GapMind for catabolism of small carbon sources

 

propionate catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

putP, prpE, pccA, pccB, epi, mcm-large, mcm-small

Also see fitness data for the top candidates

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
putP propionate transporter; proline:Na+ symporter
prpE propionyl-CoA synthetase Echvi_1268
pccA propionyl-CoA carboxylase, alpha subunit Echvi_3962 Echvi_0191
pccB propionyl-CoA carboxylase, beta subunit Echvi_0160 Echvi_0113
epi methylmalonyl-CoA epimerase Echvi_0089
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Echvi_4683 Echvi_2441
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Echvi_4683
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Echvi_4039
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Echvi_4039
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase Echvi_4069 Echvi_0069
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Echvi_0481
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Echvi_2441 Echvi_4683
mctC propionate:H+ symporter Echvi_1267
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Echvi_3962 Echvi_0191
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit Echvi_0275
pco propanyl-CoA oxidase Echvi_0738 Echvi_2990
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase Echvi_3057
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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 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:

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