catabolism of small carbon sources in Thermovenabulum gondwanense R270

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Thermovenabulum gondwanense R270

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
mannitol	cmtA, cmtB, mtlD
asparagine	ans, glt
2-oxoglutarate	Psest_0084 *, Psest_0085
tryptophan	tnaT, tnaA
alanine	alsT
aspartate	glt
deoxyinosine	nupA, nupB, nupC', bmpA, deoD, deoB, deoC, ald-dh-CoA
NAG	nagEcba, nagA, nagB
xylitol	EIIA-Axl, EIIB-Axl, EIIC-Axl, x5p-reductase
ethanol	etoh-dh-nad, ald-dh-CoA
glucosamine	gamP, nagB
glutamate	gltP, gdhA
glucose	ptsG-crr
isoleucine	livF, livG, livJ, livH, livM, vorA *, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
threonine	tdcC, ltaE, ald-dh-CoA, grdA, grdE, grdB, grdD, grdC, ackA
glucuronate	dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda
thymidine	nupG, deoA, deoB, deoC, ald-dh-CoA
glycerol	glpF, dhaD, dhaK, dhaL, dhaM, tpi
citrate	tctA, tctB, tctC, acn, icd
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
acetate	actP, ackA, pta
L-lactate	lctP, lctO, ackA, pta
proline	proY, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
arginine	rocE, arcA, arcB, arcC, rocD, PRO3, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
valine	livF, livG, livJ, livH, livM, vorA *, vorB, vorC, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
histidine	permease, hutH, hutU, hutI, hutG
D-serine	cycA, dsdA
serine	serP, sdaB
fumarate	dctM, dctP, dctQ
L-malate	dctM, dctP, dctQ
succinate	dctQ, dctM, dctP
leucine	leuT, ilvE, vorA *, vorB, vorC, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
propionate	putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
cellobiose	cdt, cbp, pgmA, glk
deoxyribose	deoP, deoK, deoC, ald-dh-CoA
fructose	fruII-ABC, 1pfk, fba, tpi
trehalose	TRET1, PsTP, pgmA, glk
glucose-6-P	uhpT
pyruvate	SLC5A8
maltose	susB, ptsG-crr
mannose	manP, manA
sorbitol	mtlA, srlD
sucrose	ams, ptsG-crr
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
gluconate	gntT, gntK, edd, eda
D-alanine	cycA, dadA
D-lactate	lctP, D-LDH
ribose	rbsU, rbsK
xylose	xylT, xylA, xylB
myoinositol	iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
galactose	galP, galK, galT, galE, pgmA
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
arabinose	araE, araA, araB, araD
tyrosine	aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
putrescine	puuP, patA, patD, gabT, gabD
lysine	lysP, lysDH, amaB, lysN, hglS, ydiJ
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
phenylalanine	aroP, ARO8, iorA, iorB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
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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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