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