HHsearch alignment for GI: 254780134 and conserved domain: cd00799

>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.
Probab=100.00  E-value=4.7e-32  Score=226.93  Aligned_cols=242  Identities=19%  Similarity=0.180  Sum_probs=181.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCC--CCHHHCCHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---
Q ss_conf             78899999999999999569--995896999999988751--59978999999999999964455200105665103---
Q gi|254780134|r   89 VNSRISFESYFDQIIRKSGD--FDYRKITTKHIRSGVESR--KHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSV---  161 (348)
Q Consensus        89 ~~T~~~~~~~~~~~~~~~g~--~~l~~it~~~i~~~~~~~--~~~~~t~n~~~~~l~~~~~~a~~~~~i~~NP~~~v---  161 (348)
T Consensus         1 enT~~aY~~~l~~f~~wc~~~~~~~~~~t~~~v~~yl~~L~~~~~~~Ti~~~lsalr~~~~~~~~~~~~~~~~~~~~~~~   80 (287)
T cd00799           1 DNTRKAYLSDWRRFAAWCQAHGRTPLPASPETVTLYLTDLADSLAPSTISRRLSALSQLHRRSGLPSPADSPLVRLVLRG   80 (287)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH
T ss_conf             90599999999999999997499978899999999999998477876999999999999999705886547148887532


Q ss_pred             -CCCC-CCCCCCCCCCHHHHHHHHHHHCC-----CCHHHHHHHHHHHCCCCCCCCCCCCCCEEEE---E--CCCCCCCCC
Q ss_conf             -4643-24444211652344566664037-----8089999898986188731002566401443---0--233211331
Q gi|254780134|r  162 -ERPK-RKTEGIRPWTKEDMQQFKSFWSE-----GSQPRLAFEFLLYSGLRCSDSCRAGVQHLQN---N--IFSIKTQKT  229 (348)
Q Consensus       162 -~~~~-~~~~~~~~~t~~ei~~~~~~~~~-----~~~~~~~~~l~~~TG~R~~Ei~~L~~~did~---~--~i~~~~~Kt  229 (348)
T Consensus        81 ~~r~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~Rd~ail~ll~~tGlR~~El~~L~~~di~~~~~~~~~i~~~~~K~  160 (287)
T cd00799          81 IRREEARPKRQALAILPEDLDKLRSLLDESDTLRDLRDLALLLLGFAGLLRRSELVRLRWEDLTFTDGGGLLVTLRRSKT  160 (287)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCEEEEEECCCCE
T ss_conf             11236887657898999999999862555787587999999999998623899997183987185789717999558740


Q ss_pred             HHHH------HHCCHHHHHHH----HHHHCCCCCCCCCC------CCCCCCCHHHHHHHHHHHHHHCCCC---CCCCHHH
Q ss_conf             0243------31121689999----96420133221122------2457758778999999999983889---9814026
Q gi|254780134|r  230 GTII------TVELPDGFMKL----LAMTPIGKETFFIN------NDKQKMNATQFSIWFKAKATKAGVN---KSAHGVR  290 (348)
Q Consensus       230 ~~~~------~vpl~~~l~~~----l~~~~~~~~~~~~~------~~g~~~~~~~~~~~~~~~~~~agi~---~~~H~lR  290 (348)
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lF~~~~~~~~~~~~~ls~~~v~~~~~~~~~~ag~~~~~~s~H~lR  240 (287)
T cd00799         161 DQSGLGVLKLIPPLTTCPVRALERWLEAARIPKGPLFRRIDRWGVLGPGALSDNSLNRILKRLAEAAGLRSGSWSGHSLR  240 (287)
T ss_pred             EECCCCCEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCH
T ss_conf             35487836750621589999999999872567664302444467757887878999999999999859999998975138


Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf             9999999984899889999964999899999999998999
Q gi|254780134|r  291 KFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIR  330 (348)
Q Consensus       291 ht~at~l~~~G~~~~~i~~~lGHss~~~t~~Y~~~~~~~r  330 (348)
T Consensus       241 Ht~At~ll~~G~~l~~Iq~~lGH~s~~tt~~Y~~~~d~~~  280 (287)
T cd00799         241 RGFATEAARAGYSLLEIMRQGRWRSPKMVSRYIRDADRFQ  280 (287)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHC
T ss_conf             9999999987999999999858999889999853713101