GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Beijerinckia indica subsp. indica ATCC 9039

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component BIND_RS12580 BIND_RS13980
PS417_11890 myo-inositol ABC transporter, ATPase component BIND_RS14235 BIND_RS14440
PS417_11895 myo-inositol ABC transporter, permease component BIND_RS14230 BIND_RS14435
iolG myo-inositol 2-dehydrogenase BIND_RS14260 BIND_RS14255
iolE scyllo-inosose 2-dehydratase BIND_RS14295
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase BIND_RS14290
iolB 5-deoxy-D-glucuronate isomerase
iolC 5-dehydro-2-deoxy-D-gluconate kinase
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase
mmsA malonate-semialdehyde dehydrogenase BIND_RS03185 BIND_RS00885
tpi triose-phosphate isomerase BIND_RS07360 BIND_RS17620
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BIND_RS14470 BIND_RS03240
HMIT myo-inositol:H+ symporter BIND_RS00535 BIND_RS12565
iatA myo-inositol ABC transporter, ATPase component IatA BIND_RS14235 BIND_RS14440
iatP myo-inositol ABC transporter, permease component IatP BIND_RS14230 BIND_RS14435
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 BIND_RS00535 BIND_RS12565
kdgK 2-keto-3-deoxygluconate kinase BIND_RS14505 BIND_RS12545
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 BIND_RS14235 BIND_RS14440
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase BIND_RS04765

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