GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Chlorobium limicola DSM 245

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argJ ornithine acetyltransferase CLIM_RS06235
argB N-acylglutamate kinase CLIM_RS06240
argC N-acylglutamylphosphate reductase CLIM_RS06230
argD N-acetylornithine aminotransferase CLIM_RS09840 CLIM_RS12010
carA carbamoyl phosphate synthase subunit alpha CLIM_RS11545
carB* carbamoyl phosphate synthase subunit beta CLIM_RS02385 with CLIM_RS09890
argI ornithine carbamoyltransferase CLIM_RS06245 CLIM_RS09010
argG arginosuccinate synthetase CLIM_RS06255
argH argininosuccinate lyase CLIM_RS06260
Alternative steps:
argA N-acylglutamate synthase CLIM_RS06235 CLIM_RS11470
argD'B N-succinylornithine aminotransferase CLIM_RS12160 CLIM_RS12010
argE N-acetylornithine deacetylase CLIM_RS06275
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase CLIM_RS06245
argF'B N-succinylornithine carbamoyltransferase
argX glutamate--LysW ligase
lysJ [LysW]-glutamate-semialdehyde aminotransferase CLIM_RS12010 CLIM_RS09840
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase CLIM_RS06230
lysZ [LysW]-glutamate kinase

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