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). # Bacteroides use succinylated intermediates (PMID:16704984), so their proteins are probably # N-succinylglutamate synthases. # (These enzymes are also known as argA2, see PMC9026213.) # uniprot:Q8P8J6 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. # It is not clear if mnaT (ecocyc:G6759-MONOMER) would acetylate arginine, so it is ignored. # Some EC 2.3.1.35 enzymes are probably dedicated for converting N-acetylornithine back to ornithine, # while others are bifunctional for N-acetylglutamate formation as well (argJ); # so similarity to this EC number is inconclusive. # For some CharProtDB entries it is unclear if they have this activity or not, while others are # labeled with this function but without the EC number. # uniprot:Q9I3W7 is annotated as this in BRENDA but we did not find experimental evidence of its activity # on glutamate, so it is ignored. # In Steroidobacter denitrificans, argA is missing but the arginine synthesis cluster includes a # potential N-acetyltransferase ACG33_RS14135 (uniprot:A0A127FCT3). Homologs of this protein are # conserved in the cluster, and it is never found together with argA; it is distantly related to # D-glutamate acetyltransferase dgcN (formerly DUF1611, see PMC10030869). argA N-acylglutamate synthase EC:2.3.1.1 term:N-succinylglutamate synthase uniprot:Q8A1A5_BACTN uniprot:L0G3H4_ECHVK curated:BRENDA::A0A0H2X8L7 curated:BRENDA::Q8P8J6 ignore:ecocyc::G6759-MONOMER ignore_other:EC 2.3.1.35 ignore:CharProtDB::CH_123299 curated:CharProtDB::CH_122594 ignore:BRENDA::Q9I3W7 ignore:BRENDA::Q8P8J6 predicted:A0A127FCT3 # 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. # uniprot:O67848 in BRENDA seems likely to be argB but is misannotated as a deacetylase; # also, uniprot:Q87EL2 is likely to be argB as well as argA. # CH_123299 has a broader annotation but probably has this activity. # argB N-acylglutamate kinase EC:2.7.2.8 term:N-succinylglutamate kinase ignore:BRENDA::O67848 ignore:BRENDA::Q87EL2 curated:CharProtDB::CH_123299 # ArgC includes Bacteroides proteins that probably act # on N-succinylglutamylphosphate instead of N-acetylglutamylphosphate (i.e. BT3759). # CH_123299 has a broader annotation but probably has this activity. # HP15_352 (uniprot:E4PLW0) from Marinobacter adhaerens HP15 is important for fitness in most # minimal media, unless arginine is provided. argC N-acylglutamylphosphate reductase EC:1.2.1.38 term:N-succinylglutamylphosphate reductase curated:CharProtDB::CH_123299 uniprot:E4PLW0 # This aminotransferase for converting N-acetylglutamate semialdehyde to acetylornithine is # often similar to succinylornithine transaminases (EC:2.6.1.81), # 4-aminobutyrate aminotransferases (EC:2.6.1.19), or # 5-aminovalerate transaminases (EC:2.6.1.48). (Succinylornithine and 4-aminobutyrate transaminases # are also reported to be active on N-acetylornithine and this seems likely for 5-aminovalerate # transaminases as well.) # metacyc:MONOMER-18314 is given this EC nmber but is actually LysW-lysine/ornithine aminotransferase (LysJ). # PMID:A0A806JQF3 show that Rv1655 (uniprot:A0A806JQF3) from Mycobacterium tuberculosis is argD. argD N-acetylornithine aminotransferase EC:2.6.1.11 ignore_other:EC 2.6.1.81 ignore_other:EC 2.6.1.19 ignore:metacyc::MONOMER-18314 ignore_other:EC 2.6.1.48 uniprot:A0A806JQF3 # This EC number also includes N-acetylcitrulline deacetylase, which is part of pathway III. # A putative amidohydrolase "ArgA3" (W3Y6L2) is in a conserved # operon with ornithine carbamoyltransferase (the next step) in Veillonella and # related genera (PMC9026213). The genome context includes other # arginine