HHsearch alignment for GI: 254781004 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=100.00  E-value=0  Score=506.78  Aligned_cols=245  Identities=23%  Similarity=0.407  Sum_probs=213.8

Q ss_pred             HCCEEEECCCCCCEEEEECCHHHHHHHHHHHHHHHHH-CCCEEEECCCCCCCCCC-CCCCCCCCCCCCCCEEECCCCCCC
Q ss_conf             1440442267874356501078999999999998876-89638555432443100-011210012555420100145677
Q gi|254781004|r  252 EMDLFHIAEDGSGVIFWHRKGWKIFQTLISYMRRKIK-DDYEEINTPQVLDQHLW-QQSGHWDSYRANMFAVKCADDTIK  329 (652)
Q Consensus       252 ~~~lf~~~~~~~G~~~wlP~G~~i~~~ie~~ir~~~~-~G~~eV~tP~l~~~~Lw-~~SGh~~~y~~~mf~~~~~~~~~~  329 (652)
T Consensus        12 ~~~l~d~~-pv~G~~~~lP~G~~i~~~l~~~~r~~~~~~G~~ev~~P~l~~~~~~~k~sgh~~~y~~emf~v~~-~g~~~   89 (261)
T cd00778          12 KAELIDYG-PVKGCMVFRPYGYAIWENIQKILDKEIKETGHENVYFPLLIPESELEKEKEHIEGFAPEVAWVTH-GGLEE   89 (261)
T ss_pred             HHCCCCCC-CCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHCHHHCCCCCCEEEEC-CCCCC
T ss_conf             81772247-99830888632899999999999999998699699883327889999742814305765335521-68520


Q ss_pred             CCCEEEECCCCHHHHHHHHHHCCCCHHHCCHHHHHHEEEECCCCCCCCEEEEECCCCCCCCCE-EECCHHHHHHHHHHHH
Q ss_conf             782377434312577776520122223104320001000127876452000105635334421-0105376788789999
Q gi|254781004|r  330 DLRTFALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAH-VFCTKEQMFNECLKIH  408 (652)
Q Consensus       330 ~~~~~~LkPmncp~h~~i~~~~~~SYrdLPlrl~e~~~~~R~E~sg~l~GL~R~ReF~~~Dah-~F~~~eq~~~e~~~~~  408 (652)
T Consensus        90 ~d~~y~LkPmne~~~~~i~~~~~~SYRdLPlrl~q~g~~~R~E~s~-~~gL~RvReF~~dDahs~~~t~eq~~~e~~~~~  168 (261)
T cd00778          90 LEEPLALRPTSETAIYPMFSKWIRSYRDLPLKINQWVNVFRWETKT-TRPFLRTREFLWQEGHTAHATEEEAEEEVLQIL  168 (261)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHCCCEECCCCCC-CCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             1356034788869999999735054022782555304224377888-876532542523423365589999999999999


Q ss_pred             HHHHHHHHHHCCCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCC
Q ss_conf             99887665521332100014653112586035778999999999850212125667520555555455432110021103
Q gi|254781004|r  409 NLIISIYKDFGFEKIMVKLSTRPEKRVGSDALWDDAENIMKGVLDTIKNSSQDRINTGVLLGEGAFYGPKFEYILKDAIG  488 (652)
Q Consensus       409 ~~~~~v~~~~g~~~~~~~ls~~~~~~~g~~~~~~~ae~~l~~~l~~~~~~~~~~~~~~~~~g~~afygpkid~~~~d~~g  488 (652)
T Consensus       169 ~~y~~i~~~l~~~--~~~~~~~~~--------~d--------------------------k~~Ga~y~~~id~~~~d--g  210 (261)
T cd00778         169 DLYKEFYEDLLAI--PVVKGRKTE--------WE--------------------------KFAGADYTYTIEAMMPD--G  210 (261)
T ss_pred             HHHHHHHHHHCCE--EEEEECCCH--------HC--------------------------CCCCCCCCEEEEEECCC--C
T ss_conf             9999999984781--578605652--------11--------------------------16785100014787478--8


Q ss_pred             CCCCCCCC-CHHHHCCCCCCCEEEEECCCEEEEEEEEECCCHHHHHHHHHHHH
Q ss_conf             31001211-01110223467416731797213799640341037899999999
Q gi|254781004|r  489 RDWQCGTI-QVDFNLPSRFNAFYVNSHSEKCHPVMIHRAVFGSIERFIGIMIE  540 (652)
Q Consensus       489 r~~~~~ti-q~df~~p~~f~l~y~~~dg~~~~pvmihr~~~Gs~eR~ia~liE  540 (652)
T Consensus       211 r~~q~gti~~l~~~~s~~f~l~y~~~dg~~~~p---hr~~~G~~eR~ig~lI~  260 (261)
T cd00778         211 RALQSGTSHNLGQNFSKAFDIKYQDKDGQKEYV---HQTSWGISTRLIGAIIM  260 (261)
T ss_pred             CEEEEEHHHHCCCCHHHHCCCEEECCCCCCCCC---EEEEEEHHHHHHHHHHC
T ss_conf             704675102027653563798999999998085---57412499899889734