GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Pedobacter sp. GW460-11-11-14-LB5

Best path

argA, argB, argC, argD'B, argF'B, argE'B, 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
argA N-acylglutamate synthase CA265_RS18550 CA265_RS00200
argB N-acylglutamate kinase CA265_RS18510
argC N-acylglutamylphosphate reductase CA265_RS18540
argD'B N-succinylornithine aminotransferase CA265_RS18530 CA265_RS15205
argF'B N-succinylornithine carbamoyltransferase CA265_RS18520
argE'B N-succinylcitrulline desuccinylase CA265_RS18500 CA265_RS00205
argG arginosuccinate synthetase CA265_RS18545
argH arginosuccinate lyase CA265_RS18485
Alternative steps:
argD N-acetylornithine aminotransferase CA265_RS15205 CA265_RS18530
argE N-acetylornithine deacetylase
argF' acetylornithine transcarbamoylase CA265_RS18520
argI ornithine carbamoyltransferase CA265_RS14660 CA265_RS18520
argJ ornithine acetyltransferase
argX glutamate--LysW ligase
carA carbamoyl phosphate synthase subunit alpha CA265_RS15240
carB carbamoyl phosphate synthase subunit beta CA265_RS20080
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase CA265_RS18530 CA265_RS15205
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase CA265_RS18540
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase CA265_RS18510

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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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