GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Rhizobium johnstonii 3841

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component RL_RS23965 RL_RS36325
PS417_11890 myo-inositol ABC transporter, ATPase component RL_RS23960 RL_RS36695
PS417_11895 myo-inositol ABC transporter, permease component RL_RS23955 RL_RS09080
iolG myo-inositol 2-dehydrogenase RL_RS18660 RL_RS30160
iolE scyllo-inosose 2-dehydratase RL_RS07755 RL_RS07360
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase RL_RS07760
iolB 5-deoxy-D-glucuronate isomerase RL_RS07750 RL_RS28805
iolC 5-dehydro-2-deoxy-D-gluconate kinase RL_RS07765
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase RL_RS07765 RL_RS33900
mmsA malonate-semialdehyde dehydrogenase RL_RS04070 RL_RS18615
tpi triose-phosphate isomerase RL_RS12945 RL_RS33970
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase RL_RS21465 RL_RS04780
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA RL_RS12630 RL_RS23960
iatP myo-inositol ABC transporter, permease component IatP RL_RS26950 RL_RS09080
ibpA myo-inositol ABC transporter, substrate-binding component IbpA RL_RS23965 RL_RS09085
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase RL_RS03430 RL_RS09770
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase RL_RS35835
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase RL_RS18270 RL_RS03385
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component RL_RS33925
PGA1_c07320 myo-inositol ABC transporter, ATPase component RL_RS29725 RL_RS02570
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase RL_RS26165 RL_RS19890
uxuB D-mannonate dehydrogenase RL_RS00525 RL_RS21725

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.

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