GapMind for Amino acid biosynthesis


L-arginine biosynthesis in Steroidobacter denitrificans DSM 18526

Best path

argA, argB, argC, argD, carA?, carB, argF', argE?, 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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap Known gap?
argA N-acylglutamate synthase ACG33_RS14135 ACG33_RS14155    
argB N-acylglutamate kinase ACG33_RS14155    
argC N-acylglutamylphosphate reductase ACG33_RS14140    
argD N-acetylornithine aminotransferase ACG33_RS14145 ACG33_RS02865    
carA? carbamoyl phosphate synthase subunit alpha spurious  
carB carbamoyl phosphate synthase subunit beta ACG33_RS06825    
argF' acetylornithine transcarbamoylase ACG33_RS14150    
argE? N-acetylornithine deacetylase   known gap
argG arginosuccinate synthetase ACG33_RS14130    
argH argininosuccinate lyase ACG33_RS14160    
Alternative steps:
argD'B N-succinylornithine aminotransferase ACG33_RS14145 ACG33_RS06630    
argE'B N-succinylcitrulline desuccinylase    
argF'B N-succinylornithine carbamoyltransferase ACG33_RS14150    
argI ornithine carbamoyltransferase ACG33_RS14150 ACG33_RS01435    
argJ ornithine acetyltransferase    
argX glutamate--LysW ligase    
lysJ [LysW]-glutamate-semialdehyde aminotransferase ACG33_RS14145 ACG33_RS06630    
lysK [LysW]-ornithine hydrolase    
lysW 2-aminoadipate/glutamate carrier protein    
lysY [LysW]-glutamate-6-phosphate reductase ACG33_RS14140    
lysZ [LysW]-glutamate kinase ACG33_RS14155    

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