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