catabolism of small carbon sources in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Dyella japonica UNC79MFTsu3.2

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
galactose	ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
fucose	fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
xylose	xylF, xylG, xylH, xylA, xylB
gluconate	gntT, gntK, edd, eda
NAG	nagP, nagK, nagA, nagB
cellobiose	bgl, MFS-glucose, glk
ethanol	etoh-dh-nad, adh, acs
proline	N515DRAFT_2924, put1, putA
acetate	deh, acs
asparagine	ans, BPHYT_RS17540
fructose	fruP, scrK
glucose	MFS-glucose, glk
glutamate	gltP, gdhA
pyruvate	cstA, ybdD
alanine	cycA
aspartate	BPHYT_RS17540
fumarate	dctA
L-malate	dctA
2-oxoglutarate	kgtP
succinate	dctA
arabinose	araUsh, araVsh, araWsh, araZsh, xacB, xacC, xacD, xacE, xacF
threonine	RR42_RS28305, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
tyrosine	aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
glucosamine	nagX, nagP, nagK, nagA, nagB
glycerol	glpF, glpK, glpD, tpi
maltose	malI, susB, glk
mannose	gluP, man-isomerase, scrK
sucrose	ams, MFS-glucose, glk
trehalose	treF, MFS-glucose, glk
D-alanine	cycA, dadA
D-serine	cycA, dsdA
leucine	leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
histidine	PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
lactose	lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
isoleucine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
propionate	putP, prpE, prpC, acnD, prpF, acn, prpB
arginine	rocE, rocF, rocD, PRO3, put1, putA
thymidine	nupG, deoA, deoB, deoC, adh, acs
citrate	SLC13A5, acn, icd
deoxyribose	deoP, deoK, deoC, adh, acs
L-lactate	lctP, L-LDH
ribose	rbsU, rbsK
serine	serP, sdaB
deoxyinosine	nupG, deoD, deoB, deoC, adh, acs
sorbitol	SOT, sdh, scrK
tryptophan	aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
glucose-6-P	uhpT
D-lactate	lctP, D-LDH
mannitol	PLT5, mt2d, scrK
xylitol	PLT5, xdhA, xylB
valine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
putrescine	puuP, patA, patD, gabT, gabD
citrulline	PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA
lysine	lysP, lat, amaB, lysN, hglS, ydiJ
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
glucuronate	exuT, uxaC, uxuB, uxuA, kdgK, eda
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
myoinositol	iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
phenylacetate	H281DRAFT_04042, 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 17 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