HHsearch alignment for GI: 254780191 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=91.94 E-value=0.29 Score=28.73 Aligned_cols=29 Identities=21% Similarity=0.297 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHCCCCCCCHH
Q ss_conf 5657665310175799999998879853005
Q gi|254780191|r 216 RFILPKMSIDTGMGLERMATVLQEKTNNYDI 246 (898)
Q Consensus 216 ~~~Lp~~~IDTGmGLERl~~vlqg~~s~ydt 246 (898)
T Consensus 107 LagLPrPdv--Glg~eki~~Ie~~gid~~de 135 (558)
T TIGR00470 107 LAGLPRPDV--GLGAEKIRIIEDLGIDVSDE 135 (558)
T ss_pred HCCCCCCCC--CCCCHHHHHHHHCCCCCCCC
T ss_conf 257878863--55602778888707742101