GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Nocardiopsis baichengensis YIM 90130

Best path

iolF, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
iolF myo-inositol:H+ symporter C892_RS0122390
iolG myo-inositol 2-dehydrogenase C892_RS0103825 C892_RS0117125
iolE scyllo-inosose 2-dehydratase C892_RS0103800
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase C892_RS0103805
iolB 5-deoxy-D-glucuronate isomerase C892_RS0103810
iolC 5-dehydro-2-deoxy-D-gluconate kinase C892_RS0103820 C892_RS0106910
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase C892_RS0103820 C892_RS0106910
mmsA malonate-semialdehyde dehydrogenase C892_RS0108545 C892_RS0126085
tpi triose-phosphate isomerase C892_RS0126430 C892_RS0126425
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase C892_RS0102105
HMIT myo-inositol:H+ symporter C892_RS0102035
iatA myo-inositol ABC transporter, ATPase component IatA C892_RS0117120 C892_RS0109575
iatP myo-inositol ABC transporter, permease component IatP C892_RS0117115 C892_RS0117110
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolM 2-inosose 4-dehydrogenase
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter C892_RS0102035
kdgK 2-keto-3-deoxygluconate kinase C892_RS0104700 C892_RS0106910
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component C892_RS0103790
PGA1_c07320 myo-inositol ABC transporter, ATPase component C892_RS0103785 C892_RS0113100
PS417_11885 myo-inositol ABC transporter, substrate-binding component
PS417_11890 myo-inositol ABC transporter, ATPase component C892_RS0117120 C892_RS0109575
PS417_11895 myo-inositol ABC transporter, permease component C892_RS0117115 C892_RS0113105
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase

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