HHsearch alignment for GI: 254780234 and conserved domain: TIGR02432

>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase; InterPro: IPR012795 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This domain is found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain architecture of this protein is variable; some, including characterised proteins of Escherichia coli and Bacillus subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family. It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016879 ligase activity forming carbon-nitrogen bonds, 0008033 tRNA processing, 0005737 cytoplasm.
Probab=98.40  E-value=6.8e-06  Score=62.58  Aligned_cols=150  Identities=18%  Similarity=0.287  Sum_probs=94.5

Q ss_pred             EEEEEECCCHHHHHHHHHHHH---HCCCE-------EEEEEEECCC----CC-HHHHHHHHHHHCCCEEEEEEC-H--HH
Q ss_conf             899991477259999999987---18986-------9999945787----11-068999999973980799820-0--89
Q gi|254780234|r    7 KVVLAYSGGLDTSIILKWLQV---EKGLE-------VIVFIADLGQ----GE-ELKIASDKARLLGAKEVYVKD-L--RR   68 (404)
Q Consensus         7 kVvlaySGGLDTSv~i~~L~~---e~g~e-------Vi~~~~d~Gq----~~-d~~~~~~~A~~~Ga~~~~v~D-~--r~   68 (404)
T Consensus         1 ~~lvAvSGG~DS~aLL~~L~~~~~~~~~~~~~~~~~~~a~h~nH~lR~~s~~~~~~~v~~~c~~~~~-~~~~~~~~~~~~   79 (204)
T TIGR02432         1 KILVAVSGGVDSMALLHLLLKLQPKLKISWQIKDFKLIAAHVNHGLRPESAQEEAEFVQQFCEKLNI-PLEIKKLVDVKA   79 (204)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHCCC-CEEEEEEECCCC
T ss_conf             9788862864279999999997663278778875068999961778841589999999999996189-569984212411


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC-CCEEECHHHCCCCHHHH--HHHHHHHHCCC----C
Q ss_conf             99998799997368654787420130124335999999988568-92875001116821567--99999985879----7
Q gi|254780234|r   69 EFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETG-ADAIAHGSTGKGNDQVR--FELSAYSLNSD----I  141 (404)
Q Consensus        69 ef~~~~i~~~I~ana~Yeg~Ypl~tslaRplia~~lv~~a~~~g-a~~iaHG~TgkGNDQvR--Fe~~~~~l~P~----l  141 (404)
T Consensus        80 ~-~~~~-~~~~E-------------~~AR~~RY~~f~~~~~~~~~~~~i~tAH--h~dDq~ET~L~rL~RG~~~~Gl~g~  142 (204)
T TIGR02432        80 L-AKGK-KKNLE-------------EAAREARYAFFEEIAKKHGKADYILTAH--HADDQAETILMRLLRGSGLRGLSGM  142 (204)
T ss_pred             C-CCCC-CCCHH-------------HHHHHHHHHHHHHHHHHCCCCEEEEECC--CCCCHHHHHHHHHHHCCCCCHHHHH
T ss_conf             0-1224-76778-------------9999999999999999729940899724--8322799999987516870001110


Q ss_pred             EEEEEE------------CC-CCCCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             077441------------00-68763799999999708967566567
Q gi|254780234|r  142 EIIAPW------------RH-WSFKGRQDLIDFAEKHAIPIDKNKRG  175 (404)
Q Consensus       142 ~viaP~------------Rd-~~~~sRe~~i~ya~~~gIpv~~~~~~  175 (404)
T Consensus       143 ~~~~~~~~~g~~~~~~~~RPLL~~-~k~ei~~y~~~~~l~~~eD~tN  188 (204)
T TIGR02432       143 PEIRPLGSLGWYKGGQIIRPLLNI-SKSEIEEYLKENGLPYFEDETN  188 (204)
T ss_pred             CCCCCCCCCCCCCCEEEEECCCCC-CHHHHHHHHHHCCCCEEECCCC
T ss_conf             133663324422563277077567-7899999999668965657888