GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Nocardioides dokdonensis FR1436

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
ethanol etoh-dh-nad, adh, acs
fumarate sdcL
L-malate sdlC
succinate sdc
leucine natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
threonine braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
propionate mctC, prpE, pccA, pccB, epi, mcm-large, mcm-small
proline natA, natB, natC, natD, natE, put1, putA
fructose fruII-ABC, 1pfk, fba, tpi
L-lactate Shew_2731, Shew_2732, lctO, acs
sucrose ams, fruII-ABC, 1pfk, fba, tpi
serine braC, braD, braE, braF, braG, sdaB
gluconate gntT, gntK, gnd
glycerol glpF, glpK, glpD, tpi
alanine braC, braD, braE, braF, braG
acetate actP, acs
asparagine ans, glt
glutamate gltP, gdhA
aspartate glt
pyruvate mctC
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
arginine rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
valine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
histidine natA, natB, natC, natD, natE, hutH, hutU, hutI, hutF, hutG'
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
thymidine nupC, deoA, deoB, deoC, adh, acs
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
trehalose thuE, thuF, thuG, thuK, treF, glk
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
phenylalanine livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
deoxyribose deoP, deoK, deoC, adh, acs
cellobiose bgl, MFS-glucose, glk
citrate SLC13A5, acn, icd
maltose MAL11, susB, glk
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
galactose galP, galK, galT, galE, pgmA
glucose MFS-glucose, glk
D-lactate lctP, D-LDH
mannitol mtlA, mtlD
sorbitol mtlA, srlD
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
lysine lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
glucose-6-P uhpT
2-oxoglutarate kgtP
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
ribose rbsU, rbsK
xylitol fruI, x5p-reductase
D-alanine cycA, dadA
glucosamine gamP, nagB
mannose manP, manA
D-serine cycA, dsdA
tryptophan aroP, tnaA
NAG nagEcba, nagA, nagB
xylose xylT, xylA, xylB
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
arabinose araE, araA, araB, araD
glucuronate exuT, udh, gci, garL, garR, garK
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda

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