GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

exuT, 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
exuT D-galacturonate transporter ExuT AO356_14055 AO356_15575
udh D-galacturonate dehydrogenase AO356_23065 AO356_14875
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF) AO356_23060 AO356_20235
garD meso-galactarate dehydratase (L-threo-forming) GarD AO356_07170 AO356_24195
kdgD 5-dehydro-4-deoxyglucarate dehydratase AO356_07185 AO356_04530
dopDH 2,5-dioxopentanonate dehydrogenase AO356_24600 AO356_07180
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO356_05150 AO356_20285
gatA D-galacturonate transporter gatA AO356_27270
gci D-galactarolactone cycloisomerase AO356_20290 AO356_26155
gli D-galactarolactone isomerase
kdgK 2-keto-3-deoxygluconate kinase AO356_28555 AO356_00445
PS417_04205 D-galacturonate transporter AO356_07175 AO356_20295
uxaA D-altronate dehydratase AO356_27460 AO356_24195
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 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, 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