q Consensus       325 ~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k-~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~  403 (653)
                      +|+|++|+||.++..+.+|||||+|++|+++++|++| +|++..||+|+|+|+|+.+|+|||||++|..        |+.
T Consensus         1 ~y~F~~i~di~~~~~~~~vDViGvv~~v~~~~~i~~k~~g~~~~kR~i~i~D~t~~~i~vtLWg~~a~~--------~~~   72 (122)
T d1jmca2           1 QFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADK--------FDG   72 (122)
T ss_dssp             CCCBCCGGGGGGSCTTCEEEEEEEEEEECCCEEEEETTTTEEEEEEEEEEECTTCCEEEEEEEHHHHHH--------CCC
T ss_pred             CcccEeHHHhhccCCCCeEEEEEEEEEccCcEEEEEcCCCCceeEEEEEEEcCCCCEEEEEEEchHhhh--------hCC
Confidence            4899999999998889999999999999999999887 6999999999999999999999999999876        445


Q ss_pred             CCCcEEEEEeeEeecCCCceeccccceEEEEcCChHHHHHHHHHHhcCCC
Q 006263          404 GFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELREWFDSGGK  453 (653)
Q Consensus       404 ~~~~Vvaik~~rV~~f~G~sLs~~~~S~i~inPdipe~~~l~~w~~~~g~  453 (653)
                      ..+|||+|+++||++|+|++|++.++|+|++|||+|||++||.||.++|+
T Consensus        73 ~~~~Vi~~k~~~v~~~~g~sL~~~~~s~i~~Npdi~ea~~Lr~wy~~~g~  122 (122)
T d1jmca2          73 SRQPVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKLRGWFDAEGQ  122 (122)
T ss_dssp             TTCCEEEEEEEEEECTTSSEEECCSSCEEESSCCSHHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeeeEEeeccCceEeccCcceEEECCCcHHHHHHHHHHHhcCC
Confidence            57899999999999999999999999999999999999999999999874

>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

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=99.96  E-value=6.1e-30  Score=227.65  Aligned_cols=115  Identities=47%  Similarity=0.921  Sum_probs=109.2

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      .++||++|+|++++|+|+|||++||++|+|++++|+|++|+|+|+|+.| +|+|++|++.+++|++.|++|+||+|++|.
T Consensus         1 ~~~PI~~L~p~~~~~~I~~RV~~k~~~r~f~~~~~~g~v~~~~l~De~G-~I~~t~~~~~~~~f~~~l~~G~vy~i~~~~   79 (116)
T d1jmca1           1 KVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESG-EIRATAFNEQVDKFFPLIEVNKVYYFSKGT   79 (116)
T ss_dssp             CBCCGGGCCTTCCCCEEEEEEEEECCCEEEECSSCEEEEEEEEEECSSC-EEEEEEEHHHHHHHGGGCCTTCEEEEECCE
T ss_pred             CcEeHHHcCCCCCCEEEEEEEEEeccceEEECCCCCceEEEEEEEcCCC-CEEEEEchhhhhhhHhhcccCCEEEEcceE
Confidence            3789999999999999999999999999999999999999999999655 899999999999999999999999999999


Q ss_pred             EecCCCcccCCCCceEEEeccccEEEeccCCCCCCCc
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPK  323 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~~~~d~~~~iP~  323 (653)
                      |++++++|+.++|+|||.|+.+|+|++|+| +.+||.
T Consensus        80 V~~~~~~y~~~~~~yei~f~~~T~I~~~~d-~~~iP~  115 (116)
T d1jmca1          80 LKIANKQFTAVKNDYEMTFNNETSVMPCED-DHHLPT  115 (116)
T ss_dssp             EEECCGGGCCCCCSEEEECCTTCEEEECCS-CSCCCC
T ss_pred             EEEccCcEeccCCcEEEEECCCcEEEECCC-CCCCCC
Confidence            999999999999999999999999999964 667885

>d2b3ga1 b.40.4.3 (A:3-114) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

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=99.94  E-value=2e-27  Score=206.93  Aligned_cols=103  Identities=36%  Similarity=0.595  Sum_probs=94.1

Q ss_pred             CCCHHHHHHHhC-CCCCCCCeEEEEEEEEcC--CCCceEEEEEecccceee-eeecccchhhcccCCcccCcEEEEeeeE
Q 006263            4 NLTPNSISLING-GDVNSKPLVQVMDIKLIG--STQERYRFLISDSVSTQH-AMLATQLNDRVKTGQVKKGSVVQLIDYI   79 (653)
Q Consensus         4 ~Lt~Gai~~i~~-~~~~~~pvvQVl~ik~~~--~~~~ryr~~lSDG~~~~~-~ml~t~ln~~v~~~~l~~~sIIkl~~y~   79 (653)
                      +||+|||.+||+ ++...+|||||+++|++.  .+.+|||++||||.|+++ |||+||||+++++|+|++||||||++|.
T Consensus         2 qLT~GAi~~I~~~~~~~~~PVlQVl~~k~i~~~~~~~RyR~~lSDG~~~~~~amLatqln~~v~~g~l~~~sii~l~~y~   81 (112)
T d2b3ga1           2 QLSEGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFI   81 (112)
T ss_dssp             GSCTTHHHHHHHHCCCCCCCEEEEEEEEEEC---CCCEEEEEEECSSEEEEEEEECGGGHHHHHTTSSCTTCEEEEEEEE
T ss_pred             ccCHHHHHHHHhCCCCCCCCEEEEEeeEeccCCCCcceEEEEEECcchhhhhhhhhhhhhhhhhcCCccCCCEEEEeEEE
Confidence            799999999997 555788999999999995  357899999999999997 8999999999999999999999999999


Q ss_pred             eeeec-CeEEEEEEeeeEeecC---CcccCC
Q 006263           80 CSTVQ-NRKIIVVLNMETIILD---CEPIGN  106 (653)
Q Consensus        80 ~~~~~-~k~~iii~~~evl~~~---~~~iG~  106 (653)
                      |+.++ +|+++||+++||+.++   +++||+
T Consensus        82 ~n~i~~~k~vlIIldleVl~~~~ev~~kIGn  112 (112)
T d2b3ga1          82 VNTLKDGRRVVILMELEVLKSAEAVGVKIGN  112 (112)
T ss_dssp             EEECTTSCEEEEEEEEEEEECHHHHCSCCSC
T ss_pred             EccccCCceEEEEeeeEEeccccccccccCC
Confidence            99998 5999999999999975   567886

>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Archaeal ssDNA-binding protein
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=99.49  E-value=9.1e-14  Score=121.92  Aligned_cols=95  Identities=15%  Similarity=0.219  Sum_probs=86.2

Q ss_pred             eccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEec
Q 006263          210 PIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLKP  289 (653)
Q Consensus       210 pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~~  289 (653)
                      .|++|+|++.+|+|.|||++++++|+|....|+|+++++.|.| ++|.|++++|++.+    +.|++|++|.|.|+.|+.
T Consensus         4 kI~dL~pg~~~v~i~~~V~~~~~~r~~~~~~g~~~v~~~~i~D-eTG~i~~~~W~~~~----~~l~~Gdvv~i~na~v~~   78 (115)
T d1o7ia_           4 KVGNLKPNMESVNVTVRVLEASEARQIQTKNGVRTISEAIVGD-ETGRVKLTLWGKHA----GSIKEGQVVKIENAWTTA   78 (115)
T ss_dssp             CGGGCCTTCSSEEEEEEEEEECCCEEECCTTCCEEEEEEEEEE-TTEEEEEEEEGGGT----TCCCTTCEEEEEEEEEEE
T ss_pred             cHHHCCCCCCCEEEEEEEEECCCCceeecCCCCEEEEEEEEEc-CCCeEEEEEecccc----ccCCCCCEEEEeeEEEEE
Confidence            6999999999999999999999999999888899999999999 78899999999754    579999999999999976


