HHsearch alignment for GI: 254780680 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=99.89  E-value=1.3e-22  Score=188.82  Aligned_cols=241  Identities=22%  Similarity=0.243  Sum_probs=209.6

Q ss_pred             CHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHHHHHH-HHHCHHHHHHHHH
Q ss_conf             202211731000112221675301056488999999999998622320320212356202788986-5514224767764
Q gi|254780680|r  143 EIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDEAMYG-TGQIPKFADDMFC  221 (430)
Q Consensus       143 elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~~~~g-tG~lp~f~~~~y~  221 (430)
T Consensus         8 ~~~~~~~l~d~-~--pv~--G~~~~lP~G~~i~~~l~~~~r~~-~~~~G~~ev~~P~l~~~~~~~k~sgh~~~y~~emf~   81 (261)
T cd00778           8 EVITKAELIDY-G--PVK--GCMVFRPYGYAIWENIQKILDKE-IKETGHENVYFPLLIPESELEKEKEHIEGFAPEVAW   81 (261)
T ss_pred             HHHHHHCCCCC-C--CCC--CEEEECCCHHHHHHHHHHHHHHH-HHHCCCEEEECCCCCCHHHHHHHHCHHHCCCCCCEE
T ss_conf             99998177224-7--998--30888632899999999999999-998699699883327889999742814305765335


Q ss_pred             HH--------HCCEECCCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEE-ECCCC
Q ss_conf             31--------0002313454114544534205955504208853221078843355434321222210200212-12786
Q gi|254780680|r  222 TT--------DGRWLIPTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELV-SITRE  292 (430)
Q Consensus       222 ~~--------d~l~Li~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~-~~~~p  292 (430)
T Consensus        82 v~~~g~~~~d~~y~LkPmne~~~~~i~~~~~~SYRdLPlrl~q~g~~~R~E~s--~--~~gL~RvReF~~dDahs~~~t~  157 (261)
T cd00778          82 VTHGGLEELEEPLALRPTSETAIYPMFSKWIRSYRDLPLKINQWVNVFRWETK--T--TRPFLRTREFLWQEGHTAHATE  157 (261)
T ss_pred             EECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHCCCEECCCCC--C--CCCCCEEEEEEEECCCCCCCCH
T ss_conf             52168520135603478886999999973505402278255530422437788--8--8765325425234233655899


Q ss_pred             CCHHHHHHHHHHHHHHHHHH-HCCHHHHCCCCCHHCCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEECC
Q ss_conf             50145789899999999998-41067530378011784434024101101004833237531021007645326847338
Q gi|254780680|r  293 EDSFTEHERMLSCAEEILKR-LDLHYRVVSLCTGDLGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYRDP  371 (430)
Q Consensus       293 e~S~~~~e~~~~~~~~i~~~-L~lpyRvv~~~sgdlg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~~~  371 (430)
T Consensus       158 eq~~~e~~~~~~~y~~i~~~l~~~~~~~~~~~~~dk~~Ga~y~~~id~~~~d-gr~~q~gti~~l~~~~s~~f~l~y~~~  236 (261)
T cd00778         158 EEAEEEVLQILDLYKEFYEDLLAIPVVKGRKTEWEKFAGADYTYTIEAMMPD-GRALQSGTSHNLGQNFSKAFDIKYQDK  236 (261)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCHHCCCCCCCCCEEEEEECCC-CCEEEEEHHHHCCCCHHHHCCCEEECC
T ss_conf             9999999999999999999847815786056521116785100014787478-870467510202765356379899999


Q ss_pred             CCCCCCEEEE-ECCCHHHHHHHHHHHHH
Q ss_conf             9984101042-00432289999999988
Q gi|254780680|r  372 NSKSLKFTHT-LNGSGVAVGRCLIAILE  398 (430)
Q Consensus       372 ~~~~~~~~ht-lNgt~~A~~R~l~ailE  398 (430)
T Consensus       237 dg~~-~~phr~~~G~~---eR~ig~lI~  260 (261)
T cd00778         237 DGQK-EYVHQTSWGIS---TRLIGAIIM  260 (261)
T ss_pred             CCCC-CCCEEEEEEHH---HHHHHHHHC
T ss_conf             9998-08557412499---899889734