synthesis genes as well. Although ArgA3 was proposed to be a N-acetylglutamate # synthase, it is related to N-acetyl-cysteine deacetylase, and the genomes with "ArgA3" # are lacking argE as well; so we think argE is the more likely function. argE N-acetylornithine deacetylase EC:3.5.1.16 term:N-acetylcitrulline deacetylase predicted:W3Y6L2 # 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 synthetase%large 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.) # Some putrescine carbamoyltransferases (EC 2.1.3.6) are also active on ornithine (uniprot:Q837U7) so # any similarity to those is ignored. argI ornithine carbamoyltransferase EC:2.1.3.3 ignore_other:EC 2.1.3.6 # 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 # Some ArgH proteins also funciton as Delta crystallin I, so ignore any similarity to those (even # proteins not so annotated may be bifuncational). argH argininosuccinate lyase EC:4.3.2.1 term:argininosuccinate lyase term:arginosuccinate lyase ignore_other:Delta crystallin ### 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 term:N-succinylcitrulline desuccinylase # 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 to N-succinylcitrulline and then deacetylated. # (This deacetylation reaction has the same EC number as acetylornithine deacetylase, # so both are included in argE.) argF' acetylornithine transcarbamoylase EC:2.1.3.9 # LysW is amino group carrier protein import lys.steps:lysW # 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 many of the enzymes are bifunctional. But the initial ligation of LysW to arginine # has a dedicated enzyme in many archaea. # uniprot:Q970U6 is given a generic EC number in SwissProt, but has this function. # EC:6.4.2.43 (LysW-2-aminoadipate ligases) are ignored because some are bifunctional (PMC5076833). argX glutamate--LysW ligase EC:6.3.2.60 curated:SwissProt::Q970U6 ignore_other:6.3.2.43 # TK0276 from Thermococcus kodakarensis (uniprot:Q5JFW2) is bifunctional, for lysine and ornithine synthesis (PMC5076833). # In Haloferax volcanii, the putative [LysW]-glutamate kinase (HVO_RS04915, uniprot:D4GYN9) is in a # conserved operon with LysW and with other arginine synthesis genes; this protein is more similar to # a characterized [LysW]-2-aminoadipate 6-kinase, but haloarchaea do not use the aminoadipate pathway # (PMC93780, PMC8305020). lysZ [LysW]-glutamate kinase EC:2.7.2.19 uniprot:Q5JFW2 predicted:D4GYN9 # TK0277 from Thermococcus kodakarensis (uniprot:Q5JFW1) is bifunctional, for lysine and ornithine synthesis (PMC5076833). lysY [LysW]-glutamate-6-phosphate reductase EC:1.2.1.106 uniprot:Q5JFW1 # TK0275 from Thermococcus kodakarensis (uniprot:Q5JFW3) is bifunctional, for lysine and ornithine synthesis (PMC5076833). # Similarity to EC:2.6.1.118 ([LysW]-aminoadipate semialdehyde aminotransferase) is ignored because some are bifunctional (PMC5076833). lysJ [LysW]-glutamate-semialdehyde aminotransferase EC:2.6.1.124 ignore_other:2.6.1.118 # TK0274 from Thermococcus kodakarensis (uniprot:Q5JFW4) is bifunctional, for lysine and ornithine synthesis (PMC5076833). # NMAR_RS06940 (uniprot:A9A1L3) is probably bifunctional for [LysW]-ornithine and [LysW]-lysined hydrolase; # this would explain how ornithine is formed in Nitrosopumilus maritimus, and # it is similar to [LysW]-lysine hydrolyze uniprot:Q8VUS5, # which is reported to hydrolyze acetyllysine or acetylornithine in vitro. lysK [LysW]-ornithine hydrolase EC:3.5.1.132 predicted:A9A1L3 # 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
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:
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:
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