GapMind for catabolism of small carbon sources

 

propionate catabolism in Moritella dasanensis ArB 0140

Best path

lctP, prpE, prpC, acnD, prpF, acn, prpB

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease A923_RS0106030
prpE propionyl-CoA synthetase A923_RS0118350 A923_RS0102085
prpC 2-methylcitrate synthase A923_RS0100240 A923_RS0113605
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) A923_RS0100245
prpF methylaconitate isomerase A923_RS0100250
acn (2R,3S)-2-methylcitrate dehydratase A923_RS0111105 A923_RS0100245
prpB 2-methylisocitrate lyase A923_RS0100235
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase A923_RS0108520
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase A923_RS0116325 A923_RS0104120
iolA malonate semialdehyde dehydrogenase (CoA-acylating) A923_RS0115330 A923_RS0108515
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit A923_RS0101145
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components A923_RS0101145
mctC propionate:H+ symporter A923_RS0113640
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit A923_RS0118365 A923_RS0101000
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit A923_RS0118365 A923_RS0101000
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit A923_RS0101010
pco propanyl-CoA oxidase
prpD 2-methylcitrate dehydratase
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 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