GapMind for Amino acid biosynthesis

 

L-proline biosynthesis in Bacteroides thetaiotaomicron VPI-5482

Best path

proB, proA, proC

Also see fitness data for the top candidates

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 also is reported in the archaeon Thermococcus kodakarensis (PMC5846162).

17 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proB glutamate 5-kinase BT3719 BT3718
proA gamma-glutamylphosphate reductase BT3718
proC pyrroline-5-carboxylate reductase BT3757
Alternative steps:
argA N-acylglutamate synthase BT3761
argB N-acylglutamate kinase BT3395
argC N-acylglutamylphosphate reductase BT3759
argD N-acetylornithine aminotransferase BT3758 BT1442
argE N-acetylornithine deacetylase
argJ ornithine acetyltransferase
argX glutamate--LysW ligase
cyclodeaminase ornithine cyclodeaminase
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase BT3758 BT1442
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase BT3759
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase BT3395
OAT L-ornithine 5-aminotransferase BT1442 BT3758

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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