GapMind for catabolism of small carbon sources

 

propionate catabolism in Herbaspirillum seropedicae SmR1

Best path

putP, prpE, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter
prpE propionyl-CoA synthetase HSERO_RS15645 HSERO_RS07770
prpC 2-methylcitrate synthase HSERO_RS15655 HSERO_RS14890
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) HSERO_RS11425 HSERO_RS14940
prpF methylaconitate isomerase HSERO_RS11420 HSERO_RS07335
acn (2R,3S)-2-methylcitrate dehydratase HSERO_RS11425 HSERO_RS14940
prpB 2-methylisocitrate lyase HSERO_RS10565 HSERO_RS15660
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase HSERO_RS24000 HSERO_RS23855
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase HSERO_RS19405 HSERO_RS12745
iolA malonate semialdehyde dehydrogenase (CoA-acylating) HSERO_RS24005 HSERO_RS23245
lctP propionate permease
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HSERO_RS21740
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
mctC propionate:H+ symporter
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit HSERO_RS23460 HSERO_RS01925
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit HSERO_RS01925 HSERO_RS20550
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit HSERO_RS23455
pco propanyl-CoA oxidase HSERO_RS23440
prpD 2-methylcitrate dehydratase
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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