catabolism of small carbon sources in Thermoactinomyces daqus H-18

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Thermoactinomyces daqus H-18

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
arginine	rocE, rocF, rocD, PRO3, put1, putA
fructose	fruII-ABC, 1pfk, fba, tpi
glycerol	glpF, glpK, glpD, tpi
maltose	malAP, susB, glk
mannitol	cmtA, cmtB, mtlD
acetate	ybhL, acs
asparagine	ans, glt
glutamate	gltP, gdhA
pyruvate	cstA, ybdD
aspartate	glt
glucose	ptsG-crr
deoxyinosine	nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
thymidine	nupC, deoA, deoB, deoC, adh, acs
NAG	nagEIIA, nagPcb, nagA, nagB
proline	opuBA, opuBB, put1, putA
trehalose	treEIIA, treB, treC, glk
ethanol	etoh-dh-nad, adh, acs
gluconate	gntT, gntK, gnd
glucosamine	gamP, nagB
mannose	manP, manA
alanine	cycA
fumarate	dctA
L-malate	dctA
succinate	dctA
D-serine	dsdX, dsdA
isoleucine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
leucine	leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
threonine	tdcC, tdh, kbl, gcvP, gcvT, gcvH, lpd
sucrose	ams, fruII-ABC, 1pfk, fba, tpi
L-lactate	lctP, lutA, lutB, lutC
deoxyribose	deoP, deoK, deoC, adh, acs
galactose	galP, galK, galT, galE, pgmA
histidine	PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
cellobiose	bglG, ascB, glk
citrate	SLC13A5, acn, icd
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
ribose	rbsU, rbsK
serine	serP, sdaB
tryptophan	aroP, tnaA
phenylalanine	aroP, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
arabinose	araE, araA, araB, araD
glucose-6-P	uhpT
2-oxoglutarate	kgtP
D-alanine	cycA, dadA
sorbitol	mtlA, srlD
xylitol	fruI, x5p-reductase
propionate	putP, prpE, prpC, prpD, acn, prpB
phenylacetate	paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
xylose	xylT, xylA, xylB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
D-lactate	lctP, glcD, glcE, glcF
valine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
lysine	lysP, kamA, kamD, kamE, kdd, kce, kal, bcd, etfA, etfB, ctfA, ctfB, atoB
putrescine	puuP, patA, patD, gabT, gabD
glucuronate	exuT, udh, gci, garL, garR, garK
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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