Q ss_pred             CCCcccCCCCceEEEeccccEEEeccC
Q 006263          290 AQKNFNHLKNEWEIFLEATSTVDLCTE  316 (653)
Q Consensus       290 a~~~f~~~~~~yei~f~~~T~I~~~~d  316 (653)
                      .+       ..++|.++..|.|+++.+
T Consensus        79 ~~-------g~~el~~~~~s~i~~~~d   98 (115)
T d1o7ia_          79 FK-------GQVQLNAGSKTKIAEASE   98 (115)
T ss_dssp             ET-------TEEEEEECTTCEEEECCC
T ss_pred             EC-------CeEEEEECCCeEEEECCC
Confidence            33       469999999999999853

>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Archaeal ssDNA-binding protein
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=98.93  E-value=3.2e-09  Score=92.35  Aligned_cols=94  Identities=21%  Similarity=0.344  Sum_probs=78.3

Q ss_pred             chhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEE
Q 006263          330 HISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVL  409 (653)
Q Consensus       330 ~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vv  409 (653)
                      +|+||..  ....+++.|.|.+++++.++.+++|. ...+++.|.|+|| +|+++||+++|..        +  ..|.+|
T Consensus         4 kI~dL~p--g~~~v~i~~~V~~~~~~r~~~~~~g~-~~v~~~~i~DeTG-~i~~~~W~~~~~~--------l--~~Gdvv   69 (115)
T d1o7ia_           4 KVGNLKP--NMESVNVTVRVLEASEARQIQTKNGV-RTISEAIVGDETG-RVKLTLWGKHAGS--------I--KEGQVV   69 (115)
T ss_dssp             CGGGCCT--TCSSEEEEEEEEEECCCEEECCTTCC-EEEEEEEEEETTE-EEEEEEEGGGTTC--------C--CTTCEE
T ss_pred             cHHHCCC--CCCCEEEEEEEEECCCCceeecCCCC-EEEEEEEEEcCCC-eEEEEEecccccc--------C--CCCCEE
Confidence            4455543  23479999999999999999888774 5678999999999 8999999998643        2  368999


Q ss_pred             EEEeeEeecCCCc-eeccccceEEEEcCC
Q 006263          410 SVKSGKVNDFSGK-SIGTIPSTQLFINPD  437 (653)
Q Consensus       410 aik~~rV~~f~G~-sLs~~~~S~i~inPd  437 (653)
                      .|++++|++|+|+ .|+....|+|...++
T Consensus        70 ~i~na~v~~~~g~~el~~~~~s~i~~~~d   98 (115)
T d1o7ia_          70 KIENAWTTAFKGQVQLNAGSKTKIAEASE   98 (115)
T ss_dssp             EEEEEEEEEETTEEEEEECTTCEEEECCC
T ss_pred             EEeeEEEEEECCeEEEEECCCeEEEECCC
Confidence            9999999999996 899999999988775

>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Hypothetical protein At4g28440 (F20O9.120)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.72  E-value=3.5e-08  Score=88.99  Aligned_cols=98  Identities=11%  Similarity=0.174  Sum_probs=83.6

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCC----------CCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhccc
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNAR----------GDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEV  276 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~----------g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~e  276 (653)
                      .++.|++|.|++.+-+|.|||+...++|.|....          +++++.++.+.| ++|.|+.++|++.++    .|++
T Consensus        15 ~~~kI~dL~pg~~~vnl~vkVl~~~~~~~~~r~~~~~~~~~~~g~~~~v~~~~v~D-eTG~i~~tlW~~~~~----~l~~   89 (145)
T d1wjja_          15 VFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGD-ETGCILFTARNDQVD----LMKP   89 (145)
T ss_dssp             SSCCSTTCCTTCCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEEC-SSCEEEEEECTTHHH----HTCT
T ss_pred             ceeEHHHCCCCCCCceEEEEEEEcccceeecccccccccccccCCCcEEEEEEEEc-cCCeEEEEEEecccc----ccCc
Confidence            4789999999999999999999999888776432          234799999999 899999999998764    5899


Q ss_pred             CcEEEEeceEEecCCCcccCCCCceEEEeccccEEEeccC
Q 006263          277 GRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTE  316 (653)
Q Consensus       277 G~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~~d  316 (653)
                      |++|.|.|+.++.-+       ...+|.++..+.|++..+
T Consensus        90 Gd~v~i~na~v~~~~-------G~~~L~vg~~g~I~~~~e  122 (145)
T d1wjja_          90 GATVILRNSRIDMFK-------GTMRLGVDKWGRIEATGA  122 (145)
T ss_dssp             TCEEEEEEEEEEEET-------TEEEEEECTTCCBCCCSC
T ss_pred             CCEEEEeeEEEEEEC-------CEEEEEECCCEEEEECCC
Confidence            999999999987643       348999999999998854

>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Hypothetical protein At4g28440 (F20O9.120)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.54  E-value=6.1e-08  Score=87.37  Aligned_cols=102  Identities=16%  Similarity=0.199  Sum_probs=82.3

Q ss_pred             cccceecchhhhhhcccCccccEEEEEEEecCceeEEec---------CCceeeEEEEEEEeCCCCEEEEEEccchhhhh
Q 006263          323 KQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRK---------NGMETQRRILNLKDTSGRSVELTLWGDFCNKE  393 (653)
Q Consensus       323 ~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k---------~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~  393 (653)
                      +....|++|+||..  ...-|++.+.|.++.+...+.++         +|.+...+++.|.|+|| .|++|||++++.. 
T Consensus        11 ~~k~~~~kI~dL~p--g~~~vnl~vkVl~~~~~~~~~r~~~~~~~~~~~g~~~~v~~~~v~DeTG-~i~~tlW~~~~~~-   86 (145)
T d1wjja_          11 KRKPVFVKVEQLKP--GTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETG-CILFTARNDQVDL-   86 (145)
T ss_dssp             CCCCSSCCSTTCCT--TCCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSC-EEEEEECTTHHHH-
T ss_pred             ccCCceeEHHHCCC--CCCCceEEEEEEEcccceeecccccccccccccCCCcEEEEEEEEccCC-eEEEEEEeccccc-
Confidence            33557999999875  34569999999999987665543         44555688999999999 8999999998643 


Q ss_pred             hhhHHHhhccCCCcEEEEEeeEeecCCCc-eeccccceEEEEcCC
Q 006263          394 GQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SIGTIPSTQLFINPD  437 (653)
Q Consensus       394 ~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sLs~~~~S~i~inPd  437 (653)
                             +  ..+.+|.|+++.+++|+|+ .|+....++|...++
T Consensus        87 -------l--~~Gd~v~i~na~v~~~~G~~~L~vg~~g~I~~~~e  122 (145)
T d1wjja_          87 -------M--KPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGA  122 (145)
T ss_dssp             -------T--CTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCSC
T ss_pred             -------c--CcCCEEEEeeEEEEEECCEEEEEECCCEEEEECCC
Confidence                   2  3689999999999999996 899988888877664

>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

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=98.33  E-value=1.8e-06  Score=74.56  Aligned_cols=100  Identities=16%  Similarity=0.104  Sum_probs=78.6

Q ss_pred             ecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCc
Q 006263          328 FRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFP  407 (653)
Q Consensus       328 f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~  407 (653)
                      .+||++|..  ....+-+.|.|+..+++.+++.++| +....++.|.|++| .|++|+|++.|..|...|      ..|.
T Consensus         2 ~~PI~~L~p--~~~~~~I~~RV~~k~~~r~f~~~~~-~g~v~~~~l~De~G-~I~~t~~~~~~~~f~~~l------~~G~   71 (116)
T d1jmca1           2 VVPIASLTP--YQSKWTICARVTNKSQIRTWSNSRG-EGKLFSLELVDESG-EIRATAFNEQVDKFFPLI------EVNK   71 (116)
T ss_dssp             BCCGGGCCT--TCCCCEEEEEEEEECCCEEEECSSC-EEEEEEEEEECSSC-EEEEEEEHHHHHHHGGGC------CTTC
T ss_pred             cEeHHHcCC--CCCCEEEEEEEEEeccceEEECCCC-CceEEEEEEEcCCC-CEEEEEchhhhhhhHhhc------ccCC
Confidence            467888764  2345679999999999999987665 45668999999999 799999999998864433      3689


