GapMind for Amino acid biosynthesis


L-proline biosynthesis in Sinorhizobium medicae WSM419

Best path

argA, argB, argC, argD, argE, cyclodeaminase


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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argA N-acylglutamate synthase SMED_RS12595 SMED_RS00365
argB N-acylglutamate kinase SMED_RS00365
argC N-acylglutamylphosphate reductase SMED_RS04275
argD N-acetylornithine aminotransferase SMED_RS00640 SMED_RS23385
argE N-acetylornithine deacetylase SMED_RS27795 SMED_RS00865
cyclodeaminase ornithine cyclodeaminase SMED_RS21845
Alternative steps:
argJ ornithine acetyltransferase SMED_RS12595
argX glutamate--LysW ligase
lysJ [LysW]-glutamate-semialdehyde aminotransferase SMED_RS00640 SMED_RS23385
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase
lysZ [LysW]-glutamate kinase SMED_RS00365
OAT L-ornithine 5-aminotransferase SMED_RS23385 SMED_RS00640
proA gamma-glutamylphosphate reductase SMED_RS15110
proB glutamate 5-kinase SMED_RS15105 SMED_RS15110
proC pyrroline-5-carboxylate reductase SMED_RS11225 SMED_RS27190

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