HHsearch alignment for GI: 254780419 and conserved domain: cd00496

>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.
Probab=99.20  E-value=1.3e-10  Score=95.45  Aligned_cols=89  Identities=25%  Similarity=0.422  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHHHCCCEEEEECCCCCC--------CCCCCCCCCCCCCCCCHHHHHH-------CC--CCHHHHHHHHHCC
Q ss_conf             99999998752036514620332112--------4645664543222221034431-------12--3854564433105
Q gi|254780419|r  146 TRIINSMRCRMIAENFIECSTPILTA--------SSPEGARDFLVPSRVNQGSFYA-------LP--QAPQQYKQLLMAS  208 (622)
Q Consensus       146 s~i~~~~R~~l~~~gF~EveTP~L~k--------sTpeGArdFlVPsR~~~g~fYA-------Lp--QSPQlyKQlLmv~  208 (622)
T Consensus         4 ~~~~~~i~~~f~~~GF~~~~gp~ie~~~~NFD~Ln~P~d-----HPaR~~~DTfy~~~~~~~lLRtHTS~~q~r~l~~~~   78 (218)
T cd00496           4 NKVIEEIEDIFVSMGFTEVEGPEVETDFYNFDALNIPQD-----HPARDMQDTFYINDPARLLLRTHTSAVQARALAKLK   78 (218)
T ss_pred             HHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHHCCCCC-----CCCCCCCCEEEECCCCCCEECCCCCHHHHHHHHHCC
T ss_conf             899999999998779868228951231030453385988-----755372432786377660215787566799997458


Q ss_pred             CHHHHEEEHHHHCCCCCCCCCCCCCEEEEEEE
Q ss_conf             70233110011037776655380000356541
Q gi|254780419|r  209 GFDRYFQIAPCFRDEDPRSDRLPGEFYQLDME  240 (622)
Q Consensus       209 G~dryfqiarcFRdEd~R~dRqp~EFTqlD~E  240 (622)
T Consensus        79 ~p~~~~~~G~VyR~D~iDatH~~-~FhQ~Eg~  109 (218)
T cd00496          79 PPIRIFSIGRVYRNDEIDATHLP-EFHQIEGL  109 (218)
T ss_pred             CCCEEEECCCEEECCCCCCCCCC-EEEEEEEE
T ss_conf             98179942504653889843153-12576379