GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Rhizobium etli CFN 42

Best path

PS417_11885, PS417_11890, PS417_11895, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component RHE_RS20385 RHE_RS13525
PS417_11890 myo-inositol ABC transporter, ATPase component RHE_RS20390 RHE_RS06210
PS417_11895 myo-inositol ABC transporter, permease component RHE_RS20395 RHE_RS06205
iolG myo-inositol 2-dehydrogenase RHE_RS16225 RHE_RS12040
iolE scyllo-inosose 2-dehydratase RHE_RS06860 RHE_RS28750
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase RHE_RS06865
iolB 5-deoxy-D-glucuronate isomerase RHE_RS06855
iolC 5-dehydro-2-deoxy-D-gluconate kinase RHE_RS06870
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase RHE_RS06870
mmsA malonate-semialdehyde dehydrogenase RHE_RS03695 RHE_RS16180
tpi triose-phosphate isomerase RHE_RS11180 RHE_RS26620
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase RHE_RS18590 RHE_RS04295
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA RHE_RS06210 RHE_RS27550
iatP myo-inositol ABC transporter, permease component IatP RHE_RS12255 RHE_RS06205
ibpA myo-inositol ABC transporter, substrate-binding component IbpA RHE_RS06200 RHE_RS13525
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase RHE_RS15165
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase RHE_RS28420
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase RHE_RS15865 RHE_RS06870
PGA1_c07300 myo-inositol ABC transport, substrate-binding component RHE_RS12060
PGA1_c07310 myo-inositol ABC transporter, permease component RHE_RS12055 RHE_RS26590
PGA1_c07320 myo-inositol ABC transporter, ATPase component RHE_RS12050 RHE_RS23990
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase RHE_RS22025 RHE_RS24555
uxuB D-mannonate dehydrogenase RHE_RS00455 RHE_RS18810

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 Apr 09 2024. 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