Definition of putrescine catabolism

GapMind for catabolism of small carbon sources

Definition of putrescine catabolism

# Putrescine degradation in GapMind is based on MetaCyc pathways
# putrescine degradation I via putrescine aminotransferase (metacyc:PUTDEG-PWY),
# pathway II with glutamylated intermediates (metacyc:PWY0-1221),
# pathway IV via putrescine oxidase (metacyc:PWY-2),
# or pathway V via putrescine:pyruvate aminotransferase (metacyc:PWY-3).
# Pathway III is not reported in prokaryotes, so it is not included in GapMind.

# ABC transporters:

# 4-part ABC transporters include E. coli potABCD or potGHIF, which are related to each other, and a related system,
# also named potABCD, from Streptococcus pneuomoniae.
potA	putrescine ABC transporter, ATPase component (PotA/PotG)	curated:TCDB::P31134	curated:CharProtDB::CH_024626	curated:TCDB::Q97Q42
potB	putrescine ABC transporter, permease component 1 (PotB/PotH)	curated:CharProtDB::CH_088338	curated:CharProtDB::CH_088337	curated:TCDB::Q97Q43
potC	putrescine ABC transporter, permease component 2 (PotC/PotI)	curated:CharProtDB::CH_088340	curated:SwissProt::P0AFL1	curated:TCDB::Q97Q44
# SpuD from P. aeruginosa (Q02UB7) is similar and was shown to bind putrescine
potD	putrescine ABC transporter, substrate-binding component (PotD/PotF)	curated:CharProtDB::CH_088339	curated:SwissProt::P31133	curated:TCDB::Q97Q45	curated:SwissProt::Q02UB7

# Transporters were identified using:
# query: transporter:putrescine
putrescine-transport: potA potB potC potD

# Homomeric transporters:

puuP	putrescine:H+ symporter PuuP/PlaP	curated:SwissProt::P0AA47	curated:SwissProt::P76037
putrescine-transport: puuP

potE	putrescine:H+ symporter PotE	curated:SwissProt::P0AAF1
putrescine-transport: potE

TPO1	putrescine transporter TPO1	curated:CharProtDB::CH_091011
putrescine-transport: TPO1

UGA4	putrescine transporter UGA4	curated:CharProtDB::CH_091303
putrescine-transport: UGA4

POT1	putrescine:H+ symporter POT1	curated:TCDB::Q5C8V6
putrescine-transport: POT1

# Ignored export systems, including sapBCDF, and the agmatine/putrescine antiporter AguD

# Gamma-aminobutyrate is a common intermediate, and can be oxidized to succinate
# via succinate semialdehyde

# Sama_2636 (A1S8Y2) was added because it is a transaminase involved in putrescine utilization
gabT	gamma-aminobutyrate transaminase	EC:2.6.1.19	EC:2.6.1.96	uniprot:A1S8Y2

# This may be either NADH or NADPH dependent, forming succinate in either case.
# Close homologs in Pseudomonas or Klebsiella are annotated as glutarate-semialdehyde dehydrogenases (1.2.1.20)
# or aldehyde dehydrogenases (1.2.1.3); Q9I6M5 is annotated as glutarate-semialdehyde dehydrogenase
# but with no EC number.
# Q8BUF0 appears to be misannotated in BRENDA.
gabD	succinate semialdehyde dehydrogenase	EC:1.2.1.79	EC:1.2.1.24	EC:1.2.1.16	ignore:BRENDA::Q8BUF0	ignore_other:1.2.1.20	ignore_other:1.2.1.3	ignore:SwissProt::Q9I6M5

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

# Since patA and putrescine-pyruvate transaminase (spuC) perform similar reactions and
# produce gamma-aminobutyraldehyde (4-aminobutanal), they are listed together.
# Many close homologs of patA are GABA aminotransferases (EC 2.6.1.19), so ignore those.
patA	putrescine aminotransferase (PatA/SpuC)	EC:2.6.1.82	curated:metacyc::MONOMER-17	EC:2.6.1.113	ignore_other:2.6.1.19

patD	gamma-aminobutyraldehyde dehydrogenase	EC:1.2.1.19

# In pathway I or pathway V, putrescine aminotransferase (patA or spuC) forms 4-aminobutanal,
# and dehydrogenase patD forms GABA.
putrescine-to-GABA: patA patD

puuA	glutamate-putrescine ligase	EC:6.3.1.11

# MetaCyc uses EC 1.4.3.M3; other resources uses 1.4.3.-
puuB	gamma-glutamylputrescine oxidase	term:glutamylputrescine oxidase

# The putative kauB (4-guanidinobutyraldehyde dehydrogenase) from P. putida (metacyc::MONOMER-11560)
# is included because it is closely related to P. aeruginosa kauB (PA5312), which acts on
# gamma-glutamyl-gamma-aminobutyraldehyde as well (PMID:3141581).
# Some other P. fluorescens kauB-type proteins seem to be acting in this pathway
# but were annotated with EC:1.2.1.54 instead, so these were added manually.
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	EC:1.2.1.99	curated:metacyc::MONOMER-11560	curated:reanno::pseudo13_GW456_L13:PfGW456L13_805	curated:reanno::pseudo6_N2E2:Pf6N2E2_4383	curated:reanno::pseudo5_N2C3_1:AO356_12580	curated:reanno::WCS417:GFF5420

puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	EC:3.5.1.94

# 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.
putrescine-to-GABA: puuA puuB puuC puuD

puo	putrescine oxidase	EC:1.4.3.10

# As part of pathway IV, putrescine oxidase (puo) forms 4-aminobutanal,
# which is probably converted to GABA by dehydrogenase patD.
putrescine-to-GABA: puo patD

# Gamma-aminobutyrate is a common intermediate.
putrescine-degradation: putrescine-to-GABA GABA-degradation

all: putrescine-transport putrescine-degradation

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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:

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