GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Tistlia consotensis USBA 355

Best path

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

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
iolT myo-inositol:H+ symporter
iolG myo-inositol 2-dehydrogenase B9O00_RS27225
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 B9O00_RS19815
uxuA D-mannonate dehydratase B9O00_RS19840 B9O00_RS27750
kdgK 2-keto-3-deoxygluconate kinase B9O00_RS16275 B9O00_RS13785
eda 2-keto-3-deoxygluconate 6-phosphate aldolase B9O00_RS13810 B9O00_RS09055
Alternative steps:
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA B9O00_RS21320 B9O00_RS21270
iatP myo-inositol ABC transporter, permease component IatP B9O00_RS21325 B9O00_RS01465
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 B9O00_RS18740
iolF myo-inositol:H+ symporter
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase B9O00_RS20835
mmsA malonate-semialdehyde dehydrogenase B9O00_RS16490 B9O00_RS00790
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 B9O00_RS29715 B9O00_RS13780
PS417_11885 myo-inositol ABC transporter, substrate-binding component B9O00_RS29725 B9O00_RS08780
PS417_11890 myo-inositol ABC transporter, ATPase component B9O00_RS28465 B9O00_RS21270
PS417_11895 myo-inositol ABC transporter, permease component B9O00_RS21325 B9O00_RS13775
SMIT1 myo-inositol:Na+ symporter
tpi triose-phosphate isomerase B9O00_RS25305 B9O00_RS28505

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