GapMind for Amino acid biosynthesis


L-proline biosynthesis in Nostoc punctiforme ATCC 29133; PCC 73102

Best path

argJ, argB, argC, argD, OAT, proC


Overview: Proline biosynthesis in GapMind is based on MetaCyc pathways L-proline biosynthesis I from L-glutamate (link) and III via L-ornithine aminotransferase (link). GapMind also describes proline synthesis via ornithine cyclodeaminase (PMID:11489875). Pathway II from arginine (link) should perhaps be included, but is not; it is reported in nitrogen-fixing cyanobacteria and the bacteria it was reported in also have pathway I. Pathway IV is not included because it is not reported in prokaryotes (link). Also, pathway III is described in MetaCyc as occuring only in plants, but it has been reported in the archaeon Thermococcus kodakarensis (PMC5846162).

17 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argJ ornithine acetyltransferase NPUN_RS11840
argB N-acylglutamate kinase NPUN_RS31950
argC N-acylglutamylphosphate reductase NPUN_RS07920 NPUN_RS17735
argD N-acetylornithine aminotransferase NPUN_RS25070 NPUN_RS09825
OAT L-ornithine 5-aminotransferase NPUN_RS09825 NPUN_RS17425
proC pyrroline-5-carboxylate reductase NPUN_RS08615 NPUN_RS11000
Alternative steps:
argA N-acylglutamate synthase NPUN_RS11840 NPUN_RS31950
argE N-acetylornithine deacetylase NPUN_RS04930 NPUN_RS11905
argX glutamate--LysW ligase
cyclodeaminase ornithine cyclodeaminase NPUN_RS12190
lysJ [LysW]-glutamate-semialdehyde aminotransferase NPUN_RS25070 NPUN_RS09825
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase NPUN_RS17735
lysZ [LysW]-glutamate kinase NPUN_RS31950
proA gamma-glutamylphosphate reductase NPUN_RS32875 NPUN_RS01445
proB glutamate 5-kinase NPUN_RS01680 NPUN_RS32875

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.



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