GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Dinoroseobacter shibae DFL-12

Best path

argJ, argB, argC, argD, 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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argJ ornithine acetyltransferase Dshi_3565
argB N-acylglutamate kinase Dshi_0324
argC N-acylglutamylphosphate reductase Dshi_1759
argD N-acetylornithine aminotransferase Dshi_0798 Dshi_2042
carA carbamoyl phosphate synthase subunit alpha Dshi_2387
carB carbamoyl phosphate synthase subunit beta Dshi_2639
argI ornithine carbamoyltransferase Dshi_0433 Dshi_0796
argG arginosuccinate synthetase Dshi_3472
argH argininosuccinate lyase Dshi_3062
Alternative steps:
argA N-acylglutamate synthase Dshi_3565 Dshi_0324
argD'B N-succinylornithine aminotransferase Dshi_0798 Dshi_1446
argE N-acetylornithine deacetylase Dshi_1161 Dshi_1288
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase Dshi_0796
argF'B N-succinylornithine carbamoyltransferase
argX glutamate--LysW ligase
lysJ [LysW]-glutamate-semialdehyde aminotransferase Dshi_3343 Dshi_0798
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase Dshi_1759
lysZ [LysW]-glutamate kinase Dshi_0324

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