HHsearch alignment for GI: 254780490 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=99.13 E-value=3e-11 Score=78.76 Aligned_cols=42 Identities=52% Similarity=0.756 Sum_probs=40.2
Q ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 216036389999999980899999999848888899999986
Q gi|254780490|r 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTN 43 (67)
Q Consensus 2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~ 43 (67)
T Consensus 121 ~~~~h~lRh~~~t~~~~~g~~~~~i~~~~GH~~~~~t~~Y~~ 162 (162)
T cd01182 121 RLTPHDLRHTFATRLLEAGVPLEVIQELLGHSSISTTERYLH 162 (162)
T ss_pred CCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHCCCCCC
T ss_conf 997016199999999996999999999928999898152819