GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Cronobacter condimenti 1330

Best path

iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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
iolT myo-inositol:H+ symporter BN137_RS02325 BN137_RS13235
iolG myo-inositol 2-dehydrogenase BN137_RS02310
iolE scyllo-inosose 2-dehydratase BN137_RS02320
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase BN137_RS02305
iolB 5-deoxy-D-glucuronate isomerase BN137_RS02290
iolC 5-dehydro-2-deoxy-D-gluconate kinase BN137_RS02010
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase
mmsA malonate-semialdehyde dehydrogenase BN137_RS02285 BN137_RS09185
tpi triose-phosphate isomerase BN137_RS05125 BN137_RS13275
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BN137_RS04830 BN137_RS04055
HMIT myo-inositol:H+ symporter BN137_RS13235 BN137_RS02325
iatA myo-inositol ABC transporter, ATPase component IatA BN137_RS17460 BN137_RS04555
iatP myo-inositol ABC transporter, permease component IatP BN137_RS17455 BN137_RS10225
ibpA myo-inositol ABC transporter, substrate-binding component IbpA BN137_RS17450
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase BN137_RS07350
kdgK 2-keto-3-deoxygluconate kinase BN137_RS03205 BN137_RS02010
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component BN137_RS03980
PGA1_c07320 myo-inositol ABC transporter, ATPase component BN137_RS14410 BN137_RS17460
PS417_11885 myo-inositol ABC transporter, substrate-binding component BN137_RS06865
PS417_11890 myo-inositol ABC transporter, ATPase component BN137_RS06860 BN137_RS17460
PS417_11895 myo-inositol ABC transporter, permease component BN137_RS17455 BN137_RS06855
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase BN137_RS06950 BN137_RS02770
uxuB D-mannonate dehydrogenase BN137_RS06955 BN137_RS10895

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 24 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:

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