HHsearch alignment for GI: 254780945 and conserved domain: cd03769

>cd03769 SR_IS607_transposase_like Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.
Probab=90.16  E-value=1.6  Score=23.68  Aligned_cols=93  Identities=16%  Similarity=0.224  Sum_probs=66.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHH--HHHHHHHHHHHHC-CEEEEEHHHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             88999999999841001343078862144223699--9999733444305-45886127999999998621101457865
Q gi|254780945|r  275 KSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLV--ALIAMAAAVEAGG-QAVIMAPIGILAQQHYEFIKKYTQNTQII  351 (700)
Q Consensus       275 ~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiV--A~~A~l~~~~~G~-Q~alMaPTEILA~QH~~~~~~~~~~~~i~  351 (700)
T Consensus        17 ~~Q~~~l~~~~~~~--g~--~~~i~~D~gSG~~~~Rp~l~~Ll~~~~~g~v~~vvV~~~DRL~Rfg~elle~~~~~~gv~   92 (134)
T cd03769          17 ERQIERLEAYATAQ--GW--IVEVIKDIGSGLNEKRKGLLKLLEDVLAGKVERVVITYKDRLARFGFELLEELFKAYGVE   92 (134)
T ss_pred             HHHHHHHHHHHHHC--CC--EEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCE
T ss_conf             99999999999955--98--259998567776603589999999997389878999855577876899999999986988


Q ss_pred             EEEEECCCCHHHHHHHHHHH
Q ss_conf             89962464225667687762
Q gi|254780945|r  352 VEIITGNMPQAHRRKALERI  371 (700)
Q Consensus       352 v~lLtg~~~~~er~~i~~~i  371 (700)
T Consensus        93 iivin~~~~~~~~~EL~eDl  112 (134)
T cd03769          93 IVVINQEENEELEQELVEDL  112 (134)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             99997998998689999999