Definition of L-glutamine biosynthesis

GapMind for Amino acid biosynthesis

Definition of L-glutamine biosynthesis

# Glutamine biosynthesis in GapMind is based on MetaCyc pathways
# L-glutamine biosynthesis I from glutamine (metacyc:GLNSYN-PWY)
# or glutaminyl-tRNA(Gln) biosynthesis via transamidation (metacyc:PWY-5921).
# Both of these pathways require glutamate. The biosynthesis of glutamate
# is not represented in GapMind, as glutamate can be formed by transamination of alpha-ketoglutarate,
# an interemdiate in the TCA cycle.

# A protein from Cupriavidus necator is reported to be a 3-hydroxylaminophenol mutase (see Swiss-Prot 3HAPM_CUPNJ),
# involved in 3-nitrophenol degradation. That is the only glutamine synthetase-like protein
# in the proteome of Cupriavidus necator (strain JMP 134 / LMG 1197) [see proteome UP000002697]
# and is 96% identical to the essential protein RR42_RS12995 from Cupriavidus basilensis 4G11.
# It is probably a glutamine synthetase.
# metacyc:SYNPCC7942_2156-MONOMER is annotated with the same reaction, but was not originally given this EC number.
# In SwissProt, uniprot:P81643 and uniprot:P85087 are annotated with this activity but they are very short,
# so are ignored.
# CKL_RS00630 (uniprot:A5N4G9) from Clostridium kluyveri is distantly related to
# characterized glutamine synthetases, but the active site residues and transition state binding
# residues are conserved (see alignment to 2whiA), so it is probably
# the missing glnA.
glnA	glutamine synthetase	EC:6.3.1.2	ignore_other:EC 5.4.4.3	curated:metacyc::SYNPCC7942_2156-MONOMER	ignore:SwissProt::P81643	ignore:SwissProt::P85087	predicted:A5N4G9	predicted:A5N4G9

# Glutamyl-tRNA(Glu/Gln) is usually formed by a nondescriminating glutamyl-tRNA synthetase.
# CCNA_01982 (uniprot:A0A0H3C8P5_CAUVN) from Caulobacter crescentus is the sole glutamyl-tRNA
# synthetase, there is no glutaminyl-tRNA synthetase, and gatABC are present,
# so we annotated it as non-discriminating. In contrast, as of March 2019, unirule
# UR000075658 labeled it as EC:6.1.1.17 (the discriminating kind).
# E. coli glutamine-tRNA ligase (uniprot:P00962) is misannotated in BRENDA as the non-discriminating ligase.
# uniprot:Q8DLI5 is a non-discriminating glutamyl-tRNA synthetase
# (PMID:16876193)  but is not given this EC number
# in SwissProt.
gltX	glutamyl-tRNA(Glx) synthetase	EC:6.1.1.24	uniprot:A0A0H3C8P5_CAUVN	ignore:BRENDA::P00962	curated:SwissProt::Q8DLI5

# The amidotransferase often acts on both glutamyl-tRNA(Gln) and aspartyl-tRNA(Asn) --
# do not try to distinguish.
# Note there are no hits for some of these terms -- for some reason only gatB is annotated as a
# aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit
# Need to flag the metacyc entries separately because they have HTML tags in their descriptions
gatA	aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A	hmm:TIGR00132	term:aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A	term:glutamyl-tRNA(Gln) amidotransferase subunit A	curated:metacyc::MONOMER-13955	ignore_other:EC 6.3.5.7
gatB	aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B	hmm:TIGR00133	term:aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B	term:glutamyl-tRNA(Gln) amidotransferase subunit B	curated:metacyc::MONOMER-13956	ignore_other:EC 6.3.5.7
gatC	aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C	hmm:TIGR00135	term:aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C	term:glutamyl-tRNA(Gln) amidotransferase subunit C	curated:metacyc::MONOMER-13957	ignore_other:EC 6.3.5.7

gatD	glutamyl-tRNA(Gln) amidotransferase, subunit D	hmm:TIGR02153	term:glutamyl-tRNA(Gln) amidotransferase subunit D	ignore_other:EC 6.3.5.7
gatE	glutamyl-tRNA(Gln) amidotransferase, subunit E	hmm:TIGR00134	term:glutamyl-tRNA(Gln) amidotransferase subunit E	ignore_other:EC 6.3.5.7

# Two types of glutamyl-tRNA amidotransferases are known, GatABC or GatDE.
# GatABC are generally thought to act on both glutamyl-tRNA and aspartyl-tRNA, while
# GatDE is thought to act only on glutamyl-tRNA.
transamidation: gatA gatB gatC
transamidation: gatD gatE

to_glutamine: glnA
# In the transamidation pathway, glutamate is ligated to tRNA, but free glutamine is still
# required, because amidotransferase uses a glutaminase subunit to obtain ammonia.
to_gln_tRNA: gltX glnA transamidation
all: to_glutamine
all: to_gln_tRNA

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis