GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Phaeobacter inhibens BS107

Best path

PGA1_c07300, PGA1_c07310, PGA1_c07320, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component PGA1_c07300
PGA1_c07310 myo-inositol ABC transporter, permease component PGA1_c07310 PGA1_c28050
PGA1_c07320 myo-inositol ABC transporter, ATPase component PGA1_c07320 PGA1_c28040
iolG myo-inositol 2-dehydrogenase PGA1_c07210 PGA1_c27960
iolE scyllo-inosose 2-dehydratase PGA1_c07270
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase PGA1_c07250
iolB 5-deoxy-D-glucuronate isomerase PGA1_c07230
iolC 5-dehydro-2-deoxy-D-gluconate kinase PGA1_c07240
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase PGA1_c07220 PGA1_c07240
mmsA malonate-semialdehyde dehydrogenase PGA1_c17300 PGA1_c21670
tpi triose-phosphate isomerase PGA1_c20650 PGA1_c17530
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PGA1_c28010 PGA1_c07350
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA PGA1_c23060 PGA1_c26910
iatP myo-inositol ABC transporter, permease component IatP PGA1_c23080 PGA1_c28050
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase
PS417_11885 myo-inositol ABC transporter, substrate-binding component PGA1_262p00430
PS417_11890 myo-inositol ABC transporter, ATPase component PGA1_c23060 PGA1_c26910
PS417_11895 myo-inositol ABC transporter, permease component PGA1_c28050 PGA1_c23070
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase PGA1_c13160

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