Q ss_pred             EEEEEeeEeecCCCc--------eeccccceEEEEcCC
Q 006263          408 VLSVKSGKVNDFSGK--------SIGTIPSTQLFINPD  437 (653)
Q Consensus       408 Vvaik~~rV~~f~G~--------sLs~~~~S~i~inPd  437 (653)
                      |+.|.+++|+..+++        .|.....|+|...||
T Consensus        72 vy~i~~~~V~~~~~~y~~~~~~yei~f~~~T~I~~~~d  109 (116)
T d1jmca1          72 VYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCED  109 (116)
T ss_dssp             EEEEECCEEEECCGGGCCCCCSEEEECCTTCEEEECCS
T ss_pred             EEEEcceEEEEccCcEeccCCcEEEEECCCcEEEECCC
Confidence            999999999865542        366778889888775

>d1xjva1 b.40.4.3 (A:6-145) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Protection of telomeres protein 1, Pot1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.16  E-value=4.9e-06  Score=73.93  Aligned_cols=98  Identities=12%  Similarity=0.223  Sum_probs=72.2

Q ss_pred             cceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccC
Q 006263          325 QFSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVG  404 (653)
Q Consensus       325 ~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~  404 (653)
                      +|.++++++|.   .+..|+|+|||++.++...  + .|+. -...|+|+|+|...+.|.++.+..+.+    .. . ..
T Consensus         3 ~Y~Y~~la~l~---~~~~vnv~gVV~~~~~p~~--s-~g~D-~~~tl~I~D~S~~gl~v~iF~~~~~~L----P~-v-~~   69 (140)
T d1xjva1           3 NYIYTPLNQLK---GGTIVNVYGVVKFFKPPYL--S-KGTD-YCSVVTIVDQTNVKLTCLLFSGNYEAL----PI-I-YK   69 (140)
T ss_dssp             CCCCCCGGGCC---SSEEEEEEEEEEEEEEEEE--C-SSSS-EEEEEEEECTTCCEEEEEEEESSGGGS----CC-C-CS
T ss_pred             cceEeEHHHcc---CCCEEEEEEEEeecCCCEE--c-CCCe-EEEEEEEEeCCCCCeEEEEECCChHHC----CC-C-CC
Confidence            57789999875   4789999999999998753  2 2443 466799999999999999998875542    21 1 13


Q ss_pred             CCcEEEEEeeEeecCCCc-e-eccccceEEEEc
Q 006263          405 FFPVLSVKSGKVNDFSGK-S-IGTIPSTQLFIN  435 (653)
Q Consensus       405 ~~~Vvaik~~rV~~f~G~-s-Ls~~~~S~i~in  435 (653)
                      .|+||.+++++|..|+|+ . ++....|...++
T Consensus        70 ~GDII~l~r~~v~~~~~~~~~~~~~~~ss~~F~  102 (140)
T d1xjva1          70 NGDIVRFHRLKIQVYKKETQGITSSGFASLTFE  102 (140)
T ss_dssp             TTCEEEEEEEEEEEETTEEEEEEEEEEEEEEEC
T ss_pred             CCCEEEEEEEEEEEECCeEEEEecCCEEEEEEe
Confidence            689999999999999996 3 333333334454

>d1jmca2 b.40.4.3 (A:299-420) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

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=97.57  E-value=0.00015  Score=62.73  Aligned_cols=98  Identities=15%  Similarity=0.126  Sum_probs=74.8

Q ss_pred             cceeccccCCCCC--ceEEEEEEEeeccccccccC-CC-CceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEE
Q 006263          207 RIIPIAALNPYQG--RWAIKARVTAKGDLRRYNNA-RG-DGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLI  282 (653)
Q Consensus       207 ~~~pI~~L~p~~~--~w~I~~RV~~k~~ir~~~~~-~g-~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~i  282 (653)
                      +|+||++|.....  ---|.|.|+..++++++... .| +...-++.|.|..|.+|++|+|++.+++|..  .++.|+.|
T Consensus         3 ~F~~i~di~~~~~~~~vDViGvv~~v~~~~~i~~k~~g~~~~kR~i~i~D~t~~~i~vtLWg~~a~~~~~--~~~~Vi~~   80 (122)
T d1jmca2           3 DFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADKFDG--SRQPVLAI   80 (122)
T ss_dssp             CBCCGGGGGGSCTTCEEEEEEEEEEECCCEEEEETTTTEEEEEEEEEEECTTCCEEEEEEEHHHHHHCCC--TTCCEEEE
T ss_pred             ccEeHHHhhccCCCCeEEEEEEEEEccCcEEEEEcCCCCceeEEEEEEEcCCCCEEEEEEEchHhhhhCC--CCCCEEEE
Confidence            4778888854433  36699999999999998754 23 3456789999966668999999999999864  68999999


Q ss_pred             eceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263          283 SKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       283 s~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                      .+++|+.    |+.    ..|.....|.|..-
T Consensus        81 k~~~v~~----~~g----~sL~~~~~s~i~~N  104 (122)
T d1jmca2          81 KGARVSD----FGG----RSLSVLSSSTIIAN  104 (122)
T ss_dssp             EEEEEEC----TTS----SEEECCSSCEEESS
T ss_pred             eeeEEee----ccC----ceEeccCcceEEEC
Confidence            9999963    321    34777777877653

>d1jb7a1 b.40.4.3 (A:36-204) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Telomere end binding protein alpha subunit
species: Oxytricha nova [TaxId: 200597]

Probab=97.40  E-value=0.00038  Score=63.38  Aligned_cols=101  Identities=11%  Similarity=0.170  Sum_probs=70.2

Q ss_pred             ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCC------------CCEEEEEEccchhhhh
Q 006263          326 FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTS------------GRSVELTLWGDFCNKE  393 (653)
Q Consensus       326 f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s------------~~~i~vtLWg~~A~~~  393 (653)
                      |.|++|.+... ..+..++|+|||++.++...  ++ |+ --...|+|+|+|            +..|.|.|+.+.-+. 
T Consensus         1 Y~y~~l~~a~~-~~~~~vNv~GVV~~~~~p~~--s~-g~-D~~~tl~I~D~S~~~~~~~~~~~~~~~l~v~~F~~~~~~-   74 (169)
T d1jb7a1           1 YEYVELAKASL-TSAQPQHFYAVVIDATFPYK--TN-QE-RYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFED-   74 (169)
T ss_dssp             CCBCCTTTSCS-SCCSCEEEEEEEEEECCCEE--CS-SS-CEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSGGG-
T ss_pred             CeeeeHHHHHH-hcCCeEEEEEEEeecCCcee--cC-CC-cEEEEEEEEeCCCCccccccccccCCceEEEEECCCHHH-
Confidence            56777776543 25677999999999999864  22 43 456899999997            346999999887544 


Q ss_pred             hhhHHHhhccCCCcEEEEEeeEeecCCCc-ee--ccccceE-EEEcCC
Q 006263          394 GQKLQEMVDVGFFPVLSVKSGKVNDFSGK-SI--GTIPSTQ-LFINPD  437 (653)
Q Consensus       394 ~~~l~~~~~~~~~~Vvaik~~rV~~f~G~-sL--s~~~~S~-i~inPd  437 (653)
                         |.. . ...|+||.|++++|..|+|+ .+  +....|. .+++++
T Consensus        75 ---LP~-V-~~~GDII~l~rv~i~~~~g~~~~v~~~~~~SswavF~~~  117 (169)
T d1jb7a1          75 ---LPI-I-HRAGDIIRVHRATLRLYNGQRQFNANVFYSSSWALFSTD  117 (169)
T ss_dssp             ---SCC-C-CEETCEEEEEEEEEEEETTEEEEEEETTTTCEEEEECSS
T ss_pred             ---CCC-C-CCCCCEEEEEEEEEEEECCceeEEEccccceeEEEEeCC
Confidence               221 1 12589999999999999997 33  2333344 466664

