GapMind for catabolism of small carbon sources

 

citrate catabolism in Yersinia intermedia Y228

Best path

tctA, tctB, tctC, citD, citE, citF

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tctA citrate/Na+ symporter, large transmembrane component TctA CH53_RS05810
tctB citrate/Na+ symporter, small transmembrane component TctB CH53_RS05805
tctC citrate/Na+ symporter, substrate-binding component TctC CH53_RS05800
citD citrate lyase, acyl carrier component CitD CH53_RS17025
citE citrate lyase, citryl-ACP lyase component CitE CH53_RS17030
citF citrate lyase, citrate-ACP transferase component CitF CH53_RS17035
Alternative steps:
acn aconitase CH53_RS04925 CH53_RS19290
cimH citrate:H+ symporter CimH CH53_RS18210
cit1 citrate:H+ symporter Cit1 CH53_RS10800 CH53_RS17050
citA citrate:H+ symporter CitA CH53_RS16075 CH53_RS05365
citM citrate:cation:H+ symporter CitM
citS citrate:Na+ symporter CitS
citT citrate:succinate antiporter CitT CH53_RS17050 CH53_RS10800
citW citrate exchange transporter CitW (with lactate or acetate) CH53_RS18210
fecB ferric citrate ABC transporter, substrate-binding component FecB
fecC ferric citrate ABC transporter, permease component 1 (FecC) CH53_RS06945 CH53_RS11840
fecD ferric citrate ABC transporter, permease component 2 (FecD) CH53_RS06945 CH53_RS11840
fecE ferric citrate ABC transporter, ATPase component FecE CH53_RS11830 CH53_RS04805
icd isocitrate dehydrogenase CH53_RS21660 CH53_RS05150
SLC13A5 citrate:Na+ symporter

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 24 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:

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