GapMind for catabolism of small carbon sources


myo-inositol catabolism in Dinoroseobacter shibae DFL-12

Best path

PGA1_c07300, PGA1_c07310, PGA1_c07320, 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
PGA1_c07300 myo-inositol ABC transport, substrate-binding component Dshi_1274
PGA1_c07310 myo-inositol ABC transporter, permease component Dshi_1275
PGA1_c07320 myo-inositol ABC transporter, ATPase component Dshi_1276 Dshi_0388
iolG myo-inositol 2-dehydrogenase Dshi_1265 Dshi_1270
iolE scyllo-inosose 2-dehydratase Dshi_1271
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase Dshi_1269
iolB 5-deoxy-D-glucuronate isomerase Dshi_1267 Dshi_1279
iolC 5-dehydro-2-deoxy-D-gluconate kinase Dshi_1268
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase Dshi_1266 Dshi_1268
mmsA malonate-semialdehyde dehydrogenase Dshi_1747 Dshi_0577
tpi triose-phosphate isomerase Dshi_2078 Dshi_2155
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Dshi_1768 Dshi_1241
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA Dshi_2433 Dshi_0530
iatP myo-inositol ABC transporter, permease component IatP Dshi_0518 Dshi_2431
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase Dshi_4159
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase Dshi_1268 Dshi_2797
PS417_11885 myo-inositol ABC transporter, substrate-binding component Dshi_2000
PS417_11890 myo-inositol ABC transporter, ATPase component Dshi_2433 Dshi_0530
PS417_11895 myo-inositol ABC transporter, permease component Dshi_0528 Dshi_0389
SMIT1 myo-inositol:Na+ symporter Dshi_3906 Dshi_3904
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase Dshi_0969

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