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