HHsearch alignment for GI: 254780627 and conserved domain: cd03238

>cd03238 ABC_UvrA The excision repair protein UvrA; 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=96.51  E-value=0.012  Score=38.73  Aligned_cols=110  Identities=15%  Similarity=0.199  Sum_probs=58.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHH--------HCCCCCEEEEEHHHHHHHH-HHHHH-CCCH-----------HHHHHHH
Q ss_conf             898627888857999999999986--------3068816864698889999-99986-1988-----------9999997
Q gi|254780627|r  199 LFIHASVGLGKTHLLQAIANASIK--------RQPNLRVVYLTAEYFMWRF-ASAIR-DNCA-----------LNLKDSL  257 (502)
Q Consensus       199 Lfi~G~~GlGKTHLl~ai~~~~~~--------~~~~~~v~y~~~e~F~~~~-~~a~~-~~~~-----------~~fr~~~  257 (502)
T Consensus        24 ~~iiG~nGsGKSTLl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~l~~~~~~LSGGqkQRvaiAraL~  103 (176)
T cd03238          24 VVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFIDQLQFLIDVGLGYLTLGQKLSTLSGGELQRVKLASELF  103 (176)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHCCHHHCCHHHCCCCCEEEHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99999999989999998887610311203210137553688577999997488667789916868999999999999998


Q ss_pred             HHCC--HHHHHHHHHHCCC--CHHHHHHHHHHHHHHCCCEEEEECCCCHHHHCCCCHHH
Q ss_conf             4031--0205444453175--06999999999988569879996487567613630345
Q gi|254780627|r  258 RNID--LLLIDDMQFLQGK--LIQHEFCHLLNSLLDSAKQVVAAADRPPSELESLDPRI  312 (502)
Q Consensus       258 r~~D--vLliDDiqfl~gk--~tqee~f~~~n~l~~~gkqiv~tsd~~P~~l~~l~~rL  312 (502)
T Consensus       104 ~~p~~~ililDEP--tsgLD~~~~~~l~~~l~~l~~~g~TvI~vtHd-~~~~~-~aDri  158 (176)
T cd03238         104 SEPPGTLFILDEP--STGLHQQDINQLLEVIKGLIDLGNTVILIEHN-LDVLS-SADWI  158 (176)
T ss_pred             HCCCCCEEEECCC--CCCCCHHHHHHHHHHHHHHHHCCCEEEEEECC-HHHHH-HCCEE
T ss_conf             6899868997177--44589879999999999999879989999478-79998-39999