catabolism of small carbon sources in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Trichormus variabilis ATCC 29413

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
alanine	braC, braD, braE, braF, braG
aspartate	natF, natG, natH, bgtA
pyruvate	dctM, dctP, dctQ
threonine	braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
proline	natA, natB, natC, natD, natE, put1, putA
serine	braC, braD, braE, braF, braG, sdaB
asparagine	ans, natF, natG, natH, bgtA
sucrose	ams, frcA, frcB, frcC, scrK
fructose	frcA, frcB, frcC, scrK
cellobiose	bgl, SemiSWEET, glk
ethanol	etoh-dh-nad, adh, acs
trehalose	treF, SemiSWEET, glk
glutamate	gtrA, gtrB, gtrC, aspA
glucose	SemiSWEET, glk
L-lactate	Shew_2731, Shew_2732, lctO, acs
arginine	bgtB, artP, rocF, rocD, rocA
deoxyribose	deoP, deoK, deoC, adh, acs
mannose	HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK
citrate	SLC13A5, acn, icd
gluconate	gntT, gntK, gnd
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
acetate	actP, acs
D-lactate	lctP, D-LDH
ribose	rbsU, rbsK
maltose	susB, SemiSWEET, glk
NAG	nagEcba, nagA, nagB
glucosamine	nagX, nagEcba, nagA, nagB
glycerol	glpF, glpK, glpD, tpi
fumarate	dctA
glucose-6-P	uhpT
L-malate	sdlC
2-oxoglutarate	kgtP
succinate	sdc
D-serine	cycA, dsdA
thymidine	nupC, deoA, deoB, deoC, adh, acs
mannitol	PLT5, mt2d, scrK
sorbitol	SOT, sdh, scrK
D-alanine	cycA, dadA
tryptophan	aroP, tnaA
xylitol	fruI, x5p-reductase
histidine	natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
propionate	putP, prpE, prpC, prpD, acn, prpB
lysine	bgtB, hisP, lat, amaB, lysN, hglS, ydiJ
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
xylose	xylF, xylG, xylH, xylA, xylB
galactose	galP, galK, galT, galE, pgmA
glucuronate	exuT, udh, gci, kdgD, dopDH
lactose	lacA', lacC', lacB', klh, SemiSWEET, glk
arabinose	araE, araA, araB, araD
isoleucine	natA, natB, natC, natD, natE, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
galacturonate	exuT, udh, gli, gci, kdgD, dopDH
valine	natA, natB, natC, natD, natE, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
leucine	natA, natB, natC, natD, natE, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
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 Apr 09 2024. 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