GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Sinorhizobium meliloti 1021

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 SM_b20712 SM_b20072
PS417_11890 myo-inositol ABC transporter, ATPase component SM_b20713 SM_b20673
PS417_11895 myo-inositol ABC transporter, permease component SM_b20714 SM_b21375
iolG myo-inositol 2-dehydrogenase SM_b20899 SMc04139
iolE scyllo-inosose 2-dehydratase SMc00433
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase SMc01166
iolB 5-deoxy-D-glucuronate isomerase SMc00432
iolC 5-dehydro-2-deoxy-D-gluconate kinase SMc01165
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase SMc01165 SM_b21192
mmsA malonate-semialdehyde dehydrogenase SMc00781 SM_b20891
tpi triose-phosphate isomerase SMc01023 SMc01614
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase SMc03153 SMc02043
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA SM_b21344 SMc02337
iatP myo-inositol ABC transporter, permease component IatP SMc02031 SM_b20854
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase SMc01214
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase SMa1353
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase SMc01531 SM_b21374
PGA1_c07300 myo-inositol ABC transport, substrate-binding component SMa0218
PGA1_c07310 myo-inositol ABC transporter, permease component SMa0070 SMa0217
PGA1_c07320 myo-inositol ABC transporter, ATPase component SMa0216 SMa0072
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase SM_b20446 SM_b20510
uxuB D-mannonate dehydrogenase SM_b20749 SMc01501

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 (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 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