GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Phaeacidiphilus oryzae TH49

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component BS73_RS29370
PGA1_c07310 myo-inositol ABC transporter, permease component BS73_RS29375 BS73_RS01760
PGA1_c07320 myo-inositol ABC transporter, ATPase component BS73_RS29380 BS73_RS12680
iolG myo-inositol 2-dehydrogenase BS73_RS11385 BS73_RS11380
iolE scyllo-inosose 2-dehydratase BS73_RS33095 BS73_RS11390
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase BS73_RS11410
iolB 5-deoxy-D-glucuronate isomerase BS73_RS11405
iolC 5-dehydro-2-deoxy-D-gluconate kinase BS73_RS11395
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase BS73_RS11395 BS73_RS16635
mmsA malonate-semialdehyde dehydrogenase BS73_RS14210 BS73_RS14255
tpi triose-phosphate isomerase BS73_RS12430 BS73_RS16890
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BS73_RS31540 BS73_RS13710
HMIT myo-inositol:H+ symporter BS73_RS08125 BS73_RS21865
iatA myo-inositol ABC transporter, ATPase component IatA BS73_RS32735 BS73_RS13055
iatP myo-inositol ABC transporter, permease component IatP BS73_RS01760 BS73_RS06825
ibpA myo-inositol ABC transporter, substrate-binding component IbpA BS73_RS01760
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase BS73_RS32950 BS73_RS06525
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter BS73_RS08125 BS73_RS21865
kdgK 2-keto-3-deoxygluconate kinase BS73_RS13700 BS73_RS31555
PS417_11885 myo-inositol ABC transporter, substrate-binding component BS73_RS01760 BS73_RS13050
PS417_11890 myo-inositol ABC transporter, ATPase component BS73_RS32735 BS73_RS01755
PS417_11895 myo-inositol ABC transporter, permease component BS73_RS01760 BS73_RS13060
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase BS73_RS03900
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 Apr 09 2024. 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