GapMind for catabolism of small carbon sources

 

Definition of D-glucosamine (chitosamine) catabolism

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

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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