GapMind for catabolism of small carbon sources

 

propionate catabolism in Streptacidiphilus oryzae TH49

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mctC propionate:H+ symporter BS73_RS13175 BS73_RS06885
prpE propionyl-CoA synthetase BS73_RS20690 BS73_RS35890
pccA propionyl-CoA carboxylase, alpha subunit BS73_RS23635 BS73_RS25280
pccB propionyl-CoA carboxylase, beta subunit BS73_RS07330 BS73_RS24900
epi methylmalonyl-CoA epimerase BS73_RS15090
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BS73_RS07325 BS73_RS15040
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BS73_RS23175 BS73_RS11855
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BS73_RS12710
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BS73_RS12710
dddA 3-hydroxypropionate dehydrogenase BS73_RS13540 BS73_RS01415
hpcD 3-hydroxypropionyl-CoA dehydratase BS73_RS20300 BS73_RS14910
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BS73_RS14210 BS73_RS14255
lctP propionate permease BS73_RS26640
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BS73_RS07325 BS73_RS15040
mctP propionate permease BS73_RS15850
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BS73_RS23635 BS73_RS06500
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BS73_RS32915
prpB 2-methylisocitrate lyase BS73_RS29705 BS73_RS10660
prpC 2-methylcitrate synthase BS73_RS25400 BS73_RS17760
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase BS73_RS10825 BS73_RS31830
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