HHsearch alignment for GI: 254780999 and conserved domain: TIGR02432

>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase; InterPro: IPR012795 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 . The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This domain is found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain architecture of this protein is variable; some, including characterised proteins of Escherichia coli and Bacillus subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family. It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016879 ligase activity forming carbon-nitrogen bonds, 0008033 tRNA processing, 0005737 cytoplasm.
Probab=96.51  E-value=0.0074  Score=37.89  Aligned_cols=138  Identities=15%  Similarity=0.182  Sum_probs=78.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHC---CCHH------HEEEEECCC--CCCCCC-CHHHHHHHHHHHCCCCCCCC-HHHHHH
Q ss_conf             0575215872368999999841---4954------467973246--666522-13569999997213542677-589999
Q gi|254780999|r  294 KVIIGLSGGIDSALCAAIAVDA---LGKE------NVQTIMLPY--KYTSPQ-SLEDAAACAKALGCKYDVLP-IHDLVN  360 (562)
Q Consensus       294 ~~viglSGGiDSal~a~la~~a---lg~~------~v~~~~mp~--~~~s~~-s~~~a~~la~~lg~~~~~i~-I~~~~~  360 (562)
T Consensus         1 ~~lvAvSGG~DS~aLL~~L~~~~~~~~~~~~~~~~~~~a~h~nH~lR~~s~~~~~~~v~~~c~~~~~~~~~~~~~~~~~~   80 (204)
T TIGR02432         1 KILVAVSGGVDSMALLHLLLKLQPKLKISWQIKDFKLIAAHVNHGLRPESAQEEAEFVQQFCEKLNIPLEIKKLVDVKAL   80 (204)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCC
T ss_conf             97888628642799999999976632787788750689999617788415899999999999961895699842124110


Q ss_pred             HHHHHHCCCCCCCCCCHHHHCCCC---HHHHHHHHHHHHHCC-CEECCCCC----HHHHH----------HH-----HCC
Q ss_conf             988631323468743101101233---046677988875169-54436432----44775----------41-----102
Q gi|254780999|r  361 HFFSLMSQFLQEEPSGIVAENIQS---RIRGNILMALSNHSK-AMLLTTSN----KSEIS----------VG-----YGT  417 (562)
Q Consensus       361 ~~~~~~~~~~~~~~~~~~~eN~qa---R~R~~~L~~~an~~~-~lvl~t~n----ksE~~----------~G-----y~T  417 (562)
T Consensus        81 ~---------~~~--~---~~~E~~AR~~RY~~f~~~~~~~~~~~~i~tAHh~dDq~ET~L~rL~RG~~~~Gl~g~~~~~  146 (204)
T TIGR02432        81 A---------KGK--K---KNLEEAAREARYAFFEEIAKKHGKADYILTAHHADDQAETILMRLLRGSGLRGLSGMPEIR  146 (204)
T ss_pred             C---------CCC--C---CCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCHHHHHCCCC
T ss_conf             1---------224--7---6778999999999999999972994089972483227999999875168700011101336


Q ss_pred             CCCC-----CCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             3666-----555401017763365899999963
Q gi|254780999|r  418 LYGD-----MSGGFNPLKDLYKTQVFQLASWRN  445 (562)
Q Consensus       418 ~~GD-----~~g~~~p~~~l~Kt~v~~la~~~n  445 (562)
T Consensus       147 ~~~~~g~~~~~~~~RPLL~~~k~ei~~y~~~~~  179 (204)
T TIGR02432       147 PLGSLGWYKGGQIIRPLLNISKSEIEEYLKENG  179 (204)
T ss_pred             CCCCCCCCCCEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             633244225632770775677899999999668