GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Burkholderia phytofirmans PsJN

Best path

argA, argB, argC, argD, argE, 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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argA N-acylglutamate synthase BPHYT_RS12985 BPHYT_RS17185
argB N-acylglutamate kinase BPHYT_RS01610 BPHYT_RS10930
argC N-acylglutamylphosphate reductase BPHYT_RS18340
argD N-acetylornithine aminotransferase BPHYT_RS07695 BPHYT_RS15580
argE N-acetylornithine deacetylase BPHYT_RS11720 BPHYT_RS09285
carA carbamoyl phosphate synthase subunit alpha BPHYT_RS14195
carB carbamoyl phosphate synthase subunit beta BPHYT_RS14190
argI ornithine carbamoyltransferase BPHYT_RS27685 BPHYT_RS15915
argG arginosuccinate synthetase BPHYT_RS15920
argH arginosuccinate lyase BPHYT_RS05210 BPHYT_RS21425
Alternative steps:
argD'B N-succinylornithine aminotransferase BPHYT_RS15580 BPHYT_RS07695
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase BPHYT_RS15915
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase BPHYT_RS17185
argX glutamate--LysW ligase
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase BPHYT_RS07695 BPHYT_RS22435
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase BPHYT_RS01610

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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