PaperBLAST
PaperBLAST Hits for SwissProt::Q21339 Sodium-dependent high-affinity dicarboxylate transporter 3; Na(+)/dicarboxylate cotransporter 3; NaDC-3; ceNaDC3 (Caenorhabditis elegans) (566 a.a., MSLSLHLSGW...)
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>SwissProt::Q21339 Sodium-dependent high-affinity dicarboxylate transporter 3; Na(+)/dicarboxylate cotransporter 3; NaDC-3; ceNaDC3 (Caenorhabditis elegans)
MSLSLHLSGWPENSESRQRMLESSSSTNFVQHFVSREISNKERLLSLFRRLRNGLVLVLT
PLFFGQMLNWEGPEWKCAYCVCIIAVYWMSEVMPLAVTAMLPVVLFPLVGVLDANTTAKE
YMNDTNFLFIGGLIMAAAVEKCDLHERVALSVLRCVGSEPKWIMLGFMTVTALLSSFISN
TATTAMMVPIGQSVVQQLISSFQHHPTNGERGRLGCKKMATGLVLSICFAANIGGTGTAT
GTPSNLVMLGQLSALFPKVDGSLNYVTWIFFAYPLMLLCLFVAWMTLVSFFLRDAPEKDE
AVTEMLKTRYNELPRMTYAEKSVFVCFCILLSLWVFRNPGVVPGFGVFFKKGAYTDATSA
MIVAFLLFVLPSERPDLATYIKKEDLKKRGCLMDWKTMQETFPWSVVLLLGGGFALAAGV
KESGLSLLIGNSLSSIEHLPLWILQLLTMLIAMVITNICSNTVTASIFVPIVATLAQRAG
HHPFTLMLPTTLASSFAFIFPVGTPPNAIVFGSGMVKVSDMAFVGGIISLELLVLTVLYM
NSIAYLTLPLLEFPTWAIIANSTMQQ
Running BLASTp...
Found 175 similar proteins in the literature:
NAD3_CAEEL / Q21339 Sodium-dependent high-affinity dicarboxylate transporter 3; Na(+)/dicarboxylate cotransporter 3; NaDC-3; ceNaDC3 from Caenorhabditis elegans (see paper)
TC 2.A.47.1.8 / Q21339 High affinity dicarboxylate:Na+ symporter, NaDC2 (INDY2) (relative affinities: fumarate > malate > α-ketoglutarate > maleate > succinate > lactate) (see 2 papers)
NP_001022673 Sodium-dependent high-affinity dicarboxylate transporter 3 from Caenorhabditis elegans
100% identity, 100% coverage
- function: High-affinity sodium-dicarboxylate cotransporter that accepts a range of tricarboxylic acid-cycle intermediates with 4-5 carbon atoms. There is no interaction with monocarboxylates. Plays a role in the regulation of life span.
- substrates: Alpha-ketoglutarate, Dicarboxylates, Fumarate, Lactate, Maleate, Na+, Succinate, malate
- Membrane topology structure of human high-affinity, sodium-dependent dicarboxylate transporter.
Bai, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2007 (PubMed)- GeneRIF: Topography of 11 transmembrane domains with an extracellular C terminus and an intracellular N terminus of this protein.
- Structural and functional characteristics of two sodium-coupled dicarboxylate transporters (ceNaDC1 and ceNaDC2) from Caenorhabditis elegans and their relevance to life span.
Fei, The Journal of biological chemistry 2003 (PubMed)- GeneRIF: structural and functional characteristics of two sodium-coupled dicarboxylate transporters and their relevance to life span.
