GapMind for catabolism of small carbon sources

 

citrate catabolism in Pseudomonas fluorescens FW300-N2E3

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
citA citrate:H+ symporter CitA AO353_26710 AO353_25075
acn aconitase AO353_21605 AO353_00890
icd isocitrate dehydrogenase AO353_27695 AO353_27690
Alternative steps:
cimH citrate:H+ symporter CimH AO353_24495
cit1 citrate:H+ symporter Cit1
citD citrate lyase, acyl carrier component CitD
citE citrate lyase, citryl-ACP lyase component CitE
citF citrate lyase, citrate-ACP transferase component CitF
citM citrate:cation:H+ symporter CitM AO353_11040
citS citrate:Na+ symporter CitS AO353_24495
citT citrate:succinate antiporter CitT
citW citrate exchange transporter CitW (with lactate or acetate) AO353_24495
fecB ferric citrate ABC transporter, substrate-binding component FecB
fecC ferric citrate ABC transporter, permease component 1 (FecC) AO353_13550 AO353_14445
fecD ferric citrate ABC transporter, permease component 2 (FecD) AO353_13550 AO353_14445
fecE ferric citrate ABC transporter, ATPase component FecE AO353_24045 AO353_13560
SLC13A5 citrate:Na+ symporter
tctA citrate/Na+ symporter, large transmembrane component TctA AO353_17570
tctB citrate/Na+ symporter, small transmembrane component TctB AO353_17575
tctC citrate/Na+ symporter, substrate-binding component TctC AO353_17580

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