GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Pseudomonas simiae WCS417

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component PS417_11885 PS417_11070
PS417_11890 myo-inositol ABC transporter, ATPase component PS417_11890 PS417_12065
PS417_11895 myo-inositol ABC transporter, permease component PS417_11895 PS417_12060
iolG myo-inositol 2-dehydrogenase PS417_11875 PS417_11080
iolE scyllo-inosose 2-dehydratase PS417_11855
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase PS417_11870
iolB 5-deoxy-D-glucuronate isomerase PS417_11860
iolC 5-dehydro-2-deoxy-D-gluconate kinase PS417_11850
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase PS417_11850 PS417_26415
mmsA malonate-semialdehyde dehydrogenase PS417_10925 PS417_03250
tpi triose-phosphate isomerase PS417_24000 PS417_26430
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PS417_22100 PS417_00160
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA PS417_13635 PS417_21330
iatP myo-inositol ABC transporter, permease component IatP PS417_12060 PS417_17725
ibpA myo-inositol ABC transporter, substrate-binding component IbpA PS417_17735 PS417_12055
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase PS417_26165
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase PS417_12130 PS417_12565
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 PS417_11890 PS417_13635
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase PS417_00165
uxuB D-mannonate dehydrogenase PS417_12695

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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