GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Desulfotomaculum hydrothermale Lam5

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate satP, acs
D-alanine cycA, dadA
alanine alsT
arabinose araE, araA, araB, araD
arginine rocE, rocF, rocD, PRO3, put1*, putA
asparagine ans, glt
aspartate glt
cellobiose bgl, ptsG-crr
citrate SLC13A5, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1*, putA
deoxyinosine nupC, deoD, deoB, deoC, ald-dh-CoA
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
deoxyribose deoP, deoK, deoC, ald-dh-CoA
ethanol etoh-dh-nad*, ald-dh-CoA
fructose fruII-ABC, 1pfk, fba, tpi
fucose fucP, fucU, fucI, fucK, fucA, tpi, fucO
fumarate dctA
galactose galP, galK, galT, galE, pgmA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntT, gntK, gnd
glucose ptsG-crr
glucose-6-P uhpT
glucosamine gamP, nagB
glucuronate exuT, udh, gci, kdgD, dopDH
glutamate gltP, aspA
glycerol glpF, glpK, glpD, tpi
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
isoleucine livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
D-lactate lctP, D-LDH
L-lactate lctP, L-LDH
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
leucine livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
lysine lysP, cadA, patA, patD, davT, davD, glaH, lhgD
L-malate dctA
maltose susB, ptsG-crr
mannitol PLT5, mt2d, scrK
mannose manP, manA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG nagEcba, nagA, nagB
2-oxoglutarate Psest_0084, Psest_0085
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
proline putP, put1*, putA
propionate lctP, prpE, pccA, pccB, epi, mcmA
putrescine puuP, patA, patD, gabT, gabD
pyruvate SLC5A8
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, fucO
ribose rbsA, rbsB, rbsC, rbsK
D-serine cycA, dsdA
serine serP, sdaB
sorbitol SOT, sdh, scrK
succinate dctA
sucrose ams, fruII-ABC, 1pfk, fba, tpi
threonine tdcC, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, ald-dh-CoA
trehalose treF, ptsG-crr
tryptophan trpP, ecfA1, ecfA2, ecfT, tnaA
tyrosine tyt1, HPD, hmgA, maiA, fahA, aacS, atoB
valine livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA
xylitol PLT5, xdhA, xylB
xylose xylT, xyrA, xdhA, xylB

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