HHsearch alignment for GI: 254780870 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=97.22  E-value=0.00054  Score=44.65  Aligned_cols=116  Identities=19%  Similarity=0.246  Sum_probs=70.2

Q ss_pred             HHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCHHHHHHHCCHHHCCCCCCEE--CCCCCCCCCCCHHHCCCCCCC
Q ss_conf             999999999999866988973575124689877197311222210402137862000--345554310110000134201
Q gi|254780870|r   50 LDNVNAIIREEQNRTGAIEMSVPTLQSADLWVESGRYDSYGKEMLRLADRNDKAMIY--GPTHEEVMTDIFRSHIKSYRN  127 (449)
Q Consensus        50 ~~~le~~~r~~~~~~G~~ei~tP~l~~~eL~~~SGh~d~~~~em~~~~d~~~~~~~L--rP~~~e~~~~i~~~~~~SYr~  127 (449)
T Consensus        24 Ra~~i~~iR~FF~e~G~~EV~TP~l~~~~~~D--~~l~p~~~~~l~~g~~~~~~~WL~TSP---EY~M---K~LL~~~~-   94 (330)
T TIGR00462        24 RAKIIAEIRKFFKERGLLEVETPLLSDFPVTD--LHLEPFKTEFLEPGGEQNKVLWLSTSP---EYHM---KRLLSAGK-   94 (330)
T ss_pred             HHHHHHHHHHHHHHCCCEEECCCCHHCCCCCC--EEEEEEEEEEECCCCCCCCEECCCCCC---CHHH---HHHHHHCC-
T ss_conf             99999999998861784253263010156443--022136888842665333312114587---2789---99986217-


Q ss_pred             CCEEEEECCCCCCCCCCCCCCCCCCEEEEEEECCEECCCHHHHHHHHHHHHH
Q ss_conf             3402641465334566767543453166874042211886887999999999
Q gi|254780870|r  128 LPFTFYQIQLKFRDELRPRFGVMRSREFLMKDAYSFDLTPEGSKHSYNKMFV  179 (449)
Q Consensus       128 LPlr~y~ig~~fR~E~rp~~GL~R~ReF~q~D~~~F~~~~e~~~~e~~~~~~  179 (449)
T Consensus        95 --~~iFQi~k~FRN~E~G~~---H~~EF~MLEWY~~~~d~~~Li~E~~~LL~  141 (330)
T TIGR00462        95 --GPIFQITKVFRNEEAGRL---HNPEFTMLEWYRPHYDMLRLINEVDDLLQ  141 (330)
T ss_pred             --CCEEEEEEHHHHCCCCCC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             --862310000100024675---77531001112110238999999999999