HHsearch alignment for GI: 254780432 and conserved domain: TIGR02539
>TIGR02539 SepCysS Sep-tRNA:Cys-tRNA synthase; InterPro: IPR013375 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 . Many archaeal species lack cysteinyl-tRNA synthetase, an essential enzyme that provides Cys-tRNA(Cys) in other organisms. Instead, in a two step pathway, tRNA-Cys is acylated with O-phosphoserine (Sep) to form Sep-tRNA(Cys), which is subsequently converted to Cys-tRNA(Cys) . This pathway is also thought to function as the sole route of cysteine biosynthesis in these organisms. Several other archaeal species use both this pathway and direct tRNA(Cys) aminoacylation to synthesize Cys-tRNA(Cys), but this pathway appears to be the only route for cysteine biosynthesis. Proteins in this entry catalyse the second step in this pathway using pyridoxal phosphate and a sulphur donor to synthesize Cys from Sep while attached to the tRNA..
Probab=97.75 E-value=0.00075 Score=45.63 Aligned_cols=287 Identities=16% Similarity=0.203 Sum_probs=165.1
Q ss_pred CHHHHHHHHH-HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 8189999986-520101333123565554035677766543200134786002343546565432123455321134799
Q gi|254780432|r 73 STQQEIFANH-LIHSTFADRVFFTNSGAESVECAIKTARRYHYMAGKTNKFRIVTFEGAFHGRTLATISAGGKLQYLEGF 151 (392)
Q Consensus 73 ~~~~~~la~~-L~~~~~~~~v~f~~SGseA~e~Aiklar~~~~~~g~t~r~~ii~~~~~yHG~t~~a~s~s~~~~~~~~~ 151 (392)
T Consensus 50 ~PpI~~F~~daLA~FlG~D~~R~t~GARe~KfaVM-----h--alC~~GD--~vV~D~~AHYtsyvAAEragl~v~eV-- 118 (381)
T TIGR02539 50 KPPIKDFLEDALAEFLGMDVVRVTHGAREGKFAVM-----H--ALCKEGD--VVVLDGLAHYTSYVAAERAGLNVKEV-- 118 (381)
T ss_pred CCCHHHHHHHHHHHHHCCCEEECCCCCCHHHHHHH-----H--HHCCCCC--EEEECCCCCHHHHHHHHHCCCEEEEC--
T ss_conf 88310004554266727974540677502457887-----6--4089989--89985874544589997549727881--
Q ss_pred CCCCCCCCC-----CCCHH-HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCEEEECCCCCCCCCC
Q ss_conf 986433322-----21002-688754101233222233322221124621012322110223457213101100344445
Q gi|254780432|r 152 GPKIEGFDQ-----AKFCD-LQSLKNQISNDTAAILIEPIQGEGGVRKVPEEFLQQLRKICDDIDALLIFDEVQTGYGRT 225 (392)
Q Consensus 152 ~p~~~~~~~-----~~~~d-~~~l~~~~~~~iAavi~Epv~g~~G~~~~~~~~l~~l~~lc~~~g~llI~DEV~tG~GRt 225 (392)
T Consensus 119 -Py~~g~P~Y~v~~e~Y~~viee~~d~~G~~~~LallThvDG~YGNL~-D---A~kva~vc~~~gvPlLLNCAY~-vGRm 192 (381)
T TIGR02539 119 -PYETGHPEYKVDPEGYKEVIEEVEDESGKPVALALLTHVDGEYGNLA-D---AKKVAKVCREKGVPLLLNCAYT-VGRM 192 (381)
T ss_pred -CCCCCCCEEEECHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCH-H---HHHHHHHHHHCCCCEEECCCCE-EEEE
T ss_conf -65588860764166788888655202798834899840268867511-2---4568766542078622124505-2100
Q ss_pred CCCCCCCCCCCCCCEEECC--CCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCC--------CCCCHHHHHHHHHHHH-
Q ss_conf 5531011124545302103--44444434432100011122222332-2345321--------1110012334554320-
Q gi|254780432|r 226 GKLFAYEWANVKPDIMTIA--KGMGGGFPIGACLATNEVAACMNQGS-HGSTYGG--------NVLAMVLGEKVLNIIQ- 293 (392)
Q Consensus 226 G~~f~~e~~gi~PDi~~~g--K~l~gG~P~sav~~~~~i~~~~~~~~-~~~T~~g--------npl~~aaa~a~L~~l~- 293 (392)
T Consensus 193 ----Pv~~ke~~~DFiVGSGHKSMAASaP~GvLa~~eE~~~~v~r~SslrGdvsG~~~~~KEvElLGCT~rGap~~TlmA 268 (381)
T TIGR02539 193 ----PVSAKEIKADFIVGSGHKSMAASAPCGVLAMSEEWEDKVLRKSSLRGDVSGRKFPVKEVELLGCTSRGAPIVTLMA 268 (381)
T ss_pred ----CCCCCCCCCCEEEECCCCHHHHCCCEEECCCCCCCCCCHHCCCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHH
T ss_conf ----3157777876778068513221266002145422234011023210033663447412774486324047999973
Q ss_pred C-CCCCCHHHH------HCCHHHHHHHHHHHHCCCEEEEECCCEE------EEEEEECC-------C---HHHHHHHHHH
Q ss_conf 1-222101121------0000268899998867970755046400------99987249-------9---8999999996
Q gi|254780432|r 294 S-DGFLENVIN------IAKILFEGLTAIKNRFPNMFLEVRGQGL------LIGLKTVF-------S---PALLAAKFRD 350 (392)
Q Consensus 294 ~-~~l~~~~~~------~g~~l~~~L~~l~~~~~~~v~~vRG~Gl------~~~ie~~~-------~---~~~~~~~l~~ 350 (392)
T Consensus 269 SfP~VveRV~~Wd~Ev~ktRy~v~eLE~i--------gG~~QlG~kPk~HDLv~FEtPgf~Eia~~~kr~GyFLY~ELKk 340 (381)
T TIGR02539 269 SFPHVVERVKRWDEEVKKTRYFVAELEDI--------GGFKQLGVKPKEHDLVKFETPGFHEIAKKHKRRGYFLYEELKK 340 (381)
T ss_pred CCCHHHHHCCCHHHHHHHHHHHHHHHHHC--------CCEEECCCCCCCCCCEEECCCCCHHHHCCCCCCCCCHHHHHHH
T ss_conf 28101122023156677765788876421--------7888648688825641444884013414487977640566531
Q ss_pred CCEEEEECC-CCEEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 898996268-988995589868899999999999999998
Q gi|254780432|r 351 ECLLTAPSS-DNVVRILPPLTITAEEIHEGLERIERTAIK 389 (392)
Q Consensus 351 ~Gll~~~~~-~~~irl~Ppl~it~~eid~~i~~l~~al~~ 389 (392)
T Consensus 341 Rgi~GI~~G~Tk~~K~Sv-YGL~~Eqv~~Vv~sf~eI~e~ 379 (381)
T TIGR02539 341 RGIVGIRSGQTKEIKLSV-YGLTKEQVEYVVDSFKEIVEE 379 (381)
T ss_pred CCCEECCCCCCEEEEEEE-ECCCCCHHHHHHHHHHHHHHH
T ss_conf 583001788742776433-127521144446789999985