GapMind for Amino acid biosynthesis


L-arginine biosynthesis in Pseudomonas benzenivorans DSM 8628

Best path

argA, argB, argC, argD, argE, carA, carB, argI, argG, argH


Overview: Arginine biosynthesis in GapMind is based on MetaCyc pathways L-arginine biosynthesis I via L-acetyl-ornithine (link), II (acetyl cycle) (link), III via N-acetyl-L-citrulline (link), or IV via LysW-ornithine (link). 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.

21 steps (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argA N-acylglutamate synthase BLS63_RS11100 BLS63_RS20395
argB N-acylglutamate kinase BLS63_RS18950 BLS63_RS11100
argC N-acylglutamylphosphate reductase BLS63_RS25835
argD N-acetylornithine aminotransferase BLS63_RS19255 BLS63_RS01095
argE N-acetylornithine deacetylase BLS63_RS08535 BLS63_RS11105
carA carbamoyl phosphate synthase subunit alpha BLS63_RS14385
carB carbamoyl phosphate synthase subunit beta BLS63_RS14390
argI ornithine carbamoyltransferase BLS63_RS10650 BLS63_RS23235
argG arginosuccinate synthetase BLS63_RS23185
argH argininosuccinate lyase BLS63_RS11400
Alternative steps:
argD'B N-succinylornithine aminotransferase BLS63_RS19255 BLS63_RS01095
argE'B N-succinylcitrulline desuccinylase BLS63_RS08535
argF' acetylornithine transcarbamoylase BLS63_RS23235
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase BLS63_RS20395
argX glutamate--LysW ligase BLS63_RS11035
lysJ [LysW]-glutamate-semialdehyde aminotransferase BLS63_RS19255 BLS63_RS01095
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase BLS63_RS25835
lysZ [LysW]-glutamate kinase BLS63_RS18950

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.



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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:

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