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