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 (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