>d1qzga_ b.40.4.3 (A:) Protection of telomeres protein 1, Pot1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Protection of telomeres protein 1, Pot1
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=96.98  E-value=0.00077  Score=60.85  Aligned_cols=88  Identities=19%  Similarity=0.249  Sum_probs=63.5

Q ss_pred             ceecchhhhhhcccCccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCC----CCEEEEEEccchhhhhhhhHHHhh
Q 006263          326 FSFRHISEIESAENNSIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTS----GRSVELTLWGDFCNKEGQKLQEMV  401 (653)
Q Consensus       326 f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s----~~~i~vtLWg~~A~~~~~~l~~~~  401 (653)
                      |.+.++++-. ...+..|+|+|||+++++...  ++.|..--...|+|+|.|    +..|.|.++.+..+.    |.. .
T Consensus        23 ~~~~~~~~~~-~k~~~~VnviGVV~~~~~P~r--s~~G~~Dy~~tl~I~D~S~~~~~~gl~v~iF~~~~e~----LP~-V   94 (170)
T d1qzga_          23 FQSIRSSQEL-QKKNTIVNLFGIVKDFTPSRQ--SLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGND----LPV-I   94 (170)
T ss_dssp             EECHHHHTSC-CSSCEEEEEEEEEEEEEEEEE--CSSTTCCEEEEEEEECTTSCTTSCCEEEEEEESSSSC----SCC-C
T ss_pred             eehhhhhHHH-hccCCEEEEEEEEeeccCcee--cCCCCCcEEEEEEEEcCCCCCCCCceEEEEECCChHH----CCC-c
Confidence            4444444422 236889999999999999743  444554457889999988    446999999887544    221 1


Q ss_pred             ccCCCcEEEEEeeEeecCCCc
Q 006263          402 DVGFFPVLSVKSGKVNDFSGK  422 (653)
Q Consensus       402 ~~~~~~Vvaik~~rV~~f~G~  422 (653)
                       ...|+||.+++++|..|+|+
T Consensus        95 -~~vGDII~l~rvkvq~~~g~  114 (170)
T d1qzga_          95 -KQVGQPLLLHQITLRSYRDR  114 (170)
T ss_dssp             -CSTTCEEEEEEEEEEEETTE
T ss_pred             -CCCCCEEEEEEEEEEEECCc
Confidence             13589999999999999997

>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.02  E-value=0.095  Score=49.37  Aligned_cols=181  Identities=15%  Similarity=0.155  Sum_probs=98.0

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEE------eCCC------CeEEEEEchhHHHHHHh-hcccCcEEEEec
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DSDG------GEIRVTCFNAVVDRFYE-IIEVGRVYLISK  284 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~~g------~~I~at~f~~~~~kf~~-~l~eG~vy~is~  284 (653)
                      +++-+|.||+.+--++|...+  | ..+.+|.|+      |.+|      .-+.+++|++.++.+.+ .|+.|+-+++.+
T Consensus         3 mN~v~l~G~l~~dpe~r~t~~--G-~~~~~f~lA~~~~~~~~~g~~~~~t~~~~v~~~g~~Ae~~~~~~l~KG~~V~V~G   79 (231)
T d1se8a_           3 MNHVYLIGALARDPELRYTGN--G-MAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAEWQAERNLKGGDAVVVEG   79 (231)
T ss_dssp             EEEEEEEEEESSCCEEEECTT--S-CEEEEEEEEEEEEC-------CEEEEEEEEEEESHHHHHHHHTCCCTTCEEEEEE
T ss_pred             ccEEEEEEEECcCCEEEECCC--C-CEEEEEEEEECCcEECCCCCEEeeeeeeeEEEeCchhhhhhhhccCCCCEEEEEE
Confidence            467789999999888887643  2 257777774      3222      24899999999998864 699999999996


Q ss_pred             eEEecCCCccc----CCCCceEEEeccccEEEeccCCCCCCCcccceecchhhhhhcccCccccEEEEEEEecCceeEEe
Q 006263          285 GSLKPAQKNFN----HLKNEWEIFLEATSTVDLCTEEDDSIPKQQFSFRHISEIESAENNSIVDVIGIVISVNPSVPILR  360 (653)
Q Consensus       285 ~~V~~a~~~f~----~~~~~yei~f~~~T~I~~~~d~~~~iP~~~f~f~~i~~i~~~~~~~~vDVIGvV~~v~~~~~i~~  360 (653)
                       ++...  .|.    ......+|..++   |+.+.......-...-.+.-      ...-..|-++|.|..-  ++.-.+
T Consensus        80 -~l~~~--~~~~~dG~~r~~~~i~a~~---v~~l~~~~~~~~~~~~~~~m------~~~~N~v~l~G~l~~d--pe~r~t  145 (231)
T d1se8a_          80 -TLEYR--QWEAPEGGKRSAVNVKALR---MEQLGTQPELIQDAGGGVRM------SGAMNEVLVLGNVTRD--PEIRYT  145 (231)
T ss_dssp             -EEEEE--EEC-----CEEEEEEEEEE---EEECSSCCCEEECTTSCEEE------ETCEEEEEEEEEECSC--CEEEEC
T ss_pred             -EEEee--eeECCCCCEEEEEEEEEEE---EEEccCCccccccccccccc------cccceeEEEEEEeCCC--cEEEEC
Confidence             33321  221    111223443332   33331111000000000000      0122468889988763  332234


Q ss_pred             cCCceeeEEEEEE----EeCCC------CEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEee-EeecCCCc
Q 006263          361 KNGMETQRRILNL----KDTSG------RSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSG-KVNDFSGK  422 (653)
Q Consensus       361 k~g~~~~kr~i~l----~D~s~------~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~-rV~~f~G~  422 (653)
                      .+|+.+..-.|-.    .|..|      .-+.|++||+.|+..    + .+  ..|..|++.|- +...|.++
T Consensus       146 ~~G~~~~~f~va~~~~~~~~~g~~~~~t~~~~v~~~g~~Ae~~----~-~l--~KG~~V~V~G~l~~~~~~~k  211 (231)
T d1se8a_         146 PAGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLAENM----K-EL--RKGDPVMIMGRLVNEGWTDK  211 (231)
T ss_dssp             TTCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHHHH----T-TC--CTTCEEEEEEEEEEEECC--
T ss_pred             CCCCEEEEEEEEECCCeECCCCceeeeeEEEEeEecCcHHHHh----h-hC--CCCCEEEEEEEeEeceEECC
Confidence            5676543332222    23333      259999999998652    1 12  35777777643 55677653

>d1xjva1 b.40.4.3 (A:6-145) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Protection of telomeres protein 1, Pot1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.59  E-value=0.14  Score=44.36  Aligned_cols=83  Identities=11%  Similarity=0.077  Sum_probs=65.4

Q ss_pred             cceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          207 RIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       207 ~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      .++||++|.+.. .-.+.|-|+.....+.   .+|..-...|.|+|+....+.+.+|.+..+.+=..-..||++.+++++
T Consensus         5 ~Y~~la~l~~~~-~vnv~gVV~~~~~p~~---s~g~D~~~tl~I~D~S~~gl~v~iF~~~~~~LP~v~~~GDII~l~r~~   80 (140)
T d1xjva1           5 IYTPLNQLKGGT-IVNVYGVVKFFKPPYL---SKGTDYCSVVTIVDQTNVKLTCLLFSGNYEALPIIYKNGDIVRFHRLK   80 (140)
T ss_dssp             CCCCGGGCCSSE-EEEEEEEEEEEEEEEE---CSSSSEEEEEEEECTTCCEEEEEEEESSGGGSCCCCSTTCEEEEEEEE
T ss_pred             eEeEHHHccCCC-EEEEEEEEeecCCCEE---cCCCeEEEEEEEEeCCCCCeEEEEECCChHHCCCCCCCCCEEEEEEEE
Confidence            478999998743 5678899988887664   345456788999998888999999988766665556789999999999