NAD1_CAEEL / Q93655 Sodium-dependent low-affinity dicarboxylate transporter 1; Na(+)/dicarboxylate cotransporter 1; NaDC-1; ceNaDC1 from Caenorhabditis elegans (see paper)
TC 2.A.47.1.7 / Q93655 Low affinity dicarboxylate:Na+ symporter, NaDC1 (INDY1) (relative affinities: succinate > fumarate > α-ketoglutarate > malate > lactate > maleate) (see 2 papers)
NP_510473 Sodium-dependent low-affinity dicarboxylate transporter 1 from Caenorhabditis elegans
47% identity, 87% coverage
8uvcA / Q8WWT9 Structure of nadc3-akg complex (see paper)
41% identity, 89% coverage
- Ligands: sodium ion; 2-oxoglutaric acid; cholesterol (8uvcA)
S13A5_HUMAN / Q86YT5 Na(+)/citrate cotransporter; NaCT; Sodium-coupled citrate transporter; Sodium-dependent citrate transporter; Solute carrier family 13 member 5 from Homo sapiens (Human) (see 7 papers)
TC 2.A.47.1.9 / Q86YT5 Na+-coupled citrate transporter (NaCT) (Km=20 μM) (also may transport dicarboxylates and other tricarboxylates with lower affinity) (Inoue et al., 2002b; Bergeron et al. 2013). Na+:citrate = 3-4:1 (Bergeron et al. 2013). Na+:citrate = 3-4:1 from Homo sapiens (Human) (see 5 papers)
40% identity, 86% coverage
- function: High-affinity sodium/citrate cotransporter that mediates the entry of citrate into cells, which is a critical participant of biochemical pathways (PubMed:12445824, PubMed:12826022, PubMed:26324167, PubMed:26384929, PubMed:30054523, PubMed:33597751). May function in various metabolic processes in which citrate has a critical role such as energy production (Krebs cycle), fatty acid synthesis, cholesterol synthesis, glycolysis, and gluconeogenesis (PubMed:12826022). Transports citrate into the cell in a Na(+)- dependent manner, recognizing the trivalent form of citrate (physiological pH) rather than the divalent form (PubMed:12445824, PubMed:12826022, PubMed:26324167, PubMed:26384929, PubMed:30054523, PubMed:33597751). Can recognize succinate as a substrate, but its affinity for succinate is several fold lower than for citrate (PubMed:26324167). The stoichiometry is probably 4 Na(+) for each carboxylate, irrespective of whether the translocated substrate is divalent or trivalent, rendering the process electrogenic (PubMed:12445824, PubMed:12826022). Involved in the regulation of citrate levels in the brain (By similarity).
catalytic activity: citrate(out) + 4 Na(+)(out) = citrate(in) + 4 Na(+)(in) (RHEA:65664)
subunit: Homodimer. - substrates: Citrate, Dicarboxylates, Na+, Tricarboxylates
- Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Kopel, The Biochemical journal 2021 - “...Q9UKG4 Na + /sulfate cotransporter SUT1/NaS2 Sulfate Placenta (BBM) Testis Heart 7q33 None SLC13A5 2.A.47.1.9 Q86YT5 Na + /citrate cotransporter NaCT/NaC2 Citrate Succinate Pyruvate Liver (SM/BLM) Brain (neuron) Testis (germ cell) 17p13.1 EIEE25 (DEE25) OMIM # 615905 BBM, lumen-facing brush-border membrane in kidney and intestinal epithelial...”
- Drosophila INDY and Mammalian INDY: Major Differences in Transport Mechanism and Structural Features despite Mostly Similar Biological Functions.
Jaramillo-Martinez, Metabolites 2021 - “...red boxes. The accession numbers for the protein sequences are Q9VVT2 for Drosophila INDY and Q86YT5 for human INDY. Figure 4 Inward-facing models for Drosophila INDY and human INDY (NaCT). ( A ) The 3D model for Drosophila INDY, created with AlphaFold, shows an inward-facing conformation...”
- Functional analysis of a species-specific inhibitor selective for human Na+-coupled citrate transporter (NaCT/SLC13A5/mINDY).
Higuchi, The Biochemical journal 2020 - “...7.01 software. Homology modeling The primary sequence alignments of human and mouse NaCT (accession numbers Q86YT5, Q67BT3, respectively) were performed using PROMALS3D [ 21 ]. Based on the resulting primary sequence alignment, homology models of human and mouse NaCT were computed using the MODELLER program [...”
- THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Common abreviation NaS1 NaC1 NaC3 NaS2 NaC2 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3 2 citric acid , succinic acid citric acid ,...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3 2 citric acid , succinic acid citric acid , succinic acid SO 4 2 citric acid...”
