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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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