HHsearch alignment for GI: 255764513 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=97.25 E-value=0.0061 Score=40.31 Aligned_cols=449 Identities=15% Similarity=0.148 Sum_probs=216.5
Q ss_pred CCEEEECCCCCCCCCCHHHHHHHHHHHHHH-----HHCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 770563484338878501599999999999-----971884999970486663886799999999886589888676558
Q gi|255764513|r 5 SKVRVRIAPSPTGEPHIGTAYTALFNYLIA-----KRTGGKFILRIEDTDSKRSTLESENAVMQSLKWCGLNWDEGPDIG 79 (492)
Q Consensus 5 ~~v~~RfaPsPtG~lH~G~~rtal~n~l~a-----~~~~g~f~lRieDtd~~R~~~~~~~~i~~~l~wlgl~~De~~~~~ 79 (492)
T Consensus 19 ~~~~~~~g~~p~g~~~~g~~~~~~~~d~~~~~l~~~g~~~~~~~~~d~~d~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~ 98 (539)
T TIGR00467 19 NLYTVASGITPSGHIHLGNLREVLTADAIARALLDSGGEAKLIYIADDYDPLRKLYPFLPEQEELETYLGLPLTKIPDPE 98 (539)
T ss_pred CCEEEECCCCCCCCEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 21033204676660330421456768888888750676147888524510344304567506788887410122067854
Q ss_pred CCCCCEECCCCHHHHHHHHHHHHHCCCEEEC------CC-------------CHHHHHHHHHHHHHHHCCCC---CCCCC
Q ss_conf 8767632326289999999999988982451------48-------------89997766887664310002---36655
Q gi|255764513|r 80 GAYGPYRQSERKNIYQPYVQNLLEKKLAFRC------FC-------------STERLEEMRRAQRKRNIPSR---YDGHC 137 (492)
Q Consensus 80 g~~~p~~QS~r~~~y~~~~~~L~~~g~aY~c------~~-------------t~eel~~~r~~~~~~~~~~~---Y~~~~ 137 (492)
T Consensus 99 ~~~~~~~~-~~~~~---~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~w~p~~~~c 174 (539)
T TIGR00467 99 GCCDSYAE-HFLRP---FLESLPVLGIPPEFYRADENYTEGLYDSKIKIALDNREELAEILNEYRGSPLEEDWYPISPLC 174 (539)
T ss_pred CHHHHHHH-HHHHH---HHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHH
T ss_conf 20245666-66656---676422116760211013444201012112333310678999987640465643233202433
Q ss_pred CCCCHHHHHHHHHCCCCCEEEEEECCCC-EEECCCCCCCCEEC-CCCCC-CCCCEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 5788333001120257740788622431-14304751340213-64323-564100045324898678876444444431
Q gi|255764513|r 138 LKLSSQEIERLSQEQKKHVVRLTVPNQG-SCVFQDKVYGEMEI-PWNAV-DMQVLLKSDGMPTYHLANVIDDHLMKITHV 214 (492)
Q Consensus 138 r~l~~~e~~~~~~~g~~~~iR~k~p~~~-~~~~~D~i~G~~~~-~~~~~-~D~vi~r~dg~ptY~~a~vvDD~~m~ithv 214 (492)
T Consensus 175 ~~c-----------~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~~~~~~~~~~l~w~~d-w~~~w~~~~~~~~p~g~d~~ 242 (539)
T TIGR00467 175 ENC-----------GRLTTTVVNYDDEYEWIEYECEICGNEGSVGPRYTGGGKLPWRVD-WPARWKILKVTFEPAGKDHA 242 (539)
T ss_pred HCC-----------CCCCCEEECCCCCCCEEEEEEEECCCCCCCCCCEECCCCCCEEEC-CCCCCEEEEEECCCCCCCCC
T ss_conf 203-----------531000210244322267764331665544420102311212203-10001133321043675200
Q ss_pred HCCCCCCCHHHHHHHHHHHHHHCCCH---HHHHHHHHHHHCCCCCCCCCC-CCHHHHHHCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 12235430247889999985100000---101455531101322122343-30245666297737799899850676665
