GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Nocardiopsis lucentensis DSM 44048

Best path

argJ, argB, argC?, argD, carA, carB, argI, argG, argH

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
argJ ornithine acetyltransferase D471_RS0114645  
argB N-acylglutamate kinase D471_RS0118260  
argC? N-acylglutamylphosphate reductase D471_RS0118275 spurious
argD N-acetylornithine aminotransferase D471_RS0118255 D471_RS0113530  
carA carbamoyl phosphate synthase subunit alpha D471_RS0118495  
carB carbamoyl phosphate synthase subunit beta D471_RS0118490  
argI ornithine carbamoyltransferase D471_RS0118250 D471_RS0118505  
argG arginosuccinate synthetase D471_RS0128425  
argH argininosuccinate lyase D471_RS0118240  
Alternative steps:
argA N-acylglutamate synthase D471_RS0114645 D471_RS0124725  
argD'B N-succinylornithine aminotransferase D471_RS0118255 D471_RS0111685  
argE N-acetylornithine deacetylase D471_RS0128150 D471_RS0125875  
argE'B N-succinylcitrulline desuccinylase  
argF' acetylornithine transcarbamoylase D471_RS0118250  
argF'B N-succinylornithine carbamoyltransferase  
argX glutamate--LysW ligase  
lysJ [LysW]-glutamate-semialdehyde aminotransferase D471_RS0118255 D471_RS0113530  
lysK [LysW]-ornithine hydrolase  
lysW 2-aminoadipate/glutamate carrier protein  
lysY [LysW]-glutamate-6-phosphate reductase D471_RS0118275  
lysZ [LysW]-glutamate kinase D471_RS0118260  

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