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 # TCDB::P0ABN5,ecocyc::DCUA-MONOMER,metacyc::DCUA-MONOMER # TCDB::P0ABN9,ecocyc::DCUB-MONOMER,metacyc::DCUB-MONOMER # TCDB::Q8ZLD2 # 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
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:
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