As text, or see rules and steps
# Since L-malate is a TCA cycle intermediate, catabolic reactions are not represented in GapMind. sdlC L-malate:Na+ symporter SdlC curated:TCDB::A4QAL6 curated:CharProtDB::CH_091173 curated:SwissProt::Q21339 curated:TCDB::Q2FFH9 curated:TCDB::Q65NC0 curated:TCDB::Q9KNE0 curated:SwissProt::Q99SX1 # Transporters were identified using # query: transporter:malate:L-malate:(S)-malate. # (None of these transporters seem to be specific for D-malate, although # E. coli can grow with D-malate as the sole source of carbon.) # In B. subtilis, mleN (uniprot:P54571) can contribute to growth on malate by # a malate:lactate antiport mechanism (PMID:10903309), but it is # not clear how this could be the sole malate uptake system for growth # (no fixed carbon would be available for growth), so it was excluded. L-malate-transport: sdlC dctA L-malate:H+ symporter DctA curated:TCDB::P96603 curated:TCDB::Q01857 curated:TCDB::Q1J1H5 curated:TCDB::Q848I3 curated:reanno::pseudo5_N2C3_1:AO356_18980 curated:SwissProt::Q9I4F5 curated:CharProtDB::CH_014038 L-malate-transport: dctA # This cluster seems to include both H+ and Na+ dependent malate transporters, as well # as Lactococcus lactis mleP or maeP (O07032) which also exports lactate. maeN malate transporter maeN curated:SwissProt::O05256 curated:TCDB::O07032 curated:TCDB::P94363 curated:TCDB::Q53787 L-malate-transport: maeN # 3-component TRAP transporter dctMPQ. # In Phaeobacter inhibens, the system is important for L-malate utilization: # PGA1_c20660 = dctM = I7DRS6; # PGA1_c20680 = dctP = I7END8; # PGA1_c20670 = dctQ = I7EY26. # A very similar system is present in Shewanella amazonensis SB2B, which cannot grow on L-malate; # it is still possible that this system transports L-malate, so it is marked ignore. dctM L-malate TRAP transporter, large permease component DctM curated:SwissProt::O07838 curated:reanno::PV4:5208943 curated:SwissProt::Q9HU16 uniprot:I7DRS6 ignore:reanno::SB2B:6938090 # Q9HVH5 = PA4616 is a malate-binding substrate-binding protein (PMC4310620) dctP L-malate TRAP transporter, substrate-binding component DctP curated:SwissProt::A3QCW5 curated:SwissProt::P37735 curated:SwissProt::Q9KQR9 curated:SwissProt::Q9HU18 uniprot:I7END8 ignore:reanno::SB2B:6938088 uniprot:Q9HVH5 curated:reanno::PV4:5208945 dctQ L-malate TRAP tranpsorter, small permease component DctQ curated:SwissProt::O07837 curated:reanno::PV4:5208944 uniprot:I7EY26 ignore:reanno::SB2B:6938089 L-malate-transport: dctM dctP dctQ import succinate.steps:Dshi_1194 Dshi_1195 # TRAP dicarboxylate transporter L-malate-transport: Dshi_1194 Dshi_1195 mae1 L-malate:H+ symporter Mae1 curated:CharProtDB::CH_016604 L-malate-transport: mae1 mleP malate permease MleP curated:TCDB::Q48797 L-malate-transport: mleP # Eukaryotic antiporters or carrier porters were excluded. # Eukaryotic translocators (DIT1/DIT2) which export glutamate were excluded. # Aluminum-activated efflux systems were excluded. all: L-malate-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