GapMind for catabolism of small carbon sources


Definition of acetate catabolism

As text, or see rules and steps

# After uptake, acetate can be converted to acetyl-CoA by acs or by
# ackA and pta, see MetaCyc's superpathway of acetate
# utilization and formation (metacyc:ACETATEUTIL-PWY).
# Acetyl-CoA is a central metabolic intermediate, so further reactions
# are not represented in GapMind. Acetyl-CoA may be catabolized by the TCA
# cycle or, in strict anaerobes, by the Wood-Ljungdahl pathway. If the
# TCA cycle is used, then intermediates need to be replenished
# by anaplaerotic reactions such as the glyoxylate cycle or the
# ethylmalonyl-CoA pathway.

actP	cation/acetate symporter ActP	curated:SwissProt::P32705	curated:SwissProt::Q8NS49	curated:TCDB::D5APM1	curated:TCDB::D5AU53

# Transporters were identified using
# query: transporter:acetate:acetic.
acetate-transport: actP

# Ignore the poorly characterized protein GPR1_YARLI (uniprot:P41943) from Yarrowia lipolytica
ady2	acetate permease Ady2	curated:SwissProt::P25613	curated:SwissProt::Q5B2K4	ignore:SwissProt::P41943
acetate-transport: ady2

patA	Acetate transporter PatA	curated:SwissProt::A0A075TRL0	curated:SwissProt::A1CFK8
acetate-transport: patA

# Added the singleton Deh4p (M1Q159) from Dehalococcoides mccartyi, which has the same domain
deh	acetate/haloacid transporter	curated:TCDB::F8SVK1	curated:TCDB::Q7X4L6	curated:TCDB::M1Q159
acetate-transport: deh

satP	acetate/proton symporter satP	curated:SwissProt::P0AC98
acetate-transport: satP

SLC5A8	actetate:Na+ symporter SLC5A8	curated:SwissProt::Q8N695
acetate-transport: SLC5A8

# TC 1.A.14.2.2 reports that E. coli yhbL is an acetate transporter, and cites a personal communication
# from M. Inouye.
ybhL	acetate uptake transporter YbhL	curated:TCDB::P0AAC4
acetate-transport: ybhL

# A mutant in P. chlororaphis is reported to be defective in acetate utilization, implying uptake.
# Fitness data for various strains of P. fluorescens did not indicate this, but uptake could be redundant;
# for the ortholog in P. aeruginosa (uniprot:Q9I4F5), acetate does not seem to have been considered as a potential substrate
dctA	organic acid/proton symporter DctA	curated:TCDB::Q848I3	ignore:SwissProt::Q9I4F5	ignore:reanno::pseudo5_N2C3_1:AO356_18980
acetate-transport: dctA

# Ignored efflux systems, acyl-CoA transporter (annotated as actetate non-utilizing),
# non-specific chloride channel protein, and
# citrate:acetate antiporter.

import ethanol.steps:acs ackA pta

all: acetate-transport acs
all: acetate-transport ackA pta



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