GapMind for Amino acid biosynthesis


L-arginine biosynthesis in Dechloromonas agitata is5

Best path

argJ, argB, argC, argD, 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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
argJ ornithine acetyltransferase K420_RS0108410  
argB N-acylglutamate kinase K420_RS0107980 K420_RS0101575  
argC N-acylglutamylphosphate reductase K420_RS0112240  
argD N-acetylornithine aminotransferase K420_RS0110205 K420_RS21080  
carA carbamoyl phosphate synthase subunit alpha K420_RS0100175  
carB carbamoyl phosphate synthase subunit beta K420_RS0100170  
argI ornithine carbamoyltransferase K420_RS0110210  
argG? arginosuccinate synthetase spurious
argH argininosuccinate lyase K420_RS0107040  
Alternative steps:
argA N-acylglutamate synthase K420_RS0101575 K420_RS0108410  
argD'B N-succinylornithine aminotransferase K420_RS0110205 K420_RS21080  
argE N-acetylornithine deacetylase K420_RS0114025 K420_RS0103985  
argE'B N-succinylcitrulline desuccinylase  
argF' acetylornithine transcarbamoylase K420_RS0110210  
argF'B N-succinylornithine carbamoyltransferase K420_RS0110210  
argX glutamate--LysW ligase  
lysJ [LysW]-glutamate-semialdehyde aminotransferase K420_RS0110205 K420_RS21080  
lysK [LysW]-ornithine hydrolase  
lysW 2-aminoadipate/glutamate carrier protein  
lysY [LysW]-glutamate-6-phosphate reductase  
lysZ [LysW]-glutamate kinase K420_RS0107980  

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