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:

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