GapMind for catabolism of small carbon sources

 

putrescine catabolism in Caulobacter crescentus NA1000

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) CCNA_03235 CCNA_01670
potB putrescine ABC transporter, permease component 1 (PotB/PotH) CCNA_03238
potC putrescine ABC transporter, permease component 2 (PotC/PotI) CCNA_03236
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) CCNA_03239
puuA glutamate-putrescine ligase CCNA_03230 CCNA_03240
puuB gamma-glutamylputrescine oxidase CCNA_03229
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CCNA_03243 CCNA_03695
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CCNA_03234
gabT gamma-aminobutyrate transaminase CCNA_03233 CCNA_03245
gabD succinate semialdehyde dehydrogenase CCNA_03242 CCNA_03243
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) CCNA_03233 CCNA_03245
patD gamma-aminobutyraldehyde dehydrogenase CCNA_03243 CCNA_03695
POT1 putrescine:H+ symporter POT1
potE putrescine:H+ symporter PotE CCNA_03226
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:

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