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