HHsearch alignment for GI: 254780680 and conserved domain: TIGR00468

>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit; InterPro: IPR004529 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 . Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases . This family describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this family. ; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=92.95  E-value=0.25  Score=30.67  Aligned_cols=107  Identities=10%  Similarity=0.124  Sum_probs=75.2

Q ss_pred             HHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHH-HCCHHHHCCCCCHH
Q ss_conf             55042088532210788433554343212222102002121278650145789899999999998-41067530378011
Q gi|254780680|r  248 KSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKR-LDLHYRVVSLCTGD  326 (430)
Q Consensus       248 ~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~-L~lpyRvv~~~sgd  326 (430)
T Consensus       202 ~~pp~~~~~~~~~~r~~~~d~-------~h~~~f~~~~g~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~~~p~~fp~t~  274 (362)
T TIGR00468       202 KNPPIRIFCPGRVFRRDTVDA-------THLPEFHQLEGLVVDKNVSFTNLKGLLEEFLKKLFGEDTEVRFRPSYFPFTE  274 (362)
T ss_pred             CCCCEEEEECCHHHCCCCCCC-------CCCCHHHHEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCC
T ss_conf             788625764101110233331-------0141022100235415664678899999999974132212023103366555


Q ss_pred             CCCHHHEEEEEEEECCC-CC--------CEEEEEEECCCCCHHHHHCCCE
Q ss_conf             78443402410110100-48--------3323753102100764532684
Q gi|254780680|r  327 LGFSACKTYDLEVWLAG-QN--------LYREISSCSTCGNFQSRRMNSR  367 (430)
Q Consensus       327 lg~~a~~~~DiE~w~P~-~~--------~y~Ev~S~Snc~D~QsrRl~ir  367 (430)
T Consensus       275 p~------~e~~~~~~~c~~gc~~c~~~~W~e~~g~g~~~p~~~~~~g~~  318 (362)
T TIGR00468       275 PS------AEVDVYCPECGKGCSVCKGTGWLELLGAGIFRPEVLEPLGID  318 (362)
T ss_pred             CC------CCEEEEEHHHCCCCHHHCCCCEEEEECCCCCCHHHHHHCCCC
T ss_conf             55------302442000013100101465035404553242355423787