GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Pedobacter sp. GW460-11-11-14-LB5

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate deh, ackA, pta
D-alanine cycA, dadA
alanine TRIC
arabinose araE, araA, araB, araD
arginine rocE, rocF, rocD, PRO3, put1, putA
asparagine ans, glt
aspartate glt
cellobiose bgl, SSS-glucose, glk
citrate SLC13A5, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
deoxyinosine nupG, deoD, deoB, deoC, adh, ackA, pta
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose deoP, deoK, deoC, adh, ackA, pta
ethanol etoh-dh-nad, adh, ackA, pta
fructose glcP, scrK
fucose fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
fumarate dctA
galactose galP, galK, galT, galE, pgmA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntT, gntK, gnd
glucose SSS-glucose, glk
glucose-6-P uhpT
glucosamine nagX, nagP, nagK, nagA, nagB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate gltP, gdhA
glycerol glpF, glpK, glpD, tpi
histidine LAT2, hutH, hutU, hutI, hutG
isoleucine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
D-lactate lctP, D-LDH
L-lactate lctP, L-LDH
lactose lacA', lacC', lacB', klh, SSS-glucose, glk
leucine leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate dctA
maltose malI, malP, pgmB, glk
mannitol mtlA, mtlD
mannose gluP, man-isomerase, scrK
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
NAG nagP, nagK, 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 N515DRAFT_2924, put1, putA
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
putrescine puuP, patA, patD, gabT, gabD
pyruvate SLC5A8
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
ribose rbsU, rbsK
D-serine cycA, dsdA
serine serP, sdaB
sorbitol mtlA, srlD
succinate dctA
sucrose ams, SSS-glucose, glk
threonine tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
trehalose lacA, lacC, lacB, klh, SSS-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 PLT5, xdhA, xylB
xylose xylT, xylA, 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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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