GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Kocuria flava HO-9041

Best path

iolT, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
iolT myo-inositol:H+ symporter AS188_RS06680 AS188_RS02770
iolG myo-inositol 2-dehydrogenase AS188_RS00950 AS188_RS06785
iolE scyllo-inosose 2-dehydratase AS188_RS06705
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase AS188_RS06725
iolB 5-deoxy-D-glucuronate isomerase AS188_RS06755
iolC 5-dehydro-2-deoxy-D-gluconate kinase AS188_RS06715
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase AS188_RS06715
mmsA malonate-semialdehyde dehydrogenase AS188_RS06730 AS188_RS02220
tpi triose-phosphate isomerase AS188_RS09635 AS188_RS09630
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase
HMIT myo-inositol:H+ symporter AS188_RS06680 AS188_RS02770
iatA myo-inositol ABC transporter, ATPase component IatA AS188_RS10235
iatP myo-inositol ABC transporter, permease component IatP AS188_RS10230
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase AS188_RS02405 AS188_RS07990
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
kdgK 2-keto-3-deoxygluconate kinase AS188_RS06715
PGA1_c07300 myo-inositol ABC transport, substrate-binding component AS188_RS06765
PGA1_c07310 myo-inositol ABC transporter, permease component AS188_RS06770
PGA1_c07320 myo-inositol ABC transporter, ATPase component AS188_RS06775 AS188_RS10235
PS417_11885 myo-inositol ABC transporter, substrate-binding component
PS417_11890 myo-inositol ABC transporter, ATPase component AS188_RS10235 AS188_RS06775
PS417_11895 myo-inositol ABC transporter, permease component AS188_RS10230
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase

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