GapMind for catabolism of small carbon sources


catabolism of small carbon sources in Synechococcus elongatus PCC 7942

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
alanine braC, braD, braE, braF, braG
aspartate natF, bgtB', natH, bgtA
threonine braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
asparagine ans, natF, bgtB', natH, bgtA
ethanol etoh-dh-nad, adh, acs
glutamate dmeA, aspA
serine braC, braD, braE, braF, braG, sdaB
trehalose thuE, thuF, thuG, thuK, PsTP, pgmA, glk
proline natA, natB, natC, natD, natE, put1, putA
sucrose thuE, thuF, thuG, thuK, ams, scrK, glk
citrate SLC13A5, acn, icd
NAG nagEcba, nagA, nagB
acetate actP, acs
glucose MFS-glucose, glk
glucosamine gamP, nagB
D-lactate lctP, D-LDH
cellobiose bgl, MFS-glucose, glk
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
fructose fruII-ABC, 1pfk, fba, tpi
glycerol glpF, dhaD, dhaK', tpi
fumarate dctA
glucose-6-P uhpT
L-malate sdlC
2-oxoglutarate kgtP
pyruvate SLC5A8
succinate sdc
deoxyribose deoP, deoK, deoC, adh, acs
mannose manP, manA
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
maltose thuE, thuF, thuG, thuK, susB, glk
sorbitol SOT, sdh, scrK
gluconate gntT, gntK, gnd
L-lactate lctP, lctO, acs
mannitol mtlA, mtlD
ribose rbsU, rbsK
D-serine cycA, dsdA
tryptophan aroP, tnaA
xylitol fruI, x5p-reductase
histidine natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
thymidine nupG, deoA, deoB, deoC, adh, acs
arginine rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
galactose galP, galK, galT, galE, pgmA
propionate putP, prpE, prpC, prpD, acn, prpB
xylose xylT, xylA, xylB
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
arabinose araE, araA, araB, araD
isoleucine natA, natB, natC, natD, natE, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
putrescine puuP, patA, patD, gabT, gabD
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
leucine natA, natB, natC, natD, natE, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
glucuronate exuT, udh, gci, kdgD, dopDH
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
lysine lysP, lat, amaB, lysN, hglS, ydiJ
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
valine natA, natB, natC, natD, natE, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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