GapMind for catabolism of small carbon sources

 

putrescine catabolism in Burkholderia phytofirmans PsJN

Best path

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

Also see fitness data for the top candidates

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.

18 steps (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) BPHYT_RS11445 BPHYT_RS23145
potB putrescine ABC transporter, permease component 1 (PotB/PotH) BPHYT_RS11440 BPHYT_RS23140
potC putrescine ABC transporter, permease component 2 (PotC/PotI) BPHYT_RS23135 BPHYT_RS11435
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) BPHYT_RS26645 BPHYT_RS11450
puuA glutamate-putrescine ligase BPHYT_RS23160 BPHYT_RS09955
puuB gamma-glutamylputrescine oxidase BPHYT_RS23125 BPHYT_RS23120
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase BPHYT_RS23175 BPHYT_RS29875
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase BPHYT_RS23165 BPHYT_RS15045
gabT gamma-aminobutyrate transaminase BPHYT_RS23155 BPHYT_RS22435
gabD succinate semialdehyde dehydrogenase BPHYT_RS10925 BPHYT_RS34305
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) BPHYT_RS23155 BPHYT_RS30220
patD gamma-aminobutyraldehyde dehydrogenase BPHYT_RS23175 BPHYT_RS25160
POT1 putrescine:H+ symporter POT1
potE putrescine:H+ symporter PotE
puo putrescine oxidase BPHYT_RS09910
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.

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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, 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