GapMind for catabolism of small carbon sources

 

Definition of myo-inositol catabolism

As rules and steps, or see full text

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).

Steps

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

iatP: myo-inositol ABC transporter, permease component IatP

iatA: myo-inositol ABC transporter, ATPase component IatA

ibpA: myo-inositol ABC transporter, substrate-binding component IbpA

PS417_11885: myo-inositol ABC transporter, substrate-binding component

PS417_11890: myo-inositol ABC transporter, ATPase component

PS417_11895: myo-inositol ABC transporter, permease component

iolT: myo-inositol:H+ symporter

SMIT1: myo-inositol:Na+ symporter

HMIT: myo-inositol:H+ symporter

iolF: myo-inositol:H+ symporter

kdgK: 2-keto-3-deoxygluconate kinase

eda: 2-keto-3-deoxygluconate 6-phosphate aldolase

tpi: triose-phosphate isomerase

iolG: myo-inositol 2-dehydrogenase

iolE: scyllo-inosose 2-dehydratase

iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase

iolB: 5-deoxy-D-glucuronate isomerase

iolC: 5-dehydro-2-deoxy-D-gluconate kinase

iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase

mmsA: malonate-semialdehyde dehydrogenase

iolM: 2-inosose 4-dehydrogenase

iolN: 2,4-diketo-inositol hydratase

iolO: 5-dehydro-L-gluconate epimerase

uxaE: D-tagaturonate epimerase

uxuB: D-mannonate dehydrogenase

uxuA: D-mannonate dehydratase

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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, 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