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=97.15  E-value=0.00011  Score=50.02  Aligned_cols=109  Identities=19%  Similarity=0.208  Sum_probs=64.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHH-HCCCCCCCCCCC-CC---CCHH------HHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             789789874004779778999999777-189855676881-40---2058------999999809999999999999999
Q gi|254780802|r   42 FPYPSGNIHMGHLRNYVIGDVVARFMR-ASGYSVLHPMGW-DA---FGMP------AENAAREHNVHPKMWTYQNIKVMR  110 (869)
Q Consensus        42 pPy~nG~lHiGH~~~~t~~Dv~aRy~r-m~G~~Vl~~~G~-d~---~GlP------ie~~~~e~~~~~~~~~~~~i~~~k  110 (869)
T Consensus        29 GpTVYd~~HiGhaR~~i~fD~~~R~L~d~~GY~V~yV~NiTDIGhltGdlddGDDKIIk~A~~~~~~~~~~kend-----  103 (660)
T TIGR00435        29 GPTVYDYAHIGHARTAIVFDVLRRYLEDYLGYEVQYVQNITDIGHLTGDLDDGDDKIIKRAREEGETVEEVKEND-----  103 (660)
T ss_pred             CCHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHCC-----
T ss_conf             731762103034663025788899998875886788864312000016777750489999875156478874012-----


Q ss_pred             HHHHHCCCEEECCCCEECCCHHHHHHHHHHHHHHHHCCCEEECCEEEECCCCCCCCCCHHHH
Q ss_conf             99998191766469821477359999999999999889634122133214776767789898
Q gi|254780802|r  111 KQLQSIGLSIDWSKDFATCDVDYYHCQQLLFLDFMKHNVIVRKTAQVNWDPVEQTVLANEQV  172 (869)
Q Consensus       111 ~~~~~lG~~~DW~r~y~T~d~~y~~~v~w~f~~L~~kGliyrg~~pV~wcp~~~t~la~~Ev  172 (869)
T Consensus       104 -------------tkfn---atvvdkvktalfqyinknftiqGseik-tieefetWlsnadt  148 (660)
T TIGR00435       104 -------------TKFN---ATVVDKVKTALFQYINKNFTIQGSEIK-TIEEFETWLSNADT  148 (660)
T ss_pred             -------------CHHH---HHHHHHHHHHHHHHHHHCCEECCCHHH-HHHHHHHHHHCCCC
T ss_conf             -------------2000---256778899999987520011252000-36777776520331