>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=99.78 E-value=2.6e-17 Score=128.05 Aligned_cols=316 Identities=16% Similarity=0.235 Sum_probs=218.4 Q ss_pred HHHHHHHHHHHHHCCCCCC-----CCCCC-CCCCHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHCCCCCCCCHH Q ss_conf 9999999999863786887-----22443-68858999999998401288851674166024565566631689710045 Q gi|254780486|r 47 LLREKILSSLDSKIPIGSG-----GSRLL-CGNYNQHLELEEEAADFFGFEKMLYFGSGYAANMAILSTLPQATDLIVYD 120 (381) Q Consensus 47 ~v~~a~~~a~~~~~g~~~~-----~sr~~-~G~~~~~~~lE~~lA~~~g~e~al~~~sG~~An~~~i~~l~~~~d~ii~D 120 (381) T Consensus 19 vLt~~ArkAl~-EfGDGYSVCDfC~G~Ld~v~~PpI~~F~~daLA~FlG~D~~R~t~GARe~KfaVMhalC~~GD~vV~D 97 (381) T TIGR02539 19 VLTEAARKALV-EFGDGYSVCDFCEGRLDEVTKPPIKDFLEDALAEFLGMDVVRVTHGAREGKFAVMHALCKEGDVVVLD 97 (381) T ss_pred CCHHHHHHHEE-EECCCCEEEECCCCEECCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCHHHHHHHHHHCCCCCEEEEC T ss_conf 78377871004-22685238530387703525883100045542667279745406775024578876408998989985 Q ss_pred HHCCHHHHHHHHHCCCCCEEEC-CC-------CHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHC Q ss_conf 4202677526664087640305-68-------814789976431000247860797146215766134689999986313 Q gi|254780486|r 121 KLVHASIREGINSGKAQAIAIP-HN-------NINSFAENINKWRKSGGKGFPWIVVESIYSMDGDKAPLDDLVKIANDY 192 (381) Q Consensus 121 ~~~HaSi~~g~~ls~a~~~~f~-Hn-------D~~~Le~~l~~~~~~~~~~~~~vv~egv~Sm~G~~apL~~i~~l~~~y 192 (381) T Consensus 98 ~~AHYtsyvAAEragl~v~eVPy~~g~P~Y~v~~e~Y~~viee~~d~~G~~~~LallThvDG~YGNL~DA~kva~vc~~~ 177 (381) T TIGR02539 98 GLAHYTSYVAAERAGLNVKEVPYETGHPEYKVDPEGYKEVIEEVEDESGKPVALALLTHVDGEYGNLADAKKVAKVCREK 177 (381) T ss_pred CCCCHHHHHHHHHCCCEEEECCCCCCCCEEEECHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHC T ss_conf 87454458999754972788165588860764166788888655202798834899840268867511245687665420 Q ss_pred CEEEEECCCCCCCCCCCCCCEEEEEHHCCCCCCCCCCCCCCCCCEE--EEEECCCCCCCCCCCCC--CCE---------- Q ss_conf 6089861311222347776401100001346521001346565302--67524510010000121--100---------- Q gi|254780486|r 193 DGFIVVDEAHATGVCGPLGKGLTHIIEERNNVIVMHSCSKALGSSG--ALVGSNKIIYDYLINYA--KPF---------- 258 (381) Q Consensus 193 ~~~LivDEah~~Gv~G~~G~G~~~~~~~~~~~iv~~TlsKa~g~~G--G~i~~~~~ii~~l~~~~--~~~---------- 258 (381) T Consensus 178 gvPlLLNCAY~vG---RmP---v~~ke-~~~DFiVGSGHKSMAASaP~GvLa~~eE~~~~v~r~SslrGdvsG~~~~~KE 250 (381) T TIGR02539 178 GVPLLLNCAYTVG---RMP---VSAKE-IKADFIVGSGHKSMAASAPCGVLAMSEEWEDKVLRKSSLRGDVSGRKFPVKE 250 (381) T ss_pred CCCEEECCCCEEE---EEC---CCCCC-CCCCEEEECCCCHHHHCCCEEECCCCCCCCCCHHCCCCCCCCCCCCCCCCCE T ss_conf 7862212450521---003---15777-7876778068513221266002145422234011023210033663447412 Q ss_pred ---ECCCCC-CCCHHHHHHHHHHHHHHC-CCHHHHH---HHHHHHHHHHH-HCCCCCCCCCC-EEEEEE--------CCH Q ss_conf ---001357-750257898878988627-1022478---99999999876-41797899897-289995--------897 Q gi|254780486|r 259 ---IYTTSP-SPILAVVACEALKLIKRK-PALHKSL---LQLINITDKIA-NKKIGFSSQSH-IQSIVI--------GDN 320 (381) Q Consensus 259 ---ifst~l-~P~~~aaa~aal~~l~~~-~~~~~~l---~~~~~~~~~~~-~~~~g~~~~s~-I~~v~~--------gd~ 320 (381) T Consensus 251 vElLGCT~rGap--~~TlmASfP~VveRV~~Wd~Ev~ktRy~v~eLE~igG~~QlG~kPk~HDLv~FEtPgf~Eia~~~k 328 (381) T TIGR02539 251 VELLGCTSRGAP--IVTLMASFPHVVERVKRWDEEVKKTRYFVAELEDIGGFKQLGVKPKEHDLVKFETPGFHEIAKKHK 328 (381) T ss_pred EEECCCCCCHHH--HHHHHHCCCHHHHHCCCHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCEEECCCCCHHHHCCCC T ss_conf 774486324047--999973281011220231566777657888764217888648688825641444884013414487 Q ss_pred HHHHHHHHHHHHCCEEEEEECCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999779189862288888887039996287899999999999999998873 Q gi|254780486|r 321 KSCLNIAKNLQKKGFDIRAIRPPTVPINTARLRISITLNVDEPTIVKLFDILPQIISEG 379 (381) Q Consensus 321 ~~a~~~~~~L~~~Gi~v~~i~~PtVp~~~~rlRi~v~a~~t~edi~~~~~~l~~v~~E~ 379 (381) T Consensus 329 r~GyFLY~ELKkRgi~--GI~~----G~Tk~~K~Sv-YGL~~Eqv~~Vv~sf~eI~e~~ 380 (381) T TIGR02539 329 RRGYFLYEELKKRGIV--GIRS----GQTKEIKLSV-YGLTKEQVEYVVDSFKEIVEEY 380 (381) T ss_pred CCCCCHHHHHHHCCCE--ECCC----CCCEEEEEEE-ECCCCCHHHHHHHHHHHHHHHC T ss_conf 9776405665315830--0178----8742776433-1275211444467899999854

HHsearch alignment for GI: 254780486 and conserved domain: TIGR02539