HHsearch alignment for GI: 254780928 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=99.67  E-value=9e-16  Score=121.57  Aligned_cols=149  Identities=17%  Similarity=0.134  Sum_probs=113.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCHHHHHHHHCCCCCCCCCCCCEEEEECCC----CCEEEECC
Q ss_conf             37998765886689999999999999999859848016520228875202675543332216898699----98899988
Q gi|254780928|r   10 ELPRGFADCPTKEIRIRNRILDSIRNIYENYGFDPIETPLLEYSDSLGKFLPDEDRPNKGVFSLQDDD----GQWISLRY   85 (496)
Q Consensus        10 ~~P~G~~D~~p~~~~~~~~i~~~l~~~f~~~G~~~I~tP~lE~~~~~~~~~~~~~~~~k~~y~f~D~~----g~~l~LRp   85 (496)
T Consensus        19 ~pv~G~~~~lP~G~~i~~~l~~~~r~~~~~~G~~ev~~P~l~~~~~~~k~sgh~~~y~~emf~v~~~g~~~~d~~y~LkP   98 (261)
T cd00778          19 GPVKGCMVFRPYGYAIWENIQKILDKEIKETGHENVYFPLLIPESELEKEKEHIEGFAPEVAWVTHGGLEELEEPLALRP   98 (261)
T ss_pred             CCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHCHHHCCCCCCEEEECCCCCCCCCCCCCCC
T ss_conf             79983088863289999999999999999869969988332788999974281430576533552168520135603478


Q ss_pred             CCHHHHHHHHHHHH-HHCCCCHHHHHHHHHHCCC-CCCCC--CCCCCCCCCHHHHHCCCHHHHHH---HHHHHHHHHHHC
Q ss_conf             88389999999511-2055411233101333025-87644--42111110001210000245788---999999999751
Q gi|254780928|r   86 DLTAPLARYVAENF-DTIVFPCRTYRIGPVFRNE-KHGPG--RFRQFIQCDVDNVGSSAETADAE---MCMMMADTLEAV  158 (496)
Q Consensus        86 DlT~~~aR~~~~~~-~~~~~p~k~yy~g~vfR~e-~p~~G--r~REf~Q~g~eiiG~~~~~~DaE---ii~l~~~~l~~l  158 (496)
T Consensus        99 mne~~~~~i~~~~~~SYRdLPlrl~q~g~~~R~E~s~~~gL~RvReF~~dDahs~~~t~eq~~~e~~~~~~~y~~i~~~l  178 (261)
T cd00778          99 TSETAIYPMFSKWIRSYRDLPLKINQWVNVFRWETKTTRPFLRTREFLWQEGHTAHATEEEAEEEVLQILDLYKEFYEDL  178 (261)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCHHHHHCCCEECCCCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88699999997350540227825553042243778888765325425234233655899999999999999999999984