As text, or see rules and steps
# Mannitol degradation in GapMind is based on MetaCyc pathway # mannitol degradation I via a phosphotransferase system (metacyc:MANNIDEG-PWY), # pathway II via mannitol 1-dehydrogenase (metacyc:PWY-3861), # or another oxidative pathway with mannitol 2-dehydrogenase (PMID:8254318). # Unified EII-CBA in Escherichia coli (mtlA) and Vibrio cholerae. Ignore similarity to the II-CB only systems. mtlA mannitol phosphotransferase system, EII-CBA components curated:BRENDA::P00550 curated:TCDB::Q9KKQ7 ignore:TCDB::P42956 ignore:SwissProt::P50852 ignore:SwissProt::O65989 ignore:SwissProt::P69826 ignore:SwissProt::P28008 # PTS systems forming mannitol 1-phosphate mannitol-PTS: mtlA # Two-part PTS, with EII-CB (cmtA/mtlA) separate from EII-A (cmtB/mtlF), in # Escherichia coli (cmt system), Bacillus subtilis, Staphylococcus # carnosus, Clostridium acetobutylicum, and Geobacillus stearothermophilus. # Ignore similarity to the unified systems. cmtA mannitol phosphotransferase system, EII-CB component CmtA/MtlF curated:SwissProt::P69826 curated:TCDB::P42956 curated:SwissProt::P28008 curated:SwissProt::O65989 curated:SwissProt::P50852 ignore:BRENDA::P00550 ignore:TCDB::Q9KKQ7 # For C. acetobutylicum, the mtlF component is is uniprot:O65991 # (see PMID:11160802); and in Geobacillus it is uniprot:Q45420 (PMID:824601; # Genbank U18943.1). # There is also a paper about the EII-A and EII-BC system from S. aureus, see PMID:3064811 and # SwissProt uniprot:P0A0E0, but I'm not sure this is the correct accession, so ignore it. cmtB mannitol phosphotransferase system, EII-A component CmtB/MtlF curated:ecocyc::CMTB-MONOMER curated:SwissProt::P17876 curated:TCDB::C0H3V2 uniprot:O65991 uniprot:Q45420 ignore:SwissProt::P0A0E0 mannitol-PTS: cmtA cmtB # EII-A, EII-BC1, and EII-C2 -- the sorbitol/glucitol system in E. coli, which also transports mannitol. gutB mannitol PTS system, EII-A component GutB curated:CharProtDB::CH_090883 # Ignore similarity to close homolog in Erwinia, annotated as transporting sorbitol only gutE mannitol PTS system, EII-BC1 component GutE curated:SwissProt::P56580 ignore:SwissProt::O32522 # Ignore similarity to close homolog in Erwinia, annotated as transporting sorbitol only gutA mannitol PTS system, EII-C2 component GutA curated:SwissProt::P56579 ignore:SwissProt::O32521 mannitol-PTS: gutB gutE gutA # ABC transporters # MtlEFGK in several strains of Pseudomonas fluorescens or Pseudomonas simiae, or smoEFGK in Rhodopseudomonas sphaeroides. # (The Rhodopseudomonas system was missed by the query; it is annotated as a hexitol transporter.) # For all components, ignore simlarity to close homologs in FW300-N2C3 or FW300-N2E2, annotated as transporting sorbitol only. mtlE polyol ABC transporter, substrate-binding component MtlE/SmoE curated:TCDB::O30491 curated:reanno::WCS417:GFF2493 curated:reanno::pseudo13_GW456_L13:PfGW456L13_3042 curated:reanno::pseudo3_N2E3:AO353_25880 ignore:reanno::pseudo5_N2C3_1:AO356_00025 ignore:reanno::pseudo6_N2E2:Pf6N2E2_1963 curated:TCDB::O30831 mtlF polyol ABC transporter, permease component 1 (MtlF/SmoF) curated:TCDB::O30492 curated:reanno::WCS417:GFF2492 curated:reanno::pseudo13_GW456_L13:PfGW456L13_3041 curated:reanno::pseudo3_N2E3:AO353_25885 ignore:reanno::pseudo5_N2C3_1:AO356_00020 ignore:reanno::pseudo6_N2E2:Pf6N2E2_1962 curated:TCDB::O30832 mtlG polyol ABC transporter, permease component 2 (MtlG/SmoG) curated:TCDB::O30493 curated:reanno::WCS417:GFF2491 curated:reanno::pseudo13_GW456_L13:PfGW456L13_3040 curated:reanno::pseudo3_N2E3:AO353_25890 ignore:reanno::pseudo6_N2E2:Pf6N2E2_1961 ignore:reanno::pseudo5_N2C3_1:AO356_00015 curated:TCDB::O30833 mtlK polyol ABC transporter, ATP component MtlK/SmoG curated:TCDB::O30494 curated:reanno::WCS417:GFF2490 curated:reanno::pseudo13_GW456_L13:PfGW456L13_3039 curated:reanno::pseudo3_N2E3:AO353_25895 ignore:reanno::pseudo6_N2E2:Pf6N2E2_1960 ignore:reanno::pseudo5_N2C3_1:AO356_00010 curated:TCDB::P54933 # Transporters and PTS systems were identified using # query: transporter:mannitol:D-mannitol mannitol-transport: mtlE mtlF mtlG mtlK PLT5 polyol transporter PLT5 curated:CharProtDB::CH_091483 mannitol-transport: PLT5 # Ignore erroneous annotation of the TRAP transporter component Q3J1R2 from Rhodobacter sphaeroides as SmoM # Ignore a porin from Pseudomonas aeruginosa mtlD mannitol-1-phosphate 5-dehydrogenase EC:1.1.1.17 # In pathway I, the phosphotransferase system forms mannitol 1-phosphate and # 5-dehydrogenase (mtlD) forms fructose 6-phosphate. all: mannitol-PTS mtlD mt1d mannitol 1-dehydrogenase EC:1.1.1.255 mak mannose kinase EC:2.7.1.7 import mannose.steps:manA # mannose 6-phosphate isomerase # In pathway II, mannitol is oxidized to # mannose by mt1d, phosphorylated to mannose 6-phosphate, and isomerized # to fructose 6-phosphate. all: mannitol-transport mt1d mak manA # SwissProt P33216 was shown to have this activity (PMID:2789134; PMID:8254318) mt2d mannitol 2-dehydrogenase EC:1.1.1.67 EC:1.1.1.138 uniprot:P33216 import fructose.steps:scrK # fructokinase # Alternatively, mannitol 2-dehydrogenase (mt2d) forms fructose, and fructokinase (scrK) # forms fructose 6-phosphate. all: mannitol-transport mt2d scrK
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