HHsearch alignment for GI: 254780573 and conserved domain: TIGR00467

>TIGR00467 lysS_arch lysyl-tRNA synthetase; InterPro: IPR002904 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). A refined crystal structures shows that 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=97.78  E-value=0.0038  Score=42.88  Aligned_cols=285  Identities=15%  Similarity=0.197  Sum_probs=142.6

Q ss_pred             CCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCH---------HHHHHHHHC---CCCC
Q ss_conf             9847999616788884441112799999999999997079984579960552338---------889999870---8986
Q gi|254780573|r   23 PSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYYYGEKCVTYVRNITDIDD---------KIIERARQE---HPSI   90 (461)
Q Consensus        23 ~~~v~~Y~CGpTvy~~~HiG~~r~~v~~D~l~R~L~~~~~~~~V~~v~niTDidD---------kii~~a~~~---~~~~   90 (461)
T Consensus        17 ~~~~~~~~~g~~p~g~~~~g~~~~~~~~d~~~~~l~~~g~~~~~~~~~d~~d~~~~~~~~~p~~~~~~~~~~~~~~~~p~   96 (539)
T TIGR00467        17 PANLYTVASGITPSGHIHLGNLREVLTADAIARALLDSGGEAKLIYIADDYDPLRKLYPFLPEQEELETYLGLPLTKIPD   96 (539)
T ss_pred             CCCCEEEECCCCCCCCEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHCCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             53210332046766603304214567688888887506761478885245103443045675067888874101220678


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCH--------------HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECC
Q ss_conf             4488489999999999999877626854100--------------01235677778999998741143201289287522
Q gi|254780573|r   91 PINDAISIITSKNTQQFVKDTTRLACLAPTH--------------QPRATNHIPQMIYLIQNIILHGHAYEANNEIIFDT  156 (461)
Q Consensus        91 ~~~~~~~~~a~~~~~~f~~d~~~L~v~~p~~--------------~pr~t~~i~~~i~~i~~L~~~g~aY~~~g~VyFdv  156 (461)
T Consensus        97 ~-~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~----~~~l~~~w-~p~  170 (539)
T TIGR00467        97 P-EGCCDSYAEHFLRPFLESLPVLGIPPEFYRADENYTEGLYDSKIKIALDNREELAEILNEYR----GSPLEEDW-YPI  170 (539)
T ss_pred             C-CCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCC-CCC
T ss_conf             5-42024566666656676422116760211013444201012112333310678999987640----46564323-320


Q ss_pred             HHC-CCCCCCCCCCHHHHHHHHHC--CCC-CCCCCCCCE-EEEECCCCCCCEEECCCCCCCCCCCCHHHHHHHHHCCCCE
Q ss_conf             002-45432246754666643210--222-210123512-6663377666314146776676433204777787529841
Q gi|254780573|r  157 SSI-PNYGSFSRRKIDEQKMGTRV--PEK-YHKKNPADF-ILWKRSTPMEPGWESPWGRGRPGWHIECSAMSSHYLGKVF  231 (461)
Q Consensus       157 ~~~-~~YG~Ls~~~~~~~~~g~r~--~~~-~~K~~p~DF-aLWK~~~~~e~~w~spwG~GRPGWHiECsam~~~~lg~~~  231 (461)
T Consensus       171 ~~~c~~c~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~~~~~~~~~~l~w~~dw~~~w~~----~~--------------~  232 (539)
T TIGR00467       171 SPLCENCGRLTTTVVNYDDEYEWIEYECEICGNEGSVGPRYTGGGKLPWRVDWPARWKI----LK--------------V  232 (539)
T ss_pred             HHHHHCCCCCCCEEECCCCCCCEEEEEEEECCCCCCCCCCEECCCCCCEEECCCCCCEE----EE--------------E
T ss_conf             24332035310002102443222677643316655444201023112122031000113----33--------------2


Q ss_pred             EEEEECCCCCCCCCHHHH---HHHHHHCC--CCCCHHHEECCCEEEE--EECCCCCCCCCCCCHHHHHCCCCCCCCCCCH
Q ss_conf             487413566668751366---88886408--7530121003432576--4202233233214089985025334557779
Q gi|254780573|r  232 DIHGGGLDLIFPHHENEI---AQSCCADR--IEKTANIWIHNGFLNL--EGRKMSKSNGNFITINELLETKKFGGRSWPA  304 (461)
Q Consensus       232 DIH~GG~DL~FPHHENEi---AQs~a~~~--~~~~a~yWlH~G~l~i--~geKMSKSlGN~iti~dlL~~~~~~~k~y~p  304 (461)
T Consensus       233 ~~~p~g~d~~~~gg~~d~~~~~~~~~~~~~pp~~~~~~~~~~---~~gd~~~~~~~~~g~~~~~~~~~-------~~~~p  302 (539)
T TIGR00467       233 TFEPAGKDHAAAGGSYDTGVLIAKEIFDYEPPYPVPYEWISL---KGGDKGGPLSSSKGDVLPVKDWL-------EVYPP  302 (539)
T ss_pred             ECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEEEEE---ECCCCCCCCCCCCCCEEEHHHHH-------HHCCH
T ss_conf             104367520015764102467888875057884202324565---02542332323456323233454-------42143


Q ss_pred             HHHHHHHHCCCC--CCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999842566--4321145034687776432100001
Q gi|254780573|r  305 PVIRLAMLMTHY--REPIDFTVQRLTEAEILLSKWPQTS  341 (461)
Q Consensus       305 ~viR~~lLsshY--RspLdfS~e~L~~A~~~l~kl~~~~  341 (461)
T Consensus       303 ~~~~~~~~~~~p~~~~~~~~d~~~~~d~~~~~d~~~~~~  341 (539)
T TIGR00467       303 EILRFLLLRTKPNTEKHIDFDLGKIPDLGDDYDKLEDFY  341 (539)
T ss_pred             HHHHHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHHH
T ss_conf             575554531167752122024023235677777777776