TABLE 5.
Transport-, efflux-, and secretion-related genes (265 total genes)a
| 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 |
a
Details of genes and COG designations are available in Table S3 in the supplemental material.
b
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).
c
Nha, Na+/H+ antiporter; Trk, transmembrane potassium transporter; KUP, potassium uptake protein; TAT, twin-arginine translocation.