HHsearch alignment for GI: 254780680 and conserved domain: TIGR00415
>TIGR00415 serS_MJ seryl-tRNA synthetase; InterPro: IPR004503 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 . Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa . The seryl-tRNA synthetases from a few of the archaea that belong to this group are different from the set of mutually more closely related seryl-tRNA synthetases from eubacteria, eukaryotes, and other archaea (IPR002317 from INTERPRO).; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=98.99 E-value=3.7e-09 Score=88.81 Aligned_cols=265 Identities=20% Similarity=0.337 Sum_probs=205.7
Q ss_pred EEEECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCEEHHHHHCCHH
Q ss_conf 20001565665666211220221173100011222167530105648899999999999862232032021235620278
Q gi|254780680|r 125 IRSVGKKPSAIHLSREHFEIGEALGLMDFDRATKLSGARFSVLTGHLAHLERALGQFMIDLHTSEHGYTEVSAPLLVRDE 204 (430)
Q Consensus 125 i~~~G~~~~f~f~~k~H~elge~l~liDfe~a~kvsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~Gy~~v~~P~lv~~~ 204 (430)
T Consensus 182 ~~~~~~~~~~~~~-~dp~~~~~~~gw~~-----~~pg~g~w~~~p~~~~~~~~~~~~~~~~~~~~~g~~~c~~p~~~p~~ 255 (520)
T TIGR00415 182 VAEYKAKRDFFFD-GDPTDEAEKLGWVK-----KFPGRGQWFYGPPITALFRALEELFVEEVVKPLGFVECLFPKLIPLD 255 (520)
T ss_pred HHHHHHCCCEEEC-CCCHHHHHHHCCHH-----CCCCCCCEECCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_conf 3321100120005-77345676611011-----26887620016506788888998889887654011345310010267
Q ss_pred HHHHHHHCHHHHHHHHHH--------------------------------HH-CCEECCCCCCHHHHHHHHHCCCHHHHC
Q ss_conf 898655142247677643--------------------------------10-002313454114544534205955504
Q gi|254780680|r 205 AMYGTGQIPKFADDMFCT--------------------------------TD-GRWLIPTSEVSLTNLYSHEIIESKSLP 251 (430)
Q Consensus 205 ~~~gtG~lp~f~~~~y~~--------------------------------~d-~l~Li~TaEvpL~~~~~~~~l~~~~LP 251 (430)
T Consensus 256 ~~~~~~~~~g~p~g~~~~~~p~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~dpg~~~~p~~c~p~~~~~~~~~~~~~d~p 335 (520)
T TIGR00415 256 ILYKLRYLEGLPEGLYYCCPPKRDPELFEEFKNELLINKEVPLDLLKNGLKDPGYVLAPAQCEPFYQFLEGEVVDAEDLP 335 (520)
T ss_pred HHHHHHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCEECCCCCCHHHHHHCCCCCCCCCCC
T ss_conf 77776764136545255227755635789876655420035578987530487704303110035675412110000143
Q ss_pred CEEEEE-ECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHC---------C
Q ss_conf 208853-221078843355434321222210200212127865014578989999999999841067530---------3
Q gi|254780680|r 252 LRFTTL-APSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREEDSFTEHERMLSCAEEILKRLDLHYRVV---------S 321 (430)
Q Consensus 252 ik~~~~-s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe~S~~~~e~~~~~~~~i~~~L~lpyRvv---------~ 321 (430)
T Consensus 336 ~~~~d~~gw~~~w~~gg----~~g~d~~~~~~~~~~~w~~~p~~~~~~~d~~~~~~~~~~~~~~~~~~~~~gddp~~~~g 411 (520)
T TIGR00415 336 VKFFDRSGWTYRWEGGG----AKGLDRVNEFLRVELVWLGEPGFTEETRDKTLELAEDLADELDLEWWTEVGDDPFYLEG 411 (520)
T ss_pred EEEECCCCCEEEECCCC----CCCHHHHHHHHHEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHEEECCCCCEEECC
T ss_conf 11220577424423766----32124554533111355147520123334456655555554100110011786301036
Q ss_pred C--CCHHCCCHHHEEEEEEEECCCCC---CEEEEEEECCCCCHHHHHCCCEEECCCCCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf 7--80117844340241011010048---332375310210076453268473389984101042004322899999999
Q gi|254780680|r 322 L--CTGDLGFSACKTYDLEVWLAGQN---LYREISSCSTCGNFQSRRMNSRYRDPNSKSLKFTHTLNGSGVAVGRCLIAI 396 (430)
Q Consensus 322 ~--~sgdlg~~a~~~~DiE~w~P~~~---~y~Ev~S~Snc~D~QsrRl~iry~~~~~~~~~~~htlNgt~~A~~R~l~ai 396 (430)
T Consensus 412 ~~~~~~g~~~pd~p~~~~~~~~p~~~d~~~g~~~~~~~~~g~~~~~g--~~~~~~~~~~---~w~-gc~g~g~~~w~~g~ 485 (520)
T TIGR00415 412 RKKEDRGIEFPDVPKYELRLWLPGREDERKGVAVTSANVHGTHFVEG--FRIKDYKGLN---VWT-GCTGYGLTRWVYGF 485 (520)
T ss_pred CCCCCCCCCCCCCCCHHHEEECCCCCCCCCCEEEEECCCCCCEEECC--CEEHHCCCCE---EEC-CCCCCCHHHHHHHH
T ss_conf 42000256577775201101057743111340455303344100012--1000003650---110-33322046787777
Q ss_pred HHHCCCCCC
Q ss_conf 883468998
Q gi|254780680|r 397 LENYLNADG 405 (430)
Q Consensus 397 lEn~q~~dg 405 (430)
T Consensus 486 ~~~~g~~~~ 494 (520)
T TIGR00415 486 LAQYGFEFG 494 (520)
T ss_pred HHHHCCCCC
T ss_conf 765056667