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