GapMind for catabolism of small carbon sources

 

putrescine catabolism in Escherichia coli BW25113

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) b0855 b1126
potB putrescine ABC transporter, permease component 1 (PotB/PotH) b0856 b1125
potC putrescine ABC transporter, permease component 2 (PotC/PotI) b0857 b1124
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) b0854 b1123
puuA glutamate-putrescine ligase b1297 b3870
puuB gamma-glutamylputrescine oxidase b1301
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase b1300 b3588
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase b1298
gabT gamma-aminobutyrate transaminase b2662 b1302
gabD succinate semialdehyde dehydrogenase b1300 b2661
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) b3073 b1302
patD gamma-aminobutyraldehyde dehydrogenase b1444 b1300
POT1 putrescine:H+ symporter POT1
potE putrescine:H+ symporter PotE b0692 b4115
puo putrescine oxidase b1386
puuP putrescine:H+ symporter PuuP/PlaP b1296 b2014
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