GapMind for catabolism of small carbon sources

 

Definition of putrescine catabolism

As rules and steps, or see full text

Rules

Overview: Putrescine degradation in GapMind is based on MetaCyc pathways putrescine degradation I via putrescine aminotransferase (link), pathway II with glutamylated intermediates (link), pathway IV via putrescine oxidase (link), or pathway V via putrescine:pyruvate aminotransferase (link). Pathway III is not reported in prokaryotes, so it is not included in GapMind.

Steps

potA: putrescine ABC transporter, ATPase component (PotA/PotG)

potB: putrescine ABC transporter, permease component 1 (PotB/PotH)

potC: putrescine ABC transporter, permease component 2 (PotC/PotI)

potD: putrescine ABC transporter, substrate-binding component (PotD/PotF)

puuP: putrescine:H+ symporter PuuP/PlaP

potE: putrescine:H+ symporter PotE

TPO1: putrescine transporter TPO1

UGA4: putrescine transporter UGA4

POT1: putrescine:H+ symporter POT1

gabT: gamma-aminobutyrate transaminase

gabD: succinate semialdehyde dehydrogenase

patA: putrescine aminotransferase (PatA/SpuC)

patD: gamma-aminobutyraldehyde dehydrogenase

puuA: glutamate-putrescine ligase

puuB: gamma-glutamylputrescine oxidase

puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase

puo: putrescine oxidase

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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