GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Sinorhizobium fredii NGR234

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component NGR_RS09870 NGR_RS11320
PS417_11890 myo-inositol ABC transporter, ATPase component NGR_RS09875 NGR_RS09420
PS417_11895 myo-inositol ABC transporter, permease component NGR_RS09880 NGR_RS09555
iolG myo-inositol 2-dehydrogenase NGR_RS23245 NGR_RS02130
iolE scyllo-inosose 2-dehydratase NGR_RS29605 NGR_RS02190
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase NGR_RS29610 NGR_RS24120
iolB 5-deoxy-D-glucuronate isomerase NGR_RS29600
iolC 5-dehydro-2-deoxy-D-gluconate kinase NGR_RS29615 NGR_RS24125
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase NGR_RS29615 NGR_RS24125
mmsA malonate-semialdehyde dehydrogenase NGR_RS13065 NGR_RS23205
tpi triose-phosphate isomerase NGR_RS17645 NGR_RS14620
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase NGR_RS25805 NGR_RS13545
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA NGR_RS00525 NGR_RS03630
iatP myo-inositol ABC transporter, permease component IatP NGR_RS00535 NGR_RS14580
ibpA myo-inositol ABC transporter, substrate-binding component IbpA NGR_RS14465 NGR_RS11320
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase NGR_RS26360
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase NGR_RS23025 NGR_RS24125
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component NGR_RS24155 NGR_RS00530
PGA1_c07320 myo-inositol ABC transporter, ATPase component NGR_RS24150 NGR_RS11930
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase NGR_RS09235 NGR_RS07565
uxuB D-mannonate dehydrogenase NGR_RS09970 NGR_RS23500

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.

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