GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Bradyrhizobium sp. BTAi1

Best path

PS417_11885, PS417_11890, PS417_11895, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component BBTA_RS31440 BBTA_RS09910
PS417_11890 myo-inositol ABC transporter, ATPase component BBTA_RS28795 BBTA_RS31430
PS417_11895 myo-inositol ABC transporter, permease component BBTA_RS31435 BBTA_RS11385
iolG myo-inositol 2-dehydrogenase BBTA_RS02340
iolE scyllo-inosose 2-dehydratase BBTA_RS02330
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase BBTA_RS02335
iolB 5-deoxy-D-glucuronate isomerase
iolC 5-dehydro-2-deoxy-D-gluconate kinase
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase BBTA_RS02195 BBTA_RS02170
mmsA malonate-semialdehyde dehydrogenase BBTA_RS16745 BBTA_RS30410
tpi triose-phosphate isomerase BBTA_RS20935 BBTA_RS02165
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BBTA_RS09905 BBTA_RS09630
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA BBTA_RS28795 BBTA_RS09915
iatP myo-inositol ABC transporter, permease component IatP BBTA_RS36615 BBTA_RS12645
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase BBTA_RS04360
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase BBTA_RS09900 BBTA_RS36585
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 BBTA_RS21220 BBTA_RS12640
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase BBTA_RS09890
uxuB D-mannonate dehydrogenase BBTA_RS09865

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