putrescine catabolism in Methylibium petroleiphilum PM1

GapMind for catabolism of small carbon sources

putrescine catabolism in Methylibium petroleiphilum PM1

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.

all: putrescine-transport and putrescine-degradation
putrescine-degradation: putrescine-to-GABA and GABA-degradation

Comment: Gamma-aminobutyrate is a common intermediate.

putrescine-to-GABA:

patA and patD
or puuA, puuB, puuC and puuD
or puo and patD
Comment: In pathway I or pathway V, putrescine aminotransferase (patA or spuC) forms 4-aminobutanal, and dehydrogenase patD forms GABA. In pathway II, putrescine is converted to GABA with glutamylated intermedates: puuA forms gamma-glutamyl-putrescine, an oxidase forms 4-(gamma-glutaminylamino)butanal, a dehydrogenase forms 4-(gamma-glutamylamino)butanoate, and a hydrolase releases glutamate and GABA. As part of pathway IV, putrescine oxidase (puo) forms 4-aminobutanal, which is probably converted to GABA by dehydrogenase patD.

GABA-degradation: gabT and gabD

Comment: GABA (4-aminobutanoate) is consumed by an aminotransferase (known as gabT or puuE), which forms succinate semialdehyde, and dehydrogenase gabD, which forms succinate.

putrescine-transport:

potA, potB, potC and potD
or puuP
or potE
or TPO1
or UGA4
or POT1
Comment: Transporters were identified using: query: transporter:putrescine

18 steps (12 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
potA	putrescine ABC transporter, ATPase component (PotA/PotG)	MPE_RS09590	MPE_RS00610
potB	putrescine ABC transporter, permease component 1 (PotB/PotH)	MPE_RS09595	MPE_RS17025
potC	putrescine ABC transporter, permease component 2 (PotC/PotI)	MPE_RS09600
potD	putrescine ABC transporter, substrate-binding component (PotD/PotF)	MPE_RS09585
puuA	glutamate-putrescine ligase	MPE_RS09575	MPE_RS10465
puuB	gamma-glutamylputrescine oxidase	MPE_RS09565
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	MPE_RS09615	MPE_RS03015
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	MPE_RS09570	MPE_RS05725
gabT	gamma-aminobutyrate transaminase	MPE_RS09620	MPE_RS09580
gabD	succinate semialdehyde dehydrogenase	MPE_RS11735	MPE_RS09615
Alternative steps:
patA	putrescine aminotransferase (PatA/SpuC)	MPE_RS09580	MPE_RS01880
patD	gamma-aminobutyraldehyde dehydrogenase	MPE_RS09615	MPE_RS03015
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources