GapMind for catabolism of small carbon sources

 

propionate catabolism in Rhodobacter viridis JA737

Best path

mctC, 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
mctC propionate:H+ symporter C8J30_RS03285 C8J30_RS02510
prpE propionyl-CoA synthetase C8J30_RS06475 C8J30_RS18190
pccA propionyl-CoA carboxylase, alpha subunit C8J30_RS08525 C8J30_RS00790
pccB propionyl-CoA carboxylase, beta subunit C8J30_RS08545 C8J30_RS00785
epi methylmalonyl-CoA epimerase C8J30_RS06980
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit C8J30_RS08510 C8J30_RS12470
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit C8J30_RS08510 C8J30_RS12470
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase C8J30_RS09560
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) C8J30_RS09560
dddA 3-hydroxypropionate dehydrogenase C8J30_RS06330 C8J30_RS08585
hpcD 3-hydroxypropionyl-CoA dehydratase C8J30_RS04555 C8J30_RS11890
iolA malonate semialdehyde dehydrogenase (CoA-acylating) C8J30_RS01055 C8J30_RS08590
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components C8J30_RS08510 C8J30_RS12470
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit C8J30_RS08525 C8J30_RS13905
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase C8J30_RS04420 C8J30_RS00780
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase C8J30_RS00405
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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