GapMind for catabolism of small carbon sources

 

citrate catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

citM, 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
citM citrate:cation:H+ symporter CitM Pf1N1B4_1898 Pf1N1B4_4465
acn aconitase Pf1N1B4_4564 Pf1N1B4_3821
icd isocitrate dehydrogenase Pf1N1B4_4051 Pf1N1B4_4052
Alternative steps:
cimH citrate:H+ symporter CimH
cit1 citrate:H+ symporter Cit1
citA citrate:H+ symporter CitA Pf1N1B4_686 Pf1N1B4_2033
citD citrate lyase, acyl carrier component CitD
citE citrate lyase, citryl-ACP lyase component CitE Pf1N1B4_5615
citF citrate lyase, citrate-ACP transferase component CitF
citS citrate:Na+ symporter CitS
citT citrate:succinate antiporter CitT
citW citrate exchange transporter CitW (with lactate or acetate)
fecB ferric citrate ABC transporter, substrate-binding component FecB
fecC ferric citrate ABC transporter, permease component 1 (FecC) Pf1N1B4_1341 Pf1N1B4_2867
fecD ferric citrate ABC transporter, permease component 2 (FecD) Pf1N1B4_1341 Pf1N1B4_2867
fecE ferric citrate ABC transporter, ATPase component FecE Pf1N1B4_2868 Pf1N1B4_1339
SLC13A5 citrate:Na+ symporter
tctA citrate/Na+ symporter, large transmembrane component TctA Pf1N1B4_3311 Pf1N1B4_4965
tctB citrate/Na+ symporter, small transmembrane component TctB Pf1N1B4_3312
tctC citrate/Na+ symporter, substrate-binding component TctC Pf1N1B4_3313 Pf1N1B4_4963

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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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