TIGR00168, Translation_initiation_factor_IF-3, translation initiation factor IF-3. infC uses abnormal initiation codons such as AUA, AUC, and CUG which render its expression particularly sensitive to excess of its gene product IF-3 thereby regulating its own expression [Protein synthesis, Translation factors].
TIGR03839, Adhesin_P1, adhesin P1. Members of this protein family are the major adhesin of the Mycoplasma terminal organelle. The protein is called adhesin P1, cytadhesin P1, P140, attachment protein, and MgPa, with locus names MG191 in Mycoplasma genitalium and MPN141 in M. pneumoniae. A conserved C-terminal region is shared by additional paralogs in M. pneumoniae and M. gallisepticum, as well as by the member of this family. [Cell envelope, Surface structures, Cellular processes, Pathogenesis].
TIGR00472, Phenylalanine--tRNA_ligase_beta_subunit, phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the amino end. [Protein synthesis, tRNA aminoacylation].
TIGR00005, Ribosomal_large_subunit_pseudouridine_synthase_D, pseudouridine synthase, RluA family. In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification].
TIGR00468, Phenylalanine--tRNA_ligase_alpha_subunit, phenylalanyl-tRNA synthetase, alpha subunit. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment. [Protein synthesis, tRNA aminoacylation].
TIGR00040, Putative_metallophosphoesterase, phosphoesterase, MJ0936 family. Members of this largely uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterized archaeal putative phosphoesterases described by TIGR00024. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown () to act on model phosphodiesterase substrates; a divalent cation was required. [Unknown function, Enzymes of unknown specificity].
TIGR01061, DNA_topoisomerase_4_subunit_A, DNA topoisomerase IV, A subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair].
TIGR03835, DnaJ-like_protein_MG200_homolog, terminal organelle assembly protein TopJ. This model describes TopJ (MG_200, CbpA), a DnaJ homolog and probable assembly protein of the Mycoplasma terminal organelle. The terminal organelle is involved in both cytadherence and gliding motility. [Cellular processes, Chemotaxis and motility].
TIGR00194, UvrABC_system_protein_C, excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. [DNA metabolism, DNA replication, recombination, and repair].
TIGR01058, DNA_topoisomerase_4_subunit_B, DNA topoisomerase IV, B subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair].
TIGR00235, Uridine_kinase, uridine kinase. Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides].
pfam01732, DUF31, Putative peptidase (DUF31). This domain has no known function. It is found in various hypothetical proteins and putative lipoproteins from mycoplasmas. It appears to be related to the superfamily of trypsin peptidases and so may have a peptidase function.
TIGR00136, Mitochondrial_translation_optimization_protein, glucose-inhibited division protein A. GidA, the longer of two forms of GidA-related proteins, appears to be present in all complete eubacterial genomes so far, as well as Saccharomyces cerevisiae. A subset of these organisms have a closely related protein. GidA is absent in the Archaea. It appears to act with MnmE, in an alpha2/beta2 heterotetramer, in the 5-carboxymethylaminomethyl modification of uridine 34 in certain tRNAs. The shorter, related protein, previously called gid or gidA(S), is now called TrmFO (see model TIGR00137). [Protein synthesis, tRNA and rRNA base modification].
TIGR00689, Probable_ribose-5-phosphate_isomerase_B, sugar-phosphate isomerase, RpiB/LacA/LacB family. Proteins of known function in this family act as sugar (pentose and/or hexose)-phosphate isomerases, including the LacA and LacB subunits of galactose-6-phosphate isomerases from Gram-positive bacteria and RpiB. RpiB is the second ribose phosphate isomerase of E. coli. It lacks homology to RpiA, its inducer is unknown (but is not ribose), and it can be replaced by the homologous galactose-6-phosphate isomerase of Streptococcus mutans, all of which suggests that the ribose phosphate isomerase activity of RpiB is a secondary function. On the other hand, there appear to be a significant number of species which contain rpiB, lack rpiA and seem to require rpi activity in order to complete the pentose phosphate pathway.
TIGR00552, Probable_NH3-dependent_NAD+_synthetase, NAD+ synthetase. NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the biosynthesis of the essensial cofactor NAD. The member of this family from Bacillus subtilis is a strictly NH(3)-dependent NAD(+) synthetase of 272 amino acids. Proteins consisting only of the domain modeled here may be named as NH3-dependent NAD+ synthetase. Amidotransferase activity may reside in a separate protein, or not be present. Some other members of the family, such as from Mycobacterium tuberculosis, are considerably longer, contain an apparent amidotransferase domain, and show glutamine-dependent as well as NH(3)-dependent activity. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides].
pfam11506, DUF3217, Protein of unknown function (DUF3217). This family of proteins with unknown function appears to be restricted to Mycoplasma. Some members in this family of proteins are annotated as MG376 however this cannot be confirmed.
The bacterium proteins that are colored denote the protein is present at specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin' and 'tRNA')
