HHsearch alignment for GI: 254780928 and conserved domain: TIGR00462

>TIGR00462 genX lysyl-tRNA synthetase homolog GenX; InterPro: IPR004525 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 . This entry represents lysyl-tRNA synthetases from bacteria, as well as other related proteins. Escherichia coli, Haemophilus influenzae, and Aquifex aeolicus each have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS, so they appear to be orthologous. The protein is termed PoxA or GenX after its designation in E. coli. Its function is unknown.; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=95.64  E-value=0.078  Score=31.06  Aligned_cols=102  Identities=25%  Similarity=0.366  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEECCCHHHHHHHHCCCCCCCCCCCCEEEEECCCCC-----EEEECCCCHHHHHHHH
Q ss_conf             68999999999999999985984801652022887520267554333221689869998-----8999888838999999
Q gi|254780928|r   21 KEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDDGQ-----WISLRYDLTAPLARYV   95 (496)
Q Consensus        21 ~~~~~~~~i~~~l~~~f~~~G~~~I~tP~lE~~~~~~~~~~~~~~~~k~~y~f~D~~g~-----~l~LRpDlT~~~aR~~   95 (496)
T Consensus        19 ~n~LkRa~~i~~iR~FF~e~G~~EV~TP~l~~~~~~-----D~-~l~p~~~~~l~~g~~~~~~~WL~TSPEY--~MK~LL   90 (330)
T TIGR00462        19 KNLLKRAKIIAEIRKFFKERGLLEVETPLLSDFPVT-----DL-HLEPFKTEFLEPGGEQNKVLWLSTSPEY--HMKRLL   90 (330)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEECCCCHHCCCCC-----CE-EEEEEEEEEECCCCCCCCEECCCCCCCH--HHHHHH
T ss_conf             677889999999999886178425326301015644-----30-2213688884266533331211458727--899998


Q ss_pred             HHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCC-----CCCCHHHH
Q ss_conf             951120554112331013330258764442111-----11000121
Q gi|254780928|r   96 AENFDTIVFPCRTYRIGPVFRNEKHGPGRFRQF-----IQCDVDNV  136 (496)
Q Consensus        96 ~~~~~~~~~p~k~yy~g~vfR~e~p~~Gr~REf-----~Q~g~eii  136 (496)
T Consensus        91 ~~~~----~--~iFQi~k~FRN~E~G~~H~~EF~MLEWY~~~~d~~  130 (330)
T TIGR00462        91 SAGK----G--PIFQITKVFRNEEAGRLHNPEFTMLEWYRPHYDML  130 (330)
T ss_pred             HHCC----C--CEEEEEEHHHHCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             6217----8--62310000100024675775310011121102389