GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Sporolactobacillus vineae SL153

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, ackA, pta
D-alanine cycA, dadA
alanine cycA
arabinose araE, araA, araB, araD
arginine rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
asparagine ans, BPHYT_RS17540
aspartate BPHYT_RS17540
cellobiose bgl, manX, manY, manZ
citrate citM, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
deoxyinosine nupA, nupB, nupC', bmpA, deoD, deoB, deoC, ald-dh-CoA
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose deoP, deoK, deoC, ald-dh-CoA
ethanol etoh-dh-nad, ald-dh-CoA
fructose levDE, levF, levG
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
fumarate dctA
galactose galP, galK, galT, galE, pgmA
galacturonate exuT, udh, gli, gci, kdgD, dopDH
gluconate gntT, gntK, gnd
glucose manX, manY, manZ
glucose-6-P uhpT
glucosamine gamP, nagB
glucuronate exuT, udh, gci, garL, garR, garK
glutamate yveA, aspA
glycerol glpF, dhaD, dhaK, dhaL, dhaM, tpi
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
isoleucine bcaP, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
D-lactate larD, D-LDH
L-lactate lctP, lutA, lutB, lutC
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
leucine bcaP, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine lysP, davB, davA, davT, davD, glaH, lhgD
L-malate dctA
maltose malI, malP, pgmB, glk
mannitol mtlA, mtlD
mannose manX, manY, manZ, manA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG nagEcba, nagA, nagB
2-oxoglutarate kgtP
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
proline proY, put1, putA
propionate lctP, prpE, prpC, prpD, acn, prpB
putrescine puuP, patA, patD, gabT, gabD
pyruvate mctC
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
ribose rbsU, rbsK
D-serine cycA, dsdA
serine serP, sdaB
sorbitol srlA, srlB, srlE, srlD
succinate dctA
sucrose ams, manX, manY, manZ
threonine RR42_RS28305, tdcB, tdcE, prpC, prpD, acn, prpB
thymidine nupG, deoA, deoB, deoC, ald-dh-CoA
trehalose thuE, thuF, thuG, thuK, treP, pgmB, glk
tryptophan trpP, ecfA1, ecfA2, ecfT, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine bcaP, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
xylitol fruI, x5p-reductase
xylose xylT, 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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