GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis in Beijerinckia indica subsp. indica ATCC 9039

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
argA N-acylglutamate synthase BIND_RS18605 BIND_RS16900  
argB N-acylglutamate kinase BIND_RS16900  
argC N-acylglutamylphosphate reductase BIND_RS07005  
argD N-acetylornithine aminotransferase BIND_RS00765 BIND_RS14190  
argE N-acetylornithine deacetylase BIND_RS05275  
carA carbamoyl phosphate synthase subunit alpha BIND_RS17955  
carB carbamoyl phosphate synthase subunit beta BIND_RS04420  
argI ornithine carbamoyltransferase BIND_RS00770 BIND_RS17345  
argG arginosuccinate synthetase BIND_RS06460  
argH? argininosuccinate lyase spurious
Alternative steps:
argD'B N-succinylornithine aminotransferase BIND_RS00765 BIND_RS14190  
argE'B N-succinylcitrulline desuccinylase  
argF' acetylornithine transcarbamoylase BIND_RS00770  
argF'B N-succinylornithine carbamoyltransferase  
argJ ornithine acetyltransferase BIND_RS18605  
argX glutamate--LysW ligase  
lysJ [LysW]-glutamate-semialdehyde aminotransferase BIND_RS00765 BIND_RS16295  
lysK [LysW]-ornithine hydrolase  
lysW 2-aminoadipate/glutamate carrier protein  
lysY [LysW]-glutamate-6-phosphate reductase  
lysZ [LysW]-glutamate kinase BIND_RS16900  

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.

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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