HHsearch alignment for GI: 255764498 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=1.5e-44  Score=278.41  Aligned_cols=181  Identities=24%  Similarity=0.362  Sum_probs=156.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCCCCCCCCCH
Q ss_conf             12233202469999864320012561027765431100012210013433343200000111100011-12221111100
Q gi|255764498|r   96 LPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVI  174 (300)
Q Consensus        96 ~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v-~~K~~k~R~ip  174 (300)
T Consensus         1 lpr~Ls~eEi~~Ll~a~~~-------~~~~~~Rd~ali~ll~~tGlR~~El~~L~~~Did~~~~~i~i~~~K~~k~r~vp   73 (188)
T cd01188           1 LPRALPWEDVERLLASCDR-------STPVGRRDYAILLLLARLGLRAGEVAALRLDDIDWRTGTIRVRQGKGGRVTRLP   73 (188)
T ss_pred             CCCCCCHHHHHHHHHCCCC-------CCCHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCC
T ss_conf             9699999999999957576-------884517999999999998815999985698355656897788638998533446


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             0012478875323210012467775200123--33222221111111012344201466764259885889999999858
Q gi|255764498|r  175 LSPSALHALQMYKKTCSSMKMTGNDLWLFPS--STKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGG  252 (300)
Q Consensus       175 i~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~--~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G  252 (300)
T Consensus        74 l~~~~~~~l~~~l~~~~~~---~~~~~lf~~~~~~~~~~~~~~~i~~~~~~~~~~ag~~~~~~~~H~lRHt~at~l~~~G  150 (188)
T cd01188          74 LPAEVGAALADYLRDGRPA---TDSRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLATRLLRAG  150 (188)
T ss_pred             CHHHHHHHHHHHHHHHCCC---CCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             8499999999999980767---8876443505888888766999999999999984998898787614899999999969


Q ss_pred             CCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH
Q ss_conf             8888999985589989989996459999999999
Q gi|255764498|r  253 ADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQ  286 (300)
Q Consensus       253 ~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~  286 (300)
T Consensus       151 ~~l~~vq~~lGH~si~tT~~Y~h~~~e~lr~~~~  184 (188)
T cd01188         151 APLKEIGDVLGHRSPDSTAIYAKVDVDALRAIAL  184 (188)
T ss_pred             CCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf             9999999983899889999988569999986647