GapMind for catabolism of small carbon sources

 

putrescine catabolism in Shewanella amazonensis SB2B

Best path

potE, 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
potE putrescine:H+ symporter PotE Sama_3335
puuA glutamate-putrescine ligase Sama_2644 Sama_1174
puuB gamma-glutamylputrescine oxidase Sama_2638 Sama_2647
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Sama_2648 Sama_3435
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Sama_0794 Sama_2645
gabT gamma-aminobutyrate transaminase Sama_2643 Sama_2636
gabD succinate semialdehyde dehydrogenase Sama_2637 Sama_2648
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) Sama_2643 Sama_2649
patD gamma-aminobutyraldehyde dehydrogenase Sama_2648 Sama_3435
POT1 putrescine:H+ symporter POT1
potA putrescine ABC transporter, ATPase component (PotA/PotG) Sama_2641 Sama_0668
potB putrescine ABC transporter, permease component 1 (PotB/PotH) Sama_2640
potC putrescine ABC transporter, permease component 2 (PotC/PotI) Sama_2639
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) Sama_2642
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.

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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