catabolism of small carbon sources in Bacillus velezensis CBMB205

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Bacillus velezensis CBMB205

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
deoxyinosine	nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, ackA, pta
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
thymidine	nupC, deoA, deoB, deoC, adh, ackA, pta
arginine	rocE, rocF, rocD, PRO3, put1, putA
galactose	galP, galK, galT, galE, pgmA
histidine	LAT2, hutH, hutU, hutI, hutG
sucrose	ams, fruII-ABC, 1pfk, fba, tpi
arabinose	araE, araA, araB, araD
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
trehalose	treEIIA, treB, treC, glk
citrate	cimH, acn, icd
gluconate	gntT, gntK, gnd
maltose	susB, glcU', glk
mannitol	cmtA, cmtB, mtlD
proline	proY, put1, putA
xylose	xylT, xylA, xylB
asparagine	ans, glt
glucose	glcU', glk
glutamate	gltP, gdhA
mannose	manP, manA
D-serine	cycA, dsdA
alanine	cycA
aspartate	glt
fumarate	dctA
L-malate	dctA
succinate	dctA
threonine	serP1, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
lactose	lacY, lacZ, galK, galT, galE, pgmA, glk
galacturonate	PS417_04205, uxaC, uxaB, uxaA, kdgK, eda
propionate	putP, prpE, prpC, prpD, acn, prpB
acetate	dctA, ackA, pta
cellobiose	bgl, glcU', glk
glucosamine	gamP, nagB
ribose	rbsU, rbsK
serine	serP, sdaB
glucose-6-P	uhpT
2-oxoglutarate	csbX
pyruvate	mctP
isoleucine	brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
leucine	brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
valine	brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
tryptophan	trpP, ecfA1, ecfA2, ecfT, tnaA
sorbitol	SOT, sdh, scrK
xylitol	PLT5, xdhA, xylB
D-alanine	cycA, dadA
glucuronate	exuT, uxaC, uxuB, uxuA, kdgK, eda
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
D-lactate	lctP, D-LDH
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
putrescine	puuP, patA, patD, gabT, gabD
lysine	lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
tyrosine	aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
4-hydroxybenzoate	pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose	rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
phenylacetate	H281DRAFT_04042, 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