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
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:
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