GapMind for catabolism of small carbon sources

 

propionate catabolism in Sphingomonas indica Dd16

Best path

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

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 B9N75_RS08675 B9N75_RS08985
pccA propionyl-CoA carboxylase, alpha subunit B9N75_RS06755 B9N75_RS13145
pccB propionyl-CoA carboxylase, beta subunit B9N75_RS06795 B9N75_RS13150
epi methylmalonyl-CoA epimerase B9N75_RS06780
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit B9N75_RS06775
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit B9N75_RS06775
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase B9N75_RS04320
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) B9N75_RS04320
dddA 3-hydroxypropionate dehydrogenase B9N75_RS13465
hpcD 3-hydroxypropionyl-CoA dehydratase B9N75_RS13460 B9N75_RS11255
iolA malonate semialdehyde dehydrogenase (CoA-acylating) B9N75_RS13435 B9N75_RS04360
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components B9N75_RS06775
mctC propionate:H+ symporter
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit B9N75_RS11080 B9N75_RS06755
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase B9N75_RS12195
prpB 2-methylisocitrate lyase B9N75_RS04185
prpC 2-methylcitrate synthase B9N75_RS11750
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 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