HHsearch alignment for GI: 254780680 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=97.23  E-value=0.002  Score=46.20  Aligned_cols=186  Identities=21%  Similarity=0.260  Sum_probs=114.8

Q ss_pred             HHHHHHHHHHHHCCCCEEHHHHHCCHHHHHHHHHCHHH-----HHHHHHHHHC--CEE-CCCCCCHHHHHHHHHCCCHHH
Q ss_conf             99999986223203202123562027889865514224-----7677643100--023-134541145445342059555
Q gi|254780680|r  178 LGQFMIDLHTSEHGYTEVSAPLLVRDEAMYGTGQIPKF-----ADDMFCTTDG--RWL-IPTSEVSLTNLYSHEIIESKS  249 (430)
Q Consensus       178 Li~y~ld~~~~~~Gy~~v~~P~lv~~~~~~gtG~lp~f-----~~~~y~~~d~--l~L-i~TaEvpL~~~~~~~~l~~~~  249 (430)
T Consensus         6 ~~~~i~~~f-~~~GF~~~~gp~ie~~~~NFD~Ln~P~dHPaR~~~DTfy~~~~~~~lLRtHTS~~q~r~l~~~------~   78 (218)
T cd00496           6 VIEEIEDIF-VSMGFTEVEGPEVETDFYNFDALNIPQDHPARDMQDTFYINDPARLLLRTHTSAVQARALAKL------K   78 (218)
T ss_pred             HHHHHHHHH-HHCCCEEECCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCEECCCCCHHHHHHHHHC------C
T ss_conf             999999999-877986822895123103045338598875537243278637766021578756679999745------8


Q ss_pred             HCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCC---HHHHCCCCCHH
Q ss_conf             042088532210788433554343212222102002121278650145789899999999998410---67530378011
Q gi|254780680|r  250 LPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDL---HYRVVSLCTGD  326 (430)
Q Consensus       250 LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~l---pyRvv~~~sgd  326 (430)
T Consensus        79 ~p~~~~~~G~VyR~D~iDa---tH----~~~FhQ~Eg~~v~~----~~~~~~Lk~~l~~~~~~lfg~~~~~r~r--p~-y  144 (218)
T cd00496          79 PPIRIFSIGRVYRNDEIDA---TH----LPEFHQIEGLVVDK----GLTFADLKGTLEEFAKELFGPITKVRFR--PS-Y  144 (218)
T ss_pred             CCCEEEECCCEEECCCCCC---CC----CCEEEEEEEEEEEC----CCCHHHHHHHHHHHHHHHCCCCCEEEEC--CC-C
T ss_conf             9817994250465388984---31----53125763799956----5119999999999999973876645367--78-8


Q ss_pred             CCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             784434024101101004833237531021007645326847338998410104200432289999999
Q gi|254780680|r  327 LGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIA  395 (430)
Q Consensus       327 lg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~a  395 (430)
T Consensus       145 FPFT-ePS~Evdv~~~~~~~WlEv~G~G~v~p~vL~~~G~---d--~~~~g~Af-----G~GlERlaMl  202 (218)
T cd00496         145 FPFT-EPSFEVDVYCPGCLGWLEILGCGMVRPEVLENAGI---D--EEYSGFAF-----GIGLERLAML  202 (218)
T ss_pred             CCCC-CCCEEEEEEECCCCCCEEEECCCCCCHHHHHHCCC---C--CCCEEEEE-----EECHHHHHHH
T ss_conf             9999-98269999965878714885046548899986697---9--99889998-----5258899999