GapMind for catabolism of small carbon sources


Definition of L-aspartate catabolism

As text, or see rules and steps

# Aspartate can be transaminated to oxaloacetate, which is an
# intermediate in central metabolism, so GapMind only represents uptake.

# First, the ABC transporters

# BztABCD from Rhodobacter capsulatus (Rhodopseudomonas capsulata),  TC 3.A.1.3.7.
# Ignore similarity of bztA to general amino acid porter AapJ and to broad transporter SMc02118.
bztA	aspartate/asparagine ABC transporter, substrate-binding component BztA	curated:TCDB::Q52663	ignore:TCDB::Q52812	ignore:reanno::Smeli:SMc02118
bztB	aspartate/asparagine ABC transporter, permease component 1 (BztB)	curated:CharProtDB::CH_011913
bztC	aspartate/asparagine ABC transporter, permease component 2 (BztC)	curated:TCDB::Q52665
# Ignore similarity of bztD to general amino acid porter AapP, SMc02121, Pf6N2E2_5405
bztD	aspartate/asparagine ABC transporter, ATPase component (BztD)	curated:TCDB::Q52666	ignore:TCDB::Q52815	ignore:reanno::Smeli:SMc02121

# To find transporters, used query: transporter:aspartate:L-aspartate
aspartate-transport:  bztA bztB bztC bztD

peb1A	aspartate ABC transporter, perisplasmic substrate-binding component Peb1A	curated:CharProtDB::CH_021449
peb1B	aspartate ABC transporter, permease component 1 (Peb1B)	curated:TCDB::A1VZQ3
peb1C	aspartate ABC transporter, ATPase component Peb1C	curated:TCDB::A3ZI83

# Pep1ABC from Campylobacter jejuni, TC 3.A.1.3.16, is listed with three components,
# but a second permease subunit (CJJ81176_0926 = Cj0919c = A0A0H3PA28) is conserved nearby, and
# a genetic study (PMC5438104) found a similar phenotype for this putative subunit as for
# peb1A/peb1B. We named it peb1D.
peb1D	aspartate ABC transporter, permease component 2 (Peb1D)	uniprot:A0A0H3PA28

aspartate-transport: peb1A peb1B peb1C peb1D

# AatJMQP from Pseudomonas putida KT2440, TC 3.A.1.3.19,
# is quite similar to an aspartate ABC transporter from P. fluorescens N2E3
# and to GltIJKL from E. coli.
# It is also very similar to asparagine/glutamate transporters from other Pseudomonas, which might transport
# aspartate as well.
# (aatJ = PP1071 or AO353_16290 or gltI)
aatJ	aspartate/asparagine ABC transporter, substrate-binding component AatJ	curated:TCDB::Q88NY2	curated:reanno::pseudo3_N2E3:AO353_16290	curated:reanno::pseudo1_N1B4:Pf1N1B4_771	curated:reanno::pseudo13_GW456_L13:PfGW456L13_4770	ignore:TCDB::Q9I402	curated:CharProtDB::CH_002441

# aatQ = PP1070 or AO353_16285 or gltJ
aatQ	aspartate/asparagine ABC transporter, permease component 1 (AatQ)	curated:TCDB::Q88NY3	curated:reanno::pseudo3_N2E3:AO353_16285	curated:reanno::pseudo1_N1B4:Pf1N1B4_772	curated:reanno::pseudo13_GW456_L13:PfGW456L13_4771	ignore:TCDB::Q9I403	curated:SwissProt::P0AER3

# aatM = PP1069 or AO353_16280 or gltK
aatM	aspartate/asparagine ABC transporter, permease component 2 (AatM)	curated:TCDB::Q88NY4	curated:reanno::pseudo3_N2E3:AO353_16280	curated:reanno::pseudo1_N1B4:Pf1N1B4_773	curated:reanno::pseudo13_GW456_L13:PfGW456L13_4772	ignore:TCDB::Q9I404	curated:SwissProt::P0AER5

# aatP = PP1068 or AO353_16275 or gltL
aatP	aspartate/asparagine ABC transporter, ATPase component	curated:TCDB::Q88NY5	curated:reanno::pseudo3_N2E3:AO353_16275	curated:reanno::pseudo13_GW456_L13:PfGW456L13_4773	curated:reanno::pseudo1_N1B4:Pf1N1B4_774	ignore:TCDB::Q9I405	curated:TCDB::P0AAG3

aspartate-transport: aatJ aatQ aatM aatP

# dmeA is described in TCDB as an aspartate transporter, but the cited paper (PMC:PMC4507348)
# instead suggests that Synpcc7942_0246 to Synpcc7942_0249 is an ABC transporter for aspartate and glutamate.
# 3/4 subunits are closely related to those of Anabaena N-II (NatFGH-BgtA), which is the main aspartate transporter
# (PMID:18208492).
# (For N-II, TC 3.A.1.3.18 lists 3 components NatFGH).
# Of Synpcc7942_0246 to Synpcc7942_0249: _0246 = Q31RP1 is similar to NatF,
# _0247 = Q31RP0 is a permease component and is usually named BgtB (but is *not* closely related to Anabaena BgtB),
# _0248 = Q31RN9 is NatH-like, and _0249 = Q31RN8 is BgtA-like.
# Anabaena bgtB = alr3187 is not closely related to _0247.
natF	aspartate ABC transporter, substrate-binding component NatF	curated:TCDB::Q8YPM9	uniprot:Q31RP1
bgtB'	aspartate ABC transporter, permease component 1 (BgtB)	uniprot:Q31RP0
natH	aspartate ABC transporter, permease component 2 (NatH)	curated:TCDB::Q8YPM7	uniprot:Q31RN9

