GapMind for catabolism of small carbon sources

 

propionate catabolism in Desulfovibrio oxyclinae DSM 11498

Best path

lctP, prpE, pco, hpcD, dddA, iolA

Rules

Overview: Propionate degradation in GapMind is based on MetaCyc pathways for the 2-methylcitrate cycle (link, link) and for propanoyl-CoA degradation (link, link).

24 steps (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease B149_RS0103815
prpE propionyl-CoA synthetase B149_RS0106290 B149_RS0113155
pco propanyl-CoA oxidase B149_RS0112495
hpcD 3-hydroxypropionyl-CoA dehydratase
dddA 3-hydroxypropionate dehydrogenase B149_RS0113405
iolA malonate semialdehyde dehydrogenase (CoA-acylating) B149_RS0113400 B149_RS0108900
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
epi methylmalonyl-CoA epimerase
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
mctC propionate:H+ symporter B149_RS0112850
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit B149_RS0111240 B149_RS0111475
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit B149_RS0111240 B149_RS0102080
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit B149_RS0111240
pccB propionyl-CoA carboxylase, beta subunit
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase B149_RS0113940
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
putP propionate transporter; proline:Na+ symporter
SLC5A8 sodium-coupled monocarboxylate transporter

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