HHsearch alignment for GI: 254781149 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=94.48 E-value=0.4 Score=28.03 Aligned_cols=45 Identities=18% Similarity=0.194 Sum_probs=31.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHCC---CEEECCCCCCH-----HHHHHHHHHHHH
Q ss_conf 8899899999999999997299---54747998898-----999999999999
Q gi|254781149|r 209 GEINQEQYRISQGICEKLQDFP---LIIDDRPSPGI-----MEFVHVANGLRN 253 (266)
Q Consensus 209 g~l~~~e~~~i~~a~~~l~~~p---l~IdD~~~~ti-----~~ira~aR~~k~ 253 (266)
T Consensus 168 ~~LSGGqkQRvaiAraL~~~~~~P~lllLDEPTs~LD~~~~~~l~~~l~~l~~ 220 (261)
T cd03271 168 TTLSGGEAQRIKLAKELSKRSTGKTLYILDEPTTGLHFHDVKKLLEVLQRLVD 220 (261)
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 56688999999999999725888967995486345998999999999999997