HHsearch alignment for GI: 254780332 and conserved domain: cd03271
>cd03271 ABC_UvrA_II The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins and UvrB having one ATP binding site that is structurally related to that of helicases.
Probab=97.00 E-value=0.021 Score=37.78 Aligned_cols=73 Identities=18% Similarity=0.313 Sum_probs=43.6
Q ss_pred CCCHHHH--HHHHHHHCCC-CCCCEEEECCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCC
Q ss_conf 9889999--9988640224-447467767135325664432113788999999999999882791999771382201689
Q gi|254780332|r 325 GISMSQL--ATRARRLKRQ-RGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKELNIPIIALSQLSRQVENRD 401 (504)
Q Consensus 325 ~~ti~~I--~~~~r~~~~~-~gi~~vvIDYLqli~~~~~~~~~r~~~i~~is~~lK~lA~e~~ipvi~lsQLnR~~e~r~ 401 (504)
T Consensus 169 ~LSGGqkQRvaiAraL~~~~~~P~lllLD-----EPTs~L-D--~~~~~~l~~~l~~l~~-~G~Tvi~itH--------- 230 (261)
T cd03271 169 TLSGGEAQRIKLAKELSKRSTGKTLYILD-----EPTTGL-H--FHDVKKLLEVLQRLVD-KGNTVVVIEH--------- 230 (261)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCCCEEEEC-----CCCCCC-C--HHHHHHHHHHHHHHHH-CCCEEEEEEE---------
T ss_conf 66889999999999997258889679954-----863459-9--8999999999999997-8999999847---------
Q ss_pred CCCCCCCCCCCCCHHHHHCCEEEEE
Q ss_conf 9998401014324223313878897
Q gi|254780332|r 402 NKRPQLSDLRESGSIEQDADVVLFV 426 (504)
Q Consensus 402 ~krP~lsDLr~Sg~IEqdAD~v~~l 426 (504)
T Consensus 231 -------~l--~-~~~-~aD~IivL 244 (261)
T cd03271 231 -------NL--D-VIK-CADWIIDL 244 (261)
T ss_pred -------CH--H-HHH-HCCEEEEC
T ss_conf -------78--8-997-38999993