GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Burkholderia phytofirmans PsJN

Best path

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

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component BPHYT_RS13895 BPHYT_RS12000
PGA1_c07310 myo-inositol ABC transporter, permease component BPHYT_RS13900 BPHYT_RS27190
PGA1_c07320 myo-inositol ABC transporter, ATPase component BPHYT_RS13905 BPHYT_RS22735
iolG myo-inositol 2-dehydrogenase BPHYT_RS13885 BPHYT_RS13880
iolE scyllo-inosose 2-dehydratase BPHYT_RS13920
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase BPHYT_RS13915
iolB 5-deoxy-D-glucuronate isomerase BPHYT_RS13925 BPHYT_RS28505
iolC 5-dehydro-2-deoxy-D-gluconate kinase BPHYT_RS13910 BPHYT_RS11300
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase BPHYT_RS13910 BPHYT_RS16260
mmsA malonate-semialdehyde dehydrogenase BPHYT_RS19500 BPHYT_RS28825
tpi triose-phosphate isomerase BPHYT_RS06610 BPHYT_RS16270
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BPHYT_RS16730 BPHYT_RS16945
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA BPHYT_RS28215 BPHYT_RS01820
iatP myo-inositol ABC transporter, permease component IatP BPHYT_RS16055 BPHYT_RS25825
ibpA myo-inositol ABC transporter, substrate-binding component IbpA BPHYT_RS16065
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase BPHYT_RS09175 BPHYT_RS11300
PS417_11885 myo-inositol ABC transporter, substrate-binding component BPHYT_RS01825 BPHYT_RS11220
PS417_11890 myo-inositol ABC transporter, ATPase component BPHYT_RS27185 BPHYT_RS20740
PS417_11895 myo-inositol ABC transporter, permease component BPHYT_RS16055 BPHYT_RS27190
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase BPHYT_RS28515 BPHYT_RS10980
uxuB D-mannonate dehydrogenase BPHYT_RS23425 BPHYT_RS28510

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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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