Q ss_pred             EecCCCc
Q 006263          287 LKPAQKN  293 (653)
Q Consensus       287 V~~a~~~  293 (653)
                      |+.-+.+
T Consensus        81 v~~~~~~   87 (140)
T d1xjva1          81 IQVYKKE   87 (140)
T ss_dssp             EEEETTE
T ss_pred             EEEECCe
Confidence            9876643

>d1eova1 b.40.4.1 (A:71-204) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.04  E-value=0.84  Score=38.69  Aligned_cols=98  Identities=13%  Similarity=0.124  Sum_probs=69.8

Q ss_pred             cceeccccCCC---CCceEEEEEEEeeccccccccCCCCc-eeEEEEEEeCCCCeEEEEEchhH-------HHHHHhhcc
Q 006263          207 RIIPIAALNPY---QGRWAIKARVTAKGDLRRYNNARGDG-KVFSFDLLDSDGGEIRVTCFNAV-------VDRFYEIIE  275 (653)
Q Consensus       207 ~~~pI~~L~p~---~~~w~I~~RV~~k~~ir~~~~~~g~g-k~f~~~L~D~~g~~I~at~f~~~-------~~kf~~~l~  275 (653)
                      ..+.|.+|.+.   ...-+|+|||..+   |.      .| ++.-++|.| .+|.|++.+..+.       .-++...|.
T Consensus        22 ~r~~i~dl~~~~~~g~~V~v~GwV~~~---R~------~G~kl~F~~LrD-~sg~iQ~~v~~~~~~~~~~~~~~~~~~l~   91 (134)
T d1eova1          22 KRVKFVDLDEAKDSDKEVLFRARVHNT---RQ------QGATLAFLTLRQ-QASLIQGLVKANKEGTISKNMVKWAGSLN   91 (134)
T ss_dssp             CCCCGGGCCTTTTTTCEEEEEEEEEEE---EE------CSSSEEEEEEEE-TTEEEEEEEECCSSSSSCHHHHHHHTTCC
T ss_pred             EEEEeccccchhcCCCEEEEEEEEEEE---Ee------CCCcEEEEEEEc-CCCcEEEEEEeccccchhHHHHHHHhcCC
Confidence            34566666553   2467799999874   33      24 576789999 7889999998532       224557899


Q ss_pred             cCcEEEEeceEEecCCCcccCCCCceEEEeccccEEEec
Q 006263          276 VGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       276 eG~vy~is~~~V~~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                      .|+++.+.+--+++..+.-+...++|||...+-..|..+
T Consensus        92 ~es~V~V~G~v~~~~~~~~~~~~~~~Ei~v~~i~vls~a  130 (134)
T d1eova1          92 LESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISET  130 (134)
T ss_dssp             TTCEEEEEEEEEECSSCCTTSSEEEEEEEEEEEEEEECC
T ss_pred             CCCEEEEEEEEEeCCccCCCCCCCcEEEEEEEEEEEeCC
Confidence            999999999877665554445668999999886666654

>d1xjva2 b.40.4.3 (A:149-299) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Protection of telomeres protein 1, Pot1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.64  E-value=0.71  Score=39.99  Aligned_cols=112  Identities=10%  Similarity=0.141  Sum_probs=66.6

Q ss_pred             cchhhhhhcccCccccEEEEEEEecCce--eEEec--CCceeeE--EEEEE------EeC------CCCEEEEEEccchh
Q 006263          329 RHISEIESAENNSIVDVIGIVISVNPSV--PILRK--NGMETQR--RILNL------KDT------SGRSVELTLWGDFC  390 (653)
Q Consensus       329 ~~i~~i~~~~~~~~vDVIGvV~~v~~~~--~i~~k--~g~~~~k--r~i~l------~D~------s~~~i~vtLWg~~A  390 (653)
                      ++|.||   ..+.++|+++.|..+-...  .+.-+  +|.....  .-...      .|.      -+.+|.|+||++.+
T Consensus         3 ~~l~di---~~~~~~DL~cqVv~v~~~~~~~~~L~VwDgT~~~~~~~~~~~e~~~~~gd~~~~~~~~~l~i~V~lyD~H~   79 (151)
T d1xjva2           3 LKLCDV---QPMQYFDLTCQLLGKAEVDGASFLLKVWDGTRTPFPSWRVLIQDLVLEGDLSHIHRLQNLTIDILVYDNHV   79 (151)
T ss_dssp             CCGGGC---CSSCEEEEEEEEEEEEECSSSEEEEEEECSSCCSSCBCCCCCCSSCCEECHHHHHHHGGGSEEEEEETTHH
T ss_pred             eehhhc---CCCcEEEEEEEEEEEEEecCCEEEEEEecCCCCCCcEeccccCCccccccccccccCcceEEEEEEECchH
Confidence            445555   4688999999999986542  22212  3333210  00011      111      12479999999998


Q ss_pred             hhhhhhHHHhhccCCCcEEEEEeeEeec--CCCc---ee----ccc----cceEEEEcC-ChHHHHHHHHHHhc
Q 006263          391 NKEGQKLQEMVDVGFFPVLSVKSGKVND--FSGK---SI----GTI----PSTQLFINP-DFAEAHELREWFDS  450 (653)
Q Consensus       391 ~~~~~~l~~~~~~~~~~Vvaik~~rV~~--f~G~---sL----s~~----~~S~i~inP-dipe~~~l~~w~~~  450 (653)
                      .-     +..+  ..|..|.|++++++-  -+|.   +|    ..-    ..-.|.+-| +.|.+++|+.|+++
T Consensus        80 ~~-----ar~l--K~GdfV~l~NVh~k~~~~~~~~~~~l~le~hlhgg~~y~rgI~vlp~~~~~~~~lk~~~es  146 (151)
T d1xjva2          80 HV-----ARSL--KVGSFLRIYSLHTKLQSMNSENQTMLSLEFHLHGGTSYGRGIRVLPESNSDVDQLKKDLES  146 (151)
T ss_dssp             HH-----HHHC--CTTCEEEEEEEEEEEEEECTTSCEEEEEEEEECSSCGGGCEEEEECTTSHHHHHHHHHHHH
T ss_pred             HH-----HhhC--CCCCEEEEEEEEEEeccCCCccCCcceEEEEEcCCcccCCeeEECCCCChHHHHHHHHhhh
Confidence            64     3333  578999999998852  2221   11    111    222466666 57999999999875

>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Lysyl-tRNA synthetase (LysRS)
species: Escherichia coli, gene lysU [TaxId: 562]

Probab=90.45  E-value=0.75  Score=39.58  Aligned_cols=78  Identities=18%  Similarity=0.234  Sum_probs=58.5

Q ss_pred             ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchh-----HHHHHHhhcccCcEEEEeceEEecCCCcc
Q 006263          220 RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA-----VVDRFYEIIEVGRVYLISKGSLKPAQKNF  294 (653)
Q Consensus       220 ~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~-----~~~kf~~~l~eG~vy~is~~~V~~a~~~f  294 (653)
                      .-+|.|||+.+   |.+      |++.-++|.| .+|.||+.+-.+     ..+.|...|..|+++-+.+.-.+..    
T Consensus        56 ~V~vaGRI~~~---R~~------Gk~~F~~i~D-~~g~iQi~~~~~~~~~~~~~~~~k~ld~GDiIgv~G~~~~Tk----  121 (143)
T d1e1oa1          56 EVSVAGRMMTR---RIM------GKASFVTLQD-VGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQ----  121 (143)
T ss_dssp             EEEEEEEEEEE---EEE------TTEEEEEEEE-TTEEEEEEEETTTSSTTHHHHTGGGCCTTCEEEEEEEEEECT----
T ss_pred             eEEEEEEEEEE---ccc------CCeeEEEEEe-CCceEEEEEccccchhhhHHHHHhcCCcccEEEeecccEECC----
Confidence            58899999885   443      6888899999 789999988543     3556778899999999988765443    


