HHsearch alignment for GI: 254780928 and conserved domain: TIGR00414
>TIGR00414 serS seryl-tRNA synthetase; InterPro: IPR002317 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 . Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa .; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=96.84 E-value=0.0087 Score=37.27 Aligned_cols=151 Identities=16% Similarity=0.235 Sum_probs=104.2
Q ss_pred CCCCC--CCHHHHHHHHHHHHHHHHHH-HHCCCEEEECCCHHHHHHHHCCC--CCCCCCCCCEEEEECCCCCEEEECCCC
Q ss_conf 98765--88668999999999999999-98598480165202288752026--755433322168986999889998888
Q gi|254780928|r 13 RGFAD--CPTKEIRIRNRILDSIRNIY-ENYGFDPIETPLLEYSDSLGKFL--PDEDRPNKGVFSLQDDDGQWISLRYDL 87 (496)
Q Consensus 13 ~G~~D--~~p~~~~~~~~i~~~l~~~f-~~~G~~~I~tP~lE~~~~~~~~~--~~~~~~~k~~y~f~D~~g~~l~LRpDl 87 (496)
T Consensus 190 ~g~~~~~~~~~~~~~~~al~~~~l~~~~~~~g~~~~~~p~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~l~~t~ 269 (460)
T TIGR00414 190 AGSRFYYLKGDGAKLERALINFMLDLLREKNGYSELYPPYLVNEELLDGTGFNPQLPKFEEDLFKLEDTDDEKLYLIPTA 269 (460)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCEEEEEECC
T ss_conf 10101213213678999999999986443226401014035423443102456556530234432126777504652010
Q ss_pred HHHHHHHHHHHHHH---CCCCHHHHHHHHHHCCCCCC-----CCCC--CCCCCCCHHHHHCC--CHHHHHHHHHHHHHHH
Q ss_conf 38999999951120---55411233101333025876-----4442--11111000121000--0245788999999999
Q gi|254780928|r 88 TAPLARYVAENFDT---IVFPCRTYRIGPVFRNEKHG-----PGRF--RQFIQCDVDNVGSS--AETADAEMCMMMADTL 155 (496)
Q Consensus 88 T~~~aR~~~~~~~~---~~~p~k~yy~g~vfR~e~p~-----~Gr~--REf~Q~g~eiiG~~--~~~~DaEii~l~~~~l 155 (496)
T Consensus 270 e~~~~~~~~~~~~~~~~~~lp~~~~~~~~cfr~eag~~g~~~~g~~r~h~f~k~e~~~~~~p~~~~~~~~~~~~~~~~~~ 349 (460)
T TIGR00414 270 EVPLTNLHRDEILDLPSEELPIKYTGYSPCFRSEAGSYGKDTKGLIRVHQFNKVELVKFCKPEESWEELEELLSDAEKIL 349 (460)
T ss_pred HHHHHHHHHHHHCCCCCCCCCEEHCCCCHHHHHHCCCCCCCCHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHHHHH
T ss_conf 00122222000102652103400000220233321345541000121110031024566354014899999987899999
Q ss_pred HHCCCCCC
Q ss_conf 75188877
Q gi|254780928|r 156 EAVGIKRN 163 (496)
Q Consensus 156 ~~lgl~~~ 163 (496)
T Consensus 350 ~~l~~p~~ 357 (460)
T TIGR00414 350 QELELPYR 357 (460)
T ss_pred HHHCCCHH
T ss_conf 97437511