GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Brucella inopinata BO1

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component BIBO1_RS09810
PGA1_c07310 myo-inositol ABC transporter, permease component BIBO1_RS09805 BIBO1_RS18545
PGA1_c07320 myo-inositol ABC transporter, ATPase component BIBO1_RS09800 BIBO1_RS18905
iolG myo-inositol 2-dehydrogenase BIBO1_RS16990 BIBO1_RS09815
iolE scyllo-inosose 2-dehydratase BIBO1_RS16970
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase BIBO1_RS16975
iolB 5-deoxy-D-glucuronate isomerase BIBO1_RS16965
iolC 5-dehydro-2-deoxy-D-gluconate kinase BIBO1_RS16980
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase BIBO1_RS16980 BIBO1_RS18595
mmsA malonate-semialdehyde dehydrogenase BIBO1_RS12430 BIBO1_RS10860
tpi triose-phosphate isomerase BIBO1_RS08660 BIBO1_RS18585
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BIBO1_RS15530 BIBO1_RS18915
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA BIBO1_RS19475 BIBO1_RS14060
iatP myo-inositol ABC transporter, permease component IatP BIBO1_RS11585 BIBO1_RS18545
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
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 BIBO1_RS08880 BIBO1_RS16980
PS417_11885 myo-inositol ABC transporter, substrate-binding component BIBO1_RS11580
PS417_11890 myo-inositol ABC transporter, ATPase component BIBO1_RS11590 BIBO1_RS19475
PS417_11895 myo-inositol ABC transporter, permease component BIBO1_RS11585 BIBO1_RS18545
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase

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