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 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