GapMind for Amino acid biosynthesis


L-arginine biosynthesis in Methylosarcina fibrata AML-C10

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argJ ornithine acetyltransferase A3OW_RS0106550
argB N-acylglutamate kinase A3OW_RS0105955 A3OW_RS0104920
argC N-acylglutamylphosphate reductase A3OW_RS0112385
argD N-acetylornithine aminotransferase A3OW_RS0104890 A3OW_RS0121340
carA carbamoyl phosphate synthase subunit alpha A3OW_RS0122880
carB carbamoyl phosphate synthase subunit beta A3OW_RS0122885
argI ornithine carbamoyltransferase A3OW_RS0104895 A3OW_RS0121810
argG arginosuccinate synthetase A3OW_RS0112860
argH argininosuccinate lyase A3OW_RS0115235 A3OW_RS23915
Alternative steps:
argA N-acylglutamate synthase A3OW_RS0104920 A3OW_RS0106550
argD'B N-succinylornithine aminotransferase A3OW_RS0104890 A3OW_RS0107650
argE N-acetylornithine deacetylase A3OW_RS0112425
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase
argF'B N-succinylornithine carbamoyltransferase
argX glutamate--LysW ligase A3OW_RS0117825
lysJ [LysW]-glutamate-semialdehyde aminotransferase A3OW_RS0104890 A3OW_RS0107650
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase A3OW_RS0112385
lysZ [LysW]-glutamate kinase A3OW_RS0105955

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