GapMind for catabolism of small carbon sources

 

ethanol catabolism in Chromobacterium vaccinii MWU205

Best path

etoh-dh-nad, adh, ackA, pta

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 (8 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
etoh-dh-nad ethanol dehydrogenase (NAD(P)) VL52_RS13795 VL52_RS05625
adh acetaldehyde dehydrogenase (not acylating) VL52_RS21455 VL52_RS06935
ackA acetate kinase VL52_RS15345 VL52_RS02270
pta phosphate acetyltransferase VL52_RS15350 VL52_RS02265
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming VL52_RS11020 VL52_RS20355
adhAqn ethanol dehydrogenase (quinone), subunit I
adhBqn ethanol dehydrogenase (quinone), subunit II VL52_RS18000
adhSqn ethanol dehydrogenase (quinone), subunit III
ald-dh-CoA acetaldehyde dehydrogenase, acylating VL52_RS13795
etoh-dh-c ethanol dehydrogenase (cytochrome c) VL52_RS18000

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 24 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:

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