HHsearch alignment for GI: 254780134 and conserved domain: cd01182

>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=99.85  E-value=3.5e-21  Score=156.19  Aligned_cols=145  Identities=20%  Similarity=0.298  Sum_probs=113.2

Q ss_pred             HHHHHHHCC--CCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEE--CCCCCCCCCHHHHHHCCHHHHHHHHHHHC------
Q ss_conf             566664037--80899998989861887310025664014430--23321133102433112168999996420------
Q gi|254780134|r  180 QQFKSFWSE--GSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNN--IFSIKTQKTGTIITVELPDGFMKLLAMTP------  249 (348)
Q Consensus       180 ~~~~~~~~~--~~~~~~~~~l~~~TG~R~~Ei~~L~~~did~~--~i~~~~~Kt~~~~~vpl~~~l~~~l~~~~------  249 (348)
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~l~~~tG~R~~El~~l~~~di~~~~~~i~i~~~K~~~~~~i~i~~~~~~~l~~~~~~~~~~   82 (162)
T cd01182           3 KKLLAALKKDTAPRDRALILLLLYTGLRVSELLALRWSDIDLDKGTITVRRTKTGKERTVPLSPELAELLREYLELRRPA   82 (162)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHCCHHEEECCCCEEEECCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
T ss_conf             99999975578999999999999978498889844311080679868733787762037625637767999999984223


Q ss_pred             -CCCCCCCCCCCCC--CCCHHHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             -1332211222457--75877899999999998388--998140269999999984899889999964999899999999
Q gi|254780134|r  250 -IGKETFFINNDKQ--KMNATQFSIWFKAKATKAGV--NKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTK  324 (348)
Q Consensus       250 -~~~~~~~~~~~g~--~~~~~~~~~~~~~~~~~agi--~~~~H~lRht~at~l~~~G~~~~~i~~~lGHss~~~t~~Y~~  324 (348)
T Consensus        83 ~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRh~~~t~~~~~g~~~~~i~~~~GH~~~~~t~~Y~~  162 (162)
T cd01182          83 PKPDDYLFPSRRGGPKRLTRRAVRRLLKKAGKRAGIPERLTPHDLRHTFATRLLEAGVPLEVIQELLGHSSISTTERYLH  162 (162)
T ss_pred             CCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHCCCCCC
T ss_conf             68877155426899765103567776665554137878997016199999999996999999999928999898152819