GapMind for Amino acid biosynthesis


L-arginine biosynthesis in Pseudomonas fluorescens FW300-N2E3

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 AO353_08685 AO353_03670
argB N-acylglutamate kinase AO353_09240 AO353_08685
argC N-acylglutamylphosphate reductase AO353_07155
argD N-acetylornithine aminotransferase AO353_03025 AO353_11510
argE N-acetylornithine deacetylase AO353_29125 AO353_08690
carA carbamoyl phosphate synthase subunit alpha AO353_05635 AO353_07220
carB carbamoyl phosphate synthase subunit beta AO353_05630
argI ornithine carbamoyltransferase AO353_03475 AO353_04155
argG arginosuccinate synthetase AO353_04105
argH argininosuccinate lyase AO353_09000 AO353_25585
Alternative steps:
argD'B N-succinylornithine aminotransferase AO353_03025 AO353_10500
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase AO353_04155
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase AO353_03670
argX glutamate--LysW ligase AO353_11755
lysJ [LysW]-glutamate-semialdehyde aminotransferase AO353_10500 AO353_03025
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase AO353_07155
lysZ [LysW]-glutamate kinase AO353_09240

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