GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Dyella japonica UNC79MFTsu3.2

Best path

argA, argB, argC, argD, carA, carB, argF', argE, 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 N515DRAFT_3768 N515DRAFT_3784
argB N-acylglutamate kinase N515DRAFT_3768
argC N-acylglutamylphosphate reductase N515DRAFT_3769
argD N-acetylornithine aminotransferase N515DRAFT_3308 N515DRAFT_3307
carA carbamoyl phosphate synthase subunit alpha N515DRAFT_2714
carB carbamoyl phosphate synthase subunit beta N515DRAFT_2713
argF' acetylornithine transcarbamoylase N515DRAFT_3763
argE N-acetylornithine deacetylase N515DRAFT_3767
argG arginosuccinate synthetase N515DRAFT_3766
argH arginosuccinate lyase N515DRAFT_3770
Alternative steps:
argD'B N-succinylornithine aminotransferase N515DRAFT_3308 N515DRAFT_1751
argE'B N-succinylcitrulline desuccinylase
argF'B N-succinylornithine carbamoyltransferase N515DRAFT_3763
argI ornithine carbamoyltransferase N515DRAFT_3763 N515DRAFT_1776
argJ ornithine acetyltransferase
argX glutamate--LysW ligase
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase N515DRAFT_3308 N515DRAFT_1751
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase N515DRAFT_3769
lysZ [LysW]-2-aminoadipate 6-kinase / [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 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, 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