GapMind for Amino acid biosynthesis


L-arginine biosynthesis in Pseudomonas fluorescens FW300-N2E2

Best path

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

Also see fitness data for the top candidates


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
argA N-acylglutamate synthase Pf6N2E2_4497 Pf6N2E2_5516
argB N-acylglutamate kinase Pf6N2E2_4373 Pf6N2E2_4497
argC N-acylglutamylphosphate reductase Pf6N2E2_4836 Pf6N2E2_1484
argD N-acetylornithine aminotransferase Pf6N2E2_5665 Pf6N2E2_4013
argE N-acetylornithine deacetylase Pf6N2E2_1339 Pf6N2E2_4496
carA carbamoyl phosphate synthase subunit alpha Pf6N2E2_3365 Pf6N2E2_4824
carB carbamoyl phosphate synthase subunit beta Pf6N2E2_3364
argI ornithine carbamoyltransferase Pf6N2E2_2909 Pf6N2E2_5579
argG arginosuccinate synthetase Pf6N2E2_5590
argH argininosuccinate lyase Pf6N2E2_4429 Pf6N2E2_1798
Alternative steps:
argD'B N-succinylornithine aminotransferase Pf6N2E2_5665 Pf6N2E2_5326
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase Pf6N2E2_5579
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase Pf6N2E2_5516
argX glutamate--LysW ligase Pf6N2E2_3903
lysJ [LysW]-glutamate-semialdehyde aminotransferase Pf6N2E2_2395 Pf6N2E2_5665
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase Pf6N2E2_4836
lysZ [LysW]-glutamate kinase Pf6N2E2_4373

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