GapMind for catabolism of small carbon sources

 

putrescine catabolism in Magnetospirillum magneticum AMB-1

Best path

potA, potB, potC, potD, patA, patD, gabT, gabD

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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) AMB_RS13205 AMB_RS09395
potB putrescine ABC transporter, permease component 1 (PotB/PotH) AMB_RS13200
potC putrescine ABC transporter, permease component 2 (PotC/PotI) AMB_RS13195 AMB_RS17215
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) AMB_RS13210
patA putrescine aminotransferase (PatA/SpuC) AMB_RS08515 AMB_RS04150
patD gamma-aminobutyraldehyde dehydrogenase AMB_RS06710 AMB_RS04115
gabT gamma-aminobutyrate transaminase AMB_RS08515 AMB_RS01605
gabD succinate semialdehyde dehydrogenase AMB_RS06710 AMB_RS04160
Alternative steps:
POT1 putrescine:H+ symporter POT1
potE putrescine:H+ symporter PotE
puo putrescine oxidase
puuA glutamate-putrescine ligase
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase AMB_RS04115 AMB_RS06710
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase AMB_RS20870
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