Definition of putrescine catabolism
As rules and steps, or see full text
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:
Steps
potA: putrescine ABC transporter, ATPase component (PotA/PotG)
- Curated sequence P31134: PotG aka B0855, component of Putrescine porter. putrescine ABC transporter ATP binding subunit (EC 7.6.2.16). putrescine ABC transporter ATP binding subunit (EC 7.6.2.16)
- Curated sequence CH_024626: spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31. Spermidine/putrescine import ATP-binding protein PotA; EC 7.6.2.11. Spermidine/putrescine import ATP-binding protein PotA aka B1126, component of Polyamine (putrescine/spermidine) uptake porter. spermidine preferential ABC transporter ATP binding subunit (EC 7.6.2.11; EC 7.6.2.16). spermidine preferential ABC transporter ATP binding subunit (EC 7.6.2.11; EC 7.6.2.16)
- Curated sequence Q97Q42: Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD
- Comment: 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.
- Total: 3 characterized proteins
potB: putrescine ABC transporter, permease component 1 (PotB/PotH)
- Curated sequence CH_088338: putrescine transport system permease protein PotH. PotH aka B0856, component of Putrescine porter. putrescine ABC transporter membrane subunit PotH (EC 7.6.2.16). putrescine ABC transporter membrane subunit PotH (EC 7.6.2.16)
- Curated sequence CH_088337: spermidine/putrescine ABC transporter, permease protein PotB. Spermidine/putrescine transport system permease protein PotB aka B1125, component of Polyamine (putrescine/spermidine) uptake porter. spermidine preferential ABC transporter membrane subunit PotB (EC 7.6.2.11; EC 7.6.2.16). spermidine preferential ABC transporter membrane subunit PotB (EC 7.6.2.11; EC 7.6.2.16)
- Curated sequence Q97Q43: Spermidine/putrescine ABC transporter, permease protein, component of The spermidine/putrescine uptake porter, PotABCD
- Total: 3 characterized proteins
potC: putrescine ABC transporter, permease component 2 (PotC/PotI)
- Curated sequence CH_088340: spermidine/putrescine ABC transporter, permease protein PotC. Spermidine/putrescine transport system permease protein PotC. Spermidine/putrescine transport system permease protein PotC aka B1124, component of Polyamine (putrescine/spermidine) uptake porter. spermidine preferential ABC transporter membrane subunit PotC (EC 7.6.2.11; EC 7.6.2.16). spermidine preferential ABC transporter membrane subunit PotC (EC 7.6.2.11; EC 7.6.2.16)
- Curated sequence P0AFL1: Putrescine transport system permease protein PotI. PotI aka B0857, component of Putrescine porter. putrescine ABC transporter membrane subunit PotI (EC 7.6.2.16). putrescine ABC transporter membrane subunit PotI (EC 7.6.2.16)
- Curated sequence Q97Q44: Spermidine/putrescine ABC transporter, permease protein, component of The spermidine/putrescine uptake porter, PotABCD
- Total: 3 characterized proteins
potD: putrescine ABC transporter, substrate-binding component (PotD/PotF)
- Curated sequence CH_088339: spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein PotD. Spermidine/putrescine-binding periplasmic protein; SPBP. Spermidine/putrescine-binding periplasmic protein PotD aka B1123, component of Polyamine (putrescine/spermidine) uptake porter. spermidine preferential ABC transporter periplasmic binding protein (EC 7.6.2.11; EC 7.6.2.16). spermidine preferential ABC transporter periplasmic binding protein (EC 7.6.2.11; EC 7.6.2.16)
- Curated sequence P31133: Putrescine-binding periplasmic protein. PotF aka B0854, component of Putrescine porter. putrescine ABC transporter periplasmic binding protein (EC 7.6.2.16). putrescine ABC transporter periplasmic binding protein (EC 7.6.2.16)
- Curated sequence Q97Q45: Spermidine/putrescine ABC transporter, spermidine/putrescine-binding protein, component of The spermidine/putrescine uptake porter, PotABCD
- Curated sequence Q02UB7: Putrescine-binding periplasmic protein SpuD. Putrescine-binding periplasmic protein SpuD
- Comment: SpuD from P. aeruginosa (Q02UB7) is similar and was shown to bind putrescine
- Total: 4 characterized proteins
puuP: putrescine:H+ symporter PuuP/PlaP
