GapMind for catabolism of small carbon sources

 

myo-inositol catabolism

Analysis of pathway myoinositol in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Azospirillum brasilense Sp245 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Bacteroides thetaiotaomicron VPI-5482 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Burkholderia phytofirmans PsJN PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Caulobacter crescentus NA1000 iatP, iatA, ibpA, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Cupriavidus basilensis 4G11 PS417_11885, PS417_11890, PS417_11895, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Dechlorosoma suillum PS iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfovibrio vulgaris Hildenborough iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Desulfovibrio vulgaris Miyazaki F iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Dinoroseobacter shibae DFL-12 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Dyella japonica UNC79MFTsu3.2 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Echinicola vietnamensis KMM 6221, DSM 17526 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Escherichia coli BW25113 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Herbaspirillum seropedicae SmR1 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Klebsiella michiganensis M5al PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Magnetospirillum magneticum AMB-1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Marinobacter adhaerens HP15 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Paraburkholderia bryophila 376MFSha3.1 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pedobacter sp. GW460-11-11-14-LB5 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Phaeobacter inhibens BS107 PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens FW300-N1B4 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens FW300-N2C3 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens FW300-N2E2 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens FW300-N2E3 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas fluorescens GW456-L13 iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Pseudomonas putida KT2440 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas simiae WCS417 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Pseudomonas stutzeri RCH2 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Shewanella amazonensis SB2B iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Shewanella loihica PV-4 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Shewanella oneidensis MR-1 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Shewanella sp. ANA-3 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sinorhizobium meliloti 1021 PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
Sphingomonas koreensis DSMZ 15582 iolF, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
Synechococcus elongatus PCC 7942 iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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