Definition of 2-oxoglutarate (alpha-ketoglutarate) catabolism
As rules and steps, or see full text
Rules
Overview: Since 2-oxoglutarate (also known as alpha-ketoglutarate) is a TCA cycle intermediate, GapMind represents uptake only.
- all: 2-oxoglutarate-transport
- 2-oxoglutarate-transport:
Steps
kgtP: 2-oxoglutarate:H+ symporter KgtP
- Curated sequence P0AEX3: Alpha-ketoglutarate permease. α-Ketoglutarate (oxoglutarate):H+ symporter. α-ketoglutarate:H+ symporter. α-ketoglutarate:H+ symporter
- Curated sequence AO353_03810: Alpha-ketoglutarate permease, MFS superfamily
- Curated sequence AO356_17790: alpha-ketoglutarate permease (MHS family)
- UniProt sequence D8J257: SubName: Full=Alpha-ketoglutarate permease of the major facilitator superfamily protein {ECO:0000313|EMBL:ADJ64840.1};
- Ignore hits to Q52000 when looking for 'other' hits (Dicarboxylate:H+ symporter)
- Comment: HSERO_RS16820 (D8J257) is similar and is important for 2-oxoglutarate utilization. Q52000 is a dicarboxylate transporter and could be active on 2-oxoglutarate as well, so is ignored.
- Total: 4 characterized proteins
csbX: 2-oxoglutarate permease csbX
dctP: 2-oxoglutarate TRAP transporter, solute receptor component DctP
- Curated sequence 6938088: alpha-ketoglutarate TRAP transporter, solute receptor component
- Curated sequence A3QCW5: C4-dicarboxylate-binding periplasmic protein DctP. dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), solute receptor component
- UniProt sequence I7END8: SubName: Full=C4-dicarboxylate-binding periplasmic protein DctP {ECO:0000313|EMBL:AFO91753.1};
- Ignore hits to Q9KQR9 when looking for 'other' hits (C4-dicarboxylate-binding periplasmic protein DctP)
- Ignore hits to Q9HU18 when looking for 'other' hits (C4-dicarboxylate-binding periplasmic protein DctP)
- Ignore hits to P37735 when looking for 'other' hits (C4-dicarboxylate-binding periplasmic protein DctP. DctP, component of Tripartite dicarboxylate:H+ symporter (substrates include: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate and mesaconate))
- Comment: 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.
- Total: 3 characterized proteins
dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ
- Curated sequence 6938089: alpha-ketoglutarate TRAP transporter, small permease component
- Curated sequence 5208944: dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), small permease component
- UniProt sequence I7EY26: SubName: Full=TRAP transporter, subunit DctQ {ECO:0000313|EMBL:AFO91752.1};
- Total: 3 characterized proteins
dctM: 2-oxoglutarate TRAP transporter, large permease component DctM
- Curated sequence 6938090: alpha-ketoglutarate TRAP transporter, large permease component
- Curated sequence 5208943: dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component
- UniProt sequence I7DRS6: SubName: Full=TRAP transporter, subunit DctM {ECO:0000313|EMBL:AFO91751.1};
- Ignore hits to O07838 when looking for 'other' hits (C4-dicarboxylate TRAP transporter large permease protein DctM. DctM, component of Tripartite dicarboxylate:H+ symporter (substrates include: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate and mesaconate))
- Ignore hits to Q9HU16 when looking for 'other' hits (C4-dicarboxylate TRAP transporter large permease protein DctM)
- Comment: 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.
- Total: 3 characterized proteins
Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components
- Curated sequence GFF84: alpha-ketoglutarate TRAP transporter, 4TM/12TM components
- UniProt sequence A8LI82: SubName: Full=TRAP transporter {ECO:0000313|EMBL:ABV92936.1};
- UniProt sequence E4PQE4: SubName: Full=TRAP transporter, 4TM/12TM fusion protein {ECO:0000313|EMBL:ADP96487.1};
- Total: 3 characterized proteins
Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component
- Curated sequence GFF85: alpha-ketoglutarate TRAP transporter, solute receptor component
- UniProt sequence A8LI83: SubName: Full=TRAP transporter solute receptor {ECO:0000313|EMBL:ABV92937.1};
- UniProt sequence E4PQE3: SubName: Full=Immunogenic protein {ECO:0000313|EMBL:ADP96486.1};
- Total: 3 characterized proteins
Dshi_1194: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components
- UniProt sequence A8LI82: SubName: Full=TRAP transporter {ECO:0000313|EMBL:ABV92936.1};
- UniProt sequence E4PQE4: SubName: Full=TRAP transporter, 4TM/12TM fusion protein {ECO:0000313|EMBL:ADP96487.1};
- Comment: The TRAP system Dshi_1194:Dshi_1195 (A8LI82,A8LI83) is important for utilization of succinate, fumarate, L-malate, and 2-oxoglutarate, as is the related system HP15_723:HP15_722 (E4PQE4,E4PQE3).
- Total: 2 characterized proteins
Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component
- UniProt sequence A8LI83: SubName: Full=TRAP transporter solute receptor {ECO:0000313|EMBL:ABV92937.1};
- UniProt sequence E4PQE3: SubName: Full=Immunogenic protein {ECO:0000313|EMBL:ADP96486.1};
- Total: 2 characterized proteins
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About GapMind
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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