HHsearch alignment for GI: 254780419 and conserved domain: cd00779

>cd00779 ProRS_core_prok 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 prokaryotes and from the mitochondria of eukaryotes.
Probab=98.05  E-value=1.4e-05  Score=59.37  Aligned_cols=110  Identities=25%  Similarity=0.301  Sum_probs=69.5

Q ss_pred             CHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCC-------CC-CC-CCCCCCCCCHHHHHHC-CC-----------CHH
Q ss_conf             1245899999998752036514620332112464-------56-64-5432222210344311-23-----------854
Q gi|254780419|r  141 NIVKRTRIINSMRCRMIAENFIECSTPILTASSP-------EG-AR-DFLVPSRVNQGSFYAL-PQ-----------APQ  199 (622)
Q Consensus       141 ~l~~Rs~i~~~~R~~l~~~gF~EveTP~L~ksTp-------eG-Ar-dFlVPsR~~~g~fYAL-pQ-----------SPQ  199 (622)
T Consensus        30 G~~i~~~i~~~i~~~~~~~G~~ev~~P~l~~~~l~~~sg~~~~f~~emf~v~d~--~~~~~~L~PT~E~~~~~~~~~~i~  107 (255)
T cd00779          30 GLRVLKKIENIIREEMNKIGAQEILMPILQPAELWKESGRWDAYGPELLRLKDR--HGKEFLLGPTHEEVITDLVANEIK  107 (255)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCCCCEEEEECC--CCCEEEECCCCHHHHHHHHHHHCC
T ss_conf             999999999999999998599899765347388874425301368731544537--887773168874889999986503


Q ss_pred             HHHHHHHCCCHHHHEEEHHHHCCCCCCCC---CCCCCEEEEEEEECCCCHHHHHHHHHHHHH
Q ss_conf             56443310570233110011037776655---380000356541026899999999999999
Q gi|254780419|r  200 QYKQLLMASGFDRYFQIAPCFRDEDPRSD---RLPGEFYQLDMEMSFVEQDDILNTMENVLR  258 (622)
Q Consensus       200 lyKQlLmv~G~dryfqiarcFRdEd~R~d---Rqp~EFTqlD~EmsF~~~edvm~l~E~li~  258 (622)
T Consensus       108 SyrdLPl-----~~~q~~~~fR~E~r~~~GllR~r-EF~~~d~hsf~~~~e~a~~~~~~~~~  163 (255)
T cd00779         108 SYKQLPL-----NLYQIQTKFRDEIRPRFGLMRGR-EFLMKDAYSFDIDEESLEETYEKMYQ  163 (255)
T ss_pred             CHHHCCE-----EEECCCCEECCCCCCCCCCCEEE-EEEEEHHHCCCCCHHHHHHHHHHHHH
T ss_conf             6122574-----54135335425667886632431-37700220356998999999999999