GapMind for catabolism of small carbon sources

 

L-arabinose catabolism

Analysis of pathway arabinose in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Azospirillum brasilense Sp245 gguA, gguB, chvE, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
Bacteroides thetaiotaomicron VPI-5482 BT0355, araA, araB, araD
Burkholderia phytofirmans PsJN araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Caulobacter crescentus NA1000 araE, xacB, xacC, xacD, xacE, xacF
Cupriavidus basilensis 4G11 araE, xacB, xacC, xacD, xacE, xacF
Dechlorosoma suillum PS araE, araA, araB, araD
Desulfovibrio vulgaris Hildenborough araE, araA, araB, araD
Desulfovibrio vulgaris Miyazaki F araE, araA, araB, araD
Dinoroseobacter shibae DFL-12 araE, xacB, xacC, xacD, xacE, xacF
Dyella japonica UNC79MFTsu3.2 araUsh, araVsh, araWsh, araZsh, xacB, xacC, xacD, xacE, xacF
Echinicola vietnamensis KMM 6221, DSM 17526 Echvi_1880, araA, araB, araD
Escherichia coli BW25113 araF, araG, araH, araA, araB, araD
Herbaspirillum seropedicae SmR1 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Klebsiella michiganensis M5al araF, araG, araH, araA, araB, araD
Magnetospirillum magneticum AMB-1 araE, araA, araB, araD
Marinobacter adhaerens HP15 araE, araA, araB, araD
Paraburkholderia bryophila 376MFSha3.1 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pedobacter sp. GW460-11-11-14-LB5 araE, araA, araB, araD
Phaeobacter inhibens BS107 araE, xacB, xacC, xacD, xacE, xacF
Pseudomonas fluorescens FW300-N1B4 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas fluorescens FW300-N2C3 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas fluorescens FW300-N2E2 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas fluorescens FW300-N2E3 araE, araA, araB, araD
Pseudomonas fluorescens GW456-L13 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas putida KT2440 araE, araA, araB, araD
Pseudomonas simiae WCS417 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas stutzeri RCH2 araE, araA, araB, araD
Shewanella amazonensis SB2B araE, araA, araB, araD
Shewanella loihica PV-4 Echvi_1880, araA, araB, araD
Shewanella oneidensis MR-1 araE, araA, araB, araD
Shewanella sp. ANA-3 araUsh, araVsh, araWsh, araZsh, araA, araB, araD
Sinorhizobium meliloti 1021 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Sphingomonas koreensis DSMZ 15582 araE, xacB, xacC, xacD, xacE, xacF
Synechococcus elongatus PCC 7942 araE, araA, araB, araD

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 May 21 2021. The underlying query database was built on May 21 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