catabolism of small carbon sources in Bacillus cytotoxicus NVH 391-98

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Bacillus cytotoxicus NVH 391-98

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
deoxyinosine	nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, ackA, pta
arginine	rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
thymidine	nupC, deoA, deoB, deoC, adh, ackA, pta
histidine	LAT2, hutH, hutU, hutI, hutG
ethanol	etoh-dh-nad, adh, ackA, pta
fructose	fruII-ABC, 1pfk, fba, tpi
glycerol	glpF, glpK, glpD, tpi
L-lactate	lctP, lutA, lutB, lutC
NAG	nagEIIA, nagPcb, nagA, nagB
cellobiose	bglG, ascB, glk
gluconate	gntT, gntK, gnd
maltose	susB, glcU', glk
proline	putP, put1, putA
asparagine	ans, glt
glucose	glcU', glk
glutamate	gltP, gdhA
D-lactate	lctP, D-LDH
mannose	manP, manA
pyruvate	cstA, ybdD
alanine	cycA
aspartate	glt
fumarate	dctA
L-malate	dctA
succinate	dctA
threonine	RR42_RS28305, tdcB, tdcE, prpC, prpD, acn, prpB
propionate	putP, prpE, prpC, prpD, acn, prpB
ribose	rbsA, rbsB, rbsC, rbsK
acetate	actP, ackA, pta
citrate	cimH, acn, icd
trehalose	treF, glcU', glk
glucosamine	gamP, nagB
D-serine	cycA, dsdA
glucose-6-P	uhpT
isoleucine	brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
valine	brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
leucine	brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
sucrose	ams, fruII-ABC, 1pfk, fba, tpi
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
tyrosine	aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
D-alanine	cycA, dadA
serine	serP, sdaB
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
2-oxoglutarate	kgtP
tryptophan	aroP, tnaA
xylitol	fruI, x5p-reductase
lysine	lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
galactose	galP, galK, galT, galE, pgmA
mannitol	mtlA, mtlD
sorbitol	mtlA, srlD
xylose	xylT, xylA, xylB
glucuronate	exuT, udh, gci, garL, garR, garK
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose	rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
arabinose	araE, araA, araB, araD
4-hydroxybenzoate	pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
galacturonate	exuT, udh, gli, gci, kdgD, dopDH
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 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