GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Sphingomonas koreensis DSMZ 15582

Best path

iolF, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda

Also see fitness data for the top candidates

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
iolF myo-inositol:H+ symporter Ga0059261_2621
iolG myo-inositol 2-dehydrogenase Ga0059261_0656 Ga0059261_3126
iolM 2-inosose 4-dehydrogenase
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
uxaE D-tagaturonate epimerase
uxuB D-mannonate dehydrogenase Ga0059261_2975
uxuA D-mannonate dehydratase Ga0059261_1631
kdgK 2-keto-3-deoxygluconate kinase Ga0059261_2965 Ga0059261_1055
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Ga0059261_0356 Ga0059261_1625
Alternative steps:
HMIT myo-inositol:H+ symporter Ga0059261_1891 Ga0059261_1777
iatA myo-inositol ABC transporter, ATPase component IatA
iatP myo-inositol ABC transporter, permease component IatP
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolB 5-deoxy-D-glucuronate isomerase
iolC 5-dehydro-2-deoxy-D-gluconate kinase
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
iolE scyllo-inosose 2-dehydratase
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase
iolT myo-inositol:H+ symporter Ga0059261_1891 Ga0059261_1777
mmsA malonate-semialdehyde dehydrogenase Ga0059261_3677 Ga0059261_3374
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 Ga0059261_0484 Ga0059261_3874
PS417_11885 myo-inositol ABC transporter, substrate-binding component
PS417_11890 myo-inositol ABC transporter, ATPase component
PS417_11895 myo-inositol ABC transporter, permease component
SMIT1 myo-inositol:Na+ symporter Ga0059261_1623
tpi triose-phosphate isomerase Ga0059261_0254 Ga0059261_0728

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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