HHsearch alignment for GI: 254780191 and conserved domain: cd00733

>cd00733 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. This alignment contains only sequences from the GlyRS form which heterotetramerizes. The homodimer form of GlyRS is in a different family of class II aaRS. Class II assignment is based upon structure and the presence of three characteristic sequence motifs.
Probab=98.25  E-value=0.0002  Score=53.42  Aligned_cols=169  Identities=24%  Similarity=0.372  Sum_probs=101.0

Q ss_pred             CHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCHHEEECCCCCCCCC-CCCCCCCCCCCCCCCCCCEECCCCCCCH---H
Q ss_conf             87899999999999789889116675667787100230143475540-0588799999851115432248987863---4
Q gi|254780191|r    3 NVSSIRTTFLEFFQKNGHELLPSSSLIPCNDPTLMFTNSGMVPFKNI-FTGQEKPVYQAVTTVQKCVRAGGKHNDL---D   78 (898)
Q Consensus         3 s~~eiR~~fl~fF~~~~H~~~~s~slvp~~d~~llft~Agm~~fk~~-f~G~~~p~~~r~~~~QkCiR~ggkhnDl---d   78 (898)
T Consensus         1 tfq~ii~~L~~fW~~~GC~i~qpyd~e---------~GAg--T~hp~T~lr~lg~~pw~~aYvqPsrRP----~DgRYG~   65 (279)
T cd00733           1 TFQDLILKLQKFWASQGCLIIQPYDME---------VGAG--TFHPATFLRALGPEPWNVAYVEPSRRP----TDGRYGE   65 (279)
T ss_pred             CHHHHHHHHHHHHHHCCCEEECCCCCC---------CCCC--CCCHHHHHHHCCCCCCEEEEECCCCCC----CCCCCCC
T ss_conf             978999999999987796887676542---------4646--588899886319986315542467799----9987778


Q ss_pred             HCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHH---HHHCCC-CHHHEEEC
Q ss_conf             34648850017888542231475378899989986133418981237999718828999975---663499-98997535
Q gi|254780191|r   79 NVGRTNRHHTFFEMLGNFSFGGYFKERAIQLAWDLLTKEFDLDQRRLYITVYDEDEEAFKLW---KKISGL-SADKIIRI  154 (898)
Q Consensus        79 ~VG~t~rH~TfFEMlGn~SfgdYfK~eai~~awe~lt~~~~l~~~~l~vtv~~~D~e~~~iW---~~~~gi-~~~~i~~~  154 (898)
T Consensus        66 NPNR-lq~y~QfQVilKPsp-----------------------------------~n~q~lYL~SL~~igid~~~hDIrF  109 (279)
T cd00733          66 NPNR-LQHYYQFQVIIKPSP-----------------------------------DNIQELYLESLEALGINPKEHDIRF  109 (279)
T ss_pred             CCCH-HCEEEEEEEEECCCC-----------------------------------HHHHHHHHHHHHHCCCCCCCCCEEE
T ss_conf             9323-100034579987895-----------------------------------6589999998998497954362478


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             78666545799999877046788538556898887778898268960011234430478875657665310175799999
Q gi|254780191|r  155 TTNDNFWSMAETGPCGPCSEIFFDQGECIPGGLPGSSEEGERYIEIWNLVFMQFEQQNKQERFILPKMSIDTGMGLERMA  234 (898)
Q Consensus       155 ~~~dNfW~~g~~GpcGPcsEi~~d~g~~~~~~~~~~~~~~~r~lEiwNlVFmq~~~~~~g~~~~Lp~~~IDTGmGLERl~  234 (898)
T Consensus       110 v-eDn-WEsPtLGAwGlGWEVwld------------------GMEItQFTYFQ---QvGG--i~c~pv~~EiTYGLERia  164 (279)
T cd00733         110 V-EDN-WESPTLGAWGLGWEVWLD------------------GMEVTQFTYFQ---QVGG--IPCKPISVEITYGLERIA  164 (279)
T ss_pred             E-ECC-CCCCCCCCCCCCEEEEEC------------------CEEEEEEEEEE---EECC--EECCCCCEEEEHHHHHHH
T ss_conf             6-147-878753102343499987------------------75776435121---1378--214453233101199999


Q ss_pred             HHHCCCCCCCHHH
Q ss_conf             9988798530057
Q gi|254780191|r  235 TVLQEKTNNYDID  247 (898)
Q Consensus       235 ~vlqg~~s~ydtD  247 (898)
T Consensus       165 MylQ~vd~v~dl~  177 (279)
T cd00733         165 MYLQGVDNVYDIE  177 (279)
T ss_pred             HHHHCCCHHEEEE
T ss_conf             9985754231412