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:
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