GapMind for catabolism of small carbon sources

 

acetate catabolism in Burkholderia phytofirmans PsJN

Best path

actP, ackA, pta

Also see fitness data for the top candidates

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.

11 steps (8 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
actP cation/acetate symporter ActP BPHYT_RS11800 BPHYT_RS25605
ackA acetate kinase BPHYT_RS06125 BPHYT_RS26200
pta phosphate acetyltransferase BPHYT_RS21700 BPHYT_RS27695
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming BPHYT_RS07000 BPHYT_RS27780
ady2 acetate permease Ady2 BPHYT_RS27785
dctA organic acid/proton symporter DctA BPHYT_RS02510 BPHYT_RS13510
deh acetate/haloacid transporter BPHYT_RS16375 BPHYT_RS07110
patA Acetate transporter PatA
satP acetate/proton symporter satP BPHYT_RS27785
SLC5A8 actetate:Na+ symporter SLC5A8
ybhL acetate uptake transporter YbhL

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 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