GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

PS417_04205, udh, uxuL, garD, kdgD, dopDH

Also see fitness data for the top candidates

Rules

Overview: Galacturonate utilization in GapMind is based on MetaCyc pathways D-galacturonate degradation I via tagaturonate (link), pathway II via oxidation to 5-dehydro-4-deoxy-glucarate (link), and another oxidative pathway (PMID:30249705). Pathway III via galactonate (link) is reported only in fungi and is not included in GapMind.

15 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_04205 D-galacturonate transporter Pf6N2E2_3297 Pf6N2E2_5978
udh D-galacturonate dehydrogenase Pf6N2E2_489 Pf6N2E2_4908
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF) Pf6N2E2_488 Pf6N2E2_5966
garD meso-galactarate dehydratase (L-threo-forming) GarD Pf6N2E2_3296 Pf6N2E2_860
kdgD 5-dehydro-4-deoxyglucarate dehydratase Pf6N2E2_3299 Pf6N2E2_2747
dopDH 2,5-dioxopentanonate dehydrogenase Pf6N2E2_612 Pf6N2E2_3298
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf6N2E2_2883 Pf6N2E2_5976
exuT D-galacturonate transporter ExuT Pf6N2E2_5056 Pf6N2E2_6017
gatA D-galacturonate transporter gatA Pf6N2E2_883
gci D-galactarolactone cycloisomerase Pf6N2E2_5977 Pf6N2E2_1104
gli D-galactarolactone isomerase
kdgK 2-keto-3-deoxygluconate kinase Pf6N2E2_2046 Pf6N2E2_629
uxaA D-altronate dehydratase Pf6N2E2_860 Pf6N2E2_3296
uxaB tagaturonate reductase
uxaC D-galacturonate isomerase

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 preprint 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