GapMind for catabolism of small carbon sources


putrescine catabolism in Phaeobacter inhibens BS107

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) PGA1_c34430 PGA1_c34390
potB putrescine ABC transporter, permease component 1 (PotB/PotH) PGA1_c34440 PGA1_c31290
potC putrescine ABC transporter, permease component 2 (PotC/PotI) PGA1_c34450
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) PGA1_c34420
puuA glutamate-putrescine ligase PGA1_c11520 PGA1_c11540
puuB gamma-glutamylputrescine oxidase PGA1_c11510 PGA1_78p00350
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PGA1_c32250 PGA1_c21670
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase PGA1_c09920 PGA1_c28350
gabT gamma-aminobutyrate transaminase PGA1_c34400 PGA1_c09350
gabD succinate semialdehyde dehydrogenase PGA1_c29650 PGA1_c23170
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) PGA1_c34400 PGA1_c09350
patD gamma-aminobutyraldehyde dehydrogenase PGA1_c21670 PGA1_c32250
POT1 putrescine:H+ symporter POT1
potE putrescine:H+ symporter PotE
puo putrescine oxidase
puuP putrescine:H+ symporter PuuP/PlaP
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 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, the preprint 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