GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism in Herbaspirillum seropedicae SmR1

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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-galacturonate transporter ExuT HSERO_RS23010 HSERO_RS20520
udh D-galacturonate dehydrogenase HSERO_RS23040
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF) HSERO_RS15795 HSERO_RS19370
garD meso-galactarate dehydratase (L-threo-forming) GarD HSERO_RS15800 HSERO_RS19355
kdgD 5-dehydro-4-deoxyglucarate dehydratase HSERO_RS15785
dopDH 2,5-dioxopentanonate dehydrogenase HSERO_RS00735 HSERO_RS07235
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HSERO_RS05525 HSERO_RS05155
gatA D-galacturonate transporter gatA
gci D-galactarolactone cycloisomerase HSERO_RS05150
gli D-galactarolactone isomerase
kdgK 2-keto-3-deoxygluconate kinase HSERO_RS08715 HSERO_RS07545
PS417_04205 D-galacturonate transporter HSERO_RS15805 HSERO_RS02645
uxaA D-altronate dehydratase HSERO_RS19355 HSERO_RS15800
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.

Links

Downloads

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:

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