GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Desulfotalea psychrophila LSv54

Best path

argJ, argB, argC, argD, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argJ ornithine acetyltransferase DP_RS13920
argB N-acylglutamate kinase DP_RS02185
argC N-acylglutamylphosphate reductase DP_RS06715
argD N-acetylornithine aminotransferase DP_RS02180 DP_RS04140
carA carbamoyl phosphate synthase subunit alpha DP_RS15655
carB carbamoyl phosphate synthase subunit beta DP_RS15660
argI ornithine carbamoyltransferase DP_RS02175 DP_RS00525
argG arginosuccinate synthetase DP_RS02170
argH argininosuccinate lyase DP_RS02165
Alternative steps:
argA N-acylglutamate synthase DP_RS13920 DP_RS13970
argD'B N-succinylornithine aminotransferase DP_RS02180 DP_RS11840
argE N-acetylornithine deacetylase DP_RS02255
argE'B N-succinylcitrulline desuccinylase
argF' acetylornithine transcarbamoylase DP_RS02175
argF'B N-succinylornithine carbamoyltransferase
argX glutamate--LysW ligase DP_RS12145
lysJ [LysW]-glutamate-semialdehyde aminotransferase DP_RS04140 DP_RS02180
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase DP_RS06715
lysZ [LysW]-glutamate kinase DP_RS02185

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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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:

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