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

Links

Downloads

Related tools

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