HHsearch alignment for GI: 254780882 and conserved domain: cd01193

>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element) present on various mobile gene cassettes. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.
Probab=100.00  E-value=0  Score=358.12  Aligned_cols=229  Identities=33%  Similarity=0.478  Sum_probs=203.8

Q ss_pred             CCCHHHCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             78968989999999999998612-10133211234442222333210123222222222222221211111110156787
Q gi|254780882|r   60 IQTIRQLSYTEIRAFISKRRTQK-IGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLV  138 (328)
Q Consensus        60 ~~~~~~i~~~~i~~~l~~l~~~~-~s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll  138 (328)
T Consensus         4 ~k~~~~it~~dI~~y~~~L~~~~~~s~~Tin~~l~~l~~~~~~~~~~~~---~~~~~~~~~k~~~~~~~~lt~eEi~~ll   80 (242)
T cd01193           4 GRSPDELGEEDVRAFLTLLAVEGNVSASTQNQALSALLFFYRHTLKRDL---PWLQRIRRPRKPRKLPVVLSPEEVRRLL   80 (242)
T ss_pred             CCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCC---CHHHHCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             9895889999999999999984898999999999999999999987689---6566565578999899889999999999


Q ss_pred             HHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             7653101356775775320122210011233222221122222332322033-237853100011221002343221110
Q gi|254780882|r  139 DNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLC  217 (328)
Q Consensus       139 ~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~  217 (328)
T Consensus        81 ~~~~----------~~r~~~~~~ll~~tGlR~~El~~L~~~did~~~~~i~i~~~K~~k~R~vpl~~~~~~~l~~~l~~~  150 (242)
T cd01193          81 GALT----------GLKHRLILSLLYGCGLRLSECLRLRVKDIDFDRGQIRVRQGKGGKDRYVMLPEALLELLRAYWKRA  150 (242)
T ss_pred             HCCC----------CCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEECCHHHHHHHHHHHHHH
T ss_conf             7387----------767999999999828988889878663167675179986188996058875999999999999984


Q ss_pred             CCCCCCCCCCCCCCCCCC--------CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf             012344665543211112--------211100012356789997686999880541799999999848998899998378
Q gi|254780882|r  218 PFDLNLNIQLPLFRGIRG--------KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGH  289 (328)
Q Consensus       218 ~~~~~~~~~~~lF~~~~g--------~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH  289 (328)
T Consensus       151 ~~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~H~lRHT~at~ll~~G~~l~~v~~~lGH  230 (242)
T cd01193         151 RALGRERPWQWLFPSTRRSRDPVERRHHLSERTLQRALKKAVEQAGIDKRVTPHTLRHSFATHLLEAGYDIRTIQELLGH  230 (242)
T ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHCCC
T ss_conf             65300365210135667775755367767599999999999998499999886748999999999879999999988399


Q ss_pred             CCHHHHHHHHHH
Q ss_conf             887897999961
Q gi|254780882|r  290 FRLSTTQIYTNV  301 (328)
Q Consensus       290 ~s~~tT~~Y~h~  301 (328)
T Consensus       231 ~si~tT~~Y~Hv  242 (242)
T cd01193         231 SDLKTTMIYTHV  242 (242)
T ss_pred             CCHHHHHHHHCC
T ss_conf             888899870583