pfam07751, Abi_2, Abi-like protein. This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins, which are involved in bacteriophage resistance mediated by abortive infection in Lactococcus species. The proteins are thought to have helix-turn-helix motifs, found in many DNA-binding proteins, allowing them to perform their function.
TIGR04056, OMP_RagA_SusC, TonB-linked outer membrane protein, SusC/RagA family. This model describes a distinctive clade among the TonB-linked outer membrane proteins (OMP). Members of this family are restricted to the Bacteriodetes lineage (except for Gemmatimonas aurantiaca T-27 from the novel phylum Gemmatimonadetes) and occur in high copy numbers, with over 100 members from Bacteroides thetaiotaomicron VPI-5482 alone. Published descriptions of members of this family are available for RagA from Porphyromonas gingivalis, SusC from Bacteroides thetaiotaomicron, and OmpW from Bacteroides caccae. Members form pairs with members of the SusD/RagB family (pfam07980). Transporter complexes including these outer membrane proteins are likely to import large degradation products of proteins (e.g. RagA) or carbohydrates (e.g. SusC) as nutrients, rather than siderophores. [Transport and binding proteins, Unknown substrate].
cd09597, M4_TLP, Peptidase M4 family including thermolysin, protealysin, aureolysin, and neutral protease. This peptidase M4 family includes several endopeptidases such as thermolysin (EC 3.4.24.27), aureolysin (the extracellular metalloproteinase from Staphylococcus aureus), neutral protease from Bacillus cereus, protealysin, and bacillolysin (EC 3.4.24.28). Typically, the M4 peptidases consist of a presequence (signal sequence), a propeptide sequence, and a peptidase unit. The presequence is cleaved off during export while the propeptide has inhibitory and chaperone functions and facilitates folding. The propeptide remains attached until the peptidase is secreted and can be safely activated. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. The active site is found between two sub-domains; the N-terminal domain contains the HEXXH zinc-binding motif while the helical C-terminal domain, which is unique for the family, carries the third zinc ligand. These peptidases are secreted eubacterial endopeptidases from Gram-positive or Gram-negative sources that degrade extracellular proteins and peptides for bacterial nutrition. They are selectively inhibited by Steptomyces metalloproteinase inhibitor (SMPI) as well as by phosphoramidon from Streptomyces tanashiensis. A large number of these enzymes are implicated as key factors in the pathogenesis of various diseases, including gastritis, peptic ulcer, gastric carcinoma, cholera and several types of bacterial infections, and are therefore important drug targets. Some enzymes of the family can function at extremes of temperatures, while some function in organic solvents, thus rendering them novel targets for biotechnological applications. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing. It has also been used in production of the artificial sweetener aspartame.
TIGR00545, Probable_lipoate-protein_ligase_A, lipoyltransferase and lipoate-protein ligase. One member of this group of proteins is bovine lipoyltransferase, which transfers the lipoyl group from lipoyl-AMP to the specific Lys of lipoate-dependent enzymes. However, it does not first activate lipoic acid with ATP to create lipoyl-AMP and pyrophosphate. Another member of this group, lipoate-protein ligase A from E. coli, catalyzes both the activation and the transfer of lipoate. Homology between the two is full-length, except for the bovine mitochondrial targeting signal, but is strongest toward the N-terminus. [Protein fate, Protein modification and repair].
pfam09357, RteC, RteC protein. Human colonic Bacteroides species harbor a family of large conjugative transposons, called tetracycline resistance (Tcr) elements. Activities of these elements are enhanced by pregrowth of bacteria in medium containing tetracycline, indicating that at least some Tcr element genes are regulated by tetracycline. An insertional disruption in the rteC gene abolished self-transfer of the Tcr element to Bacteroides recipients, indicating that the gene was essential for self-transfer.
TIGR02607, Virulence-associated_protein_I, addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other].
cd08977, SusD, starch binding outer membrane protein SusD. SusD-like proteins from Bacteroidetes, members of the human distal gut microbiota, are part of the starch utilization system (Sus). Sus is one of the large clusters of glycosyl hydrolases, called polysaccharide utilization loci (PULs), which play an important role in polysaccharide recognition and uptake, and it is needed for growth on amylose, amylopectin, pullulan, and maltooligosaccharides. SusD, together with SusC, a predicted beta-barrel porin, forms the minimum outer-membrane starch-binding complex. The adult human distal gut microbiota is essential for digestion of a large variety of dietary polysaccharides, for which humans lack the necessary glycosyl hydrolases.
pfam07291, MauE, Methylamine utilisation protein MauE. This family consists of several bacterial methylamine utilisation MauE proteins. Synthesis of enzymes involved in methylamine oxidation via methylamine dehydrogenase (MADH) is encoded by genes present in the mau cluster. MauE and MauD are specifically involved in the processing, transport, and/or maturation of the beta-subunit and that the absence of each of these proteins leads to production of a non-functional beta-subunit which becomes rapidly degraded.
NF012200, choice_anch_D, choice-of-anchor D domain-containing protein. This HMM describes a repeat domain just over 100 amino acids long and usually found in tandem copies. Members appear to be extracellular proteins that have some C-terminal anchoring domain, such as type IX secrection (T9SS) or PEP-CTERM.
