As text, or see rules and steps
# Since 2-oxoglutarate (also known as alpha-ketoglutarate) is a TCA cycle intermediate, # GapMind represents uptake only. # HSERO_RS16820 (D8J257) is similar and is important for 2-oxoglutarate utilization. # uniprot:Q52000 is a dicarboxylate transporter and could be active on 2-oxoglutarate as well, so is ignored. kgtP 2-oxoglutarate:H+ symporter KgtP curated:SwissProt::P0AEX3 curated:reanno::pseudo3_N2E3:AO353_03810 curated:reanno::pseudo5_N2C3_1:AO356_17790 uniprot:D8J257 ignore:TCDB::Q52000 # Transporters were identified using # query: transporter:2-ketoglutarate:alpha-ketoglutarate:ketoglutarate:2-oxoglutarate:oxoglutarate 2-oxoglutarate-transport: kgtP csbX 2-oxoglutarate permease csbX curated:TCDB::O05390 2-oxoglutarate-transport: csbX # Besides the system in Shewanellas, a similar system in Phaeobacter inhibens is important for # 2-oxoglutarate utilization: DctP = PGA1_c20680 = I7END8; DctQ = PGA1_c20670 = I7EY26; DctM = PGA1_c20660 = I7DRS6. # And for various related dctP-like components, it's not clear if alpha-ketoglutarate is a substrate or not, # so they are ignored. dctP 2-oxoglutarate TRAP transporter, solute receptor component DctP curated:reanno::SB2B:6938088 curated:SwissProt::A3QCW5 uniprot:I7END8 ignore:SwissProt::Q9KQR9 ignore:SwissProt::Q9HU18 ignore:SwissProt::P37735 dctQ 2-oxoglutarate TRAP transporter, small permease component DctQ curated:reanno::SB2B:6938089 curated:reanno::PV4:5208944 uniprot:I7EY26 # O07838 and Q9HU16 are reported to transport various dicarboxylates, and transport of # 2-oxoglutarate does not seem to have been tested, so they are marked ignore. dctM 2-oxoglutarate TRAP transporter, large permease component DctM curated:reanno::SB2B:6938090 curated:reanno::PV4:5208943 uniprot:I7DRS6 ignore:SwissProt::O07838 ignore:SwissProt::Q9HU16 2-oxoglutarate-transport: dctP dctQ dctM Psest_0084 2-oxoglutarate TRAP transporter, fused 4TM/12TM components curated:reanno::psRCH2:GFF84 uniprot:A8LI82 uniprot:E4PQE4 Psest_0085 2-oxoglutarate TRAP transporter, solute receptor component curated:reanno::psRCH2:GFF85 uniprot:A8LI83 uniprot:E4PQE3 2-oxoglutarate-transport: Psest_0084 Psest_0085 import succinate.steps:Dshi_1194 Dshi_1195 # TRAP dicarboxylate transporter 2-oxoglutarate-transport: Dshi_1194 Dshi_1195 # Eukaryotic antiporters and related carrier proteins were ignored # SdcL from Bacillus (TC 2.A.47.1.13) might be a low-affinity 2-oxoglutarate transporter; ignored all: 2-oxoglutarate-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