GapMind for catabolism of small carbon sources

 

citrate catabolism in Klebsiella michiganensis M5al

Best path

fecB, fecC, fecD, fecE, citD, citE, citF

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fecB ferric citrate ABC transporter, substrate-binding component FecB BWI76_RS11380
fecC ferric citrate ABC transporter, permease component 1 (FecC) BWI76_RS11375 BWI76_RS22470
fecD ferric citrate ABC transporter, permease component 2 (FecD) BWI76_RS11370 BWI76_RS22470
fecE ferric citrate ABC transporter, ATPase component FecE BWI76_RS11365 BWI76_RS07720
citD citrate lyase, acyl carrier component CitD BWI76_RS04440
citE citrate lyase, citryl-ACP lyase component CitE BWI76_RS04445
citF citrate lyase, citrate-ACP transferase component CitF BWI76_RS04450
Alternative steps:
acn aconitase BWI76_RS04910 BWI76_RS11940
cimH citrate:H+ symporter CimH BWI76_RS04555 BWI76_RS04430
cit1 citrate:H+ symporter Cit1 BWI76_RS16110 BWI76_RS04375
citA citrate:H+ symporter CitA BWI76_RS08245 BWI76_RS21415
citM citrate:cation:H+ symporter CitM
citS citrate:Na+ symporter CitS BWI76_RS04430
citT citrate:succinate antiporter CitT BWI76_RS16110 BWI76_RS04375
citW citrate exchange transporter CitW (with lactate or acetate) BWI76_RS04555 BWI76_RS04430
icd isocitrate dehydrogenase BWI76_RS11330 BWI76_RS10680
SLC13A5 citrate:Na+ symporter
tctA citrate/Na+ symporter, large transmembrane component TctA BWI76_RS20045
tctB citrate/Na+ symporter, small transmembrane component TctB BWI76_RS20040
tctC citrate/Na+ symporter, substrate-binding component TctC BWI76_RS20035

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