GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Novosphingobium lindaniclasticum LE124

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate deh, acs
D-alanine cycA, dadA
alanine cycA
arabinose araE, xacB, xacC, xacD, xacE, xacF
arginine rocE, astA, astB, astC, astD, astE
asparagine ans, glt
aspartate glt
cellobiose bgl, MFS-glucose, glk
citrate SLC13A5, acn, icd
citrulline PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, ocd, put1, putA
deoxyinosine nupC, 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 glcP, scrK
fucose fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
fumarate dctA
galactose HP1174, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntT, gntK, edd, eda
glucose MFS-glucose, glk
glucose-6-P uhpT
glucosamine gamP, nagB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate gltP, aspA
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, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
D-lactate lctP, D-LDH
L-lactate lctP, L-LDH
lactose lacA', lacC', lacB', klh, MFS-glucose, glk
leucine leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate dctA
maltose malI, susB, glk
mannitol PLT5, mt2d, scrK
mannose gluP, man-isomerase, scrK
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
NAG nagEcba, nagA, nagB
2-oxoglutarate kgtP
phenylacetate paaT, 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 putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
putrescine puuP, patA, patD, gabT, gabD
pyruvate cstA, ybdD
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
ribose rbsU, rbsK
D-serine cycA, dsdA
serine serP, sdaB
sorbitol SOT, sdh, scrK
succinate dctA
sucrose ams, MFS-glucose, glk
threonine tdcC, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
thymidine nupC, deoA, deoB, deoC, ald-dh-CoA
trehalose treF, MFS-glucose, glk
tryptophan aroP, 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 fruI, x5p-reductase
xylose xylT, xdh, xylC, xad, kdaD, dopDH

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.

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