HHsearch alignment for GI: 254780882 and conserved domain: TIGR02249

>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946 Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration.
Probab=100.00  E-value=0  Score=379.55  Aligned_cols=253  Identities=32%  Similarity=0.448  Sum_probs=212.1

Q ss_pred             HCCCHHHHHHHHHHHHHHHHH--HHHCCCCCCCCCCHHHCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             254889999999999999999--985121478878968989999999999998-61210133211234442222333210
Q gi|254780882|r   29 RGLSKLTLQSYECDTRQFLIF--LAFYTEEKITIQTIRQLSYTEIRAFISKRR-TQKIGDRSLKRSLSGIKSFLKYLKKR  105 (328)
Q Consensus        29 r~~s~~T~~~Y~~~l~~f~~~--~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~-~~~~s~~T~~~~ls~lr~f~~~~~~~  105 (328)
T Consensus        12 ~hYs~~T~~aY~~Wi~rfI~frG~~C-------~~hp~~~g~~eVeaFLs~LAv~~~Vs~sTQ~QAL~ALlFLY~~iL~~   84 (320)
T TIGR02249        12 RHYSKRTEEAYLHWIKRFIRFRGHNC-------LRHPSTLGDTEVEAFLSDLAVDGKVSASTQNQALAALLFLYKEILKL   84 (320)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCC-------CCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             88789999999999999998850510-------13853307567888856776425747657999999999999998468


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-HCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1232222222222222212111111101567877653-101356775775320122210011233222221122222332
Q gi|254780882|r  106 KITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVL-LHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDD  184 (328)
Q Consensus       106 ~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~-~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~  184 (328)
T Consensus        85 ~L~~---~~~~~Ra~~~~kLPvVLT~eEV~~~l~~l~eg~y-----------~L~a~LLYGsGMRlmE~LRLRikDiDF~  150 (320)
T TIGR02249        85 ELSL---MENFVRAKRPRKLPVVLTREEVARLLEHLEEGKY-----------RLIAKLLYGSGMRLMECLRLRIKDIDFD  150 (320)
T ss_pred             CCCC---HHHCCCCCCCCCCCEECCHHHHHHHHHHCCCCCH-----------HHHHHHHCCCHHHHHHHHHCCCCEEEEC
T ss_conf             8874---2222067888737733598899999842578613-----------1122231255158988875101103433


Q ss_pred             CCCEEEC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC--------------------------CCCCCCCCCC---
Q ss_conf             3220332-378531000112210023432211100123446--------------------------6554321111---
Q gi|254780882|r  185 QSTLRIQ-GKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLN--------------------------IQLPLFRGIR---  234 (328)
Q Consensus       185 ~~~i~v~-gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~--------------------------~~~~lF~~~~---  234 (328)
T Consensus       151 ~~~I~vr~GKG~KdR~v~Lp~~L~~~L~~q~~~~~~~h~~Dl~~~G~g~V~LP~AL~rKYPnA~~~~~WqylFPs~~~S~  230 (320)
T TIGR02249       151 YGEIRVRDGKGGKDRVVTLPKSLAPPLREQLERARALHEKDLLAEGYGGVYLPHALARKYPNASKEWGWQYLFPSARLSR  230 (320)
T ss_pred             CCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHCCCCCCCCCCCCEEECCCCCCCC
T ss_conf             76689973668988612681755799999999999999986405885301004554215787356678766537750155


Q ss_pred             ----CC----CCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf             ----22----111000123567899976869998805417999999998489988999983788878979999619
Q gi|254780882|r  235 ----GK----PLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVN  302 (328)
Q Consensus       235 ----g~----~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~  302 (328)
T Consensus       231 DPrsG~~~RHH~~e~~~QRav~~Av~~AGI~KpvTcHTLRHSFATHLLe~G~DIRTVQelLGHsDVkTTqIYTHVL  306 (320)
T TIGR02249       231 DPRSGRIRRHHIDEKTIQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVL  306 (320)
T ss_pred             CCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCEEEEEE
T ss_conf             7777852001067004328999999957898867887421224430565177367898861788422463453051