GapMind for Amino acid biosynthesis

 

L-proline biosynthesis in Calditerrivibrio nitroreducens DSM 19672

Best path

proB, proA, proC

Rules

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
proB glutamate 5-kinase CALNI_RS11370 CALNI_RS11305
proA gamma-glutamylphosphate reductase CALNI_RS11305
proC pyrroline-5-carboxylate reductase CALNI_RS05955
Alternative steps:
argA N-acylglutamate synthase CALNI_RS07970 CALNI_RS04530
argB N-acylglutamate kinase CALNI_RS01290
argC N-acylglutamylphosphate reductase CALNI_RS07965
argD N-acetylornithine aminotransferase CALNI_RS03705 CALNI_RS07435
argE N-acetylornithine deacetylase CALNI_RS05530
argJ ornithine acetyltransferase CALNI_RS07970
argX glutamate--LysW ligase
cyclodeaminase ornithine cyclodeaminase
lysJ [LysW]-glutamate-semialdehyde aminotransferase CALNI_RS03705 CALNI_RS07435
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase CALNI_RS07965
lysZ [LysW]-glutamate kinase CALNI_RS01290
OAT L-ornithine 5-aminotransferase CALNI_RS07435 CALNI_RS03705

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.

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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