GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Escherichia coli BW25113

Best path

iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
iolT myo-inositol:H+ symporter b4031 b2943
iolG myo-inositol 2-dehydrogenase
iolM 2-inosose 4-dehydrogenase b2545
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase b1314
uxaE D-tagaturonate epimerase
uxuB D-mannonate dehydrogenase b4323 b2172
uxuA D-mannonate dehydratase b4322 b1581
kdgK 2-keto-3-deoxygluconate kinase b3526
eda 2-keto-3-deoxygluconate 6-phosphate aldolase b1850 b4477
Alternative steps:
HMIT myo-inositol:H+ symporter b2943 b2841
iatA myo-inositol ABC transporter, ATPase component IatA b3749 b1900
iatP myo-inositol ABC transporter, permease component IatP b3750 b4086
ibpA myo-inositol ABC transporter, substrate-binding component IbpA b3751 b4088
iolB 5-deoxy-D-glucuronate isomerase
iolC 5-dehydro-2-deoxy-D-gluconate kinase
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
iolE scyllo-inosose 2-dehydratase
iolF myo-inositol:H+ symporter
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase b3137 b2096
mmsA malonate-semialdehyde dehydrogenase b2661 b0312
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 b4087 b3749
PS417_11885 myo-inositol ABC transporter, substrate-binding component b2150
PS417_11890 myo-inositol ABC transporter, ATPase component b3749 b2149
PS417_11895 myo-inositol ABC transporter, permease component b3750 b2148
SMIT1 myo-inositol:Na+ symporter
tpi triose-phosphate isomerase b3919 b2926

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