HHsearch alignment for GI: 254780317 and conserved domain: TIGR00470
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase; InterPro: IPR005246 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 . All known phenylalanyl-tRNA synthetases, excepting a monomeric mitochondrial form, have an alpha 2 beta 2 heterotetrameric structure. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains but is longer and of unknown function; more generally, it resembles class 2 aminoacyl tRNA ligases. .
Probab=100.00 E-value=2e-31 Score=250.78 Aligned_cols=258 Identities=24% Similarity=0.449 Sum_probs=204.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEECC
Q ss_conf 99999999999999999999999999856766676543100000112321226742389999999999998739876237
Q gi|254780317|r 60 VSARGAILNQLKVDISGKISARKDFIRNQLIFEQISSQSVDVSLPVFSSPCHRGRIHPVTQVIDEVTCIFMDMGFALEEG 139 (366)
Q Consensus 60 Kk~~Gk~iNelK~~Ie~~i~~kk~~L~~~~~~~kl~~E~iDVTLP~~~~~~~~G~~HPItqvi~eI~~IF~~lGF~v~eG 139 (366)
T Consensus 12 rfdikK~~eLaekDFE~AW~e~~~~l~~~---------h~d~~YP--Rl~f~~GK~Hpl~~TI~rlReAYLr~GFsE~vN 80 (558)
T TIGR00470 12 RFDIKKVLELAEKDFEAAWKESKELLKEK---------HIDEKYP--RLKFEFGKEHPLFETIERLREAYLRLGFSEMVN 80 (558)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC---------CCCCCCC--CCCCCCCCCCCHHHHHHHHHHHHHHCCCEECCC
T ss_conf 24679999975656899989867876227---------8665687--245545888756899999999986468313007
Q ss_pred CEEECHHHHHHHHCCCCCCCCCCCCC-EEEEECCC---------------------------------------------
Q ss_conf 23415889888618988773316331-27750566---------------------------------------------
Q gi|254780317|r 140 SDIETDYYNFAALNFPDDHPARQMHD-TFFVPGIA--------------------------------------------- 173 (366)
Q Consensus 140 PEIEtd~~NFdaLNiP~~HPARdmqD-TFyl~~~~--------------------------------------------- 173 (366)
T Consensus 81 Plivde~hiyk--QFGpEA~A--VLDRCFYLagLPrPdvGlg~eki~~Ie~~gid~~deK~E~L~Evfh~YKKG~idGDD 156 (558)
T TIGR00470 81 PLIVDEVHIYK--QFGPEALA--VLDRCFYLAGLPRPDVGLGAEKIRIIEDLGIDVSDEKKERLKEVFHRYKKGEIDGDD 156 (558)
T ss_pred CEEECCEEEEE--CCCCCHHH--HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCCH
T ss_conf 74653513520--37860357--753666625787886355602778888707742101340357886314676667541
Q ss_pred --------------------------------CCCCCCCCCC-CCCHHH--H-HHHHCCCEEEEEECCCCCCCCC--CCC
Q ss_conf --------------------------------6556322446-763055--5-5430363122541057647454--421
Q gi|254780317|r 174 --------------------------------GGKHKLLRTH-TSPVQI--R-VMESQDLPIKVIVPGKTYRRDS--DST 215 (366)
Q Consensus 174 --------------------------------~~~~~lLRth-TS~vQi--R-~m~~~~pP~~~~~~GrvyR~d~--D~t 215 (366)
T Consensus 157 Lv~eia~aL~V~~~~glkvLe~vFPEfkdLKP~S~tlTLRSHMTsGWFItLs~i~dk~~lPlKLFSIDRCFRREQ~ED~s 236 (558)
T TIGR00470 157 LVYEIAEALDVEDETGLKVLEEVFPEFKDLKPVSSTLTLRSHMTSGWFITLSSIADKLKLPLKLFSIDRCFRREQKEDAS 236 (558)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHCCCCCCCCCCCHHHCCCHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCC
T ss_conf 88888766256751102133330864001688655432001010027888987875158971122003231446643531
Q ss_pred CCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEC------CCCCCCCCCEEEEEEECCCCEEEECCCC
Q ss_conf 3781002005786178668999889999999970888662645423------8898526610367875058804224688
Q gi|254780317|r 216 HSPMFHQIEGLVVSDSATIANLRWVLESFCKSFFEVSSLQMRFRPS------FFPFTEPSFEVDVRCSFSDGIIKFDEGT 289 (366)
Q Consensus 216 H~~~FhQ~egl~v~~~i~~~~lk~~l~~~~~~~fg~~~~~~r~rp~------~fPftePs~Evdv~~~~~~~~~~~~~~~ 289 (366)
T Consensus 237 hLmtYhSASCVvVdeevsvDdGKaVAEgLL~qf-GF~--~FrFrpDEKkSKYYiP~TQ--TEVyAyHPkL~Gss-tkysd 310 (558)
T TIGR00470 237 HLMTYHSASCVVVDEEVSVDDGKAVAEGLLEQF-GFE--KFRFRPDEKKSKYYIPDTQ--TEVYAYHPKLKGSS-TKYSD 310 (558)
T ss_pred CCCCEEEEEEEEECCCCCCCCCHHHHHHHHHHH-CCC--CCCCCCCCCCCCCCCCCCC--CEEEEECCCCCCCC-CCCCC
T ss_conf 001134546678577124364268899999870-854--4750576464543578885--05677626456664-41047
Q ss_pred CEEEEECCCCCCHHHHHHCCCCCCCEEEEEEECCHHHHHHHHCCCCCHHHHH
Q ss_conf 3489845756388899856988000379963134469979973897058766
Q gi|254780317|r 290 EWMEILGCGMVDPRVLRGVGIDPDIYQGFAWGMGLDRIAMLKYGMPDVREFF 341 (366)
Q Consensus 290 ~WiEi~g~Gm~~p~vl~~~g~d~~~~~g~AfG~G~eRlaml~~gi~diR~~~ 341 (366)
T Consensus 311 eWiEvATFG~YSPiALa~Y~Id~pV---MNLGlGVERlAMIlygy~DVR~MV 359 (558)
T TIGR00470 311 EWIEVATFGVYSPIALAKYDIDVPV---MNLGLGVERLAMILYGYEDVRKMV 359 (558)
T ss_pred CCEEEEECCCCHHHHHHHCCCCCCE---EECCCHHHHHHHHHHCHHHHHHCC
T ss_conf 6479874343104677416849652---225631876787781403343226