GapMind for Amino acid biosynthesis

 

Definition of L-arginine biosynthesis

As text, or see rules and steps

# Arginine biosynthesis in GapMind is based on MetaCyc pathways
# L-arginine biosynthesis I via L-acetyl-ornithine (metacyc:ARGSYN-PWY),
# II (acetyl cycle) (metacyc:ARGSYNBSUB-PWY),
# III via N-acetyl-L-citrulline (metacyc:PWY-5154),
# or IV via LysW-ornithine (metacyc:PWY-7400).
# GapMind also includes L-arginine biosynthesis with succinylated intermediates, as in Bacteroidetes (PMC5764234).
# These pathways all involve the activation of glutamate (by aceylation, succinylation, or attachment of LysW),
# followed by phosphorylation, reduction and transamination, to activated ornithine.
# In most pathways, this intermediate is cleaved to ornithine before transcarbamoylation,
# but in the N-acetylcitrulline or succinylated pathways, transcarbamoylation occurs before hydrolysis.
# In the final two steps, citrulline is converted to arginine by ArgG and ArgH.

# Bacteroidetes have a divergent N-acylglutamate synthase, see BT3761 (uniprot:Q8A1A5_BACTN)
# or Echvi_3845 (uniprot:L0G3H4_ECHVK).
# Also see the related protein Cabys_1732 (uniprot: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.
# uniprot:A0A0H2X8L7 is annotated as argB in BRENDA, but it is also argA (a fusion protein).
# N515DRAFT_3768 (uniprot:A0A1I2DIM7) is similar to ArgAB fusion proteins and mutants are rescued by arginine.
argA	N-acylglutamate synthase	EC:2.3.1.1	uniprot:Q8A1A5_BACTN	uniprot:L0G3H4_ECHVK	uniprot:H1XRZ0_9BACT	curated:BRENDA::A0A0H2X8L7	uniprot:A0A1I2DIM7

# 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 uniprot:O67848 (which is probably argB), not uniprot:O67648.
# (This has since been corrected in BRENDA.)
argB	N-acylglutamate kinase	EC:2.7.2.8	ignore:BRENDA::O67848

# ArgC includes Bacteroides proteins that probably act
# on N-succinylglutamylphosphate instead of N-acetylglutamylphosphate (i.e. BT3759)
argC	N-acylglutamylphosphate reductase	EC:1.2.1.38

# This aminotransferase for converting N-acetylglutamate semialdehyde to acetylornithine is
# often similar to succinylornithine transaminases (EC:2.6.1.81)
argD	N-acetylornithine aminotransferase	EC:2.6.1.11	ignore_other:EC 2.6.1.81

# This EC number also includes N-acetylcitrulline deacetylase, which is part of pathway III.
# N515DRAFT_3767 (uniprot: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.
argE	N-acetylornithine deacetylase	EC:3.5.1.16	uniprot:A0A1I2DJB5_9GAMM

# This could obtain the amino group from glutamine (EC:6.3.5.5) or from ammonia (EC:6.3.4.16)
carA	carbamoyl phosphate synthase subunit alpha	term:carbamoyl-phosphate synthase%small	ignore_other:EC 6.3.5.5	ignore_other:EC 6.3.4.16	hmm:TIGR01368
carB	carbamoyl phosphate synthase subunit beta	term:carbamoyl-phosphate synthase%large	ignore_other:EC 6.3.5.5	ignore_other:EC 6.3.4.16	hmm:TIGR01369

# ArgI converts ornithine to citrulline. (E. coli has two paralogs, argI and argF)
argI	ornithine carbamoyltransferase	EC:2.1.3.3

# ArgG converts citrulline + aspartate to arginosuccinate.
# N515DRAFT_3766 (uniprot:A0A1I2DIG3_9GAMM) and BT3768 (uniprot:Q8A1A6_BACTN) are diverged
# and mutants are auxotrophic & rescued by arginine
argG	arginosuccinate synthetase	EC:6.3.4.5	uniprot:A0A1I2DIG3_9GAMM	uniprot:Q8A1A6_BACTN

argH	arginosuccinate lyase	EC:4.3.2.1

### Bacteroidetes pathway with succinylated intermediates
# This pathway is inferrred from a N-succinylornithine
# carbamoyltransferase (argF'B; EC 2.1.3.11) -- see
# https://www.ncbi.nlm.nih.gov/pubmed/16704984
# As discussed above the N-acylglutamate synthase (ArgA) is diverged
# and apparently acts forms N-succinylglutamate instead.  The next
# steps (ArgB and ArgC) might not be specific for N-acetyl
# vs. N-succinyl substrates, or the Bacteroidetes genes may have
# adapted to prefer N-succinyl intermediates.  The conversion of
# N-succinylgutamate semialdehyde to N-succinylornithine is probably
# carried out by a diverged argD (argD'B below), which would produce
# the substrate for argF'B.  And a diverged desuccinylase (argE'B
# below) probably acts on N-succinylornithine, because these
# Bacteroidetes have ordinary argG/argH for the conversion of
# ornithine to arginine

