HHsearch alignment for GI: 254780802 and conserved domain: TIGR00435

>TIGR00435 cysS cysteinyl-tRNA synthetase; InterPro: IPR002308 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 . Cysteinyl-tRNA synthetase (6.1.1.16 from EC) is an alpha monomer and belongs to class Ia.; GO: 0000166 nucleotide binding, 0004817 cysteine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006423 cysteinyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=99.51  E-value=1e-13  Score=111.94  Aligned_cols=127  Identities=20%  Similarity=0.259  Sum_probs=96.5

Q ss_pred             CEECCCCEEEECCCCCCHHHCCCCCCCCCCCC-CCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHH---HHHHHHHHHHHH
Q ss_conf             11048970640474210000001222210012-34633566655301332111113432101145---567788999997
Q gi|254780802|r  615 FRLSDNSKVVIGPLEKMSKSKKNVIDPMKVIK-SYGADTARLFVLSDSPPDRDIIWSNKGVDSTY---QFIQQIWRLIYN  690 (869)
Q Consensus       615 ~~~~~~~~~~~~~g~KMSKSkGNvi~p~~~i~-~yGaD~lRl~~~~~~~~~~d~~~s~~~i~~~~---rfl~kl~~l~~~  690 (869)
T Consensus       398 ~~yW~H~G~~~id~eKMSKSLgNF~~v~D~L~q~~d~~~lR~~~l~-~HYr~pLdf~e~~l~~aksfe~~~~~l~~~l~~  476 (660)
T TIGR00435       398 AKYWLHNGFLMIDNEKMSKSLGNFITVRDVLKQNYDPEVLRYLLLS-VHYRSPLDFSEELLEAAKSFENALERLYKALRN  476 (660)
T ss_pred             EEEEEECCEEEECCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHH-HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999851778976721651555688888687427689999999876-553145674788999998899999999999998


Q ss_pred             HHCCCCCCC------CH---HHHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHH
Q ss_conf             630246678------97---56999999999999999998-816889999999999999999
Q gi|254780802|r  691 AKDELQTSS------TK---KDISLISKSTKFLERIEENY-QNLSFNKAVANIHELVNVISK  742 (869)
Q Consensus       691 ~~~~~~~~~------~~---~D~~ils~~~~~i~~v~~~~-e~~~f~~ai~~i~~f~n~ls~  742 (869)
T Consensus       477 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~F~Eseskvhsa~~dDlN~a~Al~vL~el~~~~N~  538 (660)
T TIGR00435       477 LDTDLAYSKEFGENKDPKNVDEKEFEAAFEESESKVHSAMDDDLNTANALAVLFELAKSINK  538 (660)
T ss_pred             HHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf             75310342223424356642256578664320357788875057806899999999998400