HHsearch alignment for GI: 254780134 and conserved domain: cd00796
>cd00796 INT_Rci Rci recombinase, C-terminal catalytic domain. Rci enzymes are found in IncI1 incompatibility group plasmids such as R64. These recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The R64 Rci recombinase mediates site specific recombination at the highly mobile DNA segments called shufflon located in the C-terminal region of the pilV gene, which determines the recipient specificity in liquid mating. This gene encodes a thin pilus component that recognizes recipient's receptors required for liquid mating. The recombination occurs between any of the seven inverted repeats that separate four DNA segments of the shufflon. The segments can be inverted independently or in groups, resulting in a complex DNA rearrangement. The catalytic domain of Rci is linked to a variable N-terminal domain, whose function is unknown.
Probab=100.00 E-value=8.8e-38 Score=264.17 Aligned_cols=190 Identities=18% Similarity=0.236 Sum_probs=164.1
Q ss_pred HHHHHHHHHHHHHHHHHHH-H-HHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCC---CCHHHHHHHHHHHCCCCC
Q ss_conf 9999999999999644552-0-0105665103464324444211652344566664037---808999989898618873
Q gi|254780134|r 132 SAIQFLTSMRVLFKWAVRQ-E-YVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSE---GSQPRLAFEFLLYSGLRC 206 (348)
Q Consensus 132 t~n~~~~~l~~~~~~a~~~-~-~i~~NP~~~v~~~~~~~~~~~~~t~~ei~~~~~~~~~---~~~~~~~~~l~~~TG~R~ 206 (348)
T Consensus 1 Tinr~l~~L~~~f~~A~~~~~~~~~~NP~~~i~~pk~~~~r~r~lt~eE~~~ll~~~~~~~~~~~~~~~~~l~~~TG~R~ 80 (206)
T cd00796 1 TVRRELALLSHLFTVARKEWGLDVLTNPVELVRKPPVGKGRDRRLTEEEEERLLRAFGEEEGSPRLPVIILLALETAMRR 80 (206)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCH
T ss_conf 98899999999999999978887677927748588999999887999999999996764545766999999999909988
Q ss_pred CCCCCCCCCEEE--EECCCCCCCCCHHHHHHCCHHHHHHHHHHHCCC--CCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 100256640144--302332113310243311216899999642013--3221122245775877899999999998388
Q gi|254780134|r 207 SDSCRAGVQHLQ--NNIFSIKTQKTGTIITVELPDGFMKLLAMTPIG--KETFFINNDKQKMNATQFSIWFKAKATKAGV 282 (348)
Q Consensus 207 ~Ei~~L~~~did--~~~i~~~~~Kt~~~~~vpl~~~l~~~l~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~agi 282 (348)
T Consensus 81 ~Ei~~L~~~did~~~~~i~i~~~K~~~~r~vpl~~~~~~~l~~~~~~~~~~~vf------~~~~~~~~~~~~~~~~~~gi 154 (206)
T cd00796 81 GEILSLRWEQVDLKKRVAHLPDTKNGTSRDVPLSKRAVALLQMLPKVPDDGPVF------PITSDSVDAAFRRAKERAGL 154 (206)
T ss_pred HHHHHCCCCCCCCCCCEEEEEECCCCCEEEEECCHHHHHHHHHHHHCCCCCCCC------CCCHHHHHHHHHHHHHHHCC
T ss_conf 999428573345335848986367896568528899999999998614777667------88617899999999998277
Q ss_pred C-CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 9-98140269999999984899889999964999899999999998
Q gi|254780134|r 283 N-KSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGAD 327 (348)
Q Consensus 283 ~-~~~H~lRht~at~l~~~G~~~~~i~~~lGHss~~~t~~Y~~~~~ 327 (348)
T Consensus 155 ~~~~~H~lRHt~at~l~~~G~~~~~i~~~lGH~~~~~t~~Y~h~~~ 200 (206)
T cd00796 155 EDLHFHDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTHLSA 200 (206)
T ss_pred CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCH
T ss_conf 7875320489999999986989999999858999999988467399