GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Desulfovibrio vulgaris Miyazaki F

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate satP, ackA, pta
D-alanine cycA, dadA
alanine braC, braD, braE, braF, braG
arabinose araE, araA, araB, araD
arginine rocE, rocF, rocD, PRO3, put1, putA
asparagine ans, dauA
aspartate dauA
cellobiose bgl, ptsG-crr
citrate SLC13A5, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, 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 dauA
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, garL, garR, garK
glutamate dmeA, aspA
glycerol glpF, glpK, glpD, tpi
histidine hutV, hutW, hutX, hutH, hutU, hutI, hutG
isoleucine livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
D-lactate lctP, D-LDH
L-lactate lctP, lutA, lutB, lutC
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, lat, amaB, lysN, hglS, ydiJ
L-malate sdlC
maltose susB, ptsG-crr
mannitol mtlA, mtlD
mannose manP, manA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG nagEcba, nagA, nagB
2-oxoglutarate kgtP
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
proline proY, put1, putA
propionate lctP, prpE, pco, hpcD, dddA, iolA
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
pyruvate yjcH, actP
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, fucO
ribose rbsU, rbsK
D-serine cycA, dsdA
serine braC, braD, braE, braF, braG, sdaB
sorbitol mtlA, srlD
succinate dauA
sucrose sut, SUS, scrK, galU, pgmA
threonine braC, braD, braE, braF, braG, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, ald-dh-CoA
trehalose treF, ptsG-crr
tryptophan aroP, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
valine livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, bch, mmsB, mmsA, pco, hpcD, dddA, iolA
xylitol fruI, x5p-reductase
xylose xylT, xylA, 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 May 21 2021. The underlying query database was built on May 21 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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