GapMind for catabolism of small carbon sources

 

propionate catabolism in Pseudomonas taeanensis MS-3

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease TMS3_RS07620 TMS3_RS03540
prpE propionyl-CoA synthetase TMS3_RS12625 TMS3_RS07825
prpC 2-methylcitrate synthase TMS3_RS13495 TMS3_RS16560
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) TMS3_RS13490 TMS3_RS16650
prpF methylaconitate isomerase TMS3_RS13485 TMS3_RS20795
acn (2R,3S)-2-methylcitrate dehydratase TMS3_RS13490 TMS3_RS13040
prpB 2-methylisocitrate lyase TMS3_RS13500 TMS3_RS05915
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase TMS3_RS08960 TMS3_RS24785
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase TMS3_RS14965 TMS3_RS19290
iolA malonate semialdehyde dehydrogenase (CoA-acylating) TMS3_RS06795 TMS3_RS21110
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
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit TMS3_RS21950 TMS3_RS15410
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit TMS3_RS03090 TMS3_RS06040
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit TMS3_RS15400 TMS3_RS21965
pco propanyl-CoA oxidase TMS3_RS02095
prpD 2-methylcitrate dehydratase TMS3_RS13480
putP propionate transporter; proline:Na+ symporter TMS3_RS14535 TMS3_RS14485
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