catabolism of small carbon sources in Verminephrobacter eiseniae EF01-2

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Verminephrobacter eiseniae EF01-2

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
isoleucine	livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
fucose	SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
histidine	Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
rhamnose	rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
proline	HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
serine	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
sorbitol	mtlE, mtlF, mtlG, mtlK, sdh, scrK
asparagine	ans, aatJ, aatQ, aatM, aatP
mannose	frcA, frcB, frcC, man-isomerase, scrK
aspartate	aatJ, aatQ, aatM, aatP
fructose	frcA, frcB, frcC, scrK
glucose	mglA, mglB, mglC, glk
ribose	frcA, frcB, frcC, rbsK
ethanol	etoh-dh-nad, adh, acs
pyruvate	dctM, dctP, dctQ
acetate	deh, acs
fumarate	dctA
L-malate	dctA
succinate	dctA
valine	livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
leucine	livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
threonine	braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
myoinositol	PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
arabinose	gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
glycerol	glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
alanine	braC, braD, braE, braF, braG
glutamate	gltI, gltJ, gltK, gltL, gdhA
mannitol	mtlE, mtlF, mtlG, mtlK, mt2d, scrK
phenylalanine	livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
tyrosine	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
arginine	artJ, artM, artP, artQ, rocF, odc, patA, patD, gabT, gabD
xylose	xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
4-hydroxybenzoate	pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
propionate	putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
galactose	gguA, gguB, chvE, galdh, galactonolactonase, dgoD, dgoK, dgoA
deoxyinosine	H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
phenylacetate	paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
lysine	argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
cellobiose	bgl, mglA, mglB, mglC, glk
deoxyribose	deoP, deoK, deoC, adh, acs
maltose	susB, mglA, mglB, mglC, glk
sucrose	ams, mglA, mglB, mglC, glk
trehalose	treF, mglA, mglB, mglC, glk
xylitol	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
D-lactate	lctP, glcD, glcE, glcF
citrate	tctA, tctB, tctC, acn, icd
glucuronate	exuT, udh, gci, garL, garR, garK
L-lactate	lctP, lctO, acs
gluconate	gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
D-alanine	cycA, dadA
tryptophan	aroP, tnaA
glucosamine	SLC2A2, glc-kinase, nagB
glucose-6-P	uhpT
2-oxoglutarate	kgtP
lactose	lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
D-serine	cycA, dsdA
NAG	nagEcba, nagA, nagB
galacturonate	exuT, udh, uxuL, garD, kdgD, dopDH
thymidine	nupG, deoA, deoB, deoC, adh, acs

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