GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Marinomonas arctica 328

Best path

PGA1_c07300, PGA1_c07310, PGA1_c07320, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component DK187_RS08835
PGA1_c07310 myo-inositol ABC transporter, permease component DK187_RS08840 DK187_RS05065
PGA1_c07320 myo-inositol ABC transporter, ATPase component DK187_RS08845 DK187_RS19185
iolG myo-inositol 2-dehydrogenase DK187_RS08880 DK187_RS02870
iolE scyllo-inosose 2-dehydratase DK187_RS08865
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase DK187_RS08860
iolB 5-deoxy-D-glucuronate isomerase DK187_RS08875
iolC 5-dehydro-2-deoxy-D-gluconate kinase DK187_RS08855 DK187_RS16375
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase DK187_RS08855 DK187_RS03465
mmsA malonate-semialdehyde dehydrogenase DK187_RS07670 DK187_RS08870
tpi triose-phosphate isomerase DK187_RS01615 DK187_RS05025
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase DK187_RS01530 DK187_RS11900
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA DK187_RS04275 DK187_RS16470
iatP myo-inositol ABC transporter, permease component IatP DK187_RS05065 DK187_RS04235
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase DK187_RS06085
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase DK187_RS16375
PS417_11885 myo-inositol ABC transporter, substrate-binding component
PS417_11890 myo-inositol ABC transporter, ATPase component DK187_RS16470 DK187_RS04275
PS417_11895 myo-inositol ABC transporter, permease component DK187_RS04235 DK187_RS05065
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase DK187_RS02450 DK187_RS04650
uxuB D-mannonate dehydrogenase DK187_RS04655 DK187_RS13495

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.

Links

Downloads

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:

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