GapMind for catabolism of small carbon sources


catabolism of small carbon sources in Chromobacterium vaccinii MWU205

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
arginine artJ, artM, artP, artQ, astA, astB, astC, astD, astE
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
proline HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
thymidine nupC, deoA, deoB, deoC, adh, ackA, pta
serine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
asparagine ans, aatJ, aatQ, aatM, aatP
glutamate gltI, gltJ, gltK, gltL, gdhA
aspartate aatJ, aatQ, aatM, aatP
ethanol etoh-dh-nad, adh, ackA, pta
glycerol glpF, glpK, glpD, tpi
L-lactate lctP, lutA, lutB, lutC
NAG nagF, nagEcb, nagA, nagB
trehalose treEIIA, treB, treC, glk
acetate actP, ackA, pta
fumarate dctM, dctP, dctQ
L-malate dctM, dctP, dctQ
succinate dctQ, dctM, dctP
D-alanine cycA, dadA
D-lactate lctP, D-LDH
pyruvate yjcH, actP
tryptophan aroP, tnaA
alanine cycA
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
threonine tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
propionate lctP, prpE, prpC, acnD, prpF, acn, prpB
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
fructose frcA, frcB, frcC, scrK
ribose rbsA, rbsB, rbsC, rbsK
glucose ptsG, crr
glucosamine gamP, nagB
mannose manP, manA
D-serine cycA, dsdA
cellobiose bgl, ptsG, crr
maltose susB, ptsG, crr
glucose-6-P uhpT
lysine lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
deoxyribose deoP, deoK, deoC, adh, ackA, pta
gluconate gntT, gntK, edd, eda
citrate SLC13A5, acn, icd
sucrose ams, frcA, frcB, frcC, scrK
2-oxoglutarate dctP, dctQ, dctM
sorbitol SOT, sdh, scrK
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
mannitol PLT5, mt2d, scrK
galactose galP, galK, galT, galE, pgmA
xylitol fruI, x5p-reductase
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
glucuronate exuT, udh, gci, garL, garR, garK
xylose xylT, xylA, xylB
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
arabinose araE, araA, araB, araD
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
phenylacetate ppa, 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