HHsearch alignment for GI: 254780882 and conserved domain: cd00801

>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=100.00  E-value=2.8e-45  Score=302.48  Aligned_cols=275  Identities=17%  Similarity=0.188  Sum_probs=214.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-HHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4989999999999999986254889999999999999-999985121478878968989999999999998612101332
Q gi|254780882|r   10 VSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQF-LIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSL   88 (328)
Q Consensus        10 ~~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f-~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~   88 (328)
T Consensus        69 ~~~T~~~~~e~~~~~~~--~~~~~~t~~~~~~~l~~~i~p~~--------g~~~l~~It~~~i~~~~~~l~~~-~~~~ta  137 (357)
T cd00801          69 AANTFAEVAEEWLAAKK--PRWSEKHARQWRRTLEKHVLPVL--------GKKPITEITARDLLDVLRRIEAR-GALETA  137 (357)
T ss_pred             HHCHHHHHHHHHHHHHC--CCCCHHHHHHHHHHHHHHHHHHH--------CCCCHHHCCHHHHHHHHHHHHHC-CCHHHH
T ss_conf             45549999999999731--02476899999999997758987--------78748991889999999999856-989999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC--CCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCC
Q ss_conf             112344422223332101232222222222222212--111111101567877653101356775775320122210011
Q gi|254780882|r   89 KRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNS--LPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGC  166 (328)
Q Consensus        89 ~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~--~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~T  166 (328)
T Consensus       138 ~~~~~~l~~~~~~A~~~~~i~~NP~~~i~~~~~~~~~~r~r~lt~ee~~~l~~~l~~~~~~-~-----~~~~~~~l~l~T  211 (357)
T cd00801         138 RRVRQRLKQVFRYAIARGLIEANPAADLRGADGAPKKQHDRALSPDELPEFLQALDAASGS-P-----VTRLALKLLLLT  211 (357)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC-H-----HHHHHHHHHHHH
T ss_conf             9999999999999998277443657654441067887766678999999999999857788-3-----799999999997


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEE---CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CCCCCC
Q ss_conf             233222221122222332322033---237853100011221002343221110012344665543211112--211100
Q gi|254780882|r  167 GLRISEALSLTPQNIMDDQSTLRI---QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRG--KPLNPG  241 (328)
Q Consensus       167 GlR~~El~~L~~~did~~~~~i~v---~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g--~~ls~~  241 (328)
T Consensus       212 G~R~gE~~~L~w~diD~~~~~~~Ip~~~tK~~~~~~vPL~~~~~~~L~~~~~~------~~~~~~vF~~~~~~~~~~~~~  285 (357)
T cd00801         212 GVRPGELRGARWSEIDLENALWTIPAERMKTRRPHRVPLSDQALALLEELREL------SGHSEYVFPSRRDRGKPLSEN  285 (357)
T ss_pred             CCCHHHHHCCCHHHEECCCCEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHH------CCCCCEEECCCCCCCCCCCHH
T ss_conf             77888886387998777788489620236589936983989999999999886------499945825799999977489


Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHHC-HHHHHHHHH
Q ss_conf             0123567899976869998805417999999998489988999983788878979-999619-899999999
Q gi|254780882|r  242 VFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQ-IYTNVN-SKNGGDWMM  311 (328)
Q Consensus       242 ~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~-~Y~h~~-~~~~~~~l~  311 (328)
T Consensus       286 ~~~~~~~----~~~~~~~~t~HdlRhT~aT~l~~~Gv~~~~i~~~LGH~~~~~t~~~Y~h~~y~~ekr~~l~  353 (357)
T cd00801         286 TLNKALK----RMGYLGEWTPHGLRRTARTWLNELGFPPDVIERQLAHVLGGKVRAAYNRADYLEERREAMQ  353 (357)
T ss_pred             HHHHHHH----HHCCCCCCEEECCHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999----9659999503248899999999859899999998489999818999617448999999999