Q ss_pred             cCCCCceEEEeccccEEEec
Q 006263          295 NHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       295 ~~~~~~yei~f~~~T~I~~~  314 (653)
                         ..+..|...+.+....|
T Consensus       122 ---tGElsi~~~~~~lLsK~  138 (143)
T d1e1oa1         122 ---TGELSIHCTELRLLTKA  138 (143)
T ss_dssp             ---TCCEEEEEEEEEEEECC
T ss_pred             ---CCcEEEEeeEEEEeccc
Confidence               34577777666666655

>d1iyjb3 b.40.4.3 (B:2599-2731) OB-fold domains of BRCA2 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: OB-fold domains of BRCA2
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.91  E-value=0.18  Score=42.98  Aligned_cols=65  Identities=22%  Similarity=0.246  Sum_probs=48.4

Q ss_pred             HHHHHhCCCC-CCCC-eEEEEEEEEcC--------------CCCceEEEEEecccceeeeeecccchhhcccCCcccCcE
Q 006263            9 SISLINGGDV-NSKP-LVQVMDIKLIG--------------STQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSV   72 (653)
Q Consensus         9 ai~~i~~~~~-~~~p-vvQVl~ik~~~--------------~~~~ryr~~lSDG~~~~~~ml~t~ln~~v~~~~l~~~sI   72 (653)
                      ||.+|++++. ...| ||=|..|-...              .......|.|+||=|.++|.+...|..++..|.|..|.=
T Consensus         3 alrkI~E~D~~~s~~mVLcVs~I~~~~~~~~~~~~~~~~~~~~~~~~~lelTDGWYsi~a~lD~~L~~~l~~grl~vGqK   82 (133)
T d1iyjb3           3 ALKKILERDDTAAKTLVLCVSDIISLSTNVSETSGSKASSEDSNKVDTIELTDGWYAVKAQLDPPLLALVKSGRLTVGQK   82 (133)
T ss_dssp             HHHHHHTTSSTTCCSEEEEEEECCCCC-----------------CCCCEEEECSSCEEEECCCHHHHHHHHHTCSCTTCE
T ss_pred             HHHHHHhCCCCccCcEEEEEEEeeccCCccccccccccccccccccceEEEecCCEEEEEEcCHHHHHHHHcCCccccce
Confidence            7899999986 3345 45555552221              122445799999999999999999999999999999984


Q ss_pred             E
Q 006263           73 V   73 (653)
Q Consensus        73 I   73 (653)
                      +
T Consensus        83 L   83 (133)
T d1iyjb3          83 I   83 (133)
T ss_dssp             E
T ss_pred             E
Confidence            4

>d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-2 [TaxId: 274]

Probab=89.10  E-value=1.2  Score=35.21  Aligned_cols=84  Identities=13%  Similarity=0.090  Sum_probs=58.8

Q ss_pred             eccccCCCCC-ceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhcccCcEEEEeceEEe
Q 006263          210 PIAALNPYQG-RWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEIIEVGRVYLISKGSLK  288 (653)
Q Consensus       210 pI~~L~p~~~-~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l~eG~vy~is~~~V~  288 (653)
                      .|++|..+.+ .-+|+|||.++   |.      .|++.-++|.| .+|.|++.+-..      ..+..++++.+.+--++
T Consensus         4 ~I~dl~~~~g~~V~v~GwV~~~---R~------~gk~~Fi~LrD-~sg~iQ~v~~~~------~~~~~e~~v~v~G~v~~   67 (93)
T d1n9wa1           4 LVRDLKAHVGQEVELLGFLHWR---RD------LGRIQFLLLRD-RSGVVQVVTGGL------KLPLPESALRVRGLVVE   67 (93)
T ss_dssp             CGGGGGGCTTSEEEEEEEEEEE---EE------CSSEEEEEEEE-TTEEEEEEEESC------CCCCTTCEEEEEEEEEE
T ss_pred             EhHHhhhcCCCEEEEEEEEEeE---Ee------CCCcEEEEEEc-CCccceEEeccc------cccccceEEEEEEEEEE
Confidence            5777766653 68899999774   43      36788889999 688899987553      45677888888764433


Q ss_pred             cCCCcccCCCCceEEEeccccEEEec
Q 006263          289 PAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       289 ~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                      .. +    ...++||..++-..+..+
T Consensus        68 ~~-~----~~~~~Ei~v~~i~il~~a   88 (93)
T d1n9wa1          68 NA-K----APGGLEVQAKEVEVLSPA   88 (93)
T ss_dssp             CT-T----STTSEEEEEEEEEEEECC
T ss_pred             CC-C----CCCCEEEEEeEEEEEecC
Confidence            22 1    246899999776555544

>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Primosomal replication protein N, PriB
species: Escherichia coli [TaxId: 562]

Probab=88.51  E-value=0.7  Score=37.91  Aligned_cols=88  Identities=13%  Similarity=0.074  Sum_probs=60.3

Q ss_pred             CCceEEEEEEEeeccccccccCCCCceeEEEEEEe----CCCC-------eEEEEEchhHHHHHHhhcccCcEEEEeceE
Q 006263          218 QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD----SDGG-------EIRVTCFNAVVDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       218 ~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D----~~g~-------~I~at~f~~~~~kf~~~l~eG~vy~is~~~  286 (653)
                      .+.-.|.|||++.-++|...+  | ..+.+|.|.=    .+.+       .|.|++|+..++.+.+.|..|+-+.|.++.
T Consensus         6 ~N~v~L~G~l~~dpelr~T~~--G-~~v~~f~la~~~~~~e~~~~r~~~~~i~vv~~g~~Ae~~~~~l~kG~~v~v~G~L   82 (111)
T d1v1qa_           6 TNRLVLSGTVCRAPLRKVSPS--G-IPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFI   82 (111)
T ss_dssp             CEEEEEEEEEEEEEEEEECTT--C-CEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESTGGGGGGTTCCTTCEEEEEEEE
T ss_pred             eEEEEEEEEecCCcceEECCC--C-CEEEEEEEEeccEEecccceEEEEEEEEEEEeCHHHHHHHHHhcCCCEEEEEEEE
Confidence            467899999999999996532  2 2567777641    1222       389999999999999999999999999863


Q ss_pred             EecCCCcccCCCCceEEEeccccEEEec
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVDLC  314 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~~~  314 (653)
                       .  .+.|+.....+.+..   +.|+.+
T Consensus        83 -~--~~~~~~~~~r~v~~a---~~ie~l  104 (111)
T d1v1qa_          83 -S--CHKAKNGLSKMVLHA---EQIELI  104 (111)
T ss_dssp             -E--EECTTTTSCEEEEEE---EEEEET
T ss_pred             -E--EecccCCCCEEEEEE---EEEEEe
Confidence             2  234544333344332   345544

>d1jb7a1 b.40.4.3 (A:36-204) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Telomere end binding protein alpha subunit
species: Oxytricha nova [TaxId: 200597]

Probab=88.42  E-value=0.55  Score=41.65  Aligned_cols=81  Identities=11%  Similarity=0.119  Sum_probs=60.0

Q ss_pred             ceeccc--cCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCC------------CCeEEEEEchhHHHHHHhh
Q 006263          208 IIPIAA--LNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSD------------GGEIRVTCFNAVVDRFYEI  273 (653)
Q Consensus       208 ~~pI~~--L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~------------g~~I~at~f~~~~~kf~~~  273 (653)
                      ++||++  +... ..-.+-|-|+.....+.-   +|..-..+|.|+|..            +..|.+.+|.+..+.+=..
T Consensus         3 y~~l~~a~~~~~-~~vNv~GVV~~~~~p~~s---~g~D~~~tl~I~D~S~~~~~~~~~~~~~~~l~v~~F~~~~~~LP~V   78 (169)
T d1jb7a1           3 YVELAKASLTSA-QPQHFYAVVIDATFPYKT---NQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFEDLPII   78 (169)
T ss_dssp             BCCTTTSCSSCC-SCEEEEEEEEEECCCEEC---SSSCEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSGGGSCCC
T ss_pred             eeeHHHHHHhcC-CeEEEEEEEeecCCceec---CCCcEEEEEEEEeCCCCccccccccccCCceEEEEECCCHHHCCCC
Confidence            567764  3333 456899999988887652   455567889999953            3579999998876655444


