GapMind for catabolism of small carbon sources


D-galacturonate catabolism in Klebsiella michiganensis M5al

Best path

exuT, uxaC, uxaB, uxaA, kdgK, eda

Also see fitness data for the top candidates


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 BWI76_RS24735 BWI76_RS09050
uxaC D-galacturonate isomerase BWI76_RS24730 BWI76_RS23645
uxaB tagaturonate reductase BWI76_RS15180 BWI76_RS03945
uxaA D-altronate dehydratase BWI76_RS24725 BWI76_RS26325
kdgK 2-keto-3-deoxygluconate kinase BWI76_RS26750 BWI76_RS26950
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BWI76_RS18095 BWI76_RS27940
Alternative steps:
dopDH 2,5-dioxopentanonate dehydrogenase BWI76_RS05620 BWI76_RS07615
garD meso-galactarate dehydratase (L-threo-forming) GarD BWI76_RS24840 BWI76_RS13570
gatA D-galacturonate transporter gatA BWI76_RS24055 BWI76_RS23425
gci D-galactarolactone cycloisomerase BWI76_RS19325 BWI76_RS13570
gli D-galactarolactone isomerase
kdgD 5-dehydro-4-deoxyglucarate dehydratase
PS417_04205 D-galacturonate transporter BWI76_RS22835 BWI76_RS24835
udh D-galacturonate dehydrogenase
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF) BWI76_RS08665 BWI76_RS23720

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.



Related tools

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