GapMind for catabolism of small carbon sources


myo-inositol catabolism in Ruegeria conchae TW15

Best path

PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi


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
PGA1_c07300 myo-inositol ABC transport, substrate-binding component G7G_RS0103325
PGA1_c07310 myo-inositol ABC transporter, permease component G7G_RS0103330
PGA1_c07320 myo-inositol ABC transporter, ATPase component G7G_RS0103335 G7G_RS0115760
iolG myo-inositol 2-dehydrogenase G7G_RS0103275 G7G_RS0103305
iolE scyllo-inosose 2-dehydratase G7G_RS0103310
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase G7G_RS0103300
iolB 5-deoxy-D-glucuronate isomerase G7G_RS0103285
iolC 5-dehydro-2-deoxy-D-gluconate kinase G7G_RS0103290
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase G7G_RS0103280 G7G_RS0103290
mmsA malonate-semialdehyde dehydrogenase G7G_RS0106675 G7G_RS0111640
tpi triose-phosphate isomerase G7G_RS0106540 G7G_RS0114345
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase G7G_RS0112140 G7G_RS0100605
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA G7G_RS0100435 G7G_RS0100415
iatP myo-inositol ABC transporter, permease component IatP G7G_RS0100410 G7G_RS22595
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase G7G_RS0119975 G7G_RS0117160
PS417_11885 myo-inositol ABC transporter, substrate-binding component G7G_RS0115585
PS417_11890 myo-inositol ABC transporter, ATPase component G7G_RS0100435 G7G_RS0100415
PS417_11895 myo-inositol ABC transporter, permease component G7G_RS0100410 G7G_RS22595
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase G7G_RS0120435

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