HHsearch alignment for GI: 254780134 and conserved domain: pfam00589

>pfam00589 Phage_integrase Phage integrase family. Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.
Probab=99.95  E-value=3.7e-27  Score=195.10  Aligned_cols=154  Identities=22%  Similarity=0.304  Sum_probs=135.0

Q ss_pred             CCCHHHHHHHHHHHCC--CCHHHHHHHHHHHCCCCCCCCCCCCCCEEE--EECCCCCCCCCHHHHHHCCHHHHHHHHHHH
Q ss_conf             1652344566664037--808999989898618873100256640144--302332113310243311216899999642
Q gi|254780134|r  173 PWTKEDMQQFKSFWSE--GSQPRLAFEFLLYSGLRCSDSCRAGVQHLQ--NNIFSIKTQKTGTIITVELPDGFMKLLAMT  248 (348)
Q Consensus       173 ~~t~~ei~~~~~~~~~--~~~~~~~~~l~~~TG~R~~Ei~~L~~~did--~~~i~~~~~Kt~~~~~vpl~~~l~~~l~~~  248 (348)
T Consensus         2 ~lt~~e~~~ll~~~~~~~~lR~~~l~~l~~~tG~R~~El~~L~~~di~~~~~~i~i~~~K~~~~r~i~i~~~~~~~l~~~   81 (170)
T pfam00589         2 RLTEDEVERLLAALEEPLNIRDRALVELLLLTGLRISELLSLRWSDIDLDNGTIRIPQTKTRKSRTVPLSDAALEALKEW   81 (170)
T ss_pred             CCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCEEEEECCCCCCCCEECCCCHHHHHHHHHH
T ss_conf             89999999999864634597799999999996869888974213004676517873044113310014677799999999


Q ss_pred             ------CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC--CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf             ------01332211222457758778999999999983889--9814026999999998489988999996499989999
Q gi|254780134|r  249 ------PIGKETFFINNDKQKMNATQFSIWFKAKATKAGVN--KSAHGVRKFSATISADAGATAHELMATYGWKTVDQAE  320 (348)
Q Consensus       249 ------~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~agi~--~~~H~lRht~at~l~~~G~~~~~i~~~lGHss~~~t~  320 (348)
T Consensus        82 ~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~s~Hs~Rht~at~l~~~g~~~~~v~~~lGH~~~~tT~  161 (170)
T pfam00589        82 LGDRKEAEESEFLFVSRRGKPLSRSTVNRAFRRAGKRAGIEKDLTPHDLRHTFATHLAENGVPLRVIQKLLGHSSISMTM  161 (170)
T ss_pred             HHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
T ss_conf             99731467776143201688553134678888888860778767878884899999999699999999996899989999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780134|r  321 TYTKGA  326 (348)
Q Consensus       321 ~Y~~~~  326 (348)
T Consensus       162 ~Y~~~~  167 (170)
T pfam00589       162 RYTHVA  167 (170)
T ss_pred             HHCCCC
T ss_conf             820838