GapMind for catabolism of small carbon sources

 

putrescine catabolism in Pseudomonas stutzeri RCH2

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) Psest_4282 Psest_3658
potB putrescine ABC transporter, permease component 1 (PotB/PotH) Psest_4281 Psest_3656
potC putrescine ABC transporter, permease component 2 (PotC/PotI) Psest_4280 Psest_3655
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) Psest_4284 Psest_4283
puuA glutamate-putrescine ligase Psest_4288 Psest_4286
puuB gamma-glutamylputrescine oxidase Psest_1966 Psest_3795
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Psest_4305 Psest_0905
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase Psest_4287
gabT gamma-aminobutyrate transaminase Psest_4285 Psest_3653
gabD succinate semialdehyde dehydrogenase Psest_4237 Psest_3654
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) Psest_4285 Psest_4306
patD gamma-aminobutyraldehyde dehydrogenase Psest_4305 Psest_2634
POT1 putrescine:H+ symporter POT1
potE putrescine:H+ symporter PotE
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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