>TIGR00472 pheT_bact phenylalanyl-tRNA synthetase, beta subunit; InterPro: IPR004532 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 (see IPR002319 from INTERPRO). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta. 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 beta subunit. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps (see also IPR004531 from INTERPRO). This family represents the subfamily that includes the beta subunit from bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the N-terminal.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm.

Probab=97.58 E-value=0.0026 Score=45.22 Aligned_cols=220 Identities=14% Similarity=0.244 Sum_probs=144.5 Q ss_pred CCCCCHHHH-HHH---HHHHHHHHCCC-EEECCCEEECHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCC Q ss_conf 674238999-999---99999987398-7623723415889888618988773316331277505666556322446763 Q gi|254780317|r 112 RGRIHPVTQ-VID---EVTCIFMDMGF-ALEEGSDIETDYYNFAALNFPDDHPARQMHDTFFVPGIAGGKHKLLRTHTSP 186 (366) Q Consensus 112 ~G~~HPItq-vi~---eI~~IF~~lGF-~v~eGPEIEtd~~NFdaLNiP~~HPARdmqDTFyl~~~~~~~~~lLRthTS~ 186 (366) T Consensus 510 ~~~~~~~~~~~~~~~~~~~~~l~~~G~~E~itYsl~~~~--~~~~~~~~~~~~~---~~~~~i~NP~s~e~~~lR~sL~~ 584 (848) T TIGR00472 510 KNNKNNENQLLLKFLKKLRKLLVGLGLNEVITYSLVSKE--KLEKFNFPKLENL---DELVEIKNPLSEERSVLRTSLLP 584 (848) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCHH--HHHHHCCCCCCCC---HHEEEECCCCCHHHHHHHHHHHH T ss_conf 244442045788999999999984898577730138879--9987168777861---01045158983547887664468 Q ss_pred HHHHHHHH----CCCEEEEEECCCCCCCCCC---CCCCCCCCCCCEE---EE-------------CCCCCHHHHHHHHHH Q ss_conf 05555430----3631225410576474544---2137810020057---86-------------178668999889999 Q gi|254780317|r 187 VQIRVMES----QDLPIKVIVPGKTYRRDSD---STHSPMFHQIEGL---VV-------------SDSATIANLRWVLES 243 (366) Q Consensus 187 vQiR~m~~----~~pP~~~~~~GrvyR~d~D---~tH~~~FhQ~egl---~v-------------~~~i~~~~lk~~l~~ 243 (366) T Consensus 585 sLL~~~~~N~~r~~~~~~lFE~G~~f~~~~~AR~e-~~~~~~e~~~La~~~~G~~~~~~w~~~~~~~~~df~~~Kg~ve~ 663 (848) T TIGR00472 585 SLLEVLAYNQNRKNKDVKLFEIGKVFAKDGKARGE-EDEAVKEQLRLAILISGEKEPSSWNSKKKEEKVDFYDLKGIVES 663 (848) T ss_pred HHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCC-HHHHHHHHHHHEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 89999999986389715899887642688533575-01212344311002404456666600157665678899999999 Q ss_pred HHHHHCCCCCCEE-----EEEECCCCCCCCCCEEEEEEECCCCEEEECCCCC-EEEEECCCCCCHHHHHHCCCCCCCEEE Q ss_conf 9999708886626-----4542388985266103678750588042246883-489845756388899856988000379 Q gi|254780317|r 244 FCKSFFEVSSLQM-----RFRPSFFPFTEPSFEVDVRCSFSDGIIKFDEGTE-WMEILGCGMVDPRVLRGVGIDPDIYQG 317 (366) Q Consensus 244 ~~~~~fg~~~~~~-----r~rp~~fPftePs~Evdv~~~~~~~~~~~~~~~~-WiEi~g~Gm~~p~vl~~~g~d~~~~~g 317 (366) T Consensus 664 ~L~~l-~~~~~~~~~~~~~~~~~~~~~~hP~~~a~i~~-------------~~~~~~G~iG~~hp~~~~~~~l~~~~--- 726 (848) T TIGR00472 664 LLELL-GLSESAAYEVLDFKEAAENEELHPGQSAEIYL-------------KSGKLIGFIGEVHPEIAKEYDLKEPT--- 726 (848) T ss_pred HHHHH-CCCCCCHHHHHHHHHHCCCCCCCCCCEEEEEE-------------ECCEEEEEEEEECHHHHHHHCCCCCE--- T ss_conf 99970-86555302222113330565568873279998-------------26828999998855899750798635--- Q ss_pred EEEECCHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCC-CCCCCCCCCC Q ss_conf 963134469979973897058766358888874489844-6884145889 Q gi|254780317|r 318 FAWGMGLDRIAMLKYGMPDVREFFGADVRWIEHYGFSPL-DIPPLFSRLA 366 (366) Q Consensus 318 ~AfG~G~eRlaml~~gi~diR~~~~~d~rfl~qf~~~~~-~~~~~~~~~~ 366 (366) T Consensus 727 ~~~El~l~~l~~~----------~~~~~~~~~~--~~~~s~~P~~~RDi~ 764 (848) T TIGR00472 727 FVAELDLDRLLES----------LKKSRKLVPK--YRPISKFPAVTRDIS 764 (848) T ss_pred EEEEEEHHHHHHH----------HHHHCCEEEE--EECCCCCCCCCCCEE T ss_conf 9998727888865----------2242211456--532677885202288

HHsearch alignment for GI: 254780317 and conserved domain: TIGR00472