# N-succinylglutamate semialdehyde => N-succinylornithine.
# Some Bacteroides hvae a diverged argD-like gene, i.e. BT3758 (uniprot:Q8A1A8) or Echvi_3848 (uniprot:L0G5F2_ECHVK),
# which are auxotrophic and cofit with other arg genes.
# Note that this is the same reaction as found in arginine degradation by the arginine succinyltransferase (AST) pathway
argD'B	N-succinylornithine aminotransferase	EC:2.6.1.81	uniprot:Q8A1A8	uniprot:L0G5F2_ECHVK	ignore_other:EC 2.6.1.11

# In, Bacteroides fragilis, argF'B converts N-succinylornithine to N-succinylcitrulline
# (PMID:16704984). Echvi_3849 (uniprot:L0G4Z0_ECHVK) also has this activity, as it is rescued by arginine
# and Echinicola vietnamensis has similar argD'/argE'
argF'B	N-succinylornithine carbamoyltransferase	EC:2.1.3.11	uniprot:L0G4Z0_ECHVK

# The N-succinylcitrulline desuccinylase is probably BT3549 (uniprot:Q8A1V9),
# Echvi_3851 (uniprot:L0G443_ECHVK), or CA265_RS18500 (uniprot:A0A1X9Z8E1_9SPHI)
# Mutants in these genes are rescued by added arginine and they are
# distantly related to succinyl-diaminopimelate desuccinylase.
# And these bacteria have ordinary argG/argH, so citrulline is expected to be an intermediate.
argE'B	N-succinylcitrulline desuccinylase	uniprot:Q8A1V9	uniprot:L0G443_ECHVK	uniprot:A0A1X9Z8E1_9SPHI

# 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 uniprot:O94346)
argJ	ornithine acetyltransferase	EC:2.3.1.35	ignore:CharProtDB::CH_122594

# MetaCyc pathway L-arginine biosynthesis III via N-acetyl-L-citrulline

# Instead of deacetylating N-acetyl-ornithine, it is carbamoylated and then deacetylated
# The deacetylation reaction has the same EC number as acetylornithine deacetylase so do not distinguish

argF'	acetylornithine transcarbamoylase	EC:2.1.3.9

# There is also an archaeal pathway from glutamate to ornithine with LysW as the carrier protein, instead
# of N-acyl intermediates. This pathway is analogous to the conversion of alpha-aminoadipate to
# lysine, and most of the enzymes are bifunctional. The initial ligation of LysW to arginine
# has a dedicated enzyme in many archaea, but in Thermococcus kodakarensis, the ligase is
# also bifunctional (see PMC5076833).

# TK0278 (uniprot:Q5JFW0) is also a glutamate--LysW ligase, see PMC5076833.
# EC:6.4.2.43 (LysW-2-aminoadipate ligases) are ignored because some are bifunctional.
argX	glutamate--LysW ligase	term:Glutamate--LysW ligase	uniprot:Q5JFW0	ignore_other:6.3.2.43

# lysZ is the kinase, lysY is the reductase, lysJ is the aminotransferase, and lysK is the hydrolase,
# forming LysW and ornithine
import lys.steps:lysW lysZ lysY lysJ lysK

# In L-arginine biosynthesis I, ornithine forms via acetylated intermediates, argA, and argE (metacyc:ARGSYN-PWY).
ornithine: argA argB argC argD argE

# In L-arginine biosynthesis II, ornithine forms via acetylated intermediates and argJ (metacyc:ARGSYNBSUB-PWY).
ornithine: argJ argB argC argD

# In L-arginine biosynthesis IV, ornithine forms via LysW-modified intermediates (metacyc:PWY-7400).
ornithine: lysW argX lysZ lysY lysJ lysK 

# In pathways I, II, or IV, ornithine is carbamoylated by argI.
all: ornithine carA carB argI argG argH

# In pathway III (N-acetylcitrulline), N-acetylornithine is carbamoylated by argF'
# and N-acetylcitrulline is hydrolyzed by argE.
all: argA argB argC argD carA carB argF' argE argG argH

# In the pathway with succinylated intermediates, N-succinylornithine is carbamoylated by argF'B.
all: argA argB argC argD'B argF'B argE'B argG argH

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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:

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:

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:

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 preprint 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