catabolism of small carbon sources in Psychromonas ingrahamii 37

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Psychromonas ingrahamii 37

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
threonine	sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
deoxyinosine	nupC, deoD, deoB, deoC, adh, ackA, pta
propionate	lctP, prpE, prpC, acnD, prpF, acn, prpB
sucrose	aglE, aglF, aglG, aglK, ams, scrK, glk
thymidine	nupC, deoA, deoB, deoC, adh, ackA, pta
cellobiose	bgl, gtsA, gtsB, gtsC, gtsD, glk
maltose	aglE, aglF, aglG, aglK, susB, glk
fructose	fruA, fruB, 1pfk, fba, tpi
glucose	gtsA, gtsB, gtsC, gtsD, glk
L-lactate	Shew_2731, Shew_2732, lutA, lutB, lutC
proline	proV, proW, proX, put1, putA
ethanol	etoh-dh-nad, adh, ackA, pta
acetate	satP, ackA, pta
fumarate	dctM, dctP, dctQ
L-malate	dctM, dctP, dctQ
2-oxoglutarate	dctP, dctQ, dctM
succinate	dctQ, dctM, dctP
asparagine	ans, glt
glutamate	gltP, gdhA
D-lactate	lctP, D-LDH
mannitol	mtlA, mtlD
serine	sstT, sdaB
aspartate	glt
galactose	PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
arginine	artJ, artM, artP, artQ, adiA, speB, patA, patD, gabT, gabD
histidine	hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
trehalose	treEIIA, treB, treC, glk
D-alanine	Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
NAG	nagEcba, nagA, nagB
pyruvate	dctM, dctP, dctQ
glucosamine	gamP, nagB
ribose	rbsA, rbsB, rbsC, rbsK
alanine	alsT
mannose	manP, manA
phenylacetate	paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine	aroP, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
glycerol	glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
glucuronate	dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
citrate	tctA, tctB, tctC, acn, icd
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
gluconate	gntT, gntK, gnd
xylose	gtsA, gtsB, gtsC, gtsD, xylA, xylB
isoleucine	Bap2, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
sorbitol	mtlA, srlD
putrescine	puuP, patA, patD, gabT, gabD
lysine	argT, hisM, hisQ, hisP, davB, davA, davT, davD, glaH, lhgD
glucose-6-P	uhpT
xylitol	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
D-serine	cycA, dsdA
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
tryptophan	aroP, tnaA
valine	Bap2, ofo, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
myoinositol	PS417_11885, PS417_11890, PS417_11895, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
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
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
leucine	aapJ, aapQ, aapM, aapP, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB

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