HHsearch alignment for GI: 254780882 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=100.00  E-value=8.5e-44  Score=292.87  Aligned_cols=177  Identities=30%  Similarity=0.382  Sum_probs=155.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCC
Q ss_conf             1111111015678776531013567757753201222100112332222211222223323220332-378531000112
Q gi|254780882|r  125 LPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLL  203 (328)
Q Consensus       125 ~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~  203 (328)
T Consensus         1 lpr~Ls~eEi~~Ll~a~~~-----~~~~~~Rd~ali~ll~~tGlR~~El~~L~~~Did~~~~~i~i~~~K~~k~r~vpl~   75 (188)
T cd01188           1 LPRALPWEDVERLLASCDR-----STPVGRRDYAILLLLARLGLRAGEVAALRLDDIDWRTGTIRVRQGKGGRVTRLPLP   75 (188)
T ss_pred             CCCCCCHHHHHHHHHCCCC-----CCCHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCH
T ss_conf             9699999999999957576-----88451799999999999881599998569835565689778863899853344684


Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCCCCCCCCC---CCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHHCCCC
Q ss_conf             2100234322111001234466554321111---22111000123567899976869-9988054179999999984899
Q gi|254780882|r  204 PSVRKAILEYYDLCPFDLNLNIQLPLFRGIR---GKPLNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFATHLLSNGGD  279 (328)
Q Consensus       204 ~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~---g~~ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt~ll~~G~~  279 (328)
T Consensus        76 ~~~~~~l~~~l~~~~~~---~~~~~lf~~~~~~~~~~~~~~~i~~~~~~~~~~ag~~~~~~~~H~lRHt~at~l~~~G~~  152 (188)
T cd01188          76 AEVGAALADYLRDGRPA---TDSRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLATRLLRAGAP  152 (188)
T ss_pred             HHHHHHHHHHHHHHCCC---CCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCC
T ss_conf             99999999999980767---887644350588888876699999999999998499889878761489999999996999


Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHCHHHHHHH
Q ss_conf             889999837888789799996198999999
Q gi|254780882|r  280 LRSIQSILGHFRLSTTQIYTNVNSKNGGDW  309 (328)
Q Consensus       280 ~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~  309 (328)
T Consensus       153 l~~vq~~lGH~si~tT~~Y~h~~~e~lr~~  182 (188)
T cd01188         153 LKEIGDVLGHRSPDSTAIYAKVDVDALRAI  182 (188)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999999838998899999885699999866