>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=1.4e-45 Score=285.16 Aligned_cols=202 Identities=26% Similarity=0.393 Sum_probs=172.9 Q ss_pred HHHHHHHHHHHHHHHHCCC-CC-CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCH Q ss_conf 5322101123343210001-22-222212222121222111223320246999986432001256102776543110001 Q gi|255764498|r 58 SQRRKISVIRQFYNFLCYE-GL-RKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIEL 135 (300) Q Consensus 58 T~~~~~~~l~~~~~~~~~~-~~-~~~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~l 135 (300) T Consensus 1 Tinr~l~~L~~~f~~A~~~~~~~~~~NP~~~i~~pk~~~~r~r~lt~eE~~~ll~~~~~~~~--------~~~~~~~~~l 72 (206) T cd00796 1 TVRRELALLSHLFTVARKEWGLDVLTNPVELVRKPPVGKGRDRRLTEEEEERLLRAFGEEEG--------SPRLPVIILL 72 (206) T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC--------CHHHHHHHHH T ss_conf 98899999999999999978887677927748588999999887999999999996764545--------7669999999 Q ss_pred HHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 2210013433343200000111100011-122211111000012478875323210012467775200123332222211 Q gi|255764498|r 136 LYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSR 214 (300) Q Consensus 136 l~~tGlR~~Ei~~L~~~di~~~~~~i~v-~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~ 214 (300) T Consensus 73 ~~~TG~R~~Ei~~L~~~did~~~~~i~i~~~K~~~~r~vpl~~~~~~~l~~~~~~-------~~~~~vf~-------~~~ 138 (206) T cd00796 73 ALETAMRRGEILSLRWEQVDLKKRVAHLPDTKNGTSRDVPLSKRAVALLQMLPKV-------PDDGPVFP-------ITS 138 (206) T ss_pred HHHHCCCHHHHHHCCCCCCCCCCCEEEEEECCCCCEEEEECCHHHHHHHHHHHHC-------CCCCCCCC-------CCH T ss_conf 9990998899942857334533584898636789656852889999999999861-------47776678-------861 Q ss_pred CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHH Q ss_conf 111110123442014667642598858899999998588888999985589989989996459999999 Q gi|255764498|r 215 QVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQK 283 (300) Q Consensus 215 ~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~ 283 (300) T Consensus 139 ~~~~~~~~~~~~~~gi~--~~~~H~lRHt~at~l~~~G~~~~~i~~~lGH~~~~~t~~Y~h~~~e~L~~ 205 (206) T cd00796 139 DSVDAAFRRAKERAGLE--DLHFHDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTHLSAEDLAE 205 (206) T ss_pred HHHHHHHHHHHHHHCCC--CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHC T ss_conf 78999999999982777--87532048999999998698999999985899999998846739988704

HHsearch alignment for GI: 255764498 and conserved domain: cd00796