GapMind for catabolism of small carbon sources


myo-inositol catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

PS417_11885, PS417_11890, PS417_11895, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component Pf1N1B4_4285 Pf1N1B4_4386
PS417_11890 myo-inositol ABC transporter, ATPase component Pf1N1B4_4286 Pf1N1B4_410
PS417_11895 myo-inositol ABC transporter, permease component Pf1N1B4_4287 Pf1N1B4_6033
iolG myo-inositol 2-dehydrogenase Pf1N1B4_4280 Pf1N1B4_4388
iolE scyllo-inosose 2-dehydratase Pf1N1B4_4275
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase Pf1N1B4_4279
iolB 5-deoxy-D-glucuronate isomerase Pf1N1B4_4276
iolC 5-dehydro-2-deoxy-D-gluconate kinase Pf1N1B4_4274
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase Pf1N1B4_4274 Pf1N1B4_2402
mmsA malonate-semialdehyde dehydrogenase Pf1N1B4_4277 Pf1N1B4_1238
tpi triose-phosphate isomerase Pf1N1B4_1164 Pf1N1B4_2399
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf1N1B4_587 Pf1N1B4_399
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA Pf1N1B4_410 Pf1N1B4_4286
iatP myo-inositol ABC transporter, permease component IatP Pf1N1B4_4287 Pf1N1B4_6033
ibpA myo-inositol ABC transporter, substrate-binding component IbpA Pf1N1B4_4386
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase Pf1N1B4_5603
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase Pf1N1B4_5638 Pf1N1B4_4765
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 Pf1N1B4_4286 Pf1N1B4_410
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase Pf1N1B4_398 Pf1N1B4_3383
uxuB D-mannonate dehydrogenase Pf1N1B4_4846

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.



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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