GapMind for catabolism of small carbon sources

 

putrescine catabolism

Analysis of pathway putrescine in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 puuP, patA, patD, gabT, gabD
Azospirillum brasilense Sp245 potA, potB, potC, potD, patA, patD, gabT, gabD
Bacteroides thetaiotaomicron VPI-5482 potA, potB, potC, potD, patA, patD, gabT, gabD
Burkholderia phytofirmans PsJN potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Caulobacter crescentus NA1000 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Cupriavidus basilensis 4G11 puuP, patA, patD, gabT, gabD
Dechlorosoma suillum PS puuP, patA, patD, gabT, gabD
Desulfovibrio vulgaris Hildenborough potA, potB, potC, potD, patA, patD, gabT, gabD
Desulfovibrio vulgaris Miyazaki F potA, potB, potC, potD, patA, patD, gabT, gabD
Dinoroseobacter shibae DFL-12 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Dyella japonica UNC79MFTsu3.2 puuP, patA, patD, gabT, gabD
Echinicola vietnamensis KMM 6221, DSM 17526 puuP, patA, patD, gabT, gabD
Escherichia coli BW25113 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Herbaspirillum seropedicae SmR1 puuP, patA, patD, gabT, gabD
Klebsiella michiganensis M5al potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Magnetospirillum magneticum AMB-1 potA, potB, potC, potD, patA, patD, gabT, gabD
Marinobacter adhaerens HP15 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Paraburkholderia bryophila 376MFSha3.1 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Pedobacter sp. GW460-11-11-14-LB5 puuP, patA, patD, gabT, gabD
Phaeobacter inhibens BS107 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens FW300-N1B4 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens FW300-N2C3 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens FW300-N2E2 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens FW300-N2E3 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas fluorescens GW456-L13 potA, potB, potC, potD, patA, patD, gabT, gabD
Pseudomonas putida KT2440 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Pseudomonas simiae WCS417 potA, potB, potC, potD, patA, patD, gabT, gabD
Pseudomonas stutzeri RCH2 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella amazonensis SB2B potE, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella loihica PV-4 potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella oneidensis MR-1 puuP, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella sp. ANA-3 puuP, puuA, puuB, puuC, puuD, gabT, gabD
Sinorhizobium meliloti 1021 potE, patA, patD, gabT, gabD
Sphingomonas koreensis DSMZ 15582 puuP, patA, patD, gabT, gabD
Synechococcus elongatus PCC 7942 puuP, 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 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