Q gi|255764513|r 215 ARGEEWISSVPKHILLYQYFNFPIPE---FIHLPLIKNPDKSKLSKRRNP-TSISYYSAMGYLPEALINFLALLFVHKSE 290 (492)
Q Consensus 215 iRg~d~~~~t~~q~~l~~al~~~~p~---f~H~pli~~~~g~klSKR~~~-~~i~~~~~~GylPeAilNyLalLGws~~~ 290 (492)
T Consensus 243 ~~gg~~d~~~~~~---~~~~~~~pp~~~~~~~~~~~~gd~~~~~~~~~g~~~~~~~~~~-~~~p~-~~~~~~~~-~~p~~ 316 (539)
T TIGR00467 243 AAGGSYDTGVLIA---KEIFDYEPPYPVPYEWISLKGGDKGGPLSSSKGDVLPVKDWLE-VYPPE-ILRFLLLR-TKPNT 316 (539)
T ss_pred CCCCCCHHHHHHH---HHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCEEEHHHHHH-HCCHH-HHHHHHHH-CCCCC
T ss_conf 1576410246788---8875057884202324565025423323234563232334544-21435-75554531-16775
Q ss_pred CCHHHCCHHHHHHHH-HHHHCCCCCCC------CHHHHHHHHHHHHHHCC-CCHH--------HHHHHHHHHHC---CCC
Q ss_conf 530110146777652-02113755442------01565566435555126-9989--------99986444200---001
Q gi|255764513|r 291 DDDELMDMQQLIHHF-DLHHLSKAGAV------FDKQKLDWLNGRWIREK-LSTT--------EFLSRVSQWMK---EKD 351 (492)
Q Consensus 291 ~d~Eifsl~eli~~F-dL~~I~Ks~A~------FD~eKL~wlN~qyIr~~-l~~~--------el~~~l~~~l~---~~~ 351 (492)
T Consensus 317 ~~~~~~d~~~~~d~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d 396 (539)
T TIGR00467 317 EKHIDFDLGKIPDLGDDYDKLEDFYYGFKDKDELSEKKRAFKRIYELSTPYLPGETVPYDVPFRHLSVIGQLFEDEEKED 396 (539)
T ss_pred CEEEECCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHCCHHHHHHHHHHHCCCCHHH
T ss_conf 21220240232356777777777762232034544566666655420255434442100024046666665540100000
Q ss_pred C-CCCHHHHHHHCCCHHHHHHH---------------HHHHHHCCCCCCCHH-HHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf 2-32206888725320356677---------------556752246788854-554331486679999999999840588
Q gi|255764513|r 352 R-LTQALTLAQSRITTLSALPQ---------------MTDFLFKSDLHLTAE-SFKSTALCPEEIIDILKTTQEEFEVIQ 414 (492)
Q Consensus 352 ~-l~~il~likeRi~tL~Di~~---------------~~~ffF~~~~~~d~e-~~~k~~~~~e~~~~iL~~~~~~L~~~~ 414 (492)
T Consensus 397 ~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 476 (539)
T TIGR00467 397 WDLEKVLEILKRTGYTVDDVDDFSLKLLEKRLLCARNWLLKYAPEDVKFSLPEKEDVYEELEEEEKKWLKELAEKLKKDF 476 (539)
T ss_pred CCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 00899999986315531003466788888888888888875041000320202456788764457899999999864210
Q ss_pred CC-CHHHHHHHHHHHHHHHCCCHHHHCCEEEEEEECCCCCCCHHHHHHHHCHHHHHHHHHHH
Q ss_conf 89-98889999999999957982331012678896488888899999884959999999999
Q gi|255764513|r 415 IW-KRENIETALRNVAQHREKSLKIIVKPLFLAITGSKYSLPLFDSIEILGRSVVYFRLRHA 475 (492)
Q Consensus 415 ~w-~~e~Ie~~ik~i~e~~giK~k~l~~PLRiALTG~~~GP~L~eil~lLGkeetl~RL~~a 475 (492)
T Consensus 477 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gp~~~~~~~~~g~~~~~~~~~~~ 538 (539)
T TIGR00467 477 EPALEQDLHNLIYDVSKELGLEPALAFQAIYKILLGKEYGPKLGGFLKTLGVDWVEKRTSLY 538 (539)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 02333467889988776506635688999999883343452256788875367788887641