- The Concise Guide to PHARMACOLOGY 2013/14: transporters
Alexander, British journal of pharmacology 2013 - “...NaC1 NaC3 NaS2 NaC2 HGNC, UniProt SLC13A1, Q9BZW2 SLC13A2, Q13183 SLC13A3, Q8WWT9 SLC13A4, Q9UKG4 SLC13A5, Q86YT5 Endogenous substrates SeO42-, S2O32-, SO42- citric acid, succinic acid citric acid, succinic acid SO42- citric acid, pyruvic acid Stoichiometry 3 Na + : 1 SO 4 2- (in) 3 Na...”
XP_425404 solute carrier family 13 member 2 from Gallus gallus
40% identity, 88% coverage
S13A2_MOUSE / Q9ES88 Solute carrier family 13 member 2; Na(+)/dicarboxylate cotransporter 1; NaDC-1; Renal sodium/dicarboxylate cotransporter from Mus musculus (Mouse) (see 2 papers)
NP_071856 solute carrier family 13 member 2 from Mus musculus
40% identity, 83% coverage
- function: Low-affinity sodium-dicarboxylate cotransporter, that mediates the entry of citric acid cycle intermediates, such as succinate, citrate, fumarate and alpha-ketoglutarate (2-oxoglutarate) into the small intestine and renal proximal tubule (By similarity) (PubMed:10966927). Can transport citrate in a Na(+)-dependent manner, recognizing the divalent form of citrate rather than the trivalent form which is normally found in blood (PubMed:10966927). Transports the dicarboxylate into the cell with a probable stoichiometry of 3 Na(+) for 1 divalent dicarboxylate, rendering the process electrogenic (By similarity). Has a critical role in renal dicarboxylate transport (PubMed:17410095).
catalytic activity: succinate(out) + 3 Na(+)(out) = succinate(in) + 3 Na(+)(in) (RHEA:71919)
catalytic activity: fumarate(out) + 3 Na(+)(out) = fumarate(in) + 3 Na(+)(in) (RHEA:71931)
catalytic activity: 2-oxoglutarate(out) + 3 Na(+)(out) = 2-oxoglutarate(in) + 3 Na(+)(in) (RHEA:71939)
disruption phenotype: Deficient mice display increased urinary excretion of citrate, alpha-ketoglutarate, fumarate, and malate and a modest increase in succinate. Despite the increased excretion, there is no significant change in plasma citrate concentration. No other phenotypic change is identified in these mice. Transporter deficiency do not affect renal function under normal physiological conditions, nor to response to renal injury. - Regulation of renal NaDC1 expression and citrate excretion by NBCe1-A.
Osis, American journal of physiology. Renal physiology 2019 - GeneRIF: NaDC1 expression increased only in the proximal convoluted tubules and proximal straight tubules in knockout mice blocked both the citrate and NaDC1 changes
- SLC26A6 and NaDC-1 transporters interact to regulate oxalate and citrate homeostasis.
Ohana, Journal of the American Society of Nephrology : JASN 2013 - GeneRIF: Slc26a6-null mice exhibit increased renal and intestinal sodium-dependent succinate uptake, as well as urinary hyperoxaluria and hypocitraturia, but no change in urinary pH, indicating enhanced transport activity of NaDC-1.
- Acid regulation of NaDC-1 requires a functional endothelin B receptor.
Liu, Kidney international 2010 (PubMed)- GeneRIF: The acid-activated pathway mediating stimulation of kidney NaDC-1 activity requires a functional ET(B) receptor in vivo and in vitro.
- Generation and characterization of sodium-dicarboxylate cotransporter-deficient mice.
Ho, Kidney international 2007 (PubMed)- GeneRIF: Sodium dicarboxylate cotransporter is involved in regulating levels of various Krebs cycle intermediates in the kidney, although impaired uptake of these intermediates does not significantly affect renal function under normal or ischemic stress.
- Transmembrane helices 3 and 4 are involved in substrate recognition by the Na+/dicarboxylate cotransporter, NaDC1.
Oshiro, Biochemistry 2006 (PubMed)- GeneRIF: Substrate-dependent inward currents, measured using two-electrode voltage clamp, were similar for glutarate & succinate in Xenopus oocytes expressing mouse NaDC1. Currents evoked by glutarate in rabbit NaDC1 were about 5% of succinate-dependent currents.
