Definition of L-asparagine catabolism

GapMind for catabolism of small carbon sources

Definition of L-asparagine catabolism

# Asparagine catabolism in GapMind is based on asparaginase, which forms ammonia and aspartate.
# The asparaginase may be secreted or cytoplasmic.
# Asparatate can be transaminated to oxaloacetate, which is an intermediate in central metabolism.

# ABC transporters

# AatJMPQ from Pseudomonas or BztBACD from Rhodobacter capsulatus
import aspartate.steps:bztA bztB bztC bztD aatJ aatQ aatM aatP

# Transporters were identified using
# query: transporter:asparagine:L-asparagine
asparagine-transport: aatJ aatQ aatM aatP
asparagine-transport: bztA bztB bztC bztD

# glnQP from Lactococcus lactis, TC 3.A.1.3.25
glnQ	L-asparagine ABC transporter, ATPase component GlnQ	curated:TCDB::Q9CES4
glnP	L-asparagine ABC transporter, fused permease and substrate-binding components GlnP	curated:TCDB::Q9CES5
asparagine-transport: glnQ glnP


# AapJQMP from Rhizobium leguminosarum is described in glutamate.steps
import glutamate.steps:aapJ aapQ aapM aapP
asparagine-transport: aapJ aapQ aapM aapP

# Other transporters

ansP	L-asparagine permease AnsP	curated:SwissProt::P77610	curated:TCDB::P40812
asparagine-transport: ansP

AGP1	L-asparagine permease AGP1	curated:CharProtDB::CH_091105
asparagine-transport: AGP1

yhiT	probable L-asparagine transporter YhiT	curated:TCDB::Q8ZLD2
asparagine-transport: yhiT

agcS	Probable asparagine:Na+ symporter AgcS	curated:TCDB::W0WFC6
asparagine-transport: agcS

# Ignored the export protein EamA
# Ignored SLC38A3, which is a sodium/amino acid antiporter
# Ignored gerBB (P39570), which is part of a receptor complex; it is not clear if it is
#   actually an amino acid transporter (see PMID:24488313)
# Ignored the non-specific human permease SLC7A8 (TC 2.A.3.8.20)

# Because many of the asparaginases are periplasmic, allow uptake of aspartate as well
# (Also, some aspartate transporters probably transport asparagine as well.)
import aspartate.steps:aspartate-transport

# Isoaspartyl peptidases such as E. coli iaaA have this activity and are labeled heteromeric,
# because the proenzyme is cleaved into two subunits; this need not be represented here.
# TIGR00519 is not used because it hits GatD, a subunit of glutamyl-tRNA(Gln) amidotransferase
ans	asparaginase	EC:3.5.1.1	EC:3.5.1.38	ignore_hmm:TIGR00519

all: ans aspartate-transport
all: asparagine-transport ans

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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, or view the source code.

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 catabolism of small carbon sources