TABLE 5.
Classb | No. of genes | General functionc |
---|---|---|
ABC transporter | 87 | Uptake and efflux substrates/toxins |
Complete uptake systems (9) with ATPase, inner membrane, and periplasmic binding subunits | 30 | Sulfate/molybdate, spermidine/putrescine, ferric iron, phosphate, Mn2+/Zn2+, resistance to organic solvents (3), dipeptide/oligopeptide/nickel, cation/multidrug |
Efflux pumps | 35 | Iron (cobalamin, Fe-S assembly, heme, siderophore), antimicrobial peptide, multidrug, lysophospholipase L1 biosynthesis, polysaccharide/polyol phosphate, protease/lipase, bacteriocin/antibiotic export |
Periplasmic binding protein | 7 | Iron (hydroxymate), sulfate, branched-chain amino acid, organic solvents |
Auxiliary proteins | 4 | |
Unknown or orphans | 10 | |
Pseudogene | 1 | |
P-ATPase | 5 | Cation uptake/efflux ATPase |
Iron uptake | 21 | |
TonB/ExbB/ExbD | 12 | |
TonB-dependent receptors | 9 | Siderophore/cobamalamin |
Transport of simple organic N compounds | 14 | |
Urea | 1 | |
FNT | 1 | Formate/nitrite |
Na+/metabolite symporter | 3 | |
Na+/H+ antiporter | 2 | NhaA, NhaD |
K+ antiporter | 4 | TrkA |
Antiporter flippases | 3 | |
Efflux | 22 | |
CDF | 1 | Co/Zn/Cd |
CopD | 2 | Copper |
TerC | 2 | Tellurium resistance |
DMT superfamily | 4 | Cationic drug resistance |
RND | 13 | Multidrug/cation/metals |
Permease | 24 | |
Ammonia | 1 | |
MFS | 10 | Nitrate/nitrite, sulfate, and six uncharacterized efflux proteins |
Tellurite resistance | 1 | |
Amino acid | 2 | |
YjgP/YjgQ | 2 | |
Uncharacterized | 8 | |
Potassium uptake | 1 | KUP |
Transport of ions | 13 | |
Potassium | 2 | |
MgtE | 6 | Magnesium and cobalt transport |
ZIP | 1 | Heavy metal cation transport |
Mechanosensitive channel | 2 | |
Unknown | 2 | |
Porins | 14 | |
Phosphate | 3 | OprP |
Carbohydrate | 1 | OprB |
Lipoprotein | 3 | |
Polysaccharide | 2 | |
Other | 5 | |
Phosphotransferase | 3 | Fructose IIa, HPr, phosphoenolpyruvate phosphotransferase |
Protein secretion | 17 | Sec pathway and TAT translocases |
Type II secretion | 28 | General protein secretion/pilus formation |
Type III secretion | 11 | Flagellum biosynthesis |
Type IV secretion | 5 | TraG; DNA transfer during conjugation |
Details of genes and COG designations are available in Table S3 in the supplemental material.
TNT, formate nitrate transporter; CDF, cation diffusion facilitator; DMT, drug metabolite transporter; RND, resistance nodulation division; MFS, major facilitator superfamily; ZIP, zinc transport (Zrt/Irt-like proteins).
Nha, Na+/H+ antiporter; Trk, transmembrane potassium transporter; KUP, potassium uptake protein; TAT, twin-arginine translocation.