GapMind for catabolism of small carbon sources

 

Definition of sucrose catabolism

As text, or see rules and steps

# Sucrose utilization in GapMind is based on MetaCyc pathways
# sucrose degradation I via sucrose 6-phosphate hydrolase (metacyc:SUCUTIL-PWY),
# pathway II via sucrose synthase (metacyc:PWY-3801),
# pathway III via invertase (metacyc:PWY-621),
# and pathway IV via sucrose phosphorylase (metacyc:PWY-5384).
# Pathway V is similar to pathway III and is not reported in prokaryotes, so it is not included.
# There is no pathway VI.
# Pathway VII (via sucrose 3-dehydrogenase, metacyc:SUCROSEUTIL2-PWY)
# is too poorly understood to include in GapMind.

# ABC transporters

# ThuEFGK in Sinorhizobium meliloti and TTC1627:TTC1629 + MalK1 in Thermus thermophilus.
# Also, a thuEFGK homolog in various Pseudomonas is important for fitness on sucrose,
# i.e., Pf1N1B4_5112:5116 or Psyr_0762:Psyr_0759, and is presumably a sucrose transporter.
# The N1B4 system is A0A166QFS3 A0A166QFV1 A0A161ZE72 A0A166QFW2.
thuE	sucrose ABC transporter, substrate-binding component ThuE	curated:TCDB::Q72H68	curated:TCDB::Q9R9Q7	uniprot:A0A166QFS3
thuF	sucrose ABC transporter, permease component 1 (ThuF)	curated:TCDB::Q72H67	curated:reanno::Smeli:SM_b20326	uniprot:A0A166QFV1
thuG	sucrose ABC transporter, permease component 2 (ThuG)	curated:TCDB::Q72H66	curated:reanno::Smeli:SM_b20327	uniprot:A0A161ZE72
# aglK (Q9Z3R9, SMc03065) also clustered with thuK but is not that similar (56% identity) so is marked ignore
thuK	sucrose ABC transporter, ATPase component ThuK	curated:TCDB::Q72L52	curated:TCDB::Q9R9Q4	ignore:reanno::Smeli:SMc03065	uniprot:A0A166QFW2

# Transporters and PTS systems were analyzed using
# query: transporter:sucrose
sucrose-transport: thuE thuF thuG thuK

# AglEFGK in Sinorhizobium meliloti.
# A similar system from Dinoroseobacter shibae, Dshi_1652:Dshi_1648, is involved in sucrose uptake.
# Dinoroseobacter shibae aglE = Dshi_1652 = A8LLL6.
aglE	sucrose ABC transporter, substrate-binding component AglK	curated:TCDB::Q9Z3R5	uniprot:A8LLL6

# Dinoroseobacter shibae aglF = Dshi_1651 = A8LLL5.
aglF	sucrose ABC transporter, permease component 1 (AglF)	curated:reanno::Smeli:SMc03062	uniprot:A8LLL5

# Dinoroseobacter shibae aglG = Dshi_1650 = A8LLL4.
aglG	sucrose ABC transporter, permease component 2 (AglG)	curated:reanno::Smeli:SMc03063	uniprot:A8LLL4

# Dinoroseobacter shibae aglK = Dshi_1648 = A8LLL2.
aglK	sucrose ABC transporter, ATPase component AglK	curated:reanno::Smeli:SMc03065	uniprot:A8LLL2

sucrose-transport: aglE aglF aglG aglK

# phosphotransferase systems

# This is PTS-II-BC system (TIGR01996).
# TIGRFam describes it as relying on the glucose II-A protein (crr).
# But in B. subtilis, many different II-A proteins can phosphorylate the II-B domains
# (PMID:30038046). So, treat it as a single-component system. Since the II-A component
# is not specific, describe it as a 1-component system.
sacP	sucrose phosphotransferase enzyme EII-BC	curated:BRENDA::P27219	curated:BRENDA::P51184	curated:SwissProt::P15400	curated:TCDB::P05306	curated:TCDB::P08470

# PTS form sucrose 6-phosphate.
sucrose-PTS: sacP

ptsS	sucrose phosphotransferase enzyme EII-BCA	curated:BRENDA::P12655	curated:TCDB::Q8NMD6
sucrose-PTS: ptsS

# Other heteromeric transporters

TMT1	heteromeric sucrose:H+ symporter, TMT1 component	curated:TCDB::Q96290
TMT2	heteromeric sucrose:H+ symporter, TMT2 component	curated:TCDB::Q8LPQ8
sucrose-transport: TMT1 TMT2

# Monomeric transporters

sut	sucrose:proton symporter SUT/SUC	curated:CharProtDB::CH_091525	curated:CharProtDB::CH_091608	curated:SwissProt::A2ZN77	curated:SwissProt::Q0ILJ3	curated:SwissProt::Q10R54	curated:SwissProt::Q39231	curated:SwissProt::Q67YF8	curated:SwissProt::Q69JW3	curated:SwissProt::Q6YK44	curated:SwissProt::Q948L0	curated:SwissProt::Q9C8X2	curated:SwissProt::Q9FE59	curated:SwissProt::Q9FG00	curated:SwissProt::Q9ZVK6	curated:TCDB::D1GC38	curated:TCDB::Q9SXM0	curated:metacyc::MONOMER-18237	curated:metacyc::MONOMER-18241
sucrose-transport: sut

