GapMind for catabolism of small carbon sources

 

putrescine catabolism in Chromobacterium vaccinii MWU205

Best path

potA, potB, potC, potD, puuA, puuB, puuC, puuD, 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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) VL52_RS11120 VL52_RS13280
potB putrescine ABC transporter, permease component 1 (PotB/PotH) VL52_RS04805 VL52_RS13285
potC putrescine ABC transporter, permease component 2 (PotC/PotI) VL52_RS04810 VL52_RS13290
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) VL52_RS04800 VL52_RS13295
puuA glutamate-putrescine ligase VL52_RS07080 VL52_RS11885
puuB gamma-glutamylputrescine oxidase VL52_RS11115
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase VL52_RS07105 VL52_RS21455
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase VL52_RS07085
gabT gamma-aminobutyrate transaminase VL52_RS20935 VL52_RS07075
gabD succinate semialdehyde dehydrogenase VL52_RS20535 VL52_RS20940
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) VL52_RS07075 VL52_RS18210
patD gamma-aminobutyraldehyde dehydrogenase VL52_RS07105 VL52_RS21455
POT1 putrescine:H+ symporter POT1
potE putrescine:H+ symporter PotE VL52_RS02850
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 24 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