HHsearch alignment for GI: 254780419 and conserved domain: TIGR00459

>TIGR00459 aspS_bact aspartyl-tRNA synthetase; InterPro: IPR004524 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module . This family represents aspartyl-tRNA synthetases from the bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=1730.52  Aligned_cols=587  Identities=42%  Similarity=0.716  Sum_probs=567.4

Q ss_pred             CCC-CCHHHCCHHHCCCEEEEEEEEC-CCCCCCC-EEEEEEECCCC-EEEEEECCC--CHHHHHHHCCCCCCEEEEEEEE
Q ss_conf             774-2042369799898899997980-0444698-79999977982-599997488--1578998528988589999999
Q gi|254780419|r    4 YRT-HSCGDLGVSDVGSFVRLSGWVH-RVRPHGG-IIFLDIRDHYG-ITQVVANPD--SACFEIAKSVRSEWVLCIDGLV   77 (622)
Q Consensus         4 ~Rt-h~cg~l~~~~~g~~V~i~GwV~-~~R~~g~-l~F~~lrD~sG-~~Q~v~~~~--~~~~~~~~~l~~esvv~v~G~V   77 (622)
T Consensus         2 ~r~t~~cg~l~~~~~G~~Vtl~GWv~qr~rdlG~nliFidlRD~~GdivQv~~~p~~~~~a~~~a~~lr~E~vv~v~G~v   81 (653)
T TIGR00459         2 MRTTHYCGQLSEKHLGKTVTLAGWVKQRRRDLGGNLIFIDLRDRSGDIVQVVCDPDVSKDALELAKGLRNEDVVQVKGKV   81 (653)
T ss_pred             CCCEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCEEEEEEECCCCCEEEEEECCCCCHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             86304501343011687799985431340115881799986258888899986775678899999733552289999999


Q ss_pred             EECCCCCCCCCCCCCEEEEEEEEEEEEE-CCCCCCCCCCC-CCCCCHH---HHCCCCCEEECCCCCCCCHHHHHHHHHHH
Q ss_conf             9758655588777865999988999950-21179986457-6678987---82112320001211112124589999999
Q gi|254780419|r   78 MSRSAETINANIITGQIELSAQKIEILS-VAEELPLPVFG-EREYPES---IRFKYRFLDLRRDTLHKNIVKRTRIINSM  152 (622)
Q Consensus        78 ~~r~~~~~n~~~~tG~~Ei~~~~~~il~-~a~~~P~~~~~-~~~~~e~---~rl~~R~LdLR~~~~~~~l~~Rs~i~~~~  152 (622)
T Consensus        82 ~~R~~~~~~~~l~tg~~Ei~~~~i~~~NG~s~~~P~~~~Df~~~a~e~~EDvRLkYRYLDLRrp~~~~~L~lR~~v~~~~  161 (653)
T TIGR00459        82 SARPEGSINRNLDTGEIEILAEEITLLNGKSKTPPLIIEDFKTDAEEEREDVRLKYRYLDLRRPEMQQRLKLRHKVTKAV  161 (653)
T ss_pred             EECCCCCCCCCCCCCEEEEECCCEEEEECCCCCCCCEEECCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             86585344655676348898186268612126879403235200000101666100222204878999986688989999


