As text, or see rules and steps
# The canonical pathway for glucosamine utilization involves
# glucosamine 6-phosphate as an intermediate, as in N-acetylglucosamine utilization (metacyc:GLUAMCAT-PWY).
# GapMind also includes two other pathways: an oxidative pathway via glucosaminate ammonia-lyase, and
# a transmembrane transacetylase (NagX) pathway.
# ABC transporters:
# A 4-part system in Sinorhizobium meliloti was identified from genetic data;
# expression of this system is also induced by glucosamine or galactosamine (PMC1635973).
SM_b21216 ABC transporter for D-Glucosamine, ATPase component curated:reanno::Smeli:SM_b21216
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 curated:reanno::Smeli:SM_b21219
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 curated:reanno::Smeli:SM_b21220
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein curated:reanno::Smeli:SM_b21221
# Transporters and PTS systems were identified using
# query: transporter:glucosamine:D-glucosamine:CPD-12538:CPD-12539
glucosamine-transport: SM_b21216 SM_b21219 SM_b21220 SM_b21221
# Pseudomonas oxidize glucosamine to glucosaminate using glucose dehydrogenase (PMID:1849886),
# which is a periplasmic enzyme.
# So these 4-part "glucosamine" ABC transporters,
# which were identified by genetic data from various Pseudomonas,
# are probably glucosaminate transporters
AO353_21715 glucosaminate ABC transporter, permease component 1 curated:reanno::pseudo3_N2E3:AO353_21715 curated:reanno::pseudo6_N2E2:Pf6N2E2_2052 curated:reanno::pseudo5_N2C3_1:AO356_00475
AO353_21720 glucosaminate ABC transporter, permease component 2 curated:reanno::pseudo3_N2E3:AO353_21720 curated:reanno::pseudo5_N2C3_1:AO356_00470
AO353_21725 glucosaminate ABC transporter, ATPase component curated:reanno::pseudo3_N2E3:AO353_21725 curated:reanno::pseudo5_N2C3_1:AO356_00465 curated:reanno::pseudo6_N2E2:Pf6N2E2_2050
AO353_21710 glucosaminate ABC transporter, substrate-binding component curated:reanno::pseudo3_N2E3:AO353_21710 curated:reanno::pseudo5_N2C3_1:AO356_00480 curated:reanno::pseudo6_N2E2:Pf6N2E2_2053
glucosaminate-transport: AO353_21715 AO353_21720 AO353_21725 AO353_21710
# Unified EII-CBA systems from E. coli ("nagE") or B. subtilis ("gamP").
# Ignore a close homolog of NagE from Klebsiella, annotated as a NAG PTS system, which is not well studied
# and may well act on glucosamine as well.
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) curated:BRENDA::P09323 curated:SwissProt::P39816 ignore:BRENDA::P45604
# PTS systems (forming glucosamine-6-phosphate)
glucosamine-PTS: gamP
# The manXYZ system from E. coli where manX has EII-AB, manY has EII-C, and manZ has EII-D.
# (manZ is listed twice with slightly different sequence lengths)
manX glucosamine PTS system, EII-AB component ManX curated:CharProtDB::CH_088329
manY glucosamine PTS system, EII-C component ManY curated:CharProtDB::CH_088330
manZ glucosamine PTS system, EII-D component ManZ curated:SwissProt::P69805 curated:TCDB::P69805
glucosamine-PTS: manX manY manZ
# Other transporters:
SLC2A2 glucosamine transporter SLC2A2 curated:SwissProt::P11168
glucosamine-transport: SLC2A2
# periplasmic glucose dehydrogenase
import glucose.steps:gdh
# nagB is glucosamine 6-phosphate deaminase (isomerizing)
import NAG.steps:NAG-utilization nagB
# A purified glucosaminate dehydratase "alpha subunit" was determined to be
# thioredoxin (SwissProt Q93HX6), which seems unlikely to physiologically relevant.
glucosaminate-lyase glucosaminate ammonia-lyase EC:4.3.1.9 ignore:SwissProt::Q93HX6
# The entry for Q9ZU29 is erroneous (the correct accession is Q97U29).
# EcoCyc 2-dehydro-3-deoxygalactonokinase (dgoK) is given this EC number as well but
# I could not determine why. It doesn't link to the ketodeoxygluconate kinase reaction.
kdgK 2-keto-3-deoxygluconate kinase EC:2.7.1.45 EC:2.7.1.178 ignore:BRENDA::Q9ZU29 ignore:ecocyc::DEHYDDEOXGALACTKIN-MONOMER
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 EC:4.1.2.55
# The glucosaminate pathway begins with the periplasmic glucose dehydrogenase (gdh; PMID:1849886).
# (It is not clear if gdh forms glucosaminate directly or forms a lactone intermediate;
# the latter seems more likely but has not been demonstrated, nor has a lactonase
# been identified by genetics; or the lactone might hydrolyze
# spontaneously.)
# Glucosaminate is then taken up and converted to 2-keto-3-deoxygluconate by an
# ammonia-lyase (EC:4.3.1.9) and phosphorylated (by kdgK) to enter the Entner-Doudoroff pathway.
# (No phenotypes for kdgK were identified in the genetic data, but this step could be genetically redundant.
# It is also reported that the glucosaminate dehydratase has
# some aldolase activity, producing glyceraldehye and pyruvate (PMID:7766176).)
all: gdh glucosaminate-transport glucosaminate-lyase kdgK kdgA
# Fitness data confirms that SM_b21217 (Q92VI2), a proposed glucosamine kinase, is involved in glucosamine utilization.
glc-kinase glucosamine kinase EC:2.7.1.8 EC:2.7.1.147 uniprot:Q92VI2
# Alternatively, glucosamine kinase forms glucosamine-6-phosphate,
# which can be converted by nagB (glucosamine 6-phosphate deaminase (isomerizing))
# to fructose-6-phosphate.
all: glucosamine-transport glc-kinase nagB
# Glucosamine 6-phosphate can also be formed by PTS systems.
all: glucosamine-PTS nagB
# These NagX proteins are distantly related to human HGSNAT (uniprot:Q68CP4),
# which is a transmembrane acetyl-CoA:alpha-glucosaminide N-acetyltransferase.
# Genetic data suggests that these bacterial homologs are involved in glucosamine
# utilization, but not as a transporter -- N-acetylglucosamine utilization
# genes are also involved. So, they appear to be transmembrane N-acetyltransferases
# for glucosamine. The key histidine which holds the acetyl group as it passes
# through the membrane (His269 in NG_009552.1, or His297
# in Q68CP4) is conserved in these proteins.
# The bacterial proteins with clear evidence for this role are:
# Shewana3_3111 (A0KZW6), Sama_0947 (A1S448), and Echvi_1106 (L0FVP4).
nagX transmembrane glucosamine N-acetyltransferase NagX uniprot:A0KZW6 uniprot:A1S448 uniprot:L0FVP4
# Alternatively, the transmembrane transacetylase (NagX) route involves
# conversion in the periplasm to N-acetylglucosamine.
all: nagX NAG-utilization
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:
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 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