HHsearch alignment for GI: 254780602 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=99.25 E-value=2.9e-11 Score=88.65 Aligned_cols=295 Identities=17% Similarity=0.195 Sum_probs=181.0
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCC-CCCCCCC
Q ss_conf 9999999864210133332233233454333322222223322322223333-2322222222222222222-2222322
Q gi|254780602|r 73 LREAIVEKFRRDNDLHYTSDQIIVGTGAKHVIFNALMATVNMGDEVLIPRPY-WVSYPDMVALCGGIPVFVD-TQQDDNF 150 (400)
Q Consensus 73 lR~aia~~~~~~~g~~~~~e~I~it~G~~~~l~~~~~~~~~~Gd~Vlv~~P~-y~~y~~~~~~~g~~~~~v~-~~~~~~~ 150 (400)
T Consensus 57 ~~daLA~Fl----G~----D~~R~t~GARe~KfaVMhalC~~GD~vV~D~~AHYtsyv-AAEragl~v~eVPy~~g~P~Y 127 (381)
T TIGR02539 57 LEDALAEFL----GM----DVVRVTHGAREGKFAVMHALCKEGDVVVLDGLAHYTSYV-AAERAGLNVKEVPYETGHPEY 127 (381)
T ss_pred HHHHHHHHH----CC----CEEECCCCCCHHHHHHHHHHCCCCCEEEECCCCCHHHHH-HHHHCCCEEEECCCCCCCCEE
T ss_conf 455426672----79----745406775024578876408998989985874544589-997549727881655888607
Q ss_pred CCHHHHHHCCCCC-------CCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf 2103331000122-------122012113542100001233332111223333320111012211000001223322211
Q gi|254780602|r 151 QVSPEKLEQAITP-------KTKWLFLNSPSNPSGVVYSQNRLRALADVLVRNPHVHIISDDIYEHIVYRNCQFSNIVNV 223 (400)
Q Consensus 151 ~~d~~~l~~~i~~-------~~k~i~l~nP~NPTG~v~s~~~l~~i~~~~a~~~~i~ii~De~Y~~l~~~~~~~~s~~~~ 223 (400)
T Consensus 128 ~v~~e~Y~~viee~~d~~G~~~~LallThvDG~YGNL---~DA~kva~vc-~~~gvPlLLNCAY~v----GRmPv~~ke~ 199 (381)
T TIGR02539 128 KVDPEGYKEVIEEVEDESGKPVALALLTHVDGEYGNL---ADAKKVAKVC-REKGVPLLLNCAYTV----GRMPVSAKEI 199 (381)
T ss_pred EECHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCC---HHHHHHHHHH-HHCCCCEEECCCCEE----EEECCCCCCC
T ss_conf 6416678888865520279883489984026886751---1245687665-420786221245052----1003157777
Q ss_pred CCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC---C------------CCCCCCCCCCCCCCCCCCCCC
Q ss_conf 1233322574146544322344544422110122687531001---2------------223322222222222234676
Q gi|254780602|r 224 EPSLYERTLVVNGVSKAYAMTGLRIGYAAGALSLIKSMIVLQG---Q------------QTSGACSIAQWAAVEALNGPQ 288 (400)
Q Consensus 224 ~~~~~~~~i~~~S~SK~~~~~G~RiG~~v~~~~li~~l~~~~~---~------------~~~~~~~~~q~a~~~~l~~~~ 288 (400)
T Consensus 200 ~~-----DFiVGSGHKSMAASa-P~GvLa~~eE~~~~v~r~SslrGdvsG~~~~~KEvElLGCT~r--Gap~~Tlm-ASf 270 (381)
T TIGR02539 200 KA-----DFIVGSGHKSMAASA-PCGVLAMSEEWEDKVLRKSSLRGDVSGRKFPVKEVELLGCTSR--GAPIVTLM-ASF 270 (381)
T ss_pred CC-----CEEEECCCCHHHHCC-CEEECCCCCCCCCCHHCCCCCCCCCCCCCCCCCEEEECCCCCC--HHHHHHHH-HCC
T ss_conf 87-----677806851322126-6002145422234011023210033663447412774486324--04799997-328
Q ss_pred CCCCCCCCCCC---CCCCCHHHHHHCCCCCEE--EECCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEE
Q ss_conf 43222222110---000000245530477603--3027408998626410233211332248989999999987397998
Q gi|254780602|r 289 DFVVNNRKIFE---YRRDLCVAQLQGVPGIRY--MIPDGAFYLYPSCQDLIGKKSPSGDVIRTDLDFVNGLLEIEKVAVV 363 (400)
Q Consensus 289 ~~~~~~~~~~~---~~r~~~~~~L~~~~g~~~--~~p~g~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ll~~~gV~v~ 363 (400)
T Consensus 271 P~VveRV~~Wd~Ev~ktRy~v~eLE~igG~~QlG~kPk~HDLv~FEtPgf~---Eia~~~kr~GyFLY~EL-KkRgi~-- 344 (381)
T TIGR02539 271 PHVVERVKRWDEEVKKTRYFVAELEDIGGFKQLGVKPKEHDLVKFETPGFH---EIAKKHKRRGYFLYEEL-KKRGIV-- 344 (381)
T ss_pred CHHHHHCCCHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCEEECCCCCH---HHHCCCCCCCCCHHHHH-HHCCCE--
T ss_conf 101122023156677765788876421788864868882564144488401---34144879776405665-315830--
Q ss_pred CCCCCCCCCEEEEEE-ECCHHHHHHHHHHHHHHHHHCC
Q ss_conf 350228997289996-2999999999999999998609
Q gi|254780602|r 364 QGSSFGHGPSIRISY-AVSDAILEEACVRIKRFCHSLQ 400 (400)
Q Consensus 364 pG~~Fg~~~~iRis~-~~~~e~l~~al~rl~~~l~~l~ 400 (400)
T Consensus 345 -GI~~G~Tk~~K~SvYGL~~Eqv~~Vv~sf~eI~e~~~ 381 (381)
T TIGR02539 345 -GIRSGQTKEIKLSVYGLTKEQVEYVVDSFKEIVEEYK 381 (381)
T ss_pred -ECCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHCC
T ss_conf -0178874277643312752114444678999998549