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