GapMind for catabolism of small carbon sources

 

ethanol catabolism in Herbaspirillum seropedicae SmR1

Best path

etoh-dh-nad, adh, acs

Also see fitness data for the top candidates

Rules

Overview: Ethanol can pass through biological membranes, so no transporter is required. Ethanol degradation in GapMind is based on MetaCyc pathways ethanol degradation I (oxidation to acetyl-CoA, link) and II (oxidation to acetate and activation, link). Pathways III (with ethanol monooxygenase, link) and IV (with ethanol peroxidase, link) are not reported to occur in prokaryotes and are not included.

10 steps (7 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
etoh-dh-nad ethanol dehydrogenase (NAD(P)) HSERO_RS23855 HSERO_RS04830
adh acetaldehyde dehydrogenase (not acylating) HSERO_RS05115 HSERO_RS09465
acs acetyl-CoA synthetase, AMP-forming HSERO_RS07770 HSERO_RS23535
Alternative steps:
ackA acetate kinase HSERO_RS01305 HSERO_RS11090
adhAqn ethanol dehydrogenase (quinone), subunit I
adhBqn ethanol dehydrogenase (quinone), subunit II HSERO_RS16735 HSERO_RS22390
adhSqn ethanol dehydrogenase (quinone), subunit III
ald-dh-CoA acetaldehyde dehydrogenase, acylating
etoh-dh-c ethanol dehydrogenase (cytochrome c) HSERO_RS16735 HSERO_RS22390
pta phosphate acetyltransferase HSERO_RS12030 HSERO_RS01300

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