GapMind for catabolism of small carbon sources

 

citrate catabolism in Cupriavidus basilensis 4G11

Best path

citA, acn, icd

Also see fitness data for the top candidates

Rules

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.

20 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
citA citrate:H+ symporter CitA RR42_RS27250 RR42_RS07875
acn aconitase RR42_RS23515 RR42_RS11270
icd isocitrate dehydrogenase RR42_RS28800 RR42_RS17135
Alternative steps:
cimH citrate:H+ symporter CimH RR42_RS29530
cit1 citrate:H+ symporter Cit1
citD citrate lyase, acyl carrier component CitD
citE citrate lyase, citryl-ACP lyase component CitE RR42_RS24350 RR42_RS25095
citF citrate lyase, citrate-ACP transferase component CitF
citM citrate:cation:H+ symporter CitM
citS citrate:Na+ symporter CitS
citT citrate:succinate antiporter CitT
citW citrate exchange transporter CitW (with lactate or acetate) RR42_RS29530
fecB ferric citrate ABC transporter, substrate-binding component FecB
fecC ferric citrate ABC transporter, permease component 1 (FecC) RR42_RS16135
fecD ferric citrate ABC transporter, permease component 2 (FecD) RR42_RS16135
fecE ferric citrate ABC transporter, ATPase component FecE RR42_RS16130 RR42_RS12250
SLC13A5 citrate:Na+ symporter
tctA citrate/Na+ symporter, large transmembrane component TctA RR42_RS20610 RR42_RS15180
tctB citrate/Na+ symporter, small transmembrane component TctB
tctC citrate/Na+ symporter, substrate-binding component TctC RR42_RS03285 RR42_RS20620

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 (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 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