catabolism of small carbon sources in Lactobacillus shenzhenensis LY-73

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Lactobacillus shenzhenensis LY-73

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
deoxyinosine	nupA, nupB, nupC', bmpA, deoD, deoB, deoC, ald-dh-CoA
galactose	ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA
glycerol	glpF, glpK, glpO, tpi
cellobiose	bglG, ascB, glk
asparagine	ans, acaP
ethanol	etoh-dh-nad, ald-dh-CoA
serine	serP, sdaB
aspartate	acaP
L-malate	mleP
lactose	lacE, lacF, lacG, lacK, lacL, lacM, galK, galT, galE, pgmA, glk
maltose	malX_Sm, malF_Sm, malG_Sm, malK_Sm, malP, pgmB, glk
L-lactate	larD, lctO, ackA, pta
trehalose	malF, malG, malK, malX, treF, glk
arabinose	araUsh, araVsh, araWsh, araZsh, araA, araB, araD
sucrose	sacP, scrB, scrK
glucose	MFS-glucose, glk
mannose	manP, manA
D-serine	cycA, dsdA
alanine	cycA
D-lactate	larD, D-LDH
glucuronate	exuT, uxaC, uxuB, uxuA, kdgK, eda
thymidine	nupG, deoA, deoB, deoC, ald-dh-CoA
citrate	SLC13A5, citD, citE, citF
deoxyribose	deoP, deoK, deoC, ald-dh-CoA
fructose	fruII-ABC, 1pfk, fba, tpi
acetate	actP, ackA, pta
gluconate	gntT, gntK, gnd
NAG	nagEcba, nagA, nagB
putrescine	potA, potB, potC, potD, patA, patD, gabT, gabD
tryptophan	trpP, ecfA1, ecfA2, ecfT, tnaA
glucosamine	gamP, nagB
glutamate	acaP, gdhA
ribose	rbsU, rbsK
xylitol	fruI, x5p-reductase
sorbitol	SOT, sdh, scrK
rhamnose	rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
fumarate	dctA
glucose-6-P	uhpT
2-oxoglutarate	kgtP
pyruvate	SLC5A8
succinate	sdc
threonine	sstT, tdh, tynA, yvgN, aldA, lctO, ackA, pta
D-alanine	cycA, dadA
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
mannitol	PLT5, mt2d, scrK
proline	opuBA, opuBB, put1, putA
xylose	xylT, xylA, xylB
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
arginine	bgtB, artP, rocF, odc, patA, patD, gabT, gabD
myoinositol	iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
histidine	bgtA, bgtB, hutH, hutU, hutI, hutG
propionate	putP, prpE, pccA, pccB, epi, mcmA
lysine	bgtB, hisP, lat, amaB, lysN, hglS, ydiJ
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, patA, patD, gabT, gabD
leucine	leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
isoleucine	Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
valine	Bap2, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA
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