GapMind for catabolism of small carbon sources

 

Definition of ethanol catabolism

As text, or see rules and steps

# 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, metacyc:ETOH-ACETYLCOA-ANA-PWY)
# and II (oxidation to acetate and activation, metacyc:PWY66-21).
# Pathways III (with ethanol monooxygenase, metacyc:PWY66-161) and
# IV (with ethanol peroxidase, metacyc:PWY66-162) are not reported to
# occur in prokaryotes and are not included.

# CH_121261 seems to be a sequence fragment
etoh-dh-nad	ethanol dehydrogenase (NAD(P))	EC:1.1.1.1	ignore:CharProtDB::CH_121261	EC:1.1.1.71
etoh-dh-c	ethanol dehydrogenase (cytochrome c)	EC:1.1.2.8	ignore_other:1.1.2.8

# (The enzyme from Zymomonas is NAD-dependent, but is misannotated as quinone-dependent in MetaCyc.)
adhAqn	ethanol dehydrogenase (quinone), subunit I	curated:BRENDA::Q44002	curated:BRENDA::P18278	curated:BRENDA::Q93RE9	curated:SwissProt::O05542	curated:SwissProt::P28036	ignore_other:1.1.2.8
adhBqn	ethanol dehydrogenase (quinone), subunit II	curated:SwissProt::P0A388	curated:SwissProt::Q47945	ignore_other:1.1.2.8
adhSqn	ethanol dehydrogenase (quinone), subunit III	curated:SwissProt::O05544

# Bacterial quinone-dependent enzymes (EC 1.1.5.5) have 3 subunits.
etoh-dh-qn: adhAqn adhBqn adhSqn

# Three types of ethanol dehydrogenases: NAD(P) dependent, cytochrome c dependent, or quinone dependent.
etoh-dh: etoh-dh-nad
etoh-dh: etoh-dh-c
etoh-dh: etoh-dh-qn

# Many enzymes are multifunctional alcohol/acetaldehyde dehydrogenases,
# and many close homologs have just one annotation.
# EC:1.2.1.57 is acylating butanal dehydrogenase, which may also act on acetaldehyde.
# Q2XQZ7 is probably misannotated.
ald-dh-CoA	acetaldehyde dehydrogenase, acylating	EC:1.2.1.10	ignore_other:1.1.1.1	ignore_other:1.1.1.71	ignore_other:1.2.1.57	ignore:BRENDA::Q2XQZ7

adh	acetaldehyde dehydrogenase (not acylating)	EC:1.2.1.3

acs	acetyl-CoA synthetase, AMP-forming	EC:6.2.1.1

ackA	acetate kinase	EC:2.7.2.1	EC:2.7.2.15

# BRENDA misannotates yeast's carnitine acetyltransferase with EC:2.3.1.8
pta	phosphate acetyltransferase	EC:2.3.1.8	ignore:BRENDA::P32796

# Acetaldehyde can be oxidized to acetyl-CoA, or oxidized to acetate and activated to acetyl-CoA
# by either acetyl-CoA synthetase (acs)
# or by acetate kinase (ackA) and phosphate acetyltransferase (pta).
acetaldehyde-degradation: ald-dh-CoA
acetaldehyde-degradation: adh acs
acetaldehyde-degradation: adh ackA pta

# Ethanol is consumed by oxidation to acetaldehyde
all: etoh-dh acetaldehyde-degradation

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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, 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