>TIGR00250 TIGR00250 conserved hypothetical protein TIGR00250; InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VIIcolicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma urealyticum (Q9PQY7 from SWISSPROT, ). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase . This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC . ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0004518 nuclease activity, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus.

Probab=90.26  E-value=0.27  Score=28.89  Aligned_cols=90  Identities=16%  Similarity=0.179  Sum_probs=55.5

Q ss_pred             EEECCCCCEEEEEEEEE-ECCEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEHHHH-CCCHHHHHHH
Q ss_conf             99978887205899997-199689998336873889998889999999899986227962778850332-0241247889
Q gi|254780554|r    8 IGIDPGLRRTGWGIVDV-AGDNLCFVSSGTIVSCVRQSLAFRLCQLYEGLTDVIKNWRPEEAAVEQVFV-NKDAVATLKL   85 (169)
Q Consensus         8 LGIDPGl~~tG~avie~-~~~~~~li~~g~I~t~~~~~~~~Rl~~I~~~l~~ii~~~~Pd~vaiE~~F~-~~n~~t~~~l   85 (169)
T Consensus         1 LglD~GtK~iGvA~g~~~tG~tA~gi~--tik~~~~~~d~-G----l~~i~~l~ke~~~d~~vvGlP~nM~Gt~g~--~~   71 (133)
T TIGR00250         1 LGLDLGTKSIGVAVGQDITGLTAQGIP--TIKAQDGEPDW-G----LSRIEELLKEWKVDKIVVGLPLNMDGTVGP--LT   71 (133)
T ss_pred             CCCCCCCCEEEEEECCCCCCCEECCCH--HHHHCCCCCCC-C----HHHHHHHHHHCCCCEEEECCCCCCCCCCCH--HH
T ss_conf             963246413546763667552104403--11210488862-1----799999873158897886178787887250--26


Q ss_pred             HHHHHHHHHHHHHCCCCEEEE
Q ss_conf             999999999998601617752
Q gi|254780554|r   86 GQARAIAILSPALARIPVSEY  106 (169)
Q Consensus        86 g~arGvi~l~~~~~~i~v~ey  106 (169)
T Consensus        72 ~~~~kFA~r~~~~~~v~v~l~   92 (133)
T TIGR00250        72 KRAQKFAKRLEGRFGVPVELM   92 (133)
T ss_pred             HHHHHHHHHHHHHHCCCEEEE
T ss_conf             888999988655406643786