HHsearch alignment for GI: 254780928 and conserved domain: TIGR00470

>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase; InterPro: IPR005246 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 . All known phenylalanyl-tRNA synthetases, excepting a monomeric mitochondrial form, have an alpha 2 beta 2 heterotetrameric structure. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains but is longer and of unknown function; more generally, it resembles class 2 aminoacyl tRNA ligases. .
Probab=95.17  E-value=0.038  Score=33.11  Aligned_cols=80  Identities=18%  Similarity=0.281  Sum_probs=48.4

Q ss_conf             89998888389999999511205541123310133302587-64442111110001210000245788999999999751
Q Consensus        80 ~l~LRpDlT~~~aR~~~~~~~~~~~p~k~yy~g~vfR~e~p-~~Gr~REf~Q~g~eiiG~~~~~~DaEii~l~~~~l~~l  158 (496)
T Consensus       192 tlTLRSHMTsGWFItLs~i~dk~~lPlKLFSIDRCFRREQ~ED~shLmtYhSASCVvVdeevsvDdG--KaVAEgLL~qf  269 (558)
T ss_conf             4320010100278889878751589711220032314466435310011345466785771243642--68899999870

Q ss_pred             CCC
Q ss_conf             888
Q gi|254780928|r  159 GIK  161 (496)
Q Consensus       159 gl~  161 (496)
T Consensus       270 GF~  272 (558)
T TIGR00470       270 GFE  272 (558)
T ss_pred             CCC
T ss_conf             854