GapMind for catabolism of small carbon sources


myo-inositol catabolism in Caulobacter crescentus NA1000

Best path

iatP, iatA, ibpA, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

Also see fitness data for the top candidates


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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
iatP myo-inositol ABC transporter, permease component IatP CCNA_00904
iatA myo-inositol ABC transporter, ATPase component IatA CCNA_00903
ibpA myo-inositol ABC transporter, substrate-binding component IbpA CCNA_00902
iolG myo-inositol 2-dehydrogenase CCNA_01354 CCNA_02094
iolE scyllo-inosose 2-dehydratase CCNA_01358
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase CCNA_01357
iolB 5-deoxy-D-glucuronate isomerase CCNA_01359
iolC 5-dehydro-2-deoxy-D-gluconate kinase CCNA_01356
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase CCNA_01356 CCNA_03360
mmsA malonate-semialdehyde dehydrogenase CCNA_01360 CCNA_02357
tpi triose-phosphate isomerase CCNA_01970 CCNA_03359
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CCNA_01562 CCNA_00825
HMIT myo-inositol:H+ symporter CCNA_00857
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 CCNA_00857
kdgK 2-keto-3-deoxygluconate kinase CCNA_01110 CCNA_01563
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component CCNA_00904
PGA1_c07320 myo-inositol ABC transporter, ATPase component CCNA_01670 CCNA_03235
PS417_11885 myo-inositol ABC transporter, substrate-binding component
PS417_11890 myo-inositol ABC transporter, ATPase component CCNA_00903
PS417_11895 myo-inositol ABC transporter, permease component CCNA_00904
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase CCNA_02903 CCNA_00566
uxuB D-mannonate dehydrogenase CCNA_01554

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.



Related tools

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