GapMind for catabolism of small carbon sources

 

propionate catabolism in Pseudomonas benzenivorans DSM 8628

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease BLS63_RS14320 BLS63_RS18840
prpE propionyl-CoA synthetase BLS63_RS26090 BLS63_RS23690
prpC 2-methylcitrate synthase BLS63_RS00670 BLS63_RS00165
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BLS63_RS00675 BLS63_RS00030
prpF methylaconitate isomerase BLS63_RS00680 BLS63_RS13860
acn (2R,3S)-2-methylcitrate dehydratase BLS63_RS00675 BLS63_RS00850
prpB 2-methylisocitrate lyase BLS63_RS00665 BLS63_RS21130
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase BLS63_RS09135 BLS63_RS14560
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase BLS63_RS06660 BLS63_RS21705
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLS63_RS14055 BLS63_RS21720
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 BLS63_RS05935
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit BLS63_RS18330 BLS63_RS24345
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLS63_RS15655 BLS63_RS04465
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BLS63_RS24335 BLS63_RS18315
pco propanyl-CoA oxidase BLS63_RS14585
prpD 2-methylcitrate dehydratase BLS63_RS00685
putP propionate transporter; proline:Na+ symporter BLS63_RS22040
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