GapMind for Amino acid biosynthesis


L-arginine biosynthesis in Halococcus hamelinensis 100A6

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lysW 2-aminoadipate/glutamate carrier protein C447_RS04735
argX glutamate--LysW ligase C447_RS04730
lysZ [LysW]-glutamate kinase C447_RS04720
lysY [LysW]-glutamate-6-phosphate reductase C447_RS04725
lysJ [LysW]-glutamate-semialdehyde aminotransferase C447_RS04715 C447_RS11500
lysK [LysW]-ornithine hydrolase C447_RS16710 C447_RS04710
carA carbamoyl phosphate synthase subunit alpha C447_RS13765
carB carbamoyl phosphate synthase subunit beta C447_RS13780
argI ornithine carbamoyltransferase C447_RS04705 C447_RS10065
argG arginosuccinate synthetase C447_RS04745
argH argininosuccinate lyase C447_RS04740
Alternative steps:
argA N-acylglutamate synthase
argB N-acylglutamate kinase C447_RS04720
argC N-acylglutamylphosphate reductase C447_RS04725
argD N-acetylornithine aminotransferase C447_RS04715 C447_RS12035
argD'B N-succinylornithine aminotransferase C447_RS12035 C447_RS04715
argE N-acetylornithine deacetylase
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase C447_RS04705
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase

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