HHsearch alignment for GI: 254780419 and conserved domain: cd00778

>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.
Probab=97.95  E-value=4.5e-05  Score=55.78  Aligned_cols=121  Identities=17%  Similarity=0.167  Sum_probs=75.5

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCEEEEECCCCCC-C----CC---CCCCC--CCCCCCC--CHHHHHHCC-CC----HHHHH
Q ss_conf             21245899999998752036514620332112-4----64---56645--4322222--103443112-38----54564
Q gi|254780419|r  140 KNIVKRTRIINSMRCRMIAENFIECSTPILTA-S----SP---EGARD--FLVPSRV--NQGSFYALP-QA----PQQYK  202 (622)
Q Consensus       140 ~~l~~Rs~i~~~~R~~l~~~gF~EveTP~L~k-s----Tp---eGArd--FlVPsR~--~~g~fYALp-QS----PQlyK  202 (622)
T Consensus        30 ~G~~i~~~l~~~~r~~~~~~G~~ev~~P~l~~~~~~~k~sgh~~~y~~emf~v~~~g~~~~d~~y~LkPmne~~~~~i~~  109 (261)
T cd00778          30 YGYAIWENIQKILDKEIKETGHENVYFPLLIPESELEKEKEHIEGFAPEVAWVTHGGLEELEEPLALRPTSETAIYPMFS  109 (261)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHCHHHCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             28999999999999999986996998833278899997428143057653355216852013560347888699999997


Q ss_pred             HHHHCCC--H-HHHEEEHHHHCCCCCCCCCCC----CCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             4331057--0-233110011037776655380----000356541026899999999999999999998
Q gi|254780419|r  203 QLLMASG--F-DRYFQIAPCFRDEDPRSDRLP----GEFYQLDMEMSFVEQDDILNTMENVLRGVFEEF  264 (622)
Q Consensus       203 QlLmv~G--~-dryfqiarcFRdEd~R~dRqp----~EFTqlD~EmsF~~~edvm~l~E~li~~i~~~v  264 (622)
T Consensus       110 ~~~-~SYRdLPlrl~q~g~~~R~E~s-~-~~gL~RvReF~~dDahs~~~t~eq~~~e~~~~~~-~y~~i  174 (261)
T cd00778         110 KWI-RSYRDLPLKINQWVNVFRWETK-T-TRPFLRTREFLWQEGHTAHATEEEAEEEVLQILD-LYKEF  174 (261)
T ss_pred             HHH-CCCCCCCHHHHHCCCEECCCCC-C-CCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHH-HHHHH
T ss_conf             350-5402278255530422437788-8-8765325425234233655899999999999999-99999