Q ss_pred             HHHHHCCCEEEEECCCCCCCCCCCCCCCCCCCCCC----HHHHHHCCCCHHHHHHHHHCCCHHHHEEEHHHHCCCCCCCC
Q ss_conf             87520365146203321124645664543222221----03443112385456443310570233110011037776655
Q gi|254780419|r  153 RCRMIAENFIECSTPILTASSPEGARDFLVPSRVN----QGSFYALPQAPQQYKQLLMASGFDRYFQIAPCFRDEDPRSD  228 (622)
Q Consensus       153 R~~l~~~gF~EveTP~L~ksTpeGArdFlVPsR~~----~g~fYALpQSPQlyKQlLmv~G~dryfqiarcFRdEd~R~d  228 (622)
T Consensus       162 Rn~l~~~gFleiETP~LtKsTPEGARDyLVPsRv~rsdG~g~FYALpQSPQlfKQLLMvsG~drYyQIArCFRDEDLRAD  241 (653)
T TIGR00459       162 RNFLDQQGFLEIETPILTKSTPEGARDYLVPSRVHRSDGKGEFYALPQSPQLFKQLLMVSGVDRYYQIARCFRDEDLRAD  241 (653)
T ss_pred             HHHHHHCCCCEEECCCCCCCCCCCHHHCCCCCCCCCCCCCCCEECCCCCHHHHHHHHHHCCCCCCEEEEEEECCCCCCCC
T ss_conf             86664278706506777788843110157755300368588451468975689998751255531357889766256665


Q ss_pred             CCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHC---CCCCCCC---CCC-----------CCHHHHHHHCCCCCC
Q ss_conf             38000035654102689999999999999999999808---7234577---321-----------218988751367776
Q gi|254780419|r  229 RLPGEFYQLDMEMSFVEQDDILNTMENVLRGVFEEFSN---GNTVSNN---FLR-----------ICYDDAIRRYGTDKP  291 (622)
Q Consensus       229 Rqp~EFTqlD~EmsF~~~edvm~l~E~li~~i~~~v~~---~~~i~~p---F~r-----------mtY~eAm~~YGsDKP  291 (622)
T Consensus       242 RQP-EFTQiD~E~SF~~~~~vm~l~E~l~~~vf~~v~~krGl~~L~~~GtlfP~kkenGtvsifrmty~EAm~~yGsDKP  320 (653)
T TIGR00459       242 RQP-EFTQIDMEMSFMTQEDVMDLIEKLVSGVFKEVKGKRGLIDLKKPGTLFPVKKENGTVSIFRMTYQEAMERYGSDKP  320 (653)
T ss_pred             CCC-CCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCEEEEECCCCEEEEEECCHHHHHHHCCCCCC
T ss_conf             778-7324426311289356899999999999999707851375078852411221676079985567999861677687


Q ss_pred             CCCCCCCCCCCCCCCC-----CCCHHHHHHHHHCCCCCEEEEEECCCC--CCCCCCHHHHH---HHHHHHHHCCCCCEEE
Q ss_conf             4447640124431017-----875245666874037847999962787--66521035677---9998764202462355
Q gi|254780419|r  292 DLRNPIIMHNVTEHFV-----HSEFRVFSKILSVNPGYEVWAIPAKGG--GGNRAFCDRMN---EWARSQGQPGLAYIFW  361 (622)
Q Consensus       292 DLR~~lei~dit~~~~-----~~~f~vf~~~~~~~~~~~v~~i~~~~~--~~srk~~D~l~---e~ak~~g~kgL~~i~~  361 (622)
T Consensus       321 DLR~~~el~dv~d~f~afshld~~F~vF~~~~~~P-~g~v~~i~v~~~~~~ls~~~i~~l~~~~~~a~~~GakGlAy~~v  399 (653)
T TIGR00459       321 DLRFGLELIDVSDLFKAFSHLDSEFKVFSNLINAP-GGRVKAIRVKGGDAELSRKSIKELRVLIKFAKEYGAKGLAYLKV  399 (653)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCC-CCEEEEEECCCCCCCCCHHHHHHHCHHHHHHHHCCCCEEEEEEE
T ss_conf             78888346777667777664067534579998488-85577577278642255021222011445676658631566565


