GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

Also see fitness data for the top candidates

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component Pf6N2E2_522 Pf6N2E2_1793
PS417_11890 myo-inositol ABC transporter, ATPase component Pf6N2E2_523 Pf6N2E2_5969
PS417_11895 myo-inositol ABC transporter, permease component Pf6N2E2_524 Pf6N2E2_163
iolG myo-inositol 2-dehydrogenase Pf6N2E2_518 Pf6N2E2_1002
iolE scyllo-inosose 2-dehydratase Pf6N2E2_513
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase Pf6N2E2_517
iolB 5-deoxy-D-glucuronate isomerase Pf6N2E2_514
iolC 5-dehydro-2-deoxy-D-gluconate kinase Pf6N2E2_512 Pf6N2E2_629
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase Pf6N2E2_512 Pf6N2E2_4660
mmsA malonate-semialdehyde dehydrogenase Pf6N2E2_515 Pf6N2E2_3462
tpi triose-phosphate isomerase Pf6N2E2_3356 Pf6N2E2_4657
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf6N2E2_2883 Pf6N2E2_5976
HMIT myo-inositol:H+ symporter Pf6N2E2_883
iatA myo-inositol ABC transporter, ATPase component IatA Pf6N2E2_1008 Pf6N2E2_5969
iatP myo-inositol ABC transporter, permease component IatP Pf6N2E2_524 Pf6N2E2_163
ibpA myo-inositol ABC transporter, substrate-binding component IbpA Pf6N2E2_1005 Pf6N2E2_1006
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase Pf6N2E2_668 Pf6N2E2_4723
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter Pf6N2E2_883
kdgK 2-keto-3-deoxygluconate kinase Pf6N2E2_2046 Pf6N2E2_629
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component Pf6N2E2_163
PGA1_c07320 myo-inositol ABC transporter, ATPase component Pf6N2E2_523 Pf6N2E2_1456
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase Pf6N2E2_5977
uxuB D-mannonate dehydrogenase Pf6N2E2_806

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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