GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Caulobacter crescentus NA1000

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
myoinositol iatP, iatA, ibpA, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
lactose lacA', lacC', lacB', klh, MFS-glucose, glk
xylose xylT, xdh, xylC, xad, kdaD, dopDH
NAG nagF, nagEcb, nagA, nagB
sucrose scrT, ams, scrK, glk
cellobiose bgl, MFS-glucose, glk
ethanol etoh-dh-nad, adh, acs
maltose malI, susB, glk
proline CCNA_00435, put1, putA
acetate deh, acs
fructose glcP, scrK
glucose MFS-glucose, glk
glutamate gltP, gdhA
aspartate glt
fumarate dctA
L-malate dctA
2-oxoglutarate kgtP
succinate dctA
threonine snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glucosamine nagX, nagF, nagEcb, nagA, nagB
trehalose treF, MFS-glucose, glk
asparagine ans, glt
serine snatA, sdaB
alanine snatA
valine Bap2, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA
isoleucine Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
leucine leuT, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
propionate putP, prpE, pccA, pccB, epi, mcmA
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
arginine rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
galactose HP1174, galdh, galactonolactonase, dgoD, dgoK, dgoA
citrate SLC13A5, acn, icd
deoxyribose deoP, deoK, deoC, adh, acs
L-lactate lctP, L-LDH
mannose manP, manA
ribose rbsU, rbsK
arabinose araE, xacB, xacC, xacD, xacE, xacF
sorbitol SOT, sdh, scrK
gluconate gntT, gntK, edd, eda
glycerol glpF, glpK, glpD, tpi
glucose-6-P uhpT
pyruvate SLC5A8
D-serine cycA, dsdA
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, puuA, puuB, puuC, puuD, gabT, gabD
mannitol PLT5, mt2d, scrK
D-alanine cycA, dadA
D-lactate lctP, D-LDH
tryptophan aroP, tnaA
xylitol fruI, x5p-reductase
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
lysine lysP, lat, amaB, lysN, hglS, ydiJ
thymidine nupG, deoA, deoB, deoC, adh, acs
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
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.

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 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