GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Pseudomonas simiae WCS417

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argA N-acylglutamate synthase PS417_27195 PS417_22535
argB N-acylglutamate kinase PS417_27790 PS417_09570
argC N-acylglutamylphosphate reductase PS417_25660
argD N-acetylornithine aminotransferase PS417_21710 PS417_08025
argE N-acetylornithine deacetylase PS417_27200 PS417_18910
carA carbamoyl phosphate synthase subunit alpha PS417_24045 PS417_25720
carB carbamoyl phosphate synthase subunit beta PS417_24040
argI ornithine carbamoyltransferase PS417_22335 PS417_05595
argG arginosuccinate synthetase PS417_05640
argH arginosuccinate lyase PS417_27540 PS417_21780
Alternative steps:
argD'B N-succinylornithine aminotransferase PS417_21710 PS417_08025
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase PS417_22535
argX glutamate--LysW ligase PS417_01180
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase PS417_21710 PS417_08025
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase PS417_25660
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase PS417_27790

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 (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