GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component CEV31_RS01785
PGA1_c07310 myo-inositol ABC transporter, permease component CEV31_RS01780 CEV31_RS08970
PGA1_c07320 myo-inositol ABC transporter, ATPase component CEV31_RS01775 CEV31_RS18950
iolG myo-inositol 2-dehydrogenase CEV31_RS15200 CEV31_RS01790
iolE scyllo-inosose 2-dehydratase CEV31_RS15220
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase CEV31_RS15215
iolB 5-deoxy-D-glucuronate isomerase CEV31_RS15225
iolC 5-dehydro-2-deoxy-D-gluconate kinase CEV31_RS15210
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase CEV31_RS15210 CEV31_RS08915
mmsA malonate-semialdehyde dehydrogenase CEV31_RS03890 CEV31_RS08350
tpi triose-phosphate isomerase CEV31_RS12005 CEV31_RS08925
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CEV31_RS20745 CEV31_RS18545
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA CEV31_RS18890 CEV31_RS17305
iatP myo-inositol ABC transporter, permease component IatP CEV31_RS19245 CEV31_RS09010
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 CEV31_RS14425 CEV31_RS18910
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase CEV31_RS10505 CEV31_RS16720
PS417_11885 myo-inositol ABC transporter, substrate-binding component CEV31_RS19240 CEV31_RS20760
PS417_11890 myo-inositol ABC transporter, ATPase component CEV31_RS19250 CEV31_RS17255
PS417_11895 myo-inositol ABC transporter, permease component CEV31_RS19245 CEV31_RS09010
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase CEV31_RS18360
uxuB D-mannonate dehydrogenase CEV31_RS18355 CEV31_RS15260

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 24 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:

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