Q ss_pred             cccCcEEEEeceEEecCCC
Q 006263          274 IEVGRVYLISKGSLKPAQK  292 (653)
Q Consensus       274 l~eG~vy~is~~~V~~a~~  292 (653)
                      -..|||+.++++.|+.-+.
T Consensus        79 ~~~GDII~l~rv~i~~~~g   97 (169)
T d1jb7a1          79 HRAGDIIRVHRATLRLYNG   97 (169)
T ss_dssp             CEETCEEEEEEEEEEEETT
T ss_pred             CCCCCEEEEEEEEEEEECC
Confidence            5789999999999987664

>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RecG "wedge" domain
domain: RecG "wedge" domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.93  E-value=0.21  Score=44.84  Aligned_cols=72  Identities=11%  Similarity=0.243  Sum_probs=50.2

Q ss_pred             CCCcceeccccCCCCCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHHHhhc--ccCcEEE
Q 006263          204 APARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRFYEII--EVGRVYL  281 (653)
Q Consensus       204 ~~~~~~pI~~L~p~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf~~~l--~eG~vy~  281 (653)
                      ..+.+.+|++|.++. .-+|.|+|+.... +.+.    ..+.+.+.+.| ++|+|.+++|+..  -+...+  .+|+.+.
T Consensus        47 Dr~~~~~i~~l~~g~-~vti~g~V~~~~~-~~~~----~~~~~~~~v~D-~~g~i~l~fFn~~--~~~~~~k~~~G~~v~  117 (180)
T d1gm5a2          47 DRRKIFKLNDLLPGE-KVTTQGKIVSVET-KKFQ----NMNILTAVLSD-GLVHVPLKWFNQD--YLQTYLKQLTGKEVF  117 (180)
T ss_dssp             CCSCCCCSSCCCSSC-CCEEEECCCCCEE-EECS----SCEEEEEEECC-SSCCEEEEECSCC--TTHHHHHTTCSSCEE
T ss_pred             eccccccccccCcce-eeeeeeEEEeecc-cccc----ccceeEEEEEe-ccceEEEEEeCcH--HHHHHHhhhcCceEE
Confidence            334677899998874 5789999986432 2222    24678899999 6789999999963  122233  3699988


Q ss_pred             Eec
Q 006263          282 ISK  284 (653)
Q Consensus       282 is~  284 (653)
                      |++
T Consensus       118 v~G  120 (180)
T d1gm5a2         118 VTG  120 (180)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            876

>d1c0aa1 b.40.4.1 (A:1-106) Aspartyl-tRNA synthetase (AspRS) {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Escherichia coli [TaxId: 562]

Probab=86.84  E-value=2.4  Score=34.13  Aligned_cols=93  Identities=15%  Similarity=0.140  Sum_probs=61.6

Q ss_pred             ccccCCC--CCceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHHHHH--HhhcccCcEEEEeceE
Q 006263          211 IAALNPY--QGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVVDRF--YEIIEVGRVYLISKGS  286 (653)
Q Consensus       211 I~~L~p~--~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~~kf--~~~l~eG~vy~is~~~  286 (653)
                      +.+|+..  ...-+|+|+|-++   |.      .|++.-++|.| .+|.+++++..+..+.|  -..|..+.+..|.+--
T Consensus         6 cgeL~~~~~g~~V~v~GWv~~~---R~------~g~i~Fi~LRD-~~G~~Q~v~~~~~~~~~~~~~~l~~Es~v~V~G~V   75 (106)
T d1c0aa1           6 CGQLRLSHVGQQVTLCGWVNRR---RD------LGSLIFIDMRD-REGIVQVFFDPDRADALKLASELRNEFCIQVTGTV   75 (106)
T ss_dssp             GGGCCGGGTTCEEEEEEEEEEE---EE------CSSCEEEEEEE-TTEEEEEEECGGGHHHHHHHTTCCTTCEEEEEEEE
T ss_pred             cccCChHHCCCEEEEEEEEEEe---ee------CCCcEEEEEEc-CCeEEeEEecccchhHHHHHHhhCccceEEEEeEE
Confidence            3455443  2467899998663   33      36777789999 67899999987765444  3457788999998864


Q ss_pred             EecCCCccc--CCCCceEEEeccccEEEe
Q 006263          287 LKPAQKNFN--HLKNEWEIFLEATSTVDL  313 (653)
Q Consensus       287 V~~a~~~f~--~~~~~yei~f~~~T~I~~  313 (653)
                      ++...+..+  ....+|||..+.-+.+..
T Consensus        76 ~~r~~~~~n~~~~tg~iEi~v~~i~vl~~  104 (106)
T d1c0aa1          76 RARDEKNINRDMATGEIEVLASSLTIINR  104 (106)
T ss_dssp             EECCTTTCCTTSTTTTEEEEEEEEEEEEC
T ss_pred             eccCccccCCCCCCCcEEEEEeEEEEEeC
Confidence            443333332  234579999877655544

>d1b8aa1 b.40.4.1 (A:1-103) Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococcus kodakaraensis [TaxId: 311400]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Archaeon Pyrococcus kodakaraensis [TaxId: 311400]

Probab=85.70  E-value=2.5  Score=33.84  Aligned_cols=87  Identities=13%  Similarity=0.076  Sum_probs=57.6

Q ss_pred             ccccCCCC--CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhHH----HHHHhhcccCcEEEEec
Q 006263          211 IAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV----DRFYEIIEVGRVYLISK  284 (653)
Q Consensus       211 I~~L~p~~--~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~~----~kf~~~l~eG~vy~is~  284 (653)
                      +.+|++..  ..-+|+|||.++   |.      .|++.-++|.| .+|.||+.+..+.+    -++...|..|+++.+.+
T Consensus         7 ~~el~~~~~G~~V~v~Gwv~~~---R~------~g~i~Fi~LrD-~sg~iQ~v~~~~~~~~~~~~~~~~l~~es~v~V~G   76 (103)
T d1b8aa1           7 SSEITEELNGQKVKVAGWVWEV---KD------LGGIKFLWIRD-RDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEG   76 (103)
T ss_dssp             GGGCCGGGTTCEEEEEEEEEEE---EE------ETTEEEEEEEE-TTEEEEEEEETTTSCHHHHHHGGGCCTTCEEEEEE
T ss_pred             hhhCChhHCCCEEEEEEEEehh---cc------CCCcEEEEEEc-CCEeeeEEEeccccchhhhhHHhhCCcceEEEEEE
Confidence            55665542  468899999874   43      36777789999 67799999875432    23345688999999997


Q ss_pred             eEEecCCCcccCCCCceEEEeccccEEE
Q 006263          285 GSLKPAQKNFNHLKNEWEIFLEATSTVD  312 (653)
Q Consensus       285 ~~V~~a~~~f~~~~~~yei~f~~~T~I~  312 (653)
                      --.+...     ....+||....-..+.
T Consensus        77 ~v~~~~~-----~~~~iEi~v~~i~ils   99 (103)
T d1b8aa1          77 VVNFTPK-----AKLGFEILPEKIVVLN   99 (103)
T ss_dssp             EEEECTT-----STTSEEEEEEEEEEEE
T ss_pred             EEEECCC-----CCccEEEEeeEEEEEE
Confidence            5332211     2345888876644443

>d2pi2a1 b.40.4.3 (A:44-171) Replication protein A 32 KDa subunit (RPA32) fragment {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 32 KDa subunit (RPA32) fragment
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.98  E-value=1.3  Score=37.07  Aligned_cols=70  Identities=17%  Similarity=0.319  Sum_probs=43.7

