catabolism of small carbon sources in Alishewanella agri BL06

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Alishewanella agri BL06

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
propionate	lctP, prpE, prpC, acnD, prpF, acn, prpB
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
thymidine	nupC, deoA, deoB, deoC, adh, acs
ethanol	etoh-dh-nad, adh, acs
proline	putP, put1, putA
asparagine	ans, glt
glucose	MFS-glucose, glk
glutamate	gltP, gdhA
D-lactate	lctP, D-LDH
pyruvate	yjcH, actP
alanine	alsT
aspartate	glt
fumarate	sdcL
L-malate	sdlC
succinate	sdc
threonine	snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
sucrose	scrT, ams, scrK, glk
cellobiose	bgl, MFS-glucose, glk
fructose	fruP, scrK
serine	snatA, sdaB
isoleucine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
leucine	leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
valine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
tyrosine	aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
glucosamine	nagX, nagP, nagK, nagA, nagB
histidine	permease, hutH, hutU, hutI, hutG
arginine	rocE, astA, astB, astC, astD, astE
tryptophan	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
NAG	nagP, nagK, nagA, nagB
citrate	SLC13A5, acn, icd
L-lactate	lctP, lctO, acs
maltose	malI, susB, glk
trehalose	treF, MFS-glucose, glk
deoxyribose	deoP, deoK, deoC, adh, acs
galactose	HP1174, galK, galT, galE, pgmA
acetate	actP, acs
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
mannitol	PLT5, mt2d, scrK
mannose	gluP, man-isomerase, scrK
gluconate	gntT, gntK, edd, eda
glycerol	glpF, dhaD, dhaK', tpi
glucose-6-P	uhpT
2-oxoglutarate	kgtP
sorbitol	SOT, sdh, scrK
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
glucuronate	dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda
D-alanine	cycA, dadA
ribose	rbsU, rbsK
D-serine	cycA, dsdA
xylitol	fruI, x5p-reductase
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
xylose	xylT, xylA, xylB
lysine	lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE
putrescine	puuP, patA, patD, gabT, gabD
arabinose	araE, araA, araB, araD
4-hydroxybenzoate	pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose	rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
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.

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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