GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Pseudomonas fluorescens FW300-N2C3

Best path

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

Also see fitness data for the top candidates

Rules

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 AO356_13085 AO356_17930
argB N-acylglutamate kinase AO356_12525 AO356_13085
argC N-acylglutamylphosphate reductase AO356_14490 AO356_24070
argD N-acetylornithine aminotransferase AO356_18725 AO356_17010
argE N-acetylornithine deacetylase AO356_25400 AO356_13080
carA carbamoyl phosphate synthase subunit alpha AO356_07485 AO356_14430
carB carbamoyl phosphate synthase subunit beta AO356_07480
argI ornithine carbamoyltransferase AO356_05275 AO356_18275
argG arginosuccinate synthetase AO356_18325
argH arginosuccinate lyase AO356_12780 AO356_29670
Alternative steps:
argD'B N-succinylornithine aminotransferase AO356_18725 AO356_17010
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase AO356_18275
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase AO356_12410 AO356_17930
argX glutamate--LysW ligase AO356_10160
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase AO356_18725 AO356_17010
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase AO356_14490
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase AO356_12525

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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