HHsearch alignment for GI: 254781004 and conserved domain: cd00775

>cd00775 LysRS_core Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea. However, LysRS belongs to class I aaRS's in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=98.16  E-value=6.2e-06  Score=60.80  Aligned_cols=115  Identities=18%  Similarity=0.237  Sum_probs=71.8

Q ss_pred             HHHHHHHHHHHHHHH-HCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCEEEECCCCHHHHHHHHHHC
Q ss_conf             899999999999887-6896385554324431000112100125554201001456777823774343125777765201
Q gi|254781004|r  273 WKIFQTLISYMRRKI-KDDYEEINTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRTFALKPMNCPGHVAVFNHG  351 (652)
Q Consensus       273 ~~i~~~ie~~ir~~~-~~G~~eV~tP~l~~~~Lw~~SGh~~~y~~~mf~~~~~~~~~~~~~~~~LkPmncp~h~~i~~~~  351 (652)
T Consensus         8 ~~~Rs~i~~~iR~ff~~~gF~Ev~TPiL~~~~----~g~~----~~~f~~~~----~~~~~~~yL~qS-----pQl~~q~   70 (329)
T cd00775           8 FIVRSKIISYIRKFLDDRGFLEVETPMLQPIA----GGAA----ARPFITHH----NALDMDLYLRIA-----PELYLKR   70 (329)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCC----CCCC----CCCEEECC----CCCCCCCCCCCC-----HHHHHHH
T ss_conf             99999999999999998898899798655668----8756----75313224----467867230689-----8999999


Q ss_pred             CC-CHHHCCHHHHHHEEEECCCCCCCCEEEEECCCCCCCCCE-EECCHHHHHHHHHHHHHHH
Q ss_conf             22-223104320001000127876452000105635334421-0105376788789999998
Q gi|254781004|r  352 LK-SYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAH-VFCTKEQMFNECLKIHNLI  411 (652)
Q Consensus       352 ~~-SYrdLPlrl~e~~~~~R~E~sg~l~GL~R~ReF~~~Dah-~F~~~eq~~~e~~~~~~~~  411 (652)
T Consensus        71 l~~~--g~~-rvfqI~p~FR~E~~~~----rHl~EFtmle~E~~f~d~~dvm~~~E~li~~i  125 (329)
T cd00775          71 LIVG--GFE-RVYEIGRNFRNEGIDL----THNPEFTMIEFYEAYADYNDMMDLTEDLFSGL  125 (329)
T ss_pred             HHHC--CCC-CEEEEEECCCCCCCCC----CCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             9856--777-6799810224799997----74734563457774479999999999999999