catabolism of small carbon sources in Photobacterium jeanii R-40508

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Photobacterium jeanii R-40508

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
threonine	sstT, tdh, kbl, grdA, grdE, grdB, grdD, grdC, ackA
deoxyinosine	nupC, deoD, deoB, deoC, adh, ackA, pta
glycerol	glpF, glpK, glpA, glpB, glpC, glpD, tpi
thymidine	nupC, deoA, deoB, deoC, adh, ackA, pta
tyrosine	tyrP, HPD, hmgA, maiA, fahA, aacS, atoB
propionate	lctP, prpE, prpC, prpD, acn, prpB
fructose	fruA, fruB, 1pfk, fba, tpi
ethanol	etoh-dh-nad, adh, ackA, pta
acetate	satP, ackA, pta
proline	putP, put1, putA
asparagine	ans, glt
glucose	ptsG, crr
glutamate	gltS, gdhA
D-lactate	lctP, D-LDH
serine	sdaC, sdaB
alanine	alsT
aspartate	glt
fumarate	sdcL
L-malate	sdlC
succinate	sdc
arginine	artJ, artM, artP, artQ, astA, astB, astC, astD, astE
sucrose	ams, fruA, fruB, 1pfk, fba, tpi
L-lactate	Shew_2731, Shew_2732, lutA, lutB, lutC
maltose	malE, malF, malG, malK, susB, glk
histidine	hutV, hutW, hutX, hutH, hutU, hutI, hutG
cellobiose	bgl, ptsG, crr
NAG	nagEcba, nagA, nagB
trehalose	treEIIA, treB, treC, glk
glucosamine	gamP, nagB
mannose	manP, manA
ribose	rbsA, rbsB, rbsC, rbsK
glucose-6-P	uhpT
pyruvate	yjcH, actP
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
isoleucine	brnQ, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
valine	brnQ, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
leucine	brnQ, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
galactose	galP, galK, galT, galE, pgmA
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
citrate	SLC13A5, acn, icd
tryptophan	tnaB, tnaA
sorbitol	SOT, sdh, scrK
D-alanine	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
2-oxoglutarate	kgtP
xylitol	fruI, x5p-reductase
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
mannitol	PLT5, mt2d, scrK
D-serine	cycA, dsdA
gluconate	gntT, gntK, edd, eda
glucuronate	exuT, udh, gci, garL, garR, garK
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
xylose	xylT, xylA, xylB
lysine	argT, hisM, hisQ, hisP, lat, amaB, lysN, hglS, ydiJ
arabinose	araE, araA, araB, araD
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA4, aldA
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
fucose	fucP, fucU, fucI, fucK, fucA, 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