HHsearch alignment for GI: 254780419 and conserved domain: TIGR00499

>TIGR00499 lysS_bact lysyl-tRNA synthetase; InterPro: IPR002313 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 . Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and some eubacteria . Moreover in some eubacteria there is a gene X, which is similar to a part of lysyl-tRNA synthetase from class II. Lysyl-tRNA synthetase is duplicated in some species with, for example in E. coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding .; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=1.4e-45  Score=345.08  Aligned_cols=446  Identities=23%  Similarity=0.402  Sum_probs=303.4

Q ss_pred             CHHHC-CCEEEEEEEECCCC-CCCCEEEEEEECCC-----CEEEEEECCCCH------HHHHHHCC---CCCCEEEEEEE
Q ss_conf             97998-98899997980044-46987999997798-----259999748815------78998528---98858999999
Q gi|254780419|r   13 GVSDV-GSFVRLSGWVHRVR-PHGGIIFLDIRDHY-----GITQVVANPDSA------CFEIAKSV---RSEWVLCIDGL   76 (622)
Q Consensus        13 ~~~~~-g~~V~i~GwV~~~R-~~g~l~F~~lrD~s-----G~~Q~v~~~~~~------~~~~~~~l---~~esvv~v~G~   76 (622)
T Consensus        52 ~~~~~p~~~~~~~g~~~~~~~~~~~~~f~~~~~~~g~~~d~~~~~~~~~~~~gg~~p~~~~~~~~~~~~~~gd~~~~~g~  131 (538)
T TIGR00499        52 ELEEKPELEVSIAGRILALRFSGGKATFITLQDESGLKNDGQLQLYVNKDDLGGPEPDFYEFDEYLNFLDLGDIIGVTGY  131 (538)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHCCHHHCCCEEEECCC
T ss_conf             21114320001222466555412322578862566544563378887301147876430233320120102541232034


Q ss_pred             EEECCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCCCCCCCHHHHCCCCCEEE-CCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             997586555887778659999889999502117998645766789878211232000-1211112124589999999875
Q gi|254780419|r   77 VMSRSAETINANIITGQIELSAQKIEILSVAEELPLPVFGEREYPESIRFKYRFLDL-RRDTLHKNIVKRTRIINSMRCR  155 (622)
Q Consensus        77 V~~r~~~~~n~~~~tG~~Ei~~~~~~il~~a~~~P~~~~~~~~~~e~~rl~~R~LdL-R~~~~~~~l~~Rs~i~~~~R~~  155 (622)
T Consensus       132 ~g~-------~~~~~~~l~~~~~~~~~~~~~~~-~~p~~~~gl~d~e~~~~~~~~d~~~n~~~~~~~~~~~~~~~~~~~~  203 (538)
T TIGR00499       132 PGP-------FKTKTGELSLHVTELQLLTKALR-PLPDKWHGLTDQETRYRQRYLDLIVNPDSRDTFLKRSKIIAAIRRF  203 (538)
T ss_pred             CCC-------CCCCCCEEEEEEHHHHHHHHHHH-CCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             453-------22444114554013456677642-2651004665156777765543310502466778899999999998


Q ss_pred             HHCCCEEEEECCCCCCCCCCC--CCCCCCCCCCCHH----HHHHCCCCHHHHHHHHHCCCHHHHEEEHHHHCCCCCCCCC
Q ss_conf             203651462033211246456--6454322222103----4431123854564433105702331100110377766553
Q gi|254780419|r  156 MIAENFIECSTPILTASSPEG--ARDFLVPSRVNQG----SFYALPQAPQQYKQLLMASGFDRYFQIAPCFRDEDPRSDR  229 (622)
Q Consensus       156 l~~~gF~EveTP~L~ksTpeG--ArdFlVPsR~~~g----~fYALpQSPQlyKQlLmv~G~dryfqiarcFRdEd~R~dR  229 (622)
T Consensus       204 ~~~~g~~e~e~p~~~-~~~gg~~~~pf~~----~~n~~~~~~~-~~~~~e~~l~~l~~gg~~~~~e~g~~f~neg~~~~h  277 (538)
T TIGR00499       204 LDDRGFLEVETPLLQ-VIPGGANARPFIT----HHNALDLDLY-LRIAPELYLKRLVVGGLEKVYEIGRNFRNEGVDTTH  277 (538)
T ss_pred             HHHCCCEEECCCHHH-CCCCCCCCCCCEE----CCCCCCCCHH-HHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCC
T ss_conf             762484221131010-1267654465010----0232244212-112257788777640136778764333104665445


