GapMind for catabolism of small carbon sources

 

putrescine catabolism in Shewanella sp. ANA-3

Best path

puuP, 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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
puuP putrescine:H+ symporter PuuP/PlaP Shewana3_3634
puuA glutamate-putrescine ligase Shewana3_3098 Shewana3_0300
puuB gamma-glutamylputrescine oxidase Shewana3_3093 Shewana3_3101
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Shewana3_3105 Shewana3_0250
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Shewana3_3099
gabT gamma-aminobutyrate transaminase Shewana3_3091 Shewana3_3106
gabD succinate semialdehyde dehydrogenase Shewana3_3092 Shewana3_3105
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) Shewana3_3106 Shewana3_0610
patD gamma-aminobutyraldehyde dehydrogenase Shewana3_3105 Shewana3_0250
POT1 putrescine:H+ symporter POT1
potA putrescine ABC transporter, ATPase component (PotA/PotG) Shewana3_3096 Shewana3_3192
potB putrescine ABC transporter, permease component 1 (PotB/PotH) Shewana3_3095
potC putrescine ABC transporter, permease component 2 (PotC/PotI) Shewana3_3094
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) Shewana3_3097
potE putrescine:H+ symporter PotE Shewana3_3872
puo putrescine oxidase
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