# Anabanea bgtA = alr4167 = Q8YSA2.
bgtA	aspartate ABC transporter, ATPase component BgtA	uniprot:Q31RN8	curated:TCDB::Q8YSA2

aspartate-transport: natF bgtB' natH bgtA

natG	aspartate ABC transporter, permease component 1 (NatG)	curated:TCDB::Q8YPM8

aspartate-transport: natF natG natH bgtA

# AapJQMP from Rhizobium leguminosarum is described in glutamate.steps
import glutamate.steps:aapJ aapQ aapM aapP
aspartate-transport: aapJ aapQ aapM aapP

# The original cluster was entirely eukaryotic except for gltPh from Pyrococcus horikoshii.
# Added gltT from Bacillus caldotenax (CharProtDB::CH_088342), which is also an aspartate transporter.
# So, named it glt.
# Ignore Q9N280 which has a questionable annotation in BRENDA.
# But the more distantly related protein AO356_01905 (uniprot:A0A0N9WTL5) also seems to be an aspartate transporter.
# Similarly, the related protein RR42_RS03990 (A0A0C4Y5S4) is specifically important for asparagine utilization.
# Asparagine is probably cleaved in the periplasm (by RR42_RS12610 or RR42_RS26140)
# so this is probably an aspartate transporter as well.
# And the related protein uniprot:P24944 (CH_088342) or uniprot:P24943 is an aspartate transporter.
# This cluster also includes the aspartate transporter DctA from E. coli; it is almost
# 80% identical to Pseudomonas dicarboxylate transporters whose activity on
# aspartate is uncertain. As these are not important for aspartate utilization (AO356_18980, AO353_02800),
# do not mark them as ignored.
# The gltP from B. subtilis (uniprot:P39817) was added manually.
# A related aspartate/glutamate transporter was identified in Shewanella amazonensis SB2B (Sama_1319, uniprot:A1S570)
# using fitness data.
glt	aspartate:proton symporter Glt	curated:SwissProt::P21345	curated:CharProtDB::CH_014038	uniprot:A0A0N9WTL5	uniprot:A0A0C4Y5S4	curated:CharProtDB::CH_088342	curated:SwissProt::P24943	curated:SwissProt::P43003	curated:CharProtDB::CH_091614	curated:SwissProt::O35544	curated:SwissProt::O35921	curated:SwissProt::O57321	curated:SwissProt::O59010	curated:SwissProt::P24943	curated:SwissProt::P31596	curated:SwissProt::P31597	curated:SwissProt::P43004	curated:SwissProt::P43005	curated:SwissProt::P43006	curated:SwissProt::P46411	curated:SwissProt::P48664	curated:SwissProt::P51906	curated:SwissProt::P51907	curated:SwissProt::P56564	curated:SwissProt::Q9N1R2	curated:TCDB::B0W0K4	curated:TCDB::Q10901	curated:TCDB::Q8T0S9	curated:CharProtDB::CH_088342	ignore:BRENDA::Q9N280	curated:SwissProt::P39817	uniprot:A1S570

aspartate-transport: glt

# Ignore E. coli YcaM which does not seem to be characterized
acaP	aspartate permease AcaP	curated:SwissProt::A2RL65	curated:TCDB::F2HJG8	ignore:TCDB::P75835

aspartate-transport: acaP

SLC7A13	sodium-independent aspartate transporter	curated:SwissProt::Q8TCU3	curated:SwissProt::Q91WN3

aspartate-transport: SLC7A13

# BPHYT_RS17540 belongs to the APC (amino acid/polyamine/organocation) family of permeases
# and is specifically important with asparagine (or glutamine) as the sole source of carbon or nitrogen.
# Asparagine is probably cleaved in the periplasm by BPHYT_RS08815 before uptake of asparatate.
BPHYT_RS17540	aspartate:H+ (or asparagine) symporter	uniprot:B2SZ32

aspartate-transport: BPHYT_RS17540

yveA	aspartate:proton symporter YveA	curated:SwissProt::O07002

aspartate-transport: yveA

# Ignore TC 2.A.53.3.9 / A1JRS3 which has structural information only (no subunit information)
dauA	dicarboxylic acid transporter DauA	curated:SwissProt::P0AFR2	ignore:TCDB::A1JRS3

aspartate-transport: dauA

# Ignore aspartate-fumarate antiporters DcuA, DcuB, or YhiT  -- these are important for
# utilization as a nitrogen source, but does not permit utilization as a carbon source

# Similarly, ignore aspartate-alanine antiporters (AspT)
# SwissProt::Q8L3K8,TCDB::Q8L3K8
# TCDB::Q845W9

# Ignore mitochondrial glutamate/aspartate antiporters 
# CharProtDB::CH_091135,SwissProt::Q9UJS0,TCDB::Q9UJS0
# CharProtDB::CH_091355,SwissProt::O75746,TCDB::O75746
# CharProtDB::CH_091540,SwissProt::Q12482,TCDB::Q12482

all: aspartate-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