- Curated sequence P0AA47: Low-affinity putrescine importer PlaP. Low-affinity putrescine importer PlaP. putrescine:H+ symporter PlaP. putrescine:H+ symporter PlaP
- Curated sequence P76037: Putrescine importer PuuP. Putrescine importer, PuuP. putrescine:H+ symporter PuuP. putrescine:H+ symporter PuuP
- Total: 2 characterized proteins
potE: putrescine:H+ symporter PotE
- Curated sequence P0AAF1: Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter. Putrescine:ornithine antiporter for putrescine export; putrescine:H+ symporter for uptake. putrescine transporter PotE. putrescine transporter PotE
- Total: 1 characterized proteins
TPO1: putrescine transporter TPO1
- Curated sequence CH_091011: polyamine transporter 1. Polyamine transporter 1. Polyamines (spermine, spermidine, putrescine); paraquat; methylglyoxal bis(guanylhydrazone):H+ antiporter (in the plasma membrane) (activated by phosphorylation)
- Total: 1 characterized proteins
UGA4: putrescine transporter UGA4
- Curated sequence CH_091303: GABA-specific permease. GABA-specific permease; GABA-specific transport protein. γ-aminobutyric acid (GABA) permease, Uga4 (also transports the polyamine, putrescine)
- Total: 1 characterized proteins
POT1: putrescine:H+ symporter POT1
- Curated sequence Q5C8V6: The plasma membrane polyamine (putrescine, spermidine):H+ uptake symporter, LmPOT1 (inhibited by pentamidine and protonophores)
- Total: 1 characterized proteins
gabT: gamma-aminobutyrate transaminase
- Curated proteins or TIGRFams with EC 2.6.1.19
- Curated proteins or TIGRFams with EC 2.6.1.96
- UniProt sequence A1S8Y2: SubName: Full=4-aminobutyrate aminotransferase {ECO:0000313|EMBL:ABM00839.1}; EC=2.6.1.19 {ECO:0000313|EMBL:ABM00839.1};
- Comment: Sama_2636 (A1S8Y2) was added because it is a transaminase involved in putrescine utilization
- Total: 2 HMMs and 28 characterized proteins
gabD: succinate semialdehyde dehydrogenase
- Curated proteins or TIGRFams with EC 1.2.1.79
- Curated proteins or TIGRFams with EC 1.2.1.24
- Curated proteins or TIGRFams with EC 1.2.1.16
- Ignore hits to Q8BUF0 when looking for 'other' hits (succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24))
- Ignore hits to items matching 1.2.1.20 when looking for 'other' hits
- Ignore hits to items matching 1.2.1.3 when looking for 'other' hits
- Ignore hits to Q9I6M5 when looking for 'other' hits (Glutarate-semialdehyde dehydrogenase; EC 1.2.1.-. glutarate semialdehyde dehydrogenase)
- Comment: 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.
- Total: 37 characterized proteins
patA: putrescine aminotransferase (PatA/SpuC)
- Curated proteins or TIGRFams with EC 2.6.1.82
- Curated sequence MONOMER-17: putrescine-pyruvate transaminase (EC 2.6.1.113). Putrescine--pyruvate aminotransferase; PATase; Putrescine--pyruvate transaminase; EC 2.6.1.113. putrescine aminotransferase (EC 2.6.1.113)
- Curated proteins or TIGRFams with EC 2.6.1.113
- Ignore hits to items matching 2.6.1.19 when looking for 'other' hits
- Comment: 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.
- Total: 1 HMMs and 2 characterized proteins
patD: gamma-aminobutyraldehyde dehydrogenase
puuA: glutamate-putrescine ligase
puuB: gamma-glutamylputrescine oxidase
puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
- Curated proteins or TIGRFams with EC 1.2.1.99
- Curated sequence MONOMER-11560: 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)
- Curated sequence PfGW456L13_805: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54)
- Curated sequence Pf6N2E2_4383: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54)
- Curated sequence AO356_12580: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54)
- Curated sequence GFF5420: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54)
- Comment: 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.
- Total: 6 characterized proteins
puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase
puo: putrescine oxidase
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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, or view the source code.
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