HHsearch alignment for GI: 254780134 and conserved domain: cd01188
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain. This CD includes various bacterial integrases, including the predicted integrase of the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1.
Probab=99.96 E-value=6.5e-29 Score=206.50 Aligned_cols=155 Identities=20% Similarity=0.259 Sum_probs=127.7
Q ss_pred CCCCHHHHHHHHHHHCCC----CHHHHHHHHHHHCCCCCCCCCCCCCCEEE--EECCCCCCCCCHHHHHHCCHHHHHHHH
Q ss_conf 116523445666640378----08999989898618873100256640144--302332113310243311216899999
Q gi|254780134|r 172 RPWTKEDMQQFKSFWSEG----SQPRLAFEFLLYSGLRCSDSCRAGVQHLQ--NNIFSIKTQKTGTIITVELPDGFMKLL 245 (348)
Q Consensus 172 ~~~t~~ei~~~~~~~~~~----~~~~~~~~l~~~TG~R~~Ei~~L~~~did--~~~i~~~~~Kt~~~~~vpl~~~l~~~l 245 (348)
T Consensus 3 r~Ls~eEi~~Ll~a~~~~~~~~~Rd~ali~ll~~tGlR~~El~~L~~~Did~~~~~i~i~~~K~~k~r~vpl~~~~~~~l 82 (188)
T cd01188 3 RALPWEDVERLLASCDRSTPVGRRDYAILLLLARLGLRAGEVAALRLDDIDWRTGTIRVRQGKGGRVTRLPLPAEVGAAL 82 (188)
T ss_pred CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHH
T ss_conf 99999999999957576884517999999999998815999985698355656897788638998533446849999999
Q ss_pred HHH-----CC-CCCCCCCCC---CCCCCCHHHHHHHHHHHHHHCCCC---CCCCHHHHHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf 642-----01-332211222---457758778999999999983889---981402699999999848998899999649
Q gi|254780134|r 246 AMT-----PI-GKETFFINN---DKQKMNATQFSIWFKAKATKAGVN---KSAHGVRKFSATISADAGATAHELMATYGW 313 (348)
Q Consensus 246 ~~~-----~~-~~~~~~~~~---~g~~~~~~~~~~~~~~~~~~agi~---~~~H~lRht~at~l~~~G~~~~~i~~~lGH 313 (348)
T Consensus 83 ~~~l~~~~~~~~~~~lf~~~~~~~~~~~~~~~i~~~~~~~~~~ag~~~~~~~~H~lRHt~at~l~~~G~~l~~vq~~lGH 162 (188)
T cd01188 83 ADYLRDGRPATDSRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLATRLLRAGAPLKEIGDVLGH 162 (188)
T ss_pred HHHHHHHCCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 99999807678876443505888888766999999999999984998898787614899999999969999999998389
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 9989999999999
Q gi|254780134|r 314 KTVDQAETYTKGA 326 (348)
Q Consensus 314 ss~~~t~~Y~~~~ 326 (348)
T Consensus 163 ~si~tT~~Y~h~~ 175 (188)
T cd01188 163 RSPDSTAIYAKVD 175 (188)
T ss_pred CCHHHHHHHHCCC
T ss_conf 9889999988569