catabolism of small carbon sources in Haladaptatus cibarius D43

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Haladaptatus cibarius D43

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
glutamate	gltP, gdhA
aspartate	glt
propionate	mctC, prpE, pccA, pccB, epi, mcm-large, mcm-small
deoxyinosine	nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
ethanol	etoh-dh-nad, adh, acs
acetate	actP, acs
asparagine	ans, glt
pyruvate	mctC
proline	putP, put1, putA
threonine	tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
isoleucine	livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
histidine	permease, hutH, hutU, hutI, hutG
thymidine	nupG, deoA, deoB, deoC, adh, acs
citrate	SLC13A5, acn, icd
L-lactate	lctP, lctO, acs
serine	serP, sdaB
tryptophan	aroP, tnaA
glycerol	glpF, dhaD, dhaK, dhaL, dhaM, tpi
gluconate	gntT, gntK, gnd
sorbitol	SOT, sdh, scrK
fructose	fruII-ABC, 1pfk, fba, tpi
alanine	cycA
fumarate	dctA
glucose	ptsG-crr
glucose-6-P	uhpT
L-malate	sdlC
2-oxoglutarate	kgtP
succinate	sdc
deoxyribose	deoP, deoK, deoC, adh, acs
sucrose	sut, SUS, scrK, galU, pgmA
D-lactate	lctP, D-LDH
trehalose	thuE, thuF, thuG, thuK, PsTP, pgmA, glk
valine	livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
xylitol	PLT5, xdhA, xylB
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
arginine	rocE, rocF, rocD, rocA
cellobiose	cdt, cbp, pgmA, glk
galactose	galP, galK, galT, galE, pgmA
D-alanine	cycA, dadA
glucosamine	gamP, nagB
maltose	susB, ptsG-crr
mannitol	mtlA, mtlD
mannose	manP, manA
ribose	rbsU, rbsK
D-serine	cycA, dsdA
xylose	xylT, xyrA, xdhA, xylB
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
NAG	nagEcba, nagA, nagB
leucine	livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
putrescine	puuP, patA, patD, gabT, gabD
arabinose	araE, xacB, xacC, xacD, xacE, xacF
glucuronate	exuT, udh, gci, garL, garR, garK
phenylalanine	livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pfor, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
lysine	lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
phenylacetate	paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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