SLC45A2	sucrose transporter	curated:SwissProt::Q9UMX9	curated:SwissProt::P58355	curated:TCDB::Q9VSV1
sucrose-transport: SLC45A2

scrT	sucrose permease ScrT	curated:TCDB::Q07W00	curated:reanno::ANA3:7022816
sucrose-transport: scrT

sut1	alpha-glucoside permease Sut1	curated:CharProtDB::CH_091204
sucrose-transport: sut1

# PMID:29808622 report that PFL_3238 (Q4KBP0) is a sucrose permease; it is related to E. coli cscB
cscB	sucrose:H+ symporter CscB	curated:SwissProt::P30000	uniprot:Q4KBP0
sucrose-transport: cscB

SLC45A3	sucrose:H+ symporter	curated:SwissProt::Q96JT2
sucrose-transport: SLC45A3

SLC45A4	sucrose:H+ symporter	curated:TCDB::Q5BKX6
sucrose-transport: SLC45A4

# Ignore SWEET11 which is involved in efflux as well
# Ignore porin ScrY, involved in movement through the outer membrane

# This reaction does not match an EC number.
# Many invertases (EC 3.2.1.26) also have this activity, so ignore similarity to those.
# And the original reannotation of AO356_28590 as sucrose-6-phosphate hydrolase is questionable.
scrB	sucrose-6-phosphate hydrolase	curated:CAZy::CAG25843.1	curated:CAZy::S68598	curated:SwissProt::P27217	curated:SwissProt::Q09122	ignore_other:3.2.1.26	ignore:reanno::pseudo5_N2C3_1:AO356_28590

# Because sucrose can be hydrolyzed in the periplasm, need
# to represent glucose and fructose uptake

# glk is glucokinase
import glucose.steps:glucose-utilization glk

# scrK is fructokinase
import fructose.steps:fructose-utilization scrK

# Bacteroides thetaiotaomicron and Sphingomonas koreensis probably hydrolyze
# sucrose in the periplasm, followed by uptake of both fructose and glucose.

# In pathway I, a phosphotransferase system forms sucrose 6-phosphate,
# the hydrolyase scrB forms glucose-6-phosphate and fructose, and
# fructokinase forms fructose 6-phosphate.
all: sucrose-PTS scrB scrK

# Ignore sucrose-phosphate synthase BAA08304.1, given the wrong EC in CAZy,
# and similarly the sucrose-phosphate synthase from Thermosipho melanesiensis A6LKE9 (see PMID:25846332)
SUS	sucrose synthase	EC:2.4.1.13	ignore:CAZy::BAA08304.1	ignore:BRENDA::A6LKE9

# Ignore the dehydrogenase Q8GQP9, given the wrong EC in BRENDA
galU	glucose 1-phosphate uridylyltransferase	EC:2.7.7.9	EC:2.7.7.64	ignore:BRENDA::Q8GQP9

# PH0923 (MONOMER-13382) is both phosphomannomutase and phosphoglucomutase (PMID:16091590)
import galactose.steps:pgmA

# In pathway II, transport is followed by sucrose synthase (SUS) in reverse,
# forming fructose and UDP-glucose;
# the fructose is phosphorylated by scrK,
# while the UDP-glucose is transformed to glucose-6-phosphate by uridylyltransferase galU and
# phosphoglucomutase (pgmA).
all: sucrose-transport SUS scrK galU pgmA

# The annotation of P93291 (AtMg00260) in BRENDA is questionable.
# And the original reannotation of AO356_28590 was as sucrose 6-phosphate hydrolase,
# but it is probably a sucrose hydrolase. Also, PMID:29808622 has evidence that
# the related protein PFL_3237 (cscA, Q4KBP1) is a sucrose hydrolase.
# HaG from Halomonas (H3K096) hydrolyzes sucrose (PMC3298133).
# Dshi_1649 from Dinoroseobacter shibae (A8LLL3) is important for sucrose utilization and is 60% identical to HaG.
# Inulinases (3.2.1.7) often cleave sucrose and so similarity to them is ignored.
ams	sucrose hydrolase (invertase)	EC:3.2.1.26	EC:3.2.1.48	EC:3.2.1.80	term:sucrose hydrolase	ignore:BRENDA::P93291	curated:reanno::pseudo5_N2C3_1:AO356_28590	uniprot:Q4KBP1	uniprot:H3K096	uniprot:A8LLL3	ignore_other:3.2.1.7

# In pathway III, transport is followed by cleavage to glucose and fructose
# and phosphorylation of each.
all: sucrose-transport ams scrK glk

# glucosylglycerate phosphorylase (ycjM or b1309 or AAC74391.2) is misannotated as sucrose phosphorylase in CAZy
scrP	sucrose phosphorylase	EC:2.4.1.7	ignore:CAZy::AAC74391.2

# In pathway IV, transport is followed by phosphorylase scrP, producing fructose and glucose 1-phosphate,
# which are transformed by kinase scrK and phosphoglucomutase pgmA.
all: sucrose-transport scrP scrK pgmA

# Alternatively, sucrose can be hydrolyzed in the periplasm, followed by utilization of the glucose or fructose.
all: ams glucose-utilization
all: ams fructose-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 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