Definition of L-proline biosynthesis
As rules and steps, or see full text
Rules
Overview: Proline biosynthesis in GapMind is based on MetaCyc pathways L-proline biosynthesis I from L-glutamate (link) and III via L-ornithine aminotransferase (link). GapMind also describes proline synthesis via ornithine cyclodeaminase (PMID:11489875). Pathway II from arginine (link) should perhaps be included, but is not; it is reported in nitrogen-fixing cyanobacteria and the bacteria it was reported in also have pathway I. Pathway IV is not included because it is not reported in prokaryotes (link). Also, pathway III is described in MetaCyc as occuring only in plants, but it also is reported in the archaeon Thermococcus kodakarensis (PMC5846162).
- all:
- proB, proA and proC
- or ornithine, OAT and proC
- or ornithine and cyclodeaminase
- Comment: Pathway I is proBAC. Pathway II involves ornithine aminotransferase (OAT). Some methanogens synthesize proline via ornithine cyclodeaminase (PMID:11489875). Unfortunately, the cyclodeaminase has only been linked to sequence in bacteria.
- ornithine:
- argA, argB, argC, argD and argE
- or argJ, argB, argC and argD
- or lysW, argX, lysZ, lysY, lysJ and lysK
- Comment: In L-arginine biosynthesis I, ornithine forms via acetylated intermediates, argA, and argE (link). In L-arginine biosynthesis II, ornithine forms via acetylated intermediates and argJ (link). In L-arginine biosynthesis IV, ornithine forms via LysW-modified intermediates (link).
Steps
lysW: 2-aminoadipate/glutamate carrier protein
- Curated proteins matching alpha-aminoadipate%carrier
- UniProt sequence Q5JFV9: SubName: Full=Probable lysine biosynthesis protein {ECO:0000313|EMBL:BAD84468.1};
- Comment: LysW is a carrier protein for intermediates in lysine or ornithine biosynthesis. TK0279 (Q5JFV9) from Thermococcus kodakarensis was characterized, see PMC5076833.
- Total: 5 characterized proteins
lysZ: [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase
lysY: [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase
lysJ: [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase
lysK: [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
argA: N-acylglutamate synthase
- Curated proteins or TIGRFams with EC 2.3.1.1
- UniProt sequence Q8A1A5_BACTN: SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:AAO78866.1};
- UniProt sequence L0G3H4_ECHVK: SubName: Full=Acetyltransferase, N-acetylglutamate synthase {ECO:0000313|EMBL:AGA80057.1};
- UniProt sequence H1XRZ0_9BACT: SubName: Full=Acetyltransferase (GNAT) family protein {ECO:0000313|EMBL:EHO42483.1}; SubName: Full=L-amino acid N-acyltransferase YncA {ECO:0000313|EMBL:APF18481.1};
- Curated sequence A0A0H2X8L7: acetylglutamate kinase (EC 2.7.2.8)
- UniProt sequence A0A1I2DIM7: RecName: Full=Acetylglutamate kinase {ECO:0000256|ARBA:ARBA00021197, ECO:0000256|PIRNR:PIRNR036441}; EC=2.7.2.8 {ECO:0000256|ARBA:ARBA00013065, ECO:0000256|PIRNR:PIRNR036441};
- Comment: Bacteroidetes have a divergent N-acylglutamate synthase, see BT3761 (Q8A1A5_BACTN) or Echvi_3845 (L0G3H4_ECHVK). Also see the related protein Cabys_1732 (H1XRZ0_9BACT) which is reported to form N-acetylglutamate (PMID:28265262). Bacteroides use succinylated intermediates (PMID:16704984), so their proteins are probably N-succinylglutamate synthases. A0A0H2X8L7 is annotated as argB in BRENDA, but it is also argA (a fusion protein). N515DRAFT_3768 (A0A1I2DIM7) is similar to ArgAB fusion proteins and mutants are rescued by arginine.
- Total: 1 HMMs and 31 characterized proteins
argB: N-acylglutamate kinase
- Curated proteins or TIGRFams with EC 2.7.2.8
- Ignore hits to O67848 when looking for 'other' hits (UDP-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108))
- Comment: ArgB includes Bacteroides proteins that act on N-succinylglutamate instead of the usual N-acetylglutamate (i.e. BT3395). See "Discovery of novel pathways of microbial arginine biosynthesis" (2010), PhD thesis of Juan Manuel Cabrera Luque, which shows that argB from B. fragilis is N-succinylglutamate kinase. In the version of BRENDA we are using, lpxC from Aquifex aeolicus is erroneously given as O67848 (which is probably argB), not O67648. (This has since been corrected in BRENDA.)
- Total: 1 HMMs and 14 characterized proteins
argC: N-acylglutamylphosphate reductase
- Curated proteins or TIGRFams with EC 1.2.1.38
- Comment: ArgC includes Bacteroides proteins that probably act on N-succinylglutamylphosphate instead of N-acetylglutamylphosphate (i.e. BT3759)
- Total: 2 HMMs and 8 characterized proteins
argD: N-acetylornithine aminotransferase
- Curated proteins or TIGRFams with EC 2.6.1.11
- Ignore hits to items matching EC 2.6.1.81 when looking for 'other' hits
- Comment: This aminotransferase for converting N-acetylglutamate semialdehyde to acetylornithine is often similar to succinylornithine transaminases (EC 2.6.1.81)
- Total: 12 characterized proteins
argE: N-acetylornithine deacetylase
- Curated proteins or TIGRFams with EC 3.5.1.16
- UniProt sequence A0A1I2DJB5_9GAMM: RecName: Full=N-acetyl-L-citrulline deacetylase {ECO:0000256|HAMAP-Rule:MF_02236}; Short=ACDase {ECO:0000256|HAMAP-Rule:MF_02236}; Short=Acetylcitrulline deacetylase {ECO:0000256|HAMAP-Rule:MF_02236}; EC=3.5.1.- {ECO:0000256|HAMAP-Rule:MF_02236};
- Comment: This EC number also includes N-acetylcitrulline deacetylase, which is part of pathway III. N515DRAFT_3767 (A0A1I2DJB5_9GAMM) is a putative argE and is quite diverged (the closest characterized protein is 25% identity to E. coli argE). Mutants are auxotrophic and rescued by arginine.
- Total: 1 HMMs and 5 characterized proteins
argJ: ornithine acetyltransferase
- Curated proteins or TIGRFams with EC 2.3.1.35
- Ignore hits to CH_122594 when looking for 'other' hits (glutamate N-acetyltransferase (Eurofung))
- Comment: In pathway II (acetyl cycle), instead of an acetylornithine deacetylase, the acetyltransferase argJ converts N-acetylornithine to ornithine. ArgJ may also form N-acetylglutamate (replacing argA). CH_122594 lacks an EC number (not fully characterized) and is likely to be ArgJ (50% identity to O94346)
- Total: 13 characterized proteins
argX: glutamate--LysW ligase
proB: glutamate 5-kinase
proA: gamma-glutamylphosphate reductase
proC: pyrroline-5-carboxylate reductase
OAT: L-ornithine 5-aminotransferase
- Curated proteins or TIGRFams with EC 2.6.1.13
- Curated sequence CH_124176: ornithine aminotransferase
- Comment: Converts ornithine to glutamate semialdehyde. CH_124176 is annotated as ornithine transaminase but without the EC number; it probably has the same activity.
- Total: 1 HMMs and 17 characterized proteins
cyclodeaminase: ornithine cyclodeaminase
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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, or see changes to Amino acid biosynthesis since the publication.
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