As text, or see rules and steps
# Since fumarate is a TCA cycle intermediate, GapMind represent its uptake only. dctA fumarate:H+ symporter DctA curated:CharProtDB::CH_014038 curated:TCDB::P96603 curated:TCDB::Q01857 curated:TCDB::Q1J1H5 curated:TCDB::Q848I3 curated:reanno::pseudo5_N2C3_1:AO356_18980 curated:SwissProt::Q9I4F5 # Transporters were identified using # query: transporter:fumarate. # Fumarate:succinate antiporters or fumarate:proton antiporters (probably for efflux) were not included. # Subunits of succinate dehdydrogenase/fumarate reductase were also excluded. fumarate-transport: dctA sdcL fumarate:Na+ symporter SdcL curated:TCDB::A4QAL6 curated:SwissProt::Q21339 curated:TCDB::Q2FFH9 curated:TCDB::Q65NC0 curated:TCDB::Q9KNE0 curated:SwissProt::Q99SX1 curated:SwissProt::Q93655 fumarate-transport: sdcL # Could not find experimental evidence for the specificity of A1JRS3, annotated in TCDB as a sulfate transporter dauA fumarate transporter DauA curated:SwissProt::P0AFR2 ignore:TCDB::A1JRS3 fumarate-transport: dauA # Three-part TRAP transporter DctMPQ # In Phaeobacter inhibens, the system is important for fumarate utilization: # PGA1_c20660 = dctM = I7DRS6, # PGA1_c20680 = dctP = I7END8, # PGA1_c20670 = dctQ = I7EY26. # A closely related system in SB2B transports another dicarboxylate, 2-oxoglutarate, # so its components are marked ignore dctM fumarate TRAP transporter, large permease component DctM curated:SwissProt::O07838 curated:reanno::PV4:5208943 curated:SwissProt::Q9HU16 uniprot:I7DRS6 ignore:reanno::SB2B:6938090 dctP fumarate TRAP transporter, substrate-binding component DctP curated:SwissProt::A3QCW5 curated:SwissProt::P37735 ignore:reanno::SB2B:6938088 curated:SwissProt::Q9HU18 curated:SwissProt::Q9KQR9 uniprot:I7END8 dctQ fumarate TRAP transporter, small permease component DctQ curated:SwissProt::O07837 curated:reanno::PV4:5208944 ignore:reanno::SB2B:6938089 uniprot:I7EY26 fumarate-transport: dctM dctP dctQ # O07488 is annotated in TCDB as a sulfate permease, but I did not find any data supporting this annotation SLC26dg fumarate transporter SLC26dg curated:TCDB::Q1J2S8 ignore:TCDB::O07488 fumarate-transport: SLC26dg import succinate.steps:Dshi_1194 Dshi_1195 # TRAP dicarboxylate transporter fumarate-transport: Dshi_1194 Dshi_1195 all: fumarate-transport
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