GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Methylohalobius crimeensis 10Ki

Best path

argA, argB, argC, argD, argE, carA, carB, argI, argG, argH

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 H035_RS0111105 H035_RS0100440
argB N-acylglutamate kinase H035_RS0106980 H035_RS0111105
argC N-acylglutamylphosphate reductase H035_RS0106115
argD N-acetylornithine aminotransferase H035_RS0111080 H035_RS0104615
argE N-acetylornithine deacetylase H035_RS0111100 H035_RS0104000
carA carbamoyl phosphate synthase subunit alpha H035_RS0115815 H035_RS0107575
carB carbamoyl phosphate synthase subunit beta H035_RS0115810
argI ornithine carbamoyltransferase H035_RS0111085 H035_RS0110945
argG arginosuccinate synthetase H035_RS0107490
argH argininosuccinate lyase H035_RS20310 H035_RS0114795
Alternative steps:
argD'B N-succinylornithine aminotransferase H035_RS0111080 H035_RS0106595
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase H035_RS0111085
argF'B N-succinylornithine carbamoyltransferase
argJ ornithine acetyltransferase H035_RS0100440
argX glutamate--LysW ligase
lysJ [LysW]-glutamate-semialdehyde aminotransferase H035_RS0106595 H035_RS0111080
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase H035_RS0106115
lysZ [LysW]-glutamate kinase H035_RS0106980

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