Q ss_pred             ccccEEEEEEEecCceeEEecCCceeeEEEEEEEeCCCCEEEEEEccchhhhhhhhHHHhhccCCCcEEEEEeeEeecCC
Q 006263          341 SIVDVIGIVISVNPSVPILRKNGMETQRRILNLKDTSGRSVELTLWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFS  420 (653)
Q Consensus       341 ~~vDVIGvV~~v~~~~~i~~k~g~~~~kr~i~l~D~s~~~i~vtLWg~~A~~~~~~l~~~~~~~~~~Vvaik~~rV~~f~  420 (653)
                      ..|.++|+|.++....          .+-.++|-|.||..|.|..|-+.-.... . .+.+  ..+..|.+.| +++.|+
T Consensus        29 ~~V~iVG~V~~i~~~~----------t~~~y~idDgTG~~i~v~~w~~~~~~~~-~-~~~i--~~g~yVrV~G-~lk~f~   93 (128)
T d2pi2a1          29 SQVTIVGIIRHAEKAP----------TNIVYKIDDMTAAPMDVRQWVDTDDTSS-E-NTVV--PPETYVKVAG-HLRSFQ   93 (128)
T ss_dssp             SEEEEEEEEEEEEECS----------SEEEEEEECSSSSCEEEEEECC---------CCCC--CTTCEEEEEE-EEEEET
T ss_pred             EEEEEEEEEEEEEecC----------CEEEEEEECCCCCcEEEEEECCCCCCcc-c-cccc--cCCCEEEEEE-EEEeeC
Confidence            4789999999865532          3467899999998899999954321100 0 0011  2456665555 677888


Q ss_pred             Cc-eec
Q 006263          421 GK-SIG  425 (653)
Q Consensus       421 G~-sLs  425 (653)
                      |+ ++.
T Consensus        94 ~~~~i~   99 (128)
T d2pi2a1          94 NKKSLV   99 (128)
T ss_dssp             TEEEEE
T ss_pred             CeEEEE
Confidence            85 553

>d1l0wa1 b.40.4.1 (A:1-104) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-1 [TaxId: 274]

Probab=83.69  E-value=3.1  Score=33.40  Aligned_cols=93  Identities=16%  Similarity=0.085  Sum_probs=59.0

Q ss_pred             eccccCCCC--CceEEEEEEEeeccccccccCCCCceeEEEEEEeCCCCeEEEEEchhH-HHHHHhhcccCcEEEEeceE
Q 006263          210 PIAALNPYQ--GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAV-VDRFYEIIEVGRVYLISKGS  286 (653)
Q Consensus       210 pI~~L~p~~--~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D~~g~~I~at~f~~~-~~kf~~~l~eG~vy~is~~~  286 (653)
                      .+.+|++..  ..-+|+|+|-++   |.      .|++.-++|.| .+|.|++++..+. .-..-..|..+.++.+.+--
T Consensus         6 ~~geL~~~~~g~~V~l~GWV~~~---R~------~g~i~Fi~LRD-~~G~iQ~v~~~~~~~~~~~~~l~~Es~I~V~G~V   75 (104)
T d1l0wa1           6 YAGSLRETHVGEEVVLEGWVNRR---RD------LGGLIFLDLRD-REGLVQLVAHPASPAYATAERVRPEWVVRAKGLV   75 (104)
T ss_dssp             CGGGCCGGGTTCEEEEEEEEEEE---EE------CSSCEEEEEEE-TTEEEEEEECTTSTTHHHHTTCCTTCEEEEEEEE
T ss_pred             ccccCChHHCCCEEEEEEEEEeh---hc------CCCeEEEEEEC-CCCceEEecccchhHHHHHhhcCcccEEEEEEEE
Confidence            345666543  468899998663   33      36777799999 6788999987543 22233457888999998844


Q ss_pred             EecCCCcccCCCCceEEEeccccEEE
Q 006263          287 LKPAQKNFNHLKNEWEIFLEATSTVD  312 (653)
Q Consensus       287 V~~a~~~f~~~~~~yei~f~~~T~I~  312 (653)
                      .+.....-+....+|||..++-..+-
T Consensus        76 ~~r~~~n~~~~tG~iEi~v~~i~iL~  101 (104)
T d1l0wa1          76 RLRPEPNPRLATGRVEVELSALEVLA  101 (104)
T ss_dssp             EECSSCCTTSTTTTEEEEEEEEEEEE
T ss_pred             eeCCccCCCCCCCCEEEEEeEEEEEE
Confidence            33222212223457999887654443

>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Escherichia coli [TaxId: 562]

Probab=82.77  E-value=2.2  Score=36.34  Aligned_cols=65  Identities=20%  Similarity=0.232  Sum_probs=51.1

Q ss_pred             CCCceEEEEEEEeeccccccccCCCCceeEEEEEE------eC-------CCCeEEEEEchhHHHHHHhhcccCcEEEEe
Q 006263          217 YQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLL------DS-------DGGEIRVTCFNAVVDRFYEIIEVGRVYLIS  283 (653)
Q Consensus       217 ~~~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~------D~-------~g~~I~at~f~~~~~kf~~~l~eG~vy~is  283 (653)
                      .++.-+|.|||.+--++|...+  | ..+.+|.|+      |.       +..=+.+++|+..++.+...|+.|+.++|.
T Consensus         4 ~mN~v~LiG~l~~dpe~r~~~~--G-~~v~~f~va~~~~~~~~~~~~~~~~t~w~~v~~~g~~Ae~~~~~l~KG~~V~V~   80 (145)
T d1qvca_           4 GVNKVILVGNLGQDPEVRYMPN--G-GAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIE   80 (145)
T ss_dssp             CEEEEEEEEEESSCCEEECCSS--S-CCEEEEEEEECCCCSCCSSSSCCCCCEEEEEEEETHHHHHHHHHCCTTCEEEEE
T ss_pred             cceEEEEEEECCCCCEEEECCC--C-CEEEEEEEEecccccccccccccccceEEeeEEecchhhhHhhhcccCCEEEEE
Confidence            4567889999999888887643  2 257677765      22       334689999999999999999999999997


Q ss_pred             c
Q 006263          284 K  284 (653)
Q Consensus       284 ~  284 (653)
                      +
T Consensus        81 G   81 (145)
T d1qvca_          81 G   81 (145)
T ss_dssp             E
T ss_pred             E
Confidence            6

>d1ue1a_ b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.17  E-value=1.6  Score=35.86  Aligned_cols=63  Identities=19%  Similarity=0.248  Sum_probs=48.9

Q ss_pred             CceEEEEEEEeeccccccccCCCCceeEEEEEEe------CC--------CCeEEEEEchhHHHHHHhhcccCcEEEEec
Q 006263          219 GRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLD------SD--------GGEIRVTCFNAVVDRFYEIIEVGRVYLISK  284 (653)
Q Consensus       219 ~~w~I~~RV~~k~~ir~~~~~~g~gk~f~~~L~D------~~--------g~~I~at~f~~~~~kf~~~l~eG~vy~is~  284 (653)
                      +.-+|.+|+.+--++|...+  | ..+.+|.|+-      .+        ..-+.+++|+.+++.+.+.|+.|+-+++.+
T Consensus         3 N~V~L~G~l~~dpe~r~~~~--G-~~v~~f~lA~~~~~~~~~~~~~~~~~t~~~~v~~~g~~Ae~~~~~l~KG~~V~V~G   79 (118)
T d1ue1a_           3 TTITIVGNLTADPELRFTPS--G-AAVANFTVASTPRIYDRQTGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVSG   79 (118)
T ss_dssp             CEEEEEEEESSCCEEEECTT--S-CEEEEEEEEECCCCCC-----CCCCCCEEEEEEEEHHHHHHHHHHCCTTCEEEEEE
T ss_pred             CEEEEEEEcCcCCEEEECCC--C-CEEEEEEEEecccccccCCCcccccceeeEEEEeChHHHHHHHHhccCCCEEEEEe
Confidence            56789999998888887653  2 2576777642      12        235999999999999999999999999984