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