catabolism of small carbon sources in Methylobacterium gossipiicola Gh-105

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Methylobacterium gossipiicola Gh-105

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
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
acetate	actP, acs
pyruvate	yjcH, actP
fumarate	dctA
L-malate	dctA
2-oxoglutarate	kgtP
succinate	dctA
arginine	braC, braD, braE, braF, braG, rocF, odc, patA, patD, gabT, gabD
threonine	braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
propionate	lctP, prpE, pccA, pccB, epi, mcmA
ethanol	etoh-dh-nad, adh, acs
L-lactate	lctP, lctO, acs
serine	braC, braD, braE, braF, braG, sdaB
alanine	braC, braD, braE, braF, braG
mannose	manP, manA
isoleucine	livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
D-alanine	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
thymidine	nupG, deoA, deoB, deoC, adh, acs
fructose	fruA, fruI, 1pfk, fba, tpi
valine	livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA
proline	AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
gluconate	gntT, gntK, edd, eda
glycerol	glpF, glpK, glpD, tpi
deoxyribose	deoP, deoK, deoC, adh, acs
sucrose	ams, fruA, fruI, 1pfk, fba, tpi
putrescine	puuP, patA, patD, gabT, gabD
leucine	livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
sorbitol	SOT, sdh, scrK
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
glucose	ptsG-crr
glucose-6-P	uhpT
ribose	rbsU, rbsK
histidine	braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
mannitol	PLT5, mt2d, scrK
cellobiose	cdt, cbp, pgmA, glk
trehalose	TRET1, PsTP, pgmA, glk
phenylalanine	livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
tyrosine	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
glucosamine	gamP, nagB
maltose	susB, ptsG-crr
D-serine	cycA, dsdA
tryptophan	aroP, tnaA
xylitol	fruI, x5p-reductase
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
galactose	galP, galK, galT, galE, pgmA
NAG	nagEcba, nagA, nagB
xylose	xylT, xylA, xylB
glucuronate	exuT, udh, gci, kdgD, dopDH
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
arabinose	araE, araA, araB, araD
lysine	lysP, lat, amaB, lysN, hglS, ydiJ
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
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 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