Q ss_pred             CCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCC-----CCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             80000356541026899999999999999999998087234-----5773212189887513677764447640124431
Q gi|254780419|r  230 LPGEFYQLDMEMSFVEQDDILNTMENVLRGVFEEFSNGNTV-----SNNFLRICYDDAIRRYGTDKPDLRNPIIMHNVTE  304 (622)
Q Consensus       230 qp~EFTqlD~EmsF~~~edvm~l~E~li~~i~~~v~~~~~i-----~~pF~rmtY~eAm~~YGsDKPDLR~~lei~dit~  304 (622)
T Consensus       278 np-ef~~~e~y~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~p~p~~~~~~~~~~~~-------~~~~~~~~~~~~~~  349 (538)
T TIGR00499       278 NP-EFTSLEFYQAYADYEDLLDLTENLFKFLAKELLGTTKITRLPVPKTFPELTYGDLE-------LDLKKPWKRITMLD  349 (538)
T ss_pred             CC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCCCCCHHHCCCCC-------CCCCCCCHHHHHHH
T ss_conf             75-30245567765108899998999999999875321100112566543112203210-------02355400224567


Q ss_pred             CCCCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCHHHHCCHHHH
Q ss_conf             01787524566687403784799996278766521035677999876420246235520477753335702553252789
Q gi|254780419|r  305 HFVHSEFRVFSKILSVNPGYEVWAIPAKGGGGNRAFCDRMNEWARSQGQPGLAYIFWRLDESGNVAGMGPVAKHLNIVNT  384 (622)
Q Consensus       305 ~~~~~~f~vf~~~~~~~~~~~v~~i~~~~~~~srk~~D~l~e~ak~~g~kgL~~i~~~~~~~~~~~~~spi~K~l~~~~~  384 (622)
T Consensus       350 --------------------------------------~~~~~~~--~~~g~~~~-----------------~~~~~~~~  372 (538)
T TIGR00499       350 --------------------------------------ALKKYDL--LETGIDFD-----------------DLKDDETA  372 (538)
T ss_pred             --------------------------------------HHHHHHH--HCCCCCCH-----------------HCCHHHHH
T ss_conf             --------------------------------------7765200--00465400-----------------10025788


Q ss_pred             HHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEE--EEEEEECCCEEECCCCCCCCHHHCCCCCC
Q ss_conf             9999981887557269980885411001347889998773003557510--28896077053545547000211002476
Q gi|254780419|r  385 EAIRVRLDMQDGDSCFFIAGDPLKFCSFAADARNHIAQELGIINCNCFE--FCWIMDFPFYEWNEEEKKIDFAHNPFTMP  462 (622)
Q Consensus       385 ~~l~~~~~~~~GD~i~f~a~~~~~~~~~lg~lR~~ia~~l~li~~~~~~--flWV~DFPLFe~dee~~r~~s~HHPFTaP  462 (622)
T Consensus       373 ~~~~~~~~~~----~~~~~~~~--~~~~~~~~~~~~~~~--~~e~~~~~~~p~~~~~~p~-----~~~-------pl~~~  432 (538)
T TIGR00499       373 KALAKELGIK----YFEVAEDS--GPLTLGHILNELFEE--FLEHTLIQTLPTFITGYPA-----EIS-------PLAKR  432 (538)
T ss_pred             HHHHHHHHHH----HHCCCCCC--CCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHCCCH-----HHC-------CHHCC
T ss_conf             8888875433----20223457--742068899998888--7755666532143404641-----222-------10005


Q ss_pred             CCCHHHHHCCCHHHHHHHCCCEEECCEEECCCCEECCCHHHHHHHHH------HCC--CCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             64306554188777413136777756772125123156999999999------859--9989998667789999860849
Q gi|254780419|r  463 QGGMESLKGNDLLSIKAFQYDLVCNGFEIASGGIRNHMSEVMLQAFS------NVG--ISKEVVENRFGGLYRAFQCGMP  534 (622)
Q Consensus       463 ~~~~~~l~~~dp~~v~a~~YDLVlNG~EiggGSiRIHd~~iQ~~~f~------~lg--l~~ee~~~~Fg~lL~Al~yG~P  534 (622)
T Consensus       433 -------~~~~p~--~~~~fe~f~~g~e~~n~~~e~~~p~~~~~~~~~~~~~~~~gg~~~~~~~~~~d~~~~~~l~~g~p  503 (538)
T TIGR00499       433 -------NPSNPE--LTDRFELFIGGKEIANAFSELNDPLDQRERFEAQLAEKEAGGNKTDDEAPLLDEDFVEALEYGLP  503 (538)
T ss_pred             -------CCCCCC--HHHHHHHEECCHHHHCCHHHHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             -------777753--01111100101122010122046278899999988887506775410344433678888871688


Q ss_pred             CCCCEECCHHHHHHHHCCCCCCEEEECCCCCC
Q ss_conf             73422246899999983739840321378999
Q gi|254780419|r  535 PHGGIAAGIDRIVMLLLGAKNVREVSLFPMSQ  566 (622)
Q Consensus       535 PHgG~alGlDRlvmll~g~~sIRdVIaFPKt~  566 (622)
T Consensus       504 p~~g~g~g~d~l~~l~~~~~~~~~~~~fp~~~  535 (538)
T TIGR00499       504 PTGGLGIGIDRLVMLLTDSPSIRDVLLFPALR  535 (538)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCHHHHHHCCCCC
T ss_conf             65654432777877661675101332025313