GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Methylocapsa aurea KYG

Best path

argA, argB, argC, argD, argE, 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
argA N-acylglutamate synthase DL86_RS16570 DL86_RS10190
argB N-acylglutamate kinase DL86_RS10190
argC N-acylglutamylphosphate reductase DL86_RS11730
argD N-acetylornithine aminotransferase DL86_RS01865 DL86_RS06885
argE N-acetylornithine deacetylase DL86_RS12470
carA carbamoyl phosphate synthase subunit alpha DL86_RS04410
carB carbamoyl phosphate synthase subunit beta DL86_RS06900
argI ornithine carbamoyltransferase DL86_RS01860 DL86_RS03635
argG arginosuccinate synthetase DL86_RS14290
argH argininosuccinate lyase DL86_RS17270 DL86_RS03230
Alternative steps:
argD'B N-succinylornithine aminotransferase DL86_RS01865 DL86_RS06885
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase DL86_RS01860
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase DL86_RS16570
argX glutamate--LysW ligase
lysJ [LysW]-glutamate-semialdehyde aminotransferase DL86_RS01865 DL86_RS06885
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase
lysZ [LysW]-glutamate kinase DL86_RS10190

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