GapMind for catabolism of small carbon sources

 

Definition of fumarate catabolism

As text, or see rules and steps

# Since fumarate is a TCA cycle intermediate, GapMind represent its uptake only.

dctA	fumarate:H+ symporter DctA	curated:CharProtDB::CH_014038	curated:TCDB::P96603	curated:TCDB::Q01857	curated:TCDB::Q1J1H5	curated:TCDB::Q848I3	curated:reanno::pseudo5_N2C3_1:AO356_18980	curated:SwissProt::Q9I4F5

# Transporters were identified using
# query: transporter:fumarate.
# Fumarate:succinate antiporters or fumarate:proton antiporters (probably for efflux) were not included.
# Subunits of succinate dehdydrogenase/fumarate reductase were also excluded.
fumarate-transport: dctA

sdcL	fumarate:Na+ symporter SdcL	curated:TCDB::A4QAL6	curated:SwissProt::Q21339	curated:TCDB::Q2FFH9	curated:TCDB::Q65NC0	curated:TCDB::Q9KNE0	curated:SwissProt::Q99SX1	curated:SwissProt::Q93655
fumarate-transport: sdcL

# Could not find experimental evidence for the specificity of A1JRS3, annotated in TCDB as a sulfate transporter
dauA	fumarate transporter DauA	curated:SwissProt::P0AFR2	ignore:TCDB::A1JRS3
fumarate-transport: dauA

# Three-part TRAP transporter DctMPQ
# In Phaeobacter inhibens, the system is important for fumarate utilization:
# PGA1_c20660 = dctM = I7DRS6,
# PGA1_c20680 = dctP = I7END8,
# PGA1_c20670 = dctQ = I7EY26.
# A closely related system in SB2B transports another dicarboxylate, 2-oxoglutarate,
# so its components are marked ignore
dctM	fumarate TRAP transporter, large permease component DctM	curated:SwissProt::O07838	curated:reanno::PV4:5208943	curated:SwissProt::Q9HU16	uniprot:I7DRS6	ignore:reanno::SB2B:6938090

dctP	fumarate TRAP transporter, substrate-binding component DctP	curated:SwissProt::A3QCW5	curated:SwissProt::P37735	ignore:reanno::SB2B:6938088	curated:SwissProt::Q9HU18	curated:SwissProt::Q9KQR9	uniprot:I7END8

dctQ	fumarate TRAP transporter, small permease component DctQ	curated:SwissProt::O07837	curated:reanno::PV4:5208944	ignore:reanno::SB2B:6938089	uniprot:I7EY26

fumarate-transport: dctM dctP dctQ

# O07488 is annotated in TCDB as a sulfate permease, but I did not find any data supporting this annotation
SLC26dg	fumarate transporter SLC26dg	curated:TCDB::Q1J2S8	ignore:TCDB::O07488
fumarate-transport: SLC26dg

import succinate.steps:Dshi_1194 Dshi_1195 # TRAP dicarboxylate transporter
fumarate-transport: Dshi_1194 Dshi_1195

all: fumarate-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 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