GapMind for catabolism of small carbon sources

 

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

Pathways are sorted by completeness. Sort by name instead.

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