Definition of acetate catabolism
As rules and steps, or see full text
Rules
Overview: 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 (link). 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.
- all:
- acetate-transport and acs
- or acetate-transport, ackA and pta
- acetate-transport:
Steps
actP: cation/acetate symporter ActP
- Curated sequence P32705: Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP. Acetate/glyoxylate permease, ActP. acetate/glycolate:cation symporter. acetate/glycolate:cation symporter
- Curated sequence Q8NS49: Monocarboxylic acid transporter. Pyruvate/acetate/propionate: H+ symporter, MctC (DhlC; cg0953)
- Curated sequence D5APM1: Acetate permease ActP-2/ActP2/ActP3
- Curated sequence D5AU53: Acetate uptake permease, ActP1; also takes up tellurite
- Total: 4 characterized proteins
ady2: acetate permease Ady2
- Curated sequence P25613: Accumulation of dyads protein 2; Ammonia transport outward protein 1. The acetate permease, Ady2, required for normal sporulation; phosphorylated in mitochondria
- Curated sequence Q5B2K4: Acetate permease A; Monocarboxylate transporter acpA. acetate permease. The acetate permease, AcpA (Robellet et al., 2008). (induced by acetate, ethanol and ethyl acetate). This systems and its orthologs in fungi have been reviewed
- Ignore hits to P41943 when looking for 'other' hits (Glyoxylate pathway regulator. Gpr1/YarL1 glyoxylate pathway regulator)
- Comment: Ignore the poorly characterized protein GPR1_YARLI (P41943) from Yarrowia lipolytica
- Total: 2 characterized proteins
patA: Acetate transporter PatA
- Curated sequence A0A075TRL0: Acetate transporter protein patA; Patulin biosynthesis cluster protein A
- Curated sequence A1CFK8: Acetate transporter protein patA; Patulin synthesis protein A
- Total: 2 characterized proteins
deh: acetate/haloacid transporter
- Curated sequence F8SVK1: Acetate/haloacid transporter, Dehp2, with a possible atypical topology
- Curated sequence Q7X4L6: The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate)
- Curated sequence M1Q159: Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs
- Comment: Added the singleton Deh4p (M1Q159) from Dehalococcoides mccartyi, which has the same domain
- Total: 3 characterized proteins
satP: acetate/proton symporter satP
- Curated sequence P0AC98: Succinate-acetate/proton symporter SatP; Succinate-acetate transporter protein. Acetate/succinate transporter, SatP or YaaH. acetate/succinate:H+ symporter. acetate/succinate:H+ symporter
- Total: 1 characterized proteins
SLC5A8: actetate:Na+ symporter SLC5A8
- Curated sequence Q8N695: Sodium-coupled monocarboxylate transporter 1; Apical iodide transporter; Electrogenic sodium monocarboxylate cotransporter; Sodium iodide-related cotransporter; Solute carrier family 5 member 8. Na+-dependent short chain fatty acid transporter SLC5A8 (tumor suppressor gene product, down-regulated in colon cancer) (substrates: lactate, pyruvate, acetate, propionate, butyrate (Km ≈1 mM)) [propionate:Na+ = 1:3] (Miyauchi et al., 2004). Pyroglutamate (5-oxoproline) is also transported in a Na+- coupled mechanism (Miyauchi et al., 2010). SMCT1 and SMCT2 may transport monocarboxylate drugs (e.g. nicotinate and its derivatives) across the intestinal brush boarder membrane
- Total: 1 characterized proteins
ybhL: acetate uptake transporter YbhL
- Curated sequence P0AAC4: The YbhL (AceP) protein. Possibly a pmf-dependent acetate uptake transporter. [14C]Acetate uptake was inhibited by CCCP as well as cold acetate, serine, α-ketoglutarate, lactate, and succinate (M. Inouye, personal communication). Bax1-I family protein YbhL
- Comment: TC 1.A.14.2.2 reports that E. coli yhbL is an acetate transporter, and cites a personal communication from M. Inouye.
- Total: 1 characterized proteins
dctA: organic acid/proton symporter DctA
- Curated sequence Q848I3: Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs
- Ignore hits to Q9I4F5 when looking for 'other' hits (C4-dicarboxylate transport protein 2)
- Ignore hits to AO356_18980 when looking for 'other' hits (sodium:C4-dicarboxylate symporter (dctA))
- Comment: 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 (Q9I4F5), acetate does not seem to have been considered as a potential substrate
- Total: 1 characterized proteins
acs: acetyl-CoA synthetase, AMP-forming
ackA: acetate kinase
pta: phosphate acetyltransferase
- Curated proteins or TIGRFams with EC 2.3.1.8
- Ignore hits to P32796 when looking for 'other' hits (carnitine O-acetyltransferase (EC 2.3.1.7); phosphate acetyltransferase (EC 2.3.1.8). Carnitine O-acetyltransferase, mitochondrial; Carnitine acetylase; EC 2.3.1.7)
- Comment: BRENDA misannotates yeast's carnitine acetyltransferase with EC 2.3.1.8
- Total: 1 HMMs and 18 characterized proteins
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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