>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=100.00 E-value=0 Score=591.49 Aligned_cols=305 Identities=43% Similarity=0.842 Sum_probs=289.7 Q ss_pred HHHHHHHHCCCCHHH--HHHHHHHHHHHH------HHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 899987615899889--999999999999------999999999999998--5676667654310000011232122674 Q gi|254780317|r 45 ISSLLKDLKNLDSQQ--VSARGAILNQLK------VDISGKISARKDFIR--NQLIFEQISSQSVDVSLPVFSSPCHRGR 114 (366) Q Consensus 45 Lt~llK~Lk~Ls~Ee--Kk~~Gk~iNelK------~~Ie~~i~~kk~~L~--~~~~~~kl~~E~iDVTLP~~~~~~~~G~ 114 (366) T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~--~~~~~~g~ 79 (362) T TIGR00468 2 LKDLLKGLGKLSKEEELKPALGALANEVKEFLKKGIELEDELTKLKPELLDLEAGLWKKLKFEPYDVTLP--GKPIYPGG 79 (362) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEC--CCCCCCCC T ss_conf 2124444311313577777788777767887512267888888766778777765554310122111104--43114553 Q ss_pred CCHHHHHHHHHHHHHHHCCCEEECCCE-EECHHHHHHHHCCCCCCCCCCCCCEEEEECCC-------------------- Q ss_conf 238999999999999873987623723-41588988861898877331633127750566-------------------- Q gi|254780317|r 115 IHPVTQVIDEVTCIFMDMGFALEEGSD-IETDYYNFAALNFPDDHPARQMHDTFFVPGIA-------------------- 173 (366) Q Consensus 115 ~HPItqvi~eI~~IF~~lGF~v~eGPE-IEtd~~NFdaLNiP~~HPARdmqDTFyl~~~~-------------------- 173 (366) T Consensus 80 ~~p~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~f~~l~~p~~hp~r~~~d~f~~~~p~~~~~~~~~~~~~~~~~~~~~ 159 (362) T TIGR00468 80 LHPLTRVIDEIRDIFLGLGFTEEKGPEYVETDFWNFDALNLPQDHPARDLQDTFYLKDPLTGDLPPELVSDVKDAHETGG 159 (362) T ss_pred CHHHHHHHHHHHHHHHHHCCEEECCCCEECCCCCCCHHHCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCC T ss_conf 10578999999998765033010473101111001011127754543112330331374200032246776777665202 Q ss_pred --------------CCCCCCCCCCCCC---HHHHHHHHCC----CEEEEEECCCCCCCCC-CCCCCCCCCCCCEEEECCC Q ss_conf --------------6556322446763---0555543036----3122541057647454-4213781002005786178 Q gi|254780317|r 174 --------------GGKHKLLRTHTSP---VQIRVMESQD----LPIKVIVPGKTYRRDS-DSTHSPMFHQIEGLVVSDS 231 (366) Q Consensus 174 --------------~~~~~lLRthTS~---vQiR~m~~~~----pP~~~~~~GrvyR~d~-D~tH~~~FhQ~egl~v~~~ 231 (366) T Consensus 160 ~~g~~gw~~~~~~~~~~~~~lrt~~~~~~~~~~~~~~~~~~~~~pp~~~~~~~~~~r~~~~d~~h~~~f~~~~g~~~~~~ 239 (362) T TIGR00468 160 ATGSRGWRYEWDEDLARRLLLRTHTTASSAVQLRTLEENPKAKNPPIRIFCPGRVFRRDTVDATHLPEFHQLEGLVVDKN 239 (362) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHCCCCCCCCCCCHHHHEEEEEEECC T ss_conf 12232445444555665555431132135666666654101378862576410111023333101410221002354156 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEEEEECCCCEEEECCCCCEEEEECCCCCCHHHHHHCCCC Q ss_conf 66899988999999997088866264542388985266103678750588042246883489845756388899856988 Q gi|254780317|r 232 ATIANLRWVLESFCKSFFEVSSLQMRFRPSFFPFTEPSFEVDVRCSFSDGIIKFDEGTEWMEILGCGMVDPRVLRGVGID 311 (366) Q Consensus 232 i~~~~lk~~l~~~~~~~fg~~~~~~r~rp~~fPftePs~Evdv~~~~~~~~~~~~~~~~WiEi~g~Gm~~p~vl~~~g~d 311 (366) T Consensus 240 ~~~~~l~g~~~~~~~~~~~-~~~~~~~~p~~fp~t~p~~e~~~~~~~c~~gc~~c~~~~W~e~~g~g~~~p~~~~~~g~~ 318 (362) T TIGR00468 240 VSFTNLKGLLEEFLKKLFG-EDTEVRFRPSYFPFTEPSAEVDVYCPECGKGCSVCKGTGWLELLGAGIFRPEVLEPLGID 318 (362) T ss_pred CCHHHHHHHHHHHHHHHCC-CCCCEEEECCCCCCCCCCCCEEEEEHHHCCCCHHHCCCCEEEEECCCCCCHHHHHHCCCC T ss_conf 6467889999999997413-221202310336655555302442000013100101465035404553242355423787 Q ss_pred CCCEEEEEEECCHHHHHHHHCCCCCHHHHHHCCHH--HHHHCC Q ss_conf 00037996313446997997389705876635888--887448 Q gi|254780317|r 312 PDIYQGFAWGMGLDRIAMLKYGMPDVREFFGADVR--WIEHYG 352 (366) Q Consensus 312 ~~~~~g~AfG~G~eRlaml~~gi~diR~~~~~d~r--fl~qf~ 352 (366) T Consensus 319 ~~~~~~~~~g~g~~r~~~~~~~~~d~r~~~~~~~~~~~l~~~~ 361 (362) T TIGR00468 319 PEEYPGLAWGLGIERLAMLKYGLDDLRDLYENDLGDDFLRQFP 361 (362) T ss_pred CCCCEEEEECCCHHHHHHHHHCHHHHHHHHCCCCCHHHHHCCC T ss_conf 3101134321240124454513356888640332012332048

HHsearch alignment for GI: 254780317 and conserved domain: TIGR00468