GapMind for catabolism of small carbon sources


catabolism of small carbon sources in Dokdonella koreensis DS-123

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
ethanol etoh-dh-nad, adh, acs
proline N515DRAFT_2924, put1, putA
acetate deh, acs
pyruvate cstA, ybdD
aspartate dauA
fumarate dauA
2-oxoglutarate kgtP
succinate dauA
asparagine ans, dauA
glutamate gltP, gdhA
leucine leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
isoleucine Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
valine Bap2, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
threonine tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
propionate putP, prpE, prpC, prpD, acn, prpB
L-lactate lctP, lutA, lutB, lutC
arginine rocE, rocF, rocD, PRO3, put1, putA
citrate SLC13A5, acn, icd
deoxyribose deoP, deoK, deoC, adh, acs
ribose rbsU, rbsK
serine serP, sdaB
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
fructose fruII-ABC, 1pfk, fba, tpi
alanine cycA
glucose ptsG-crr
glucose-6-P uhpT
L-malate sdlC
D-alanine cycA, dadA
mannose manP, manA
D-serine cycA, dsdA
thymidine nupC, deoA, deoB, deoC, adh, acs
glycerol glpF, glpK, glpD, tpi
sucrose sut, SUS, scrK, galU, pgmA
cellobiose bgl, ptsG-crr
glucosamine gamP, nagB
D-lactate lctP, D-LDH
maltose susB, ptsG-crr
mannitol mtlA, mtlD
sorbitol mtlA, srlD
trehalose treF, ptsG-crr
tryptophan aroP, tnaA
xylitol fruI, x5p-reductase
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
galactose galP, galK, galT, galE, pgmA
gluconate gntT, gntK, gnd
NAG nagEcba, nagA, nagB
xylose xylT, xylA, xylB
putrescine puuP, patA, patD, gabT, gabD
lysine lysP, lat, amaB, lysN, hglS, ydiJ
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
arabinose araE, araA, araB, araD
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
glucuronate exuT, udh, gci, kdgD, dopDH
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.



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About GapMind

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.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

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).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory