GapMind for catabolism of small carbon sources

 

L-arginine catabolism

Analysis of pathway arginine in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Azospirillum brasilense Sp245 braC, braD, braE, braF, braG, arcA, arcB, arcC, rocD, PRO3, put1, putA
Bacteroides thetaiotaomicron VPI-5482 rocE, rocF, rocD, rocA
Burkholderia phytofirmans PsJN artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Caulobacter crescentus NA1000 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Cupriavidus basilensis 4G11 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Dechlorosoma suillum PS rocE, rocF, rocD, rocA
Desulfovibrio vulgaris Hildenborough rocE, rocF, rocD, PRO3, put1, putA
Desulfovibrio vulgaris Miyazaki F rocE, rocF, rocD, PRO3, put1, putA
Dinoroseobacter shibae DFL-12 artJ, artM, artP, artQ, arcA, arcB, arcC, ocd, put1, putA
Dyella japonica UNC79MFTsu3.2 rocE, rocF, rocD, PRO3, put1, putA
Echinicola vietnamensis KMM 6221, DSM 17526 rocE, rocF, rocD, PRO3, put1, putA
Escherichia coli BW25113 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Herbaspirillum seropedicae SmR1 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Klebsiella michiganensis M5al artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Magnetospirillum magneticum AMB-1 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Marinobacter adhaerens HP15 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Paraburkholderia bryophila 376MFSha3.1 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Pedobacter sp. GW460-11-11-14-LB5 rocE, rocF, rocD, PRO3, put1, putA
Phaeobacter inhibens BS107 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Pseudomonas fluorescens FW300-N1B4 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens FW300-N2C3 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens FW300-N2E2 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens FW300-N2E3 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens GW456-L13 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas putida KT2440 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas simiae WCS417 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas stutzeri RCH2 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella amazonensis SB2B rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella loihica PV-4 rocE, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella oneidensis MR-1 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella sp. ANA-3 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Sinorhizobium meliloti 1021 braC, braD, braE, braF, braG, arcA, arcB, arcC, ocd, put1, putA
Sphingomonas koreensis DSMZ 15582 rocE, astA, astB, astC, astD, astE
Synechococcus elongatus PCC 7942 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD

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