Table 5 Selected functional capacities
Cell function | Metabolic system/element | Putative gene/gene product |
|---|---|---|
Light energy metabolism | Oxygenic phototrophy; photorespiration | psaA-F, psaJ-L, psaX, psbA-D, psbH-P, psbU, psbV, psbW, psbZ, pcbA-C; ycf39, petA, petB, pet D, petE, hoxH/hoxY, PsbF, cyt f, cyt b 6; PC, CAT, SGAT, Fd-GOGAT, IpdA |
Dark energy metabolism | Glycolysis and gluconeogenesis; methylglyoxal metabolism, pentose phosphate pathway; Entner-Doudoroff pathway; pyruvate cleavage; TCA with glyoxylate bypass | GlcK, HxK, PPgK, PfK1, PfK2, PPiFKa, PPiFKb, Fbp_I, B, X; Fba1- 2, TpI, GADH, G3PNP, PgK, PgM, EnO, PyK, PpS, PpD, Hyp1, GPDH; MgsA, GloA-B, AldA-B, GRE2; GPDH, PLG, RisA-B, TK, TA, FPK, XPK, PglD, OpcA; AlaDH, AlaR, AlaGAT, SerD, SerT; glcB-F, HxK, GoxR, HpyrR, GalDH, AldDH, 2PGP; PyK, PpS, PpD, Pc, PEPC, ME; PDE, POX, PDC, PFORa-d, PDHA-B, DDH, OPOT, ADHA; GOX, lysR |
Lipid/pigments metabolism | Chl, iron tetrapyrrols, fatty acids, isoprenoids, phospholipids | PMgCD, PMgCH, PmgMT, ChlEAe, DVR, ChlB, ChlG, ChlL-M, POR; GltR, UroM, UroD, HemQ, HemX-Y; FabA-T, HpnE-H; CruA-G, CrtL, GlyP, GarL |
Carbon substrate intermediary metabolism | Calvin cycle; fructose, galactose, mannose, sucrose, polyglucoside, aminosugar, nucleotide sugar, C1-substrate and glycogen metabolism | PRK, Rbc, PGK, GAPDH, TPI, FBA1-2, FBP_I-X, TK, RPE; cbbL; cbbS, Ss, RBCS, RBCI, ClCP, CA; ManA-P, MalE-G, K; MsmK, LamB, MalL-K, MalA-B; NAGK1-3, NagA-E, CbSA, ChbA-C; mtdA, FTCLI; GAT_C, GAT_D, GS, GBr, GP, MP, MOTs, aAMP |
Nitrogen substrate intermediary metabolism | Nitrogen and ammonia assimilation; urea cycle | cynT, cynR, cynS, cynX; nrfB-H, niR1-3, niTa-Tc, narC, narG, narH, narI, napA-L, napR-T, nrfE-G, nrfX, GsI, GSIII, GlnE, GlnD, GOGDP1, GOGDP2, GlxC-D, GOGD, GAT, NRI, NRII, PII, PIIK, NtcA; UreD-G |
Protein metabolism | Amino acids, polyamines and glutathione biosyntheses; protein processing, degradation, modification and folding; selenoproteins | GltB, GlxC-B, GldH, AspA-C, AsnA-B, GltS, GlsA, HisA-I, AstA-E, ArgR, SpeA-C, ArcA-D, MetN-T, ThrA-C, AspC, CysB-E, Lys1, LLP, CadA-C, DavA-D, CodA, LeuA-D, TrpA-E, TyrA, PheA, ProA-C, SelD, GlyA-B, AlaB, AlaR, CsdA, SufS, SerA-C; SelA-B |
Mineral substrate metabolism | Phosphate, sulfur, iron and potassium metabolism | pho regulon; high-affinity phosphate transporter genes; siderophores; bacterioferritins; CysA, CysQ, SAT1-2, APSR, ASK, SIRFP, FPR_A; FhuB; kdpA-E, KefA-B, KefF |
Enzyme cofactor metabolism | Coenzyme B12, FAD, FMN, lipoic acid, Mo-cofactor, NAD, pterines, pyridoxin, quinone, riboflavin, thiamine biosynthesis | BioC, BioH, HoxE, HoxF, HoxH, HoxU, HoxY, CobA-C, CbiA-K, ThiB-G; UbiA-H; menA-D; PyrD, PyrR, PyrP, RSAe, FMNAT, LUMP, RK, RSA, gapA, pdxA-K, FolA-B; LipA-C, LipL-M, BirA, GlyP, PdhB, SucB, AceB, BkdB |
Secondary metabolism | Auxin, flavonoids, terpenes and derivatives biosynthesis | plant hormones (AUX1, APRT, PRAI, IGS,TSa, TM, IAH, IAD, AAD, AFTS), toxin-antitoxin replicon stabilization systems (RelB, E, F; CcdA-B, ParE-D, HigA-B, VapC-B, YoeB, YefM, YafQ, DinJ, YeeU, YkfI, YafW, YpjF, YgiZ) |
Membrane transport | ABC transporters (phnC-E, oppA-F, dppA-F), FtsY, TatA-E, MgtA-E, YcnL-K, CopC-D, CsoR, CopA, ModB; TolA, TonB, NikQ, NikM, CbiQ, CbiO, CbiM, BioM, BioN, MtsA-C, YkoC-E lipT, Sec-translocase; secretion protein type E, type IV pilus (pilA, pilT) | |
Cell division, cytoskeleton | ftsZ, ftsW, ftsB, ftsL, ftsA, ZipA, ZapA, MinC-E, ParA-B, Maf, YgiD, YeaZ(TsaB); MreB-D, RodA, MraZ | |
Regulation | kaiA-C, sasA, CikA, Pex, CPM; nrrA, groEL, grpE, dnaJ, LdpA, PSF, SigB, RsbR-W, PemK, SigF, SigG, SigFV, sig70, hetR, TyrR, IcsR, YbeD, cAMPB, FNR, CGA, dnaG, rpoD, exoY, pagA, AtxA, AtxR, hcnA-C, Clp2, ArsR, HisI, PyrC, FolE, HemB, CynT, CysS, YGR262c; SpoT, RelA, Rex, Fur_Zur, Fnr, gpp | |
Stress response | Protection from reactive oxygen species; oxidative and periplasmic stress | sodA-C, cyt c551 peroxidase, HP1; SoxS-R, OxyR, PerR, NnrS, AhpC, HemO, gshA-B, GltC, GltT, Rth, SOR, Rdx, ROO, NRO, AHR, grlA, EnvC, HbO, CHb, FHP, HmpX, Hfq, HflX-C; DegP-S, RseP, RseA-B, SurA, DegQ, HtrA |
Phages, integrons and CRISPRs | SA bacteriophages 11, TFP1-2, TFAP, TFC, Lys1-8, LysA-B, Hol1-2, TransI, endolysin; integrons (Int1-2, Int4, InyIPac); CRISPR cmr-cluster (Cmr1-6, Csx11, NEO113, TM1812, Cas02710); CasReg, Cas1-7, Csh1-2, Csd1-2, Cse1-4, Csn1-2, Csy1-4, Csa1-5, Csm1-5, Cst1-2 |