catabolism of small carbon sources in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Desulfovibrio vulgaris Miyazaki F

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
glycerol	glpF, glpK, glpD, tpi
L-lactate	lctP, lutA, lutB, lutC
acetate	satP, ackA, pta
ethanol	etoh-dh-nad, ald-dh-CoA
glutamate	dmeA, aspA
D-lactate	lctP, D-LDH
pyruvate	yjcH, actP
aspartate	dauA
fumarate	dauA
succinate	dauA
threonine	braC, braD, braE, braF, braG, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
serine	braC, braD, braE, braF, braG, sdaB
asparagine	ans, dauA
alanine	braC, braD, braE, braF, braG
citrate	SLC13A5, acn, icd
proline	proY, put1, putA
fructose	fruII-ABC, 1pfk, fba, tpi
glucose	ptsG-crr
glucose-6-P	uhpT
L-malate	sdlC
2-oxoglutarate	kgtP
mannose	manP, manA
propionate	lctP, prpE, pco, hpcD, dddA, iolA
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
deoxyinosine	nupC, deoD, deoB, deoC, ald-dh-CoA
sucrose	sut, SUS, scrK, galU, pgmA
D-alanine	cycA, dadA
cellobiose	bgl, ptsG-crr
glucosamine	gamP, nagB
maltose	susB, ptsG-crr
mannitol	mtlA, mtlD
ribose	rbsU, rbsK
D-serine	cycA, dsdA
sorbitol	mtlA, srlD
trehalose	treF, ptsG-crr
tryptophan	aroP, tnaA
xylitol	fruI, x5p-reductase
arginine	rocE, rocF, rocD, PRO3, put1, putA
leucine	livF, livG, livJ, livH, livM, ilvE, vorA *, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
deoxyribose	deoP, deoK, deoC, ald-dh-CoA
galactose	galP, galK, galT, galE, pgmA
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
glucuronate	exuT, udh, gci, garL, garR, garK
gluconate	gntT, gntK, gnd
NAG	nagEcba, nagA, nagB
xylose	xylT, xylA, xylB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
thymidine	nupG, deoA, deoB, deoC, ald-dh-CoA
arabinose	araE, araA, araB, araD
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA4, fucO
isoleucine	livF, livG, livJ, livH, livM, vorA *, vorB, vorC, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
fucose	fucP, fucU, fucI, fucK, fucA, tpi, fucO
histidine	hutV, hutW, hutX, hutH, hutU, hutI, hutG
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
lysine	lysP, lat, amaB, lysN, hglS, ydiJ
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
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
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
phenylalanine	livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources