GapMind for catabolism of small carbon sources

 

propionate catabolism in Chromobacterium vaccinii MWU205

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease VL52_RS18675
prpE propionyl-CoA synthetase VL52_RS11020 VL52_RS20355
prpC 2-methylcitrate synthase VL52_RS06910 VL52_RS01125
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) VL52_RS06920 VL52_RS13705
prpF methylaconitate isomerase VL52_RS06925 VL52_RS07045
acn (2R,3S)-2-methylcitrate dehydratase VL52_RS06920 VL52_RS16820
prpB 2-methylisocitrate lyase VL52_RS13445 VL52_RS06905
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase VL52_RS11315
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase VL52_RS18865 VL52_RS21030
iolA malonate semialdehyde dehydrogenase (CoA-acylating) VL52_RS11940 VL52_RS21020
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 VL52_RS11015 VL52_RS20390
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit VL52_RS19945 VL52_RS01580
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit VL52_RS01580 VL52_RS19945
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit VL52_RS19955
pco propanyl-CoA oxidase VL52_RS20895 VL52_RS19965
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