GapMind for Amino acid biosynthesis

 

Definition of L-proline biosynthesis

As text, or see rules and steps

# Proline biosynthesis in GapMind is based on MetaCyc pathways
# L-proline biosynthesis I from L-glutamate (metacyc:PROSYN-PWY)
# and III via L-ornithine aminotransferase (metacyc:PWY-3341).
# GapMind also describes proline synthesis via ornithine cyclodeaminase (PMID:11489875).
# Pathway II from arginine (metacyc:PWY-4981) 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 (metacyc:PWY-4281).
# Also, pathway III is described in MetaCyc as occuring only in plants, but it also is reported
# in the archaeon Thermococcus kodakarensis (PMC5846162).

import lys.steps:lysW lysZ lysY lysJ lysK # shared with ornithine biosynthesis
import arg.steps:ornithine

proB	glutamate 5-kinase	EC:2.7.2.11

# glutamyl-5-phosphate to glutamate 5-semialdehyde, which spontaneously dehydrates to 1-pyrroline-5-carboxylate
proA	gamma-glutamylphosphate reductase	EC:1.2.1.41

# pyrroline-5-carboxylate to proline
proC	pyrroline-5-carboxylate reductase	EC:1.5.1.2

# Pathway I is proBAC.
all: proB proA proC

# Converts ornithine to glutamate semialdehyde.
# CH_124176 is annotated as ornithine transaminase but without the EC number; it probably
# has the same activity.
OAT	L-ornithine 5-aminotransferase	EC:2.6.1.13	curated:CharProtDB::CH_124176

# Pathway II involves ornithine aminotransferase (OAT).
all: ornithine OAT proC

cyclodeaminase	ornithine cyclodeaminase	EC:4.3.1.12

# Some methanogens synthesize proline via ornithine cyclodeaminase (PMID:11489875).
# Unfortunately, the cyclodeaminase has only been linked to sequence in bacteria.
all: ornithine cyclodeaminase

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 (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