Q ss_pred             EECCCCCCCCCCCHHHHCCHHHHHHHHHHHCCCCCCCEE--EEECC-CCCCCCHHH--HHHHHHHHHHH--CCCCCCEEE
Q ss_conf             204777533357025532527899999981887557269--98088-541100134--78899987730--035575102
Q gi|254780419|r  362 RLDESGNVAGMGPVAKHLNIVNTEAIRVRLDMQDGDSCF--FIAGD-PLKFCSFAA--DARNHIAQELG--IINCNCFEF  434 (622)
Q Consensus       362 ~~~~~~~~~~~spi~K~l~~~~~~~l~~~~~~~~GD~i~--f~a~~-~~~~~~~lg--~lR~~ia~~l~--li~~~~~~f  434 (622)
T Consensus       400 ~~~~~~~~~~~~~i~kfL~~~~~~~~~~~t~a~~gdillnPfg~~~l~~~v~~~lgGkalRl~l~~~l~sWL~d~~~~~f  479 (653)
T TIGR00459       400 NEDAEGLEEVKSPIKKFLDEKKLKKLLERTDAQEGDILLNPFGAGDLKKIVLDALGGKALRLKLGKDLGSWLVDPDAFSF  479 (653)
T ss_pred             ECCCCCCCCCCCHHHHCCCHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCE
T ss_conf             21674102453101202473577889987421268786557786058999998504168899987653000235231471


Q ss_pred             EEEEE---------CCCEEECCCCCCCCHHHCCCCCCCCCHHHHHCCCHHHHHHHCCCEEECCEEECCCCEECCCHHHHH
Q ss_conf             88960---------770535455470002110024766430655418877741313677775677212512315699999
Q gi|254780419|r  435 CWIMD---------FPFYEWNEEEKKIDFAHNPFTMPQGGMESLKGNDLLSIKAFQYDLVCNGFEIASGGIRNHMSEVML  505 (622)
Q Consensus       435 lWV~D---------FPLFe~dee~~r~~s~HHPFTaP~~~~~~l~~~dp~~v~a~~YDLVlNG~EiggGSiRIHd~~iQ~  505 (622)
T Consensus       480 lWv~DksGkkeklaFP~fE~d~~E~~~~a~HHpFT~Pk~~~~~~lE~~p~~a~a~aYDlVlNG~ElGGGSiRIh~~~~Q~  559 (653)
T TIGR00459       480 LWVVDKSGKKEKLAFPLFEKDEEEGRLVAAHHPFTMPKPEDLEDLETAPEEALAEAYDLVLNGVELGGGSIRIHDPEVQE  559 (653)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHCCHHHHHHHCCCEEEEEEEECCCEEEECCHHHHH
T ss_conf             78983788702342765667765275584057889875122787740745541202876883069887104642878999


Q ss_pred             HHHH-HCCCCHHHHHHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             9999-859998999866778999986084973422246899999983739840321378999871034688672898899
Q gi|254780419|r  506 QAFS-NVGISKEVVENRFGGLYRAFQCGMPPHGGIAAGIDRIVMLLLGAKNVREVSLFPMSQNFCDLLMGSPSTVSVEQL  584 (622)
Q Consensus       506 ~~f~-~lgl~~ee~~~~Fg~lL~Al~yG~PPHgG~alGlDRlvmll~g~~sIRdVIaFPKt~~g~Dlm~~aPs~v~~~qL  584 (622)
T Consensus       560 ~~F~d~Lgid~eea~EkFGFLLeA~~yGaPPHgG~A~GlDRL~Mll~~~~nIRDVIAFPKt~~a~cL~T~APs~~~~~~L  639 (653)
T TIGR00459       560 KVFEDILGIDPEEAREKFGFLLEAFKYGAPPHGGLALGLDRLVMLLTGTDNIRDVIAFPKTAQASCLLTEAPSEIDEKQL  639 (653)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCHHHHHHCCCCCCCHHHH
T ss_conf             99987628898998776356875873576851015555899999980899722001788760124341148775798884


Q ss_pred             HHCCCEEE
Q ss_conf             87083560
Q gi|254780419|r  585 RELGLRIV  592 (622)
Q Consensus       585 ~e~~i~~~  592 (622)
T Consensus       640 ~~l~i~~~  647 (653)
T TIGR00459       640 EELSIKYS  647 (653)
T ss_pred             HHHHHHHC
T ss_conf             11323313