catabolism of small carbon sources in Lactobacillus delbrueckii ZN7a-9

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Lactobacillus delbrueckii ZN7a-9

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
sucrose	ams, fruII-ABC, 1pfk, fba, tpi
fructose	fruII-ABC, 1pfk, fba, tpi
L-lactate	larD, lctO, ackA, pta
mannose	manX, manY, manZ, manA
glucose	manX, manY, manZ
D-lactate	larD, D-LDH
ribose	rbsU, rbsK
maltose	malX_Sm, malF_Sm, malG_Sm, malK_Sm, malP, pgmB, glk
cellobiose	bgl, manX, manY, manZ
acetate	ybhL, ackA, pta
trehalose	treEIIA, treB, treC, glk
asparagine	ans, acaP
ethanol	etoh-dh-nad, ald-dh-CoA
glutamate	acaP, aspA
alanine	cycA
aspartate	acaP
glycerol	glpF, glpK, glpD, tpi
NAG	nagEcba, nagA, nagB
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
tryptophan	trpP, ecfA1, ecfA2, ecfT, tnaA
glucosamine	gamP, nagB
serine	serP, sdaB
xylitol	fruI, x5p-reductase
arginine	rocE, arcA, arcB, arcC, odc, patA, patD, gabT, gabD
proline	opuBA, opuBB, put1, putA
fumarate	dctA
glucose-6-P	uhpT
L-malate	sdlC
2-oxoglutarate	kgtP
pyruvate	SLC5A8
succinate	sdc
deoxyinosine	nupA, nupB, nupC', bmpA, deoD, deoB, deoC, ald-dh-CoA
threonine	serP1, tdh, tynA, yvgN, aldA, lctO, ackA, pta
D-alanine	cycA, dadA
D-serine	cycA, dsdA
gluconate	gntT, gntK, gnd
mannitol	PLT5, mt2d, scrK
sorbitol	SOT, sdh, scrK
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
deoxyribose	deoP, deoK, deoC, ald-dh-CoA
galactose	galP, galK, galT, galE, pgmA
citrate	cit1, acn, icd
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
xylose	xylT, xylA, xylB
leucine	livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
arabinose	araE, araA, araB, araD
isoleucine	livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
histidine	LAT2, hutH, hutU, hutI, hutG
thymidine	nupG, deoA, deoB, deoC, ald-dh-CoA
propionate	lctP, prpE, pccA, pccB, epi, mcmA
glucuronate	exuT, udh, gci, garL, garR, garK
lysine	bgtB, hisP, lat, amaB, lysN, hglS, ydiJ
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose	rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
valine	livF, livG, livJ, livH, livM, ofo, 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, aacS, 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 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