GapMind for catabolism of small carbon sources

 

pyruvate catabolism in Magnetospirillum magneticum AMB-1

Best path

dctM, dctP, dctQ

Also see fitness data for the top candidates

Rules

Overview: Pyruvate is a central metabolite, so GapMind represents transport only.

13 steps (6 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dctM pyruvate TRAP transporter, large permease component AMB_RS13000 AMB_RS04550
dctP pyruvate TRAP transporter, substrate-binding component AMB_RS13005
dctQ pyruvate TRAP transporter, small permease component AMB_RS12995
Alternative steps:
actP large subunit of pyruvate transporter (actP-like) AMB_RS07815 AMB_RS13720
btsT pyruvate symporter BtsT
cstA large subunit of pyruvate transporter (CstA)
JEN1 pyruvate symporter JEN1
MCT4 pyruvate symporter MCT4 (SLC16A3)
mctC pyruvate symporter MctC AMB_RS13215 AMB_RS07815
mctP pyruvate permease MctP
SLC5A8 sodium-coupled pyruvate transporter
ybdD small subunit of pyruvate transporter (YbdD)
yjcH putative small subunit of pyruvate transporter (yjcH-like) AMB_RS07810 AMB_RS13725

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 Apr 09 2024. 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