catabolism of small carbon sources in Methylobacterium sp. 4-46 Apr-46

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Methylobacterium sp. 4-46 Apr-46

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, mcmA
histidine	braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
arginine	braC, braD, braE, braF, braG, rocF, ocd, put1, putA
glycerol	glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
proline	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
D-alanine	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
glutamate	braC, braD, braE, braF, braG, gdhA
asparagine	ans, aatJ, aatQ, aatM, aatP
aspartate	aatJ, aatQ, aatM, aatP
D-lactate	lctP, glcD, glcE, glcF
citrate	citA, acn, icd
ethanol	etoh-dh-nad, adh, acs
fumarate	dctM, dctP, dctQ
L-malate	dctM, dctP, dctQ
succinate	dctQ, dctM, dctP
acetate	actP, acs
L-lactate	lctP, L-LDH
pyruvate	yjcH, actP
2-oxoglutarate	kgtP
leucine	livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
valine	livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA
threonine	braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
4-hydroxybenzoate	pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
propionate	lctP, prpE, pccA, pccB, epi, mcmA
glucuronate	exuT, udh, uxuL, gudD, garL, garR, garK
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
serine	braC, braD, braE, braF, braG, sdaB
alanine	braC, braD, braE, braF, braG
sucrose	sacP, scrB, scrK
deoxyribose	drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
lactose	lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
arabinose	araE, xacB, xacC, xacD, xacE, xacF
galactose	galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate	exuT, udh, uxuL, garD, kdgD, dopDH
phenylalanine	livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
thymidine	nupC, deoA, deoB, deoC, adh, acs
NAG	nagEcba, nagA, nagB
tyrosine	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
lysine	argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
xylose	xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
fructose	Slc2a5, scrK
glucosamine	gamP, nagB
maltose	susB, ptsG-crr
ribose	rbsU, rbsK
mannose	STP6, mannokinase, manA
sorbitol	SOT, sdh, scrK
tryptophan	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
gluconate	gntT, gntK, edd, eda
glucose	ptsG-crr
glucose-6-P	uhpT
D-serine	cycA, dsdA
trehalose	treF, ptsG-crr
mannitol	PLT5, mt2d, scrK
cellobiose	cdt, cbp, pgmA, glk
xylitol	fruI, x5p-reductase
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
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 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