HHsearch alignment for GI: 254780546 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=100.00  E-value=0  Score=404.97  Aligned_cols=188  Identities=36%  Similarity=0.510  Sum_probs=171.0

Q ss_pred             EEEEEECCCHHHHHHHHHHHHHHHHCCCC----CEEEEEEEECCCCCCCHHH-HHHHHHHHHHHCCCCEEEEE-EECCCC
Q ss_conf             39999669424899999999999864899----7299999966779878468-99999999987189889999-750478
Q gi|254780546|r   21 HILVAVSGGSDSMGLLIALHSVLSDRSFG----KIKFSAISVDHCLRETAKD-EVRYVSDVCSRLRIAHSVVS-WKNSKP   94 (423)
Q Consensus        21 ~i~vAvSGG~DS~aLl~ll~~~~~~~~~~----~~~l~a~~vdHglr~~s~~-e~~~v~~~~~~lgi~~~~~~-~~~~~~   94 (423)
T Consensus         1 ~~lvAvSGG~DS~aLL~~L~~~~~~~~~~~~~~~~~~~a~h~nH~lR~~s~~~~~~~v~~~c~~~~~~~~~~~~~~~~~~   80 (204)
T TIGR02432         1 KILVAVSGGVDSMALLHLLLKLQPKLKISWQIKDFKLIAAHVNHGLRPESAQEEAEFVQQFCEKLNIPLEIKKLVDVKAL   80 (204)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCC
T ss_conf             97888628642799999999976632787788750689999617788415899999999999961895699842124110


Q ss_pred             ----CCCCHHHHHHHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC-----CCCE
Q ss_conf             ----778037888545555432001234-420123456665668999986236544433223576410035-----7968
Q gi|254780546|r   95 ----QTGLMAAAREARYALISEHAKTIN-ATLIMTAHTFDDQLETVYMRSQRDYAEKGMGLSGMCDTILYD-----LNLW  164 (423)
Q Consensus        95 ----~~~~~~~ar~~r~~~~~~~~~~~~-~~~l~~ah~~dD~~Et~l~rl~r~sg~~g~~l~~~~~~~~~~-----~~~~  164 (423)
T Consensus        81 ~~~~~~~~E~~AR~~RY~~f~~~~~~~~~~~~i~tAHh~dDq~ET~L~rL~RG~~~~Gl--~g~~~~~~~~~~g~~~~~~  158 (204)
T TIGR02432        81 AKGKKKNLEEAAREARYAFFEEIAKKHGKADYILTAHHADDQAETILMRLLRGSGLRGL--SGMPEIRPLGSLGWYKGGQ  158 (204)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCHH--HHHCCCCCCCCCCCCCCEE
T ss_conf             12247677899999999999999997299408997248322799999987516870001--1101336633244225632


Q ss_pred             EECCHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             7101210428999998998189320266786422101899976434
Q gi|254780546|r  165 ISRPFLRCRREDIRSFLLQRNISWCEDPSNTDDRFERVRVRRFVRD  210 (423)
Q Consensus       165 i~RPLL~~~r~~l~~~~~~~~i~wveDpSN~d~~f~R~rlR~~l~~  210 (423)
T Consensus       159 ~~RPLL~~~k~ei~~y~~~~~l~~~eD~tN~~~~y~RNriR~~~~P  204 (204)
T TIGR02432       159 IIRPLLNISKSEIEEYLKENGLPYFEDETNQDDKYLRNRIRHELLP  204 (204)
T ss_pred             EEECCCCCCHHHHHHHHHHCCCCEEECCCCCCCCCCHHHHHHHHCC
T ss_conf             7707756778999999996689656578889876205899976169