catabolism of small carbon sources in Salinicoccus carnicancri Crm

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Salinicoccus carnicancri Crm

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
deoxyinosine	nupC, deoD, deoB, deoC, adh, ackA, pta
thymidine	nupC, deoA, deoB, deoC, adh, ackA, pta
fructose	fruII-ABC, 1pfk, fba, tpi
glycerol	glpF, glpK, glpD, tpi
proline	opuBA, opuBB, put1, putA
cellobiose	bglG, ascB, glk
gluconate	gntT, gntK, gnd
mannitol	cmtA, cmtB, mtlD
ribose	fru2-IIA, fru2-IIB, fru2-IIC
asparagine	ans, glt
glutamate	gltP, gdhA
maltose	susB, ptsG-crr
mannose	manP, manA
alanine	alsT
aspartate	glt
fumarate	sdcL
glucose	ptsG-crr
L-malate	sdlC
succinate	sdc
sucrose	ams, fruII-ABC, 1pfk, fba, tpi
propionate	lctP, prpE, prpC, prpD, acn, prpB
histidine	PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
ethanol	etoh-dh-nad, adh, ackA, pta
NAG	nagEIIA, nagPcb, nagA, nagB
trehalose	treEIIA, treB, treC, glk
acetate	actP, ackA, pta
citrate	citM, acn, icd
glucosamine	gamP, nagB
L-lactate	lctP, L-LDH
pyruvate	mctC
2-oxoglutarate	Psest_0084, Psest_0085
threonine	tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
arginine	rocE, rocF, rocD, PRO3, put1, putA
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
tryptophan	trpP, ecfA1, ecfA2, ecfT, kynA, kynB, kyn, antA, antB, antC, xylE, xylF, mhpD, mhpE, adh, ackA, pta
isoleucine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
sorbitol	srlA, srlB, srlE, srlD
D-lactate	lctP, D-LDH
D-serine	cycA, dsdA
serine	serP, sdaB
glucuronate	exuT, uxaC, uxuB, uxuA, kdgK, eda
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
glucose-6-P	uhpT
xylitol	fruI, x5p-reductase
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
leucine	leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
D-alanine	cycA, dadA
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
xylose	xylT, xylA, xylB
lactose	lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
putrescine	puuP, patA, patD, gabT, gabD
galactose	galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
valine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
tyrosine	aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
arabinose	araE, araA, araB, araD
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
lysine	lysP, davB, davA, davT, davD, glaH, lhgD
myoinositol	iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
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