GapMind for catabolism of small carbon sources


putrescine catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD

Also see fitness data for the top candidates


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.

18 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) Pf1N1B4_4352 Pf1N1B4_2261
potB putrescine ABC transporter, permease component 1 (PotB/PotH) Pf1N1B4_4351 Pf1N1B4_2262
potC putrescine ABC transporter, permease component 2 (PotC/PotI) Pf1N1B4_4350 Pf1N1B4_2263
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) Pf1N1B4_2259 Pf1N1B4_4349
puuA glutamate-putrescine ligase Pf1N1B4_4354 Pf1N1B4_2254
puuB gamma-glutamylputrescine oxidase Pf1N1B4_6047 Pf1N1B4_4356
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Pf1N1B4_2132 Pf1N1B4_4355
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Pf1N1B4_4353 Pf1N1B4_2255
gabT gamma-aminobutyrate transaminase Pf1N1B4_2257 Pf1N1B4_1733
gabD succinate semialdehyde dehydrogenase Pf1N1B4_1734 Pf1N1B4_5616
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) Pf1N1B4_2257 Pf1N1B4_1239
patD gamma-aminobutyraldehyde dehydrogenase Pf1N1B4_3024 Pf1N1B4_3029
POT1 putrescine:H+ symporter POT1
potE putrescine:H+ symporter PotE Pf1N1B4_4994
puo putrescine oxidase
puuP putrescine:H+ symporter PuuP/PlaP Pf1N1B4_5855
TPO1 putrescine transporter TPO1
UGA4 putrescine transporter UGA4

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.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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