catabolism of small carbon sources in Pontimonas salivibrio CL-TW6

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Pontimonas salivibrio CL-TW6

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
fumarate	SLC26dg
glycerol	glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
ethanol	etoh-dh-nad, adh, ackA, pta
alanine	TRIC
threonine	braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
deoxyinosine	H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, ackA, pta
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
thymidine	nupG, deoA, deoB, deoC, adh, ackA, pta
ribose	rbsA, rbsB, rbsC, rbsK
serine	braC, braD, braE, braF, braG, sdaB
acetate	actP, ackA, pta
citrate	SLC13A5, acn, icd
fructose	fruII-ABC, 1pfk, fba, tpi
cellobiose	bgl, mglA, mglB, mglC, glk
maltose	susB, mglA, mglB, mglC, glk
glucosamine	gamP, nagB
glutamate	gltS, aspA
L-lactate	lctP, L-LDH
mannose	manP, manA
NAG	nagEcba, nagA, nagB
aspartate	natF, natG, natH, bgtA
glucose	mglA, mglB, mglC, glk
asparagine	ans, natF, natG, natH, bgtA
glucose-6-P	uhpT
L-malate	sdlC
2-oxoglutarate	kgtP
pyruvate	SLC5A8
succinate	sdc
putrescine	puuP, patA, patD, gabT, gabD
sucrose	ams, fruII-ABC, 1pfk, fba, tpi
xylitol	PLT5, xdhA, xylB
fucose	fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
proline	natA, natB, natC, natD, natE, put1, putA
xylose	xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
gluconate	gntT, gntK, gnd
arginine	rocE, rocF, rocD, rocA
mannitol	PLT5, mt1d, mak, manA
galactose	galP, galK, galT, galE, pgmA
trehalose	treF, mglA, mglB, mglC, glk
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
D-alanine	cycA, dadA
D-lactate	lctP, D-LDH
D-serine	cycA, dsdA
sorbitol	mtlA, srlD
tryptophan	aroP, tnaA
propionate	putP, prpE, pccA, pccB, epi, mcmA
leucine	natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
arabinose	araE, xacB, xacC, xacD, xacE, xacF
lysine	lysP, cadA, patA, patD, davT, davD, glaH, lhgD
glucuronate	exuT, udh, gci, kdgD, dopDH
histidine	natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
galacturonate	exuT, udh, uxuL, garD, kdgD, dopDH
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
isoleucine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
tyrosine	aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
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 2024 update 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