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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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