HHsearch alignment for GI: 254780766 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=98.31 E-value=3.8e-06 Score=59.34 Aligned_cols=81 Identities=15% Similarity=0.242 Sum_probs=61.4
Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHCCCHHHHHHHHHHHHHC---CCCEEEEECCHHHHHHHHCC
Q ss_conf 312205899999999999999999870899789980122015989999999997417---98099980696785432126
Q gi|254780766|r 285 AHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI---GSQIFMTGTDKSVFDSLNET 361 (375)
Q Consensus 285 ~~~S~Gqqk~~~l~l~La~~~~~~~~~~~~pilLiDdi~s~LD~~~~~~ll~~l~~~---~~Qv~iTt~~~~~~~~~~~~ 361 (375)
T Consensus 168 ~~LSGGqkQRvaiAraL~~-----~~-~~P~lllLDEPTs~LD~~~~~~l~~~l~~l~~~G~Tvi~itH~l~~~~-~aD~ 240 (261)
T cd03271 168 TTLSGGEAQRIKLAKELSK-----RS-TGKTLYILDEPTTGLHFHDVKKLLEVLQRLVDKGNTVVVIEHNLDVIK-CADW 240 (261)
T ss_pred CCCCHHHHHHHHHHHHHHH-----CC-CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEECHHHHH-HCCE
T ss_conf 5668899999999999972-----58-889679954863459989999999999999978999999847788997-3899
Q ss_pred EEEEEE------CCCEEEE
Q ss_conf 007997------2896895
Q gi|254780766|r 362 AKFMRI------SNHQALC 374 (375)
Q Consensus 362 ~~~~~i------~~g~~~~ 374 (375)
T Consensus 241 --IivLg~~~g~~~G~iv~ 257 (261)
T cd03271 241 --IIDLGPEGGDGGGQVVA 257 (261)
T ss_pred --EEECCCCCCCCCCEEEE
T ss_conf --99934877789958998