GapMind for catabolism of small carbon sources


Definition of N-acetyl-D-glucosamine catabolism

As text, or see rules and steps

# 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:	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:	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:	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:

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