catabolism of small carbon sources in Candidatus Hydrogenedens sp. RI

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Candidatus Hydrogenedens sp. RI_113

Pathways are sorted by name. Sort by completeness instead.

Pathway	Steps
acetate	actP, acs
D-alanine	cycA, dadA
alanine	alsT
arabinose	Echvi_1880, araA, araB, araD
arginine	rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
asparagine	ans, dauA
aspartate	dauA
cellobiose	bglG, ascB, glk
citrate	SLC13A5, acn, icd
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
deoxyribose	deoP, deoK, deoC, adh, acs
ethanol	etoh-dh-nad, adh, acs
fructose	fruII-ABC, 1pfk, fba, tpi
fucose	HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
fumarate	sdcL
galactose	sglS, galK, galT, galE, pgmA
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate	gntT, gntK, gnd
glucose	mglA, mglB, mglC, glk
glucose-6-P	uhpT
glucosamine	nagX, nagEcba, nagA, nagB
glucuronate	exuT, udh, gci, garL, garR, garK
glutamate	gltS, gdhA
glycerol	glpF, glpK, glpD, tpi
histidine	permease, hutH, hutU, hutI, hutG
isoleucine	Bap2, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
D-lactate	lctP, D-LDH
L-lactate	Shew_2731, Shew_2732, lldE, lldF, lldG
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
leucine	leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
lysine	lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate	sdlC
maltose	susB, mglA, mglB, mglC, glk
mannitol	mtlA, mtlD
mannose	manP, manA
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG	nagEcba, nagA, nagB
2-oxoglutarate	Psest_0084, Psest_0085
phenylacetate	paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
proline	proY, put1, putA
propionate	putP, prpE, prpC, prpD, acn, prpB
putrescine	puuP, patA, patD, gabT, gabD
pyruvate	yjcH, actP
rhamnose	rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
ribose	rbsA, rbsB, rbsC, rbsK
D-serine	cycA, dsdA
serine	serP, sdaB
sorbitol	mtlA, srlD
succinate	sdc
sucrose	sut, SUS, scrK, galU, pgmA
threonine	tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
thymidine	nupG, deoA, deoB, deoC, adh, acs
trehalose	BT2158, klh, mglA, mglB, mglC, glk
tryptophan	aroP, tnaA
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
valine	Bap2, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
xylitol	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
xylose	xylF_Tm, xylE_Tm, xylK_Tm, xylA, xylB

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 Jun 22 2024. 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