>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=305.49 Aligned_cols=202 Identities=19% Similarity=0.255 Sum_probs=175.0 Q ss_pred HHHHHHHHHHHHHHHHHHH--CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCC Q ss_conf 3211234442222333210--12322222222222222121111111015678776531013567757753201222100 Q gi|254780882|r 87 SLKRSLSGIKSFLKYLKKR--KITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLY 164 (328) Q Consensus 87 T~~~~ls~lr~f~~~~~~~--~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~ 164 (328) T Consensus 1 Tinr~l~~L~~~f~~A~~~~~~~~~~NP~~~i~~pk~~~~r~r~lt~eE~~~ll~~~~~~~~------~~~~~~~~~l~~ 74 (206) T cd00796 1 TVRRELALLSHLFTVARKEWGLDVLTNPVELVRKPPVGKGRDRRLTEEEEERLLRAFGEEEG------SPRLPVIILLAL 74 (206) T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC------CHHHHHHHHHHH T ss_conf 98899999999999999978887677927748588999999887999999999996764545------766999999999 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 11233222221122222332322033-23785310001122100234322111001234466554321111221110001 Q gi|254780882|r 165 GCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVF 243 (328) Q Consensus 165 ~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i 243 (328) T Consensus 75 ~TG~R~~Ei~~L~~~did~~~~~i~i~~~K~~~~r~vpl~~~~~~~l~~~~~~-------~~~~~vf------~~~~~~~ 141 (206) T cd00796 75 ETAMRRGEILSLRWEQVDLKKRVAHLPDTKNGTSRDVPLSKRAVALLQMLPKV-------PDDGPVF------PITSDSV 141 (206) T ss_pred HHCCCHHHHHHCCCCCCCCCCCEEEEEECCCCCEEEEECCHHHHHHHHHHHHC-------CCCCCCC------CCCHHHH T ss_conf 90998899942857334533584898636789656852889999999999861-------4777667------8861789 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHH Q ss_conf 23567899976869998805417999999998489988999983788878979999619899999 Q gi|254780882|r 244 QRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGD 308 (328) Q Consensus 244 ~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~ 308 (328) T Consensus 142 ~~~~~~~~~~~gi~-~~~~H~lRHt~at~l~~~G~~~~~i~~~lGH~~~~~t~~Y~h~~~e~L~~ 205 (206) T cd00796 142 DAAFRRAKERAGLE-DLHFHDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTHLSAEDLAE 205 (206) T ss_pred HHHHHHHHHHHCCC-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHC T ss_conf 99999999982777-87532048999999998698999999985899999998846739988704

HHsearch alignment for GI: 254780882 and conserved domain: cd00796