GapMind for catabolism of small carbon sources

 

putrescine catabolism in Ochrobactrum thiophenivorans DSM 7216

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
potA putrescine ABC transporter, ATPase component (PotA/PotG) CEV31_RS15580 CEV31_RS13865
potB putrescine ABC transporter, permease component 1 (PotB/PotH) CEV31_RS15575 CEV31_RS19515
potC putrescine ABC transporter, permease component 2 (PotC/PotI) CEV31_RS15570 CEV31_RS19520
potD putrescine ABC transporter, substrate-binding component (PotD/PotF) CEV31_RS15585
puuA glutamate-putrescine ligase CEV31_RS15610 CEV31_RS09105
puuB gamma-glutamylputrescine oxidase CEV31_RS15615 CEV31_RS19040
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CEV31_RS06610 CEV31_RS16975
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase CEV31_RS02805
gabT gamma-aminobutyrate transaminase CEV31_RS17470 CEV31_RS19110
gabD succinate semialdehyde dehydrogenase CEV31_RS02995 CEV31_RS17935
Alternative steps:
patA putrescine aminotransferase (PatA/SpuC) CEV31_RS19110 CEV31_RS17470
patD gamma-aminobutyraldehyde dehydrogenase CEV31_RS19025 CEV31_RS08350
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 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