GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Nocardiopsis lucentensis DSM 44048

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, acs*
D-alanine cycA, dadA
alanine alsT
arabinose araE, araA, araB, araD
arginine rocE, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD
asparagine ans, glt
aspartate glt
cellobiose bgl, MFS-glucose, glk
citrate tctA, tctB, tctC, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
deoxyinosine nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs*
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose deoP, deoK, deoC, adh, acs*
ethanol etoh-dh-nad, adh, acs*
fructose frcA, frcB, frcC, scrK
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
fumarate sdcL
galactose galP, galK, galT, galE, pgmA
galacturonate exuT, udh, gli, gci, kdgD, dopDH
gluconate gntT, gntK, edd, eda
glucose MFS-glucose, glk
glucose-6-P uhpT
glucosamine nagX, crr, ptsB, ptsC, nagA, nagB
glucuronate exuT, udh, gci, kdgD, dopDH
glutamate gltP, gdhA
glycerol glpF, glpK, glpD, tpi
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
isoleucine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
D-lactate larD, glcD, glcE, glcF
L-lactate larD, lutA, lutB, lutC
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
leucine natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine lysL, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate sdlC
maltose susB, MFS-glucose, glk
mannitol cmtA*, cmtB, mtlD
mannose frcA, frcB, frcC, mannokinase, manA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG crr, ptsB, ptsC, nagA, nagB
2-oxoglutarate kgtP
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
proline proY, put1, putA
propionate mctC, prpE, pccA, pccB, epi, mcm-large, mcm-small
putrescine puuP, patA, patD, gabT, gabD
pyruvate mctC
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
ribose frcA, frcB, frcC, rbsK
D-serine cycA, dsdA
serine braC, braD, braE, braF, braG, sdaB
sorbitol SOT, sdh, scrK
succinate sdc
sucrose ams, frcA, frcB, frcC, scrK
threonine braC, braD, braE, braF, braG, ltaE, adh, acs*, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, adh, acs*
trehalose thuE, thuF, thuG, thuK, treF, glk
tryptophan tnaT, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
xylitol PLT5, xdhA, xylB
xylose xylT, xyrA, xdhA, 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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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