GapMind for catabolism of small carbon sources

 

Definition of L-malate catabolism

As text, or see rules and steps

# Since L-malate is a TCA cycle intermediate, catabolic reactions are not represented in GapMind.

sdlC	L-malate:Na+ symporter SdlC	curated:TCDB::A4QAL6	curated:CharProtDB::CH_091173	curated:SwissProt::Q21339	curated:TCDB::Q2FFH9	curated:TCDB::Q65NC0	curated:TCDB::Q9KNE0	curated:SwissProt::Q99SX1

# Transporters were identified using
# query: transporter:malate:L-malate:(S)-malate.
# (None of these transporters seem to be specific for D-malate, although
# E. coli can grow with D-malate as the sole source of carbon.)
# In B. subtilis, mleN (uniprot:P54571) can contribute to growth on malate by
# a malate:lactate antiport mechanism (PMID:10903309), but it is
# not clear how this could be the sole malate uptake system for growth
# (no fixed carbon would be available for growth), so it was excluded.
L-malate-transport: sdlC

dctA	L-malate:H+ symporter DctA	curated:TCDB::P96603	curated:TCDB::Q01857	curated:TCDB::Q1J1H5	curated:TCDB::Q848I3	curated:reanno::pseudo5_N2C3_1:AO356_18980	curated:SwissProt::Q9I4F5	curated:CharProtDB::CH_014038
L-malate-transport: dctA

# This cluster seems to include both H+ and Na+ dependent malate transporters, as well
# as Lactococcus lactis mleP or maeP (O07032) which also exports lactate.
maeN	malate transporter maeN	curated:SwissProt::O05256	curated:TCDB::O07032	curated:TCDB::P94363	curated:TCDB::Q53787
L-malate-transport: maeN

# 3-component TRAP transporter dctMPQ.
# In Phaeobacter inhibens, the system is important for L-malate utilization:
# PGA1_c20660 = dctM = I7DRS6;
# PGA1_c20680 = dctP = I7END8;
# PGA1_c20670 = dctQ = I7EY26.
# A very similar system is present in Shewanella amazonensis SB2B, which cannot grow on L-malate;
# it is still possible that this system transports L-malate, so it is marked ignore.
dctM	L-malate TRAP transporter, large permease component DctM	curated:SwissProt::O07838	curated:reanno::PV4:5208943	curated:SwissProt::Q9HU16	uniprot:I7DRS6	ignore:reanno::SB2B:6938090

# Q9HVH5  = PA4616 is a malate-binding substrate-binding protein (PMC4310620)
dctP	L-malate TRAP transporter, substrate-binding component DctP	curated:SwissProt::A3QCW5	curated:SwissProt::P37735	curated:SwissProt::Q9KQR9	curated:SwissProt::Q9HU18	uniprot:I7END8	ignore:reanno::SB2B:6938088	uniprot:Q9HVH5	curated:reanno::PV4:5208945

dctQ	L-malate TRAP tranpsorter, small permease component DctQ	curated:SwissProt::O07837	curated:reanno::PV4:5208944	uniprot:I7EY26	ignore:reanno::SB2B:6938089

L-malate-transport: dctM dctP dctQ

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

mae1	L-malate:H+ symporter Mae1	curated:CharProtDB::CH_016604
L-malate-transport: mae1

mleP	malate permease MleP	curated:TCDB::Q48797
L-malate-transport: mleP

# Eukaryotic antiporters or carrier porters were excluded.
# Eukaryotic translocators (DIT1/DIT2) which export glutamate were excluded.
# Aluminum-activated efflux systems were excluded.

all: L-malate-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