GapMind for Amino acid biosynthesis


L-arginine biosynthesis in Thermus aquaticus YT-1

Best path

lysW, argX, lysZ, lysY, lysJ, lysK, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
lysW 2-aminoadipate/glutamate carrier protein BVI061214_RS04195 BVI061214_RS04190  
argX glutamate--LysW ligase BVI061214_RS04200  
lysZ [LysW]-glutamate kinase BVI061214_RS04210 BVI061214_RS02685  
lysY [LysW]-glutamate-6-phosphate reductase BVI061214_RS04205 BVI061214_RS08065  
lysJ [LysW]-glutamate-semialdehyde aminotransferase BVI061214_RS04805 BVI061214_RS10655  
lysK [LysW]-ornithine hydrolase BVI061214_RS03250 BVI061214_RS04800  
carA? carbamoyl phosphate synthase subunit alpha spurious
carB carbamoyl phosphate synthase subunit beta BVI061214_RS08710  
argI ornithine carbamoyltransferase BVI061214_RS08055 BVI061214_RS07270  
argG arginosuccinate synthetase BVI061214_RS04520  
argH argininosuccinate lyase BVI061214_RS04525 BVI061214_RS10615  
Alternative steps:
argA N-acylglutamate synthase BVI061214_RS08070 BVI061214_RS04530  
argB N-acylglutamate kinase BVI061214_RS02685 BVI061214_RS04210  
argC N-acylglutamylphosphate reductase BVI061214_RS08065 BVI061214_RS04205  
argD N-acetylornithine aminotransferase BVI061214_RS10655 BVI061214_RS04805  
argD'B N-succinylornithine aminotransferase BVI061214_RS04805 BVI061214_RS10655  
argE N-acetylornithine deacetylase  
argE'B N-succinylcitrulline desuccinylase  
argF' acetylornithine transcarbamoylase BVI061214_RS08055  
argF'B N-succinylornithine carbamoyltransferase  
argJ ornithine acetyltransferase BVI061214_RS08070  

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