GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Klebsiella michiganensis M5al

Best path

PS417_11885, PS417_11890, PS417_11895, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component BWI76_RS07235 BWI76_RS00285
PS417_11890 myo-inositol ABC transporter, ATPase component BWI76_RS07240 BWI76_RS14860
PS417_11895 myo-inositol ABC transporter, permease component BWI76_RS07245 BWI76_RS14865
iolG myo-inositol 2-dehydrogenase BWI76_RS03095 BWI76_RS10220
iolE scyllo-inosose 2-dehydratase BWI76_RS03105 BWI76_RS10210
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase BWI76_RS03090
iolB 5-deoxy-D-glucuronate isomerase BWI76_RS03075
iolC 5-dehydro-2-deoxy-D-gluconate kinase BWI76_RS03085
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase BWI76_RS03085 BWI76_RS24855
mmsA malonate-semialdehyde dehydrogenase BWI76_RS03070 BWI76_RS02840
tpi triose-phosphate isomerase BWI76_RS27465 BWI76_RS23980
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BWI76_RS18095 BWI76_RS27940
HMIT myo-inositol:H+ symporter BWI76_RS24055 BWI76_RS03110
iatA myo-inositol ABC transporter, ATPase component IatA BWI76_RS00275 BWI76_RS14860
iatP myo-inositol ABC transporter, permease component IatP BWI76_RS00280 BWI76_RS14865
ibpA myo-inositol ABC transporter, substrate-binding component IbpA BWI76_RS00285 BWI76_RS07235
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 BWI76_RS10225 BWI76_RS03110
kdgK 2-keto-3-deoxygluconate kinase BWI76_RS26750 BWI76_RS26950
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component BWI76_RS14605
PGA1_c07320 myo-inositol ABC transporter, ATPase component BWI76_RS14860 BWI76_RS07240
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase BWI76_RS05650 BWI76_RS23640
uxuB D-mannonate dehydrogenase BWI76_RS05645 BWI76_RS19755

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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