Definition of N-acetyl-D-glucosamine catabolism

GapMind for catabolism of small carbon sources

Definition of N-acetyl-D-glucosamine catabolism

# N-acetylglucosamine utilization in GapMind is based on MetaCyc pathways
# N-acetylglucosamine degradation I (metacyc:GLUAMCAT-PWY)
# and pathway II (metacyc:PWY-6517).
# These pathways differ in whether uptake and phosphorylation are performed by a PTS system
# or performed separately by a transporter and a kinase.

# PTS systems:

# unified EII-ABC (as in E. coli and Klebsiella pneumoniae)
nagEcba	N-acetylglucosamine phosphotransferase system, EII-CBA components	curated:BRENDA::P09323	curated:BRENDA::P45604

# PTS systems form N-acetylglucosamine 6-phosphate
NAG-PTS: nagEcba

# nagFE, where nagF has PTS I, Hpr, and II-A, and nagE has II-CB
# (in Burkholderia phytofirmans and two Pseudomonas fluorescens, and in P. aeruginosa)
nagF	N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF)	curated:reanno::BFirm:BPHYT_RS02740	curated:reanno::pseudo3_N2E3:AO353_04460	curated:reanno::pseudo5_N2C3_1:AO356_17540	curated:TCDB::Q9HXN5
nagEcb	N-acetylglucosamine phosphotransferase system, EII-CB components	curated:reanno::BFirm:BPHYT_RS02745	curated:reanno::pseudo3_N2E3:AO353_04465	curated:reanno::pseudo5_N2C3_1:AO356_17535	curated:TCDB::Q9HXN4
NAG-PTS: nagF nagEcb

# Streptomyces coelicolor has just EII-B and EII-C (ptsB, ptsC);
#  "crr" (SCO1390 or uniprot:Q9KZP2) is the EII-A (see PMC3294797).
# Streptomyces olivaceoviridis has a related system with EII-B, EII-C, and EII-C' components (ptsBC1C2).
# Did not find any papers about the EII-A component in S. olivaceoviridis.
crr	N-acetylglucosamine phosphotransferase system, EII-A component Crr	uniprot:Q9KZP2

ptsB	N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB	curated:SwissProt::Q9S2H6	curated:TCDB::Q8GBT8

# In S. olivaceoviridis, either ptsC1 or ptsC2 suffices for xylose uptake,
# but ptsC2 is specific for NAG (PMID:12436256), so include ptsC2 here.
# Not sure if ptsC1 = uniprot:Q8GBT7 should be marked ignore or not.
ptsC	N-acetylglucosamine phosphotransferase system, EII-C component PtsC	curated:SwissProt::Q9S2H4	curated:TCDB::Q8GBT6

NAG-PTS: crr ptsB ptsC

# Bacillus subtilis has EII-CB, known as nagP.
# The major EII-A is ptsG (uniprot:P20166, see PMID:30038046),
#	which is a bit surprising as ptsG has EII-B and EII-C domains as well
#	and is thought to be specific for glucose;
#	YpqE (uniprot:P50829) or GamP (uniprot:P39816) also suffice.
#	(YpqE has EII-A only, while GamP is the EII-CBA protein for glucosamine)
nagEIIA	N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP)	curated:TCDB::P20166	uniprot:P50829	curated:SwissProt::P39816
nagPcb	N-acetylglucosamine phosphotransferase system, EII-CB component NagP	curated:SwissProt::O34521
NAG-PTS: nagEIIA nagPcb

# ABC transporters:

# Phaeobacter inhibens and Sinorhizobium meliloti have a 4-component system; name them by
# the S. meliloti components
SMc02869	N-acetylglucosamine ABC transporter, ATPase component	curated:reanno::Phaeo:GFF2754	curated:reanno::Smeli:SMc02869
SMc02872	N-acetylglucosamine ABC transporter, permease component 1	curated:reanno::Phaeo:GFF2751	curated:reanno::Smeli:SMc02872
SMc02871	N-acetylglucosamine ABC transporter, permease component 2	curated:reanno::Phaeo:GFF2752	curated:reanno::Smeli:SMc02871
SMc02873	N-acetylglucosamine ABC transporter, substrate-binding component	curated:reanno::Phaeo:GFF2750	curated:reanno::Smeli:SMc02873

# Transporters were identified using:
# query: transporter:N-acetylglucosamine:N-ACETYL-D-GLUCOSAMINE:CPD-12541
NAG-transport: SMc02869 SMc02872 SMc02871 SMc02873

# Streptomyces olivaceoviridis has ngcEFG, with the presumed ATPase component
# not identified. It probably depends on a shared ATPase component such as msiK (known in S. coelicolor)
ngcE	N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)	curated:TCDB::Q8RJV0
ngcF	N-acetylglucosamine ABC transporter, permease component 1 (NgcF)	curated:TCDB::Q8RJU9
ngcG	N-acetylglucosamine ABC transporter, permease component 2 (NgcG)	curated:TCDB::Q8RJU8
NAG-transport: ngcE ngcF ngcG

# Other transporters:

nagP	N-acetylglucosamine transporter NagP	curated:TCDB::Q8EBL0	curated:reanno::ANA3:7025962
NAG-transport: nagP

nag3	N-acetylglucosamine transporter nag3/nag4	curated:SwissProt::A0A1D8PQG0	curated:SwissProt::Q59RG0
NAG-transport: nag3

ngt1	N-acetylglucosamine:H+ symporter Ngt1	curated:CharProtDB::CH_123262
NAG-transport: ngt1

# Ignore a putative NAG deacetylase from C. albicans, not given this EC number, in CharProtDB
nagA	N-acetylglucosamine 6-phosphate deacetylase	EC:3.5.1.25	ignore:CharProtDB::CH_123434

# Add the Candida isomerase, not given this EC number by CharProtDB.
# And fitness data confirms the proposal that SM_b21218 (Q92VI1) is this enzyme.
nagB	glucosamine 6-phosphate deaminase (isomerizing)	EC:3.5.99.6	curated:CharProtDB::CH_123433	uniprot:Q92VI1

# Both pathways involve N-acetylglucosamine 6-phosphate,
# followed by deacetylase nagA and the isomerizing deaminase nagB, which produces fructose 6-phosphate,
# a central metabolic intermediate.
NAG-utilization: NAG-PTS nagA nagB

# Ignore a putative enzyme from C. albicans, not given this EC number in CharProtDB.
# PMC2832512 identified two NAG kinases in Xanthomonas campestris, XCC2886 (Q8P6S9) and XCC2943 (Q8P6M4)
nagK	N-acetylglucosamine kinase	EC:2.7.1.59	ignore:CharProtDB::CH_123431	uniprot:Q8P6S9	uniprot:Q8P6M4

NAG-utilization: NAG-transport nagK nagA nagB

all: NAG-utilization

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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

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