GapMind for catabolism of small carbon sources


Definition of citrate catabolism

As rules and steps, or see full text


Overview: Citrate is utilized via ATP-citrate lyase (link) or by oxidation to 2-oxoglutarate (part of the the TCA cycle, link). MetaCyc does not explicitly represent the TCA cycle as a means for catabolizing citrate, but it is expected to function under respiratory conditions. Fitness data confirms that in diverse bacteria, ATP-citrate lyase is not necessary for aerobic utilization of citrate.


fecB: ferric citrate ABC transporter, substrate-binding component FecB

fecC: ferric citrate ABC transporter, permease component 1 (FecC)

fecD: ferric citrate ABC transporter, permease component 2 (FecD)

fecE: ferric citrate ABC transporter, ATPase component FecE

tctA: citrate/Na+ symporter, large transmembrane component TctA

tctB: citrate/Na+ symporter, small transmembrane component TctB

tctC: citrate/Na+ symporter, substrate-binding component TctC

SLC13A5: citrate:Na+ symporter

citA: citrate:H+ symporter CitA

cimH: citrate:H+ symporter CimH

citW: citrate exchange transporter CitW (with lactate or acetate)

cit1: citrate:H+ symporter Cit1

citT: citrate:succinate antiporter CitT

citM: citrate:cation:H+ symporter CitM

citS: citrate:Na+ symporter CitS

citD: citrate lyase, acyl carrier component CitD

citE: citrate lyase, citryl-ACP lyase component CitE

citF: citrate lyase, citrate-ACP transferase component CitF

acn: aconitase

icd: isocitrate dehydrogenase



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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 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