catabolism of small carbon sources in Flammeovirga pacifica WPAGA1

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Flammeovirga pacifica WPAGA1

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
deoxyinosine	nupG, deoD, deoB, deoC, adh, ackA, pta
thymidine	nupG, deoA, deoB, deoC, adh, ackA, pta
acetate	ybhL, ackA, pta
xylose	xylT, xylA, xylB
asparagine	ans, glt
alanine	alsT
aspartate	glt
fumarate	SLC26dg
threonine	snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
galactose	galP, galK, galT, galE, pgmA
ethanol	etoh-dh-nad, adh, ackA, pta
cellobiose	bgl, SSS-glucose, glk
maltose	malI, susB, glk
proline	ectP, put1, putA
glucose	SSS-glucose, glk
glutamate	gltP, gdhA
serine	snatA, sdaB
pyruvate	dctM, dctP, dctQ
trehalose	treF, SSS-glucose, glk
succinate	satP
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
arginine	rocE, rocF, rocD, PRO3, put1, putA
propionate	putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
rhamnose	Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
histidine	permease, hutH, hutU, hutI, hutG
glucuronate	exuT, uxaC, uxuB, uxuA, kdgK, eda
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
leucine	leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
citrate	SLC13A5, acn, icd
mannose	STP6, mannokinase, manA
glycerol	glpF, glpK, glpD, tpi
L-lactate	lctP, lldE, lldF, lldG
isoleucine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
glucosamine	nagX, nagP, nagK, nagA, nagB
fructose	BT1758, scrK
D-lactate	lctP, D-LDH
ribose	BT2809, rbsK
sucrose	ams, SSS-glucose, glk
NAG	nagP, nagK, nagA, nagB
glucose-6-P	uhpT
L-malate	sdlC
2-oxoglutarate	kgtP
D-serine	cycA, dsdA
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
xylitol	PLT5, xdhA, xylB
lysine	lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
D-alanine	cycA, dadA
mannitol	mtlA, mtlD
sorbitol	mtlA, srlD
tryptophan	aroP, tnaA
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
gluconate	gntT, gntK, edd, eda
valine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
arabinose	araE, araA, araB, araD
putrescine	puuP, patA, patD, gabT, gabD
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
myoinositol	iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
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