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