GapMind for catabolism of small carbon sources

 

Definition of 2-oxoglutarate (alpha-ketoglutarate) catabolism

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

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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:

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:

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