GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Rhodobacter viridis JA737

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component C8J30_RS14095 C8J30_RS14110
PS417_11890 myo-inositol ABC transporter, ATPase component C8J30_RS14105 C8J30_RS10885
PS417_11895 myo-inositol ABC transporter, permease component C8J30_RS14100 C8J30_RS10880
iolG myo-inositol 2-dehydrogenase C8J30_RS14080
iolE scyllo-inosose 2-dehydratase C8J30_RS14060
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase C8J30_RS14065
iolB 5-deoxy-D-glucuronate isomerase C8J30_RS14055
iolC 5-dehydro-2-deoxy-D-gluconate kinase C8J30_RS14070
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase C8J30_RS14070 C8J30_RS02175
mmsA malonate-semialdehyde dehydrogenase C8J30_RS01055 C8J30_RS08590
tpi triose-phosphate isomerase C8J30_RS01230 C8J30_RS02960
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase C8J30_RS09810
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA C8J30_RS14105 C8J30_RS10885
iatP myo-inositol ABC transporter, permease component IatP C8J30_RS10880 C8J30_RS14100
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase C8J30_RS13635
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase C8J30_RS14070
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 C8J30_RS03205 C8J30_RS13475
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase C8J30_RS03255

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.

Links

Downloads

Related tools

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