HHsearch alignment for GI: 254780317 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=95.12  E-value=0.38  Score=29.39  Aligned_cols=199  Identities=13%  Similarity=0.141  Sum_probs=101.0

Q ss_pred             CCHHHHHHHHHHHHHHHCCCEEECCCEE--ECHHHH-HHHHCCCCCCCCCCCCCEEEEECC---CCCCCCCCCCCCCCHH
Q ss_conf             2389999999999998739876237234--158898-886189887733163312775056---6655632244676305
Q gi|254780317|r  115 IHPVTQVIDEVTCIFMDMGFALEEGSDI--ETDYYN-FAALNFPDDHPARQMHDTFFVPGI---AGGKHKLLRTHTSPVQ  188 (366)
Q Consensus       115 ~HPItqvi~eI~~IF~~lGF~v~eGPEI--Etd~~N-FdaLNiP~~HPARdmqDTFyl~~~---~~~~~~lLRthTS~vQ  188 (366)
T Consensus        32 ~~i~~~l~~~~r~~~~~~G~~ev~~P~l~~~~~~~k~s-------gh~~~y~~emf~v~~~g~~~~d~~y~LkPmne~~~  104 (261)
T cd00778          32 YAIWENIQKILDKEIKETGHENVYFPLLIPESELEKEK-------EHIEGFAPEVAWVTHGGLEELEEPLALRPTSETAI  104 (261)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-------CHHHCCCCCCEEEECCCCCCCCCCCCCCCCCHHHH
T ss_conf             99999999999999998699699883327889999742-------81430576533552168520135603478886999


Q ss_pred             HHHH----HH-CCCEEEEEECCCCCCCCCCCCCC----CCCCCCCEEEECC--C---CCHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             5554----30-36312254105764745442137----8100200578617--8---66899988999999997088866
Q gi|254780317|r  189 IRVM----ES-QDLPIKVIVPGKTYRRDSDSTHS----PMFHQIEGLVVSD--S---ATIANLRWVLESFCKSFFEVSSL  254 (366)
Q Consensus       189 iR~m----~~-~~pP~~~~~~GrvyR~d~D~tH~----~~FhQ~egl~v~~--~---i~~~~lk~~l~~~~~~~fg~~~~  254 (366)
T Consensus       105 ~~i~~~~~~SYRdLPlrl~q~g~~~R~E~s~~~gL~RvReF~~dDahs~~~t~eq~~~e~~~~~~~y~~i~~~l~~~~-~  183 (261)
T cd00778         105 YPMFSKWIRSYRDLPLKINQWVNVFRWETKTTRPFLRTREFLWQEGHTAHATEEEAEEEVLQILDLYKEFYEDLLAIP-V  183 (261)
T ss_pred             HHHHHHHHCCCCCCCHHHHHCCCEECCCCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCEE-E
T ss_conf             999973505402278255530422437788887653254252342336558999999999999999999999847815-7


Q ss_pred             EEEEEEC--CCCCCCCCCEEEEEEECCCCEEEECCCCCEEEEECCCCCCHHHHHHCCC---CCC-----CEEEEEEECCH
Q ss_conf             2645423--8898526610367875058804224688348984575638889985698---800-----03799631344
Q gi|254780317|r  255 QMRFRPS--FFPFTEPSFEVDVRCSFSDGIIKFDEGTEWMEILGCGMVDPRVLRGVGI---DPD-----IYQGFAWGMGL  324 (366)
Q Consensus       255 ~~r~rp~--~fPftePs~Evdv~~~~~~~~~~~~~~~~WiEi~g~Gm~~p~vl~~~g~---d~~-----~~~g~AfG~G~  324 (366)
T Consensus       184 ~~~~~~~~dk~~Ga~y~~~id~~~----------~dgr~~q~gti~~l~~~~s~~f~l~y~~~dg~~~~phr~-~~G~~-  251 (261)
T cd00778         184 VKGRKTEWEKFAGADYTYTIEAMM----------PDGRALQSGTSHNLGQNFSKAFDIKYQDKDGQKEYVHQT-SWGIS-  251 (261)
T ss_pred             EEECCCHHCCCCCCCCCEEEEEEC----------CCCCEEEEEHHHHCCCCHHHHCCCEEECCCCCCCCCEEE-EEEHH-
T ss_conf             860565211167851000147874----------788704675102027653563798999999998085574-12499-


Q ss_pred             HHHHHHHCC
Q ss_conf             699799738
Q gi|254780317|r  325 DRIAMLKYG  333 (366)
Q Consensus       325 eRlaml~~g  333 (366)
T Consensus       252 eR~ig~lI~  260 (261)
T cd00778         252 TRLIGAIIM  260 (261)
T ss_pred             HHHHHHHHC
T ss_conf             899889734