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