GapMind for catabolism of small carbon sources


myo-inositol catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

Also see fitness data for the top candidates


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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component H281DRAFT_04462
PGA1_c07310 myo-inositol ABC transporter, permease component H281DRAFT_04461 H281DRAFT_03379
PGA1_c07320 myo-inositol ABC transporter, ATPase component H281DRAFT_04460 H281DRAFT_03224
iolG myo-inositol 2-dehydrogenase H281DRAFT_04464 H281DRAFT_04465
iolE scyllo-inosose 2-dehydratase H281DRAFT_04457
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase H281DRAFT_04458
iolB 5-deoxy-D-glucuronate isomerase H281DRAFT_04456 H281DRAFT_02951
iolC 5-dehydro-2-deoxy-D-gluconate kinase H281DRAFT_04459
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase H281DRAFT_04459 H281DRAFT_04188
mmsA malonate-semialdehyde dehydrogenase H281DRAFT_02373 H281DRAFT_03264
tpi triose-phosphate isomerase H281DRAFT_04564 H281DRAFT_04190
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase H281DRAFT_04277 H281DRAFT_06295
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA H281DRAFT_01223 H281DRAFT_02174
iatP myo-inositol ABC transporter, permease component IatP H281DRAFT_01120 H281DRAFT_04148
ibpA myo-inositol ABC transporter, substrate-binding component IbpA H281DRAFT_04150
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase H281DRAFT_03278 H281DRAFT_01693
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase H281DRAFT_00856 H281DRAFT_05211
PS417_11885 myo-inositol ABC transporter, substrate-binding component H281DRAFT_02173 H281DRAFT_05225
PS417_11890 myo-inositol ABC transporter, ATPase component H281DRAFT_00426 H281DRAFT_03380
PS417_11895 myo-inositol ABC transporter, permease component H281DRAFT_04148 H281DRAFT_03379
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase H281DRAFT_02953 H281DRAFT_01518
uxuB D-mannonate dehydrogenase H281DRAFT_01519 H281DRAFT_02952

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.



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