GapMind for catabolism of small carbon sources


myo-inositol catabolism in Herbaspirillum seropedicae SmR1

Best path

PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

Also see fitness data for the top candidates


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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component HSERO_RS12110
PGA1_c07310 myo-inositol ABC transporter, permease component HSERO_RS12115 HSERO_RS05325
PGA1_c07320 myo-inositol ABC transporter, ATPase component HSERO_RS12120 HSERO_RS03640
iolG myo-inositol 2-dehydrogenase HSERO_RS12095 HSERO_RS12100
iolE scyllo-inosose 2-dehydratase HSERO_RS12135
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase HSERO_RS12130
iolB 5-deoxy-D-glucuronate isomerase HSERO_RS12140
iolC 5-dehydro-2-deoxy-D-gluconate kinase HSERO_RS12125 HSERO_RS07545
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase HSERO_RS12125 HSERO_RS03355
mmsA malonate-semialdehyde dehydrogenase HSERO_RS24005 HSERO_RS23245
tpi triose-phosphate isomerase HSERO_RS08805 HSERO_RS03345
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HSERO_RS05525 HSERO_RS05155
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA HSERO_RS03640 HSERO_RS05250
iatP myo-inositol ABC transporter, permease component IatP HSERO_RS05325 HSERO_RS03645
ibpA myo-inositol ABC transporter, substrate-binding component IbpA HSERO_RS05315
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 HSERO_RS08715 HSERO_RS07545
PS417_11885 myo-inositol ABC transporter, substrate-binding component HSERO_RS05170
PS417_11890 myo-inositol ABC transporter, ATPase component HSERO_RS05250 HSERO_RS03640
PS417_11895 myo-inositol ABC transporter, permease component HSERO_RS03645 HSERO_RS05325
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase HSERO_RS05150
uxuB D-mannonate dehydrogenase HSERO_RS02215

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:

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