HHsearch alignment for GI: 254780945 and conserved domain: TIGR00617
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1); InterPro: IPR004591 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 single-stranded DNA and function in the recognition of DNA damage for nucleotide excision repair. 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. This family is Replication factor-a protein 1 (RPA1); GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus.
Probab=95.42 E-value=0.045 Score=35.85 Aligned_cols=120 Identities=19% Similarity=0.264 Sum_probs=80.6
Q ss_pred CCCCCCCCCCCCHHHCCCC-CEEEEEEEEEEEEEECCC---C--CCEEEEEEEC-CCCEEEEEEECCCHHHHHHHCCCCC
Q ss_conf 9740134444647888998-789999999897542158---9--8338999981-8936999995188789987328988
Q gi|254780945|r 49 PSSFIDRHYRPKISEISEE-RIVTITGYISQHSSFQLQ---K--RRPYKILLND-GTGEITLLFFYRKTEMLKNVFFEGR 121 (700)
Q Consensus 49 PrrYeDr~~~~~I~~l~~g-~~vti~g~V~~~~~~~~~---~--r~~~~v~v~D-~tg~i~lvfFn~~~~yl~k~lk~G~ 121 (700)
T Consensus 205 ~~~~~t~~~v~Pi~~LsPYq~~W~IkARVT~K~~irtw~N~RGEGKlFn~~L~D~~sgeIRaTaFNe~ad~FY~~i~~g~ 284 (671)
T TIGR00617 205 PNSGSTRERVVPIESLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDSESGEIRATAFNEQADKFYDLIQVGK 284 (671)
T ss_pred HHHCCCCCCEEEECCCCCCCCCEEEEEEEEEHHCCCCCCCCCCCCEEEEEEEECCCCCEEEEECHHHHHHHHCCEEEECC
T ss_conf 12168977547712258877732898987200013302378888106555747179784677424788753213243367
Q ss_pred EEEEE-EEEEECCCEEEEECCEEEECCCCCCCCCCCCCCCCCCH-HHHHHHH
Q ss_conf 89999-89973187799977868962643344444110000000-0004543
Q gi|254780945|r 122 KITVT-GKIKKLKNRIIMVHPHYIFHNSQDVNFPLIEAVYSLPT-GLSVDLF 171 (700)
Q Consensus 122 ~v~vs-GKv~~~~~~~qi~hPe~~~~~~~~~~~~~I~PIYplt~-GLsqk~i 171 (700)
T Consensus 285 vYYiSkg~L~~AnKqF~~~~NdYE~tl~~~---t~i~~ced~~~d~~P~~~f 333 (671)
T TIGR00617 285 VYYISKGSLKPANKQFTNVKNDYEMTLDRD---TVIEECEDETADAIPKIQF 333 (671)
T ss_pred EEEEECCEECCCCCCCCCCCCCEEEECCCC---CEEEECCCCCCCCCCCEEE
T ss_conf 879973784347766677887102505867---4576146888776781464