GapMind for catabolism of small carbon sources

 

putrescine catabolism in Dyella japonica UNC79MFTsu3.2

Best path

puuP, patA, patD, 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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
puuP putrescine:H+ symporter PuuP/PlaP
patA putrescine aminotransferase (PatA/SpuC) N515DRAFT_3308 N515DRAFT_1751
patD gamma-aminobutyraldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
gabT gamma-aminobutyrate transaminase N515DRAFT_3308 N515DRAFT_1751
gabD succinate semialdehyde dehydrogenase N515DRAFT_2488 N515DRAFT_3729
Alternative steps:
POT1 putrescine:H+ symporter POT1
potA putrescine ABC transporter, ATPase component (PotA/PotG) N515DRAFT_1562 N515DRAFT_4212
potB putrescine ABC transporter, permease component 1 (PotB/PotH) N515DRAFT_1560
potC putrescine ABC transporter, permease component 2 (PotC/PotI)
potD putrescine ABC transporter, substrate-binding component (PotD/PotF)
potE putrescine:H+ symporter PotE N515DRAFT_1063
puo putrescine oxidase
puuA glutamate-putrescine ligase N515DRAFT_3024
puuB gamma-glutamylputrescine oxidase N515DRAFT_2697
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_0379
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
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, 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