GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Pseudomonas fluorescens FW300-N2C3

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component AO356_23200 AO356_29225
PS417_11890 myo-inositol ABC transporter, ATPase component AO356_23205 AO356_20250
PS417_11895 myo-inositol ABC transporter, permease component AO356_23210 AO356_00960
iolG myo-inositol 2-dehydrogenase AO356_23190 AO356_29215
iolE scyllo-inosose 2-dehydratase AO356_23165
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase AO356_23185
iolB 5-deoxy-D-glucuronate isomerase AO356_23170
iolC 5-dehydro-2-deoxy-D-gluconate kinase AO356_23160
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase AO356_23160 AO356_13705
mmsA malonate-semialdehyde dehydrogenase AO356_23175 AO356_07950
tpi triose-phosphate isomerase AO356_07440 AO356_13690
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO356_05150 AO356_20285
HMIT myo-inositol:H+ symporter AO356_27270
iatA myo-inositol ABC transporter, ATPase component IatA AO356_23205 AO356_20250
iatP myo-inositol ABC transporter, permease component IatP AO356_23210 AO356_00960
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase AO356_24895 AO356_14000
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter AO356_27270
kdgK 2-keto-3-deoxygluconate kinase AO356_28555 AO356_00445
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component AO356_00960
PGA1_c07320 myo-inositol ABC transporter, ATPase component AO356_23205 AO356_28510
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase AO356_28550 AO356_28530
uxuB D-mannonate dehydrogenase AO356_28535 AO356_27690

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