GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Pseudomonas fluorescens GW456-L13

Best path

iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda

Also see fitness data for the top candidates

Rules

Overview: Myo-inositol degradation in GapMind is based on MetaCyc pathways myo-inositol degradation I via inosose dehydratase (link) and pathway II inosose dehydrogenase (link).

29 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
iolT myo-inositol:H+ symporter
iolG myo-inositol 2-dehydrogenase PfGW456L13_2810 PfGW456L13_1420
iolM 2-inosose 4-dehydrogenase PfGW456L13_1122
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
uxaE D-tagaturonate epimerase
uxuB D-mannonate dehydrogenase PfGW456L13_3038
uxuA D-mannonate dehydratase PfGW456L13_3477 PfGW456L13_2128
kdgK 2-keto-3-deoxygluconate kinase PfGW456L13_2869 PfGW456L13_2950
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PfGW456L13_1903 PfGW456L13_2127
Alternative steps:
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA PfGW456L13_2121 PfGW456L13_3911
iatP myo-inositol ABC transporter, permease component IatP PfGW456L13_3910 PfGW456L13_2122
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolB 5-deoxy-D-glucuronate isomerase
iolC 5-dehydro-2-deoxy-D-gluconate kinase
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
iolE scyllo-inosose 2-dehydratase
iolF myo-inositol:H+ symporter
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase PfGW456L13_1069
mmsA malonate-semialdehyde dehydrogenase PfGW456L13_2 PfGW456L13_5146
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component
PGA1_c07320 myo-inositol ABC transporter, ATPase component PfGW456L13_2121 PfGW456L13_3911
PS417_11885 myo-inositol ABC transporter, substrate-binding component
PS417_11890 myo-inositol ABC transporter, ATPase component PfGW456L13_2121 PfGW456L13_3911
PS417_11895 myo-inositol ABC transporter, permease component PfGW456L13_2122 PfGW456L13_3910
SMIT1 myo-inositol:Na+ symporter
tpi triose-phosphate isomerase PfGW456L13_5091 PfGW456L13_1066

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