| Pathway | Steps | | acetate | ybhL, ackA, pta |
| D-alanine | cycA, dadA |
| alanine | snatA |
| arabinose | araE, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB |
| arginine | rocE, rocF, ocd, put1, putA |
| asparagine | ans, bztA, bztB, bztC, bztD |
| aspartate | bztA, bztB, bztC, bztD |
| cellobiose | bgl, gtsA, gtsB, gtsC, gtsD, glk |
| citrate | tctA, tctB, tctC, acn, icd |
| citrulline | PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, ocd, put1, putA |
| deoxyinosine | nupC, deoD, deoB, deoC, adh, ackA, pta |
| deoxyribonate | deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB |
| deoxyribose | deoP, deoK, deoC, adh, ackA, pta |
| ethanol | etoh-dh-nad, adh, ackA, pta |
| fructose | Slc2a5, scrK |
| fucose | fucP, fucU, fucI, fucK, fucA, tpi, aldA |
| fumarate | dctM, dctP, dctQ |
| galactose | PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA |
| galacturonate | exuT, uxaC, uxaB, uxaA, kdgK, eda |
| gluconate | gntT, gntK, edd, eda |
| glucose | gtsA, gtsB, gtsC, gtsD, glk |
| glucose-6-P | uhpT |
| glucosamine | nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB |
| glucuronate | exuT, udh, gci, garL, garR, garK |
| glutamate | bztA, bztB, bztC, gltL, gdhA |
| glycerol | glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi |
| histidine | hutV, hutW, hutX, hutH, hutU, hutI, hutF, hutG' |
| isoleucine | livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small |
| 4-hydroxybenzoate | pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta |
| D-lactate | PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF |
| L-lactate | Shew_2731, Shew_2732, L-LDH |
| lactose | lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk |
| leucine | livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB |
| lysine | lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB |
| L-malate | dctM, dctP, dctQ |
| maltose | aglE, aglF, aglG, aglK, susB, glk |
| mannitol | mtlE, mtlF, mtlG, mtlK, mt2d, scrK |
| mannose | manP, manA |
| myoinositol | PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi |
| NAG | SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB |
| 2-oxoglutarate | dctP, dctQ, dctM |
| phenylacetate | paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2 |
| phenylalanine | aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB |
| proline | natA, natB, natC, natD, natE, put1, putA |
| propionate | putP, prpE, pccA, pccB, epi, mcm-large, mcm-small |
| putrescine | potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD |
| pyruvate | yjcH, actP |
| rhamnose | rhaT, LRA1, LRA2, LRA3, LRA4, aldA |
| ribose | rbsU, rbsK |
| D-serine | cycA, dsdA |
| serine | snatA, sdaB |
| sorbitol | mtlE, mtlF, mtlG, mtlK, sdh, scrK |
| succinate | dctQ, dctM, dctP |
| sucrose | ams, gtsA, gtsB, gtsC, gtsD, glk |
| threonine | snatA, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small |
| thymidine | nupG, deoA, deoB, deoC, adh, ackA, pta |
| trehalose | treF, gtsA, gtsB, gtsC, gtsD, glk |
| tryptophan | aroP, tnaA |
| tyrosine | aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB |
| valine | natA, natB, natC, natD, natE, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small |
| xylitol | fruI, x5p-reductase |
| xylose | gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB |
This GapMind analysis is from Dec 12 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know