>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=94.31  E-value=0.018  Score=34.12  Aligned_cols=119  Identities=17%  Similarity=0.180  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHHHHCCCEEEECCC-EECCC-CCCCC-------C----CCEEEEC-------------------------
Q ss_conf             999999999999987988984782-10568-98544-------5----4124102-------------------------
Q gi|254781066|r   25 RNMIQSSLREYFVENQFIEIDSMS-LQYSP-GNETH-------I----RAFSTEL-------------------------   66 (355)
Q Consensus        25 Rs~i~~~iR~ff~~~gF~EV~TPi-L~~~~-~g~~~-------~----~~f~t~~-------------------------   66 (355)
T Consensus        83 ~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~f~~l~~p~~hp~r~~~d~f~~~~p~~~~~~~~~~~~~~~~~~~~~~~g  162 (362)
T TIGR00468        83 LTRVIDEIRDIFLGLGFTEEKGPEYVETDFWNFDALNLPQDHPARDLQDTFYLKDPLTGDLPPELVSDVKDAHETGGATG  162 (362)
T ss_pred             HHHHHHHHHHHHHHHCCEEECCCCEECCCCCCCHHHCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             78999999998765033010473101111001011127754543112330331374200032246776777665202122


Q ss_pred             -CCCCC-C----CCCCCC--CCCH----HHHHHHHHH---HHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCH
Q ss_conf             -47886-7----832000--0285----899998987---44688999886424567775448430020001157--765
Q gi|254781066|r   67 -IIQDH-I----RKPLYL--QTSP----EFSCKKLLA---AGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESY  129 (355)
Q Consensus        67 -~~~~~-~----~~~~yL--~~SP----ql~lK~ll~---~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~  129 (355)
T Consensus       163 ~~gw~~~~~~~~~~~~~lrt~~~~~~~~~~~~~~~~~~~~~pp~~~~~~~~~~r~~~~d~~h~~~f~~~~g~~~~~~~~~  242 (362)
T TIGR00468       163 SRGWRYEWDEDLARRLLLRTHTTASSAVQLRTLEENPKAKNPPIRIFCPGRVFRRDTVDATHLPEFHQLEGLVVDKNVSF  242 (362)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHCCCCCCCCCCCHHHHEEEEEEECCCCH
T ss_conf             32445444555665555431132135666666654101378862576410111023333101410221002354156646


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             78777557888776
Q gi|254781066|r  130 EQLMKDCMNIIRCA  143 (355)
Q Consensus       130 ~dlm~~~E~li~~~  143 (355)
T Consensus       243 ~~l~g~~~~~~~~~  256 (362)
T TIGR00468       243 TNLKGLLEEFLKKL  256 (362)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             78899999999974