catabolism of small carbon sources in Trichodesmium erythraeum IMS101

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Trichodesmium erythraeum IMS101

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
cellobiose	bgl, mglA, mglB, mglC, glk
aspartate	natF, bgtB', natH, bgtA
glucose	mglA, mglB, mglC, glk
L-lactate	Shew_2731, Shew_2732, lctO, acs
pyruvate	dctM, dctP, dctQ
alanine	alsT
asparagine	ans, natF, bgtB', natH, bgtA
ethanol	etoh-dh-nad, adh, acs
threonine	tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
deoxyribose	deoP, deoK, deoC, adh, acs
maltose	susB, mglA, mglB, mglC, glk
sucrose	ams, mglA, mglB, mglC, glk
trehalose	treF, mglA, mglB, mglC, glk
galactose	mglA, mglB, mglC, galK, galT, galE, pgmA
proline	proV, proW, proX, put1, putA
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
citrate	SLC13A5, acn, icd
gluconate	gntT, gntK, gnd
glucosamine	nagX, nagEcba, nagA, nagB
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
acetate	actP, acs
ribose	rbsU, rbsK
thymidine	nupC, deoA, deoB, deoC, adh, acs
NAG	nagEcba, nagA, nagB
fructose	fruII-ABC, 1pfk, fba, tpi
glycerol	glpF, glpK, glpD, tpi
D-lactate	lctP, glcD, glcE, glcF
fumarate	dctA
glucose-6-P	uhpT
L-malate	sdlC
2-oxoglutarate	kgtP
succinate	sdc
glutamate	gltS, gdhA
arginine	rocE, adiA, speB, patA, patD, gabT, gabD
lactose	lacA', lacC', lacB', klh, mglA, mglB, mglC, glk
D-alanine	cycA, dadA
mannitol	mtlA, mtlD
mannose	manP, manA
D-serine	cycA, dsdA
serine	serP, sdaB
sorbitol	mtlA, srlD
tryptophan	aroP, tnaA
xylitol	fruI, x5p-reductase
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
propionate	putP, prpE, prpC, prpD, acn, prpB
xylose	xylT, xylA, xylB
arabinose	araE, araA, araB, araD
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
glucuronate	exuT, udh, gci, kdgD, dopDH
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA4, aldA
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
histidine	permease, hutH, hutU, hutI, hutG
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
lysine	lysP, lat, amaB, lysN, hglS, ydiJ
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
isoleucine	Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
leucine	leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
valine	Bap2, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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