GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c07300 myo-inositol ABC transport, substrate-binding component HTA01S_RS06225
PGA1_c07310 myo-inositol ABC transporter, permease component HTA01S_RS06220
PGA1_c07320 myo-inositol ABC transporter, ATPase component HTA01S_RS06215 HTA01S_RS10210
iolG myo-inositol 2-dehydrogenase HTA01S_RS06235 HTA01S_RS06240
iolE scyllo-inosose 2-dehydratase HTA01S_RS06200
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase HTA01S_RS06205
iolB 5-deoxy-D-glucuronate isomerase HTA01S_RS06195
iolC 5-dehydro-2-deoxy-D-gluconate kinase HTA01S_RS06210 HTA01S_RS01875
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase HTA01S_RS06210 HTA01S_RS06295
mmsA malonate-semialdehyde dehydrogenase HTA01S_RS06165 HTA01S_RS16360
tpi triose-phosphate isomerase HTA01S_RS22235
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HTA01S_RS01685 HTA01S_RS16415
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA HTA01S_RS08955 HTA01S_RS05330
iatP myo-inositol ABC transporter, permease component IatP HTA01S_RS08960 HTA01S_RS05335
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase HTA01S_RS13475
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase HTA01S_RS13440 HTA01S_RS01875
PS417_11885 myo-inositol ABC transporter, substrate-binding component HTA01S_RS16365
PS417_11890 myo-inositol ABC transporter, ATPase component HTA01S_RS05330 HTA01S_RS08955
PS417_11895 myo-inositol ABC transporter, permease component HTA01S_RS08960 HTA01S_RS05335
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase HTA01S_RS13450 HTA01S_RS01850
uxuB D-mannonate dehydrogenase HTA01S_RS13445 HTA01S_RS01905

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