GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-galacturonate transporter ExuT H281DRAFT_05311 H281DRAFT_03828
udh D-galacturonate dehydrogenase H281DRAFT_05321 H281DRAFT_03826
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF) H281DRAFT_03238 H281DRAFT_05322
garD meso-galactarate dehydratase (L-threo-forming) GarD H281DRAFT_05320 H281DRAFT_06497
kdgD 5-dehydro-4-deoxyglucarate dehydratase H281DRAFT_05319 H281DRAFT_03816
dopDH 2,5-dioxopentanonate dehydrogenase H281DRAFT_01155 H281DRAFT_05316
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase H281DRAFT_04277 H281DRAFT_06295
gatA D-galacturonate transporter gatA
gci D-galactarolactone cycloisomerase H281DRAFT_04215 H281DRAFT_00974
gli D-galactarolactone isomerase H281DRAFT_01747 H281DRAFT_05538
kdgK 2-keto-3-deoxygluconate kinase H281DRAFT_00856 H281DRAFT_05211
PS417_04205 D-galacturonate transporter H281DRAFT_05318 H281DRAFT_03217
uxaA D-altronate dehydratase H281DRAFT_05320 H281DRAFT_00666
uxaB tagaturonate reductase H281DRAFT_02952 H281DRAFT_00668
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, 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