GapMind for Amino acid biosynthesis


L-proline biosynthesis in Dinoroseobacter shibae DFL-12

Best path

argJ, argB, argC, argD, cyclodeaminase

Also see fitness data for the top candidates


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 Dshi_3565
argB N-acylglutamate kinase Dshi_0324
argC N-acylglutamylphosphate reductase Dshi_1759
argD N-acetylornithine aminotransferase Dshi_0798 Dshi_2042
cyclodeaminase ornithine cyclodeaminase Dshi_2310 Dshi_0890
Alternative steps:
argA N-acylglutamate synthase Dshi_3565 Dshi_0324
argE N-acetylornithine deacetylase Dshi_1161 Dshi_1288
argX glutamate--LysW ligase
lysJ [LysW]-glutamate-semialdehyde aminotransferase Dshi_3343 Dshi_0798
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase Dshi_1759
lysZ [LysW]-glutamate kinase Dshi_0324
OAT L-ornithine 5-aminotransferase Dshi_2042 Dshi_1366
proA gamma-glutamylphosphate reductase Dshi_1469
proB glutamate 5-kinase Dshi_1467 Dshi_1469
proC pyrroline-5-carboxylate reductase Dshi_2645

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