S13A2_RAT / P70545 Solute carrier family 13 member 2; Intestinal sodium/dicarboxylate cotransporter; Na(+)/dicarboxylate cotransporter 1; NaDC-1 from Rattus norvegicus (Rat) (see 2 papers)
TC 2.A.47.1.3 / O35055 The brush boarder intestinal and renal electrogenic, Na -dependent, low affinity (0.1-4.0mM), dicarboxylate (succinate, fumarate, malate, α-ketoglutarate, oxaloacetate, L- and D-glutamate, and citrate):H cotransporter, NaDC-1 or SDCT1. Functions in acid regulation. An acidic pH stimullates citrate uptake; acid stimulation is mediated by endothelin-1 (ET-1) and its receptor from Rattus norvegicus (Rat) (see 4 papers)
NP_113934 solute carrier family 13 member 2 from Rattus norvegicus
41% identity, 82% coverage
- function: Low-affinity sodium-dicarboxylate cotransporter, that mediates the entry of citric acid cycle intermediates, such as succinate, citrate, fumarate and alpha-ketoglutarate (2-oxoglutarate) into the small intestine and renal proximal tubule (PubMed:9691021, PubMed:9694847). Transports the dicarboxylate into the cell with a probable stoichiometry of 3 Na(+) for 1 divalent dicarboxylate, rendering the process electrogenic (PubMed:9691021, PubMed:9694847). Citrate is transported in protonated form as a divalent anion, rather than the trivalent form which is normally found in blood (PubMed:9694847). Has a critical role in renal dicarboxylate transport (By similarity).
catalytic activity: succinate(out) + 3 Na(+)(out) = succinate(in) + 3 Na(+)(in) (RHEA:71919)
catalytic activity: fumarate(out) + 3 Na(+)(out) = fumarate(in) + 3 Na(+)(in) (RHEA:71931)
catalytic activity: 2-oxoglutarate(out) + 3 Na(+)(out) = 2-oxoglutarate(in) + 3 Na(+)(in) (RHEA:71939) - substrates: Na+
- Role of intestinal trefoil factor in protecting intestinal epithelial cells from burn-induced injury.
Hu, Scientific reports 2018 - GeneRIF: ITF can improve cytomorphosis ability for promoting cell migration with limited effect on cell proliferation, which can be enhanced with addition of mucin. The main mechanism of ITF in maintaining intestinal mucosal barrier may be attributed to acceleration of cell migration.
- Renal expression and urinary excretion of Na+/dicarboxylate cotransporter 1 (NaDC1) in obstructive nephropathy: a candidate biomarker for this pathology.
Campagno, Pflugers Archiv : European journal of physiology 2018 (PubMed)- GeneRIF: The renal expression of NaDC1 was decreased in the mouse model of obstructive nephropathy. The urinary excretion of NaDC1 increased after short times of ureteral obstruction.
- Expression of renal Oat5 and NaDC1 transporters in rats with acute biliary obstruction.
Brandoni, World journal of gastroenterology 2015 - GeneRIF: Cholestasis induced by common bile duct ligation in the rat induces upregulation of NaDC1 in kidneys.
- Localization of the calcium-regulated citrate transport process in proximal tubule cells.
Hering-Smith, Urolithiasis 2014 - GeneRIF: NaDC1 was predominantly located in discrete apical membrane or subapical areas in proximal kidney tubules.
- A short-term ingestion of fructo-oligosaccharides increases immunoglobulin A and mucin concentrations in the rat cecum, but the effects are attenuated with the prolonged ingestion.
Komura, Bioscience, biotechnology, and biochemistry 2014 (PubMed)- GeneRIF: These findings may explain the fructo-oligosaccharides-induced early elevation of IgA and mucin
- A Rhodobacter capsulatus member of a universal permease family imports molybdate and other oxyanions
Gisin, Journal of bacteriology 2010 - “...the ArsB/NhaD family AAB08008 (SacI) NP_113934 (NaDC-1) a Rhodobacter capsulatus (Alphaproteobacteria) Paracoccus denitrificans (Alphaproteobacteria)...”
- Oat5 and NaDC1 protein abundance in kidney and urine after renal ischemic reperfusion injury.
Di, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society 2009 - GeneRIF: This is the first study on Oat5 and NaDC1 detection in urine.
- Anterior segment alterations and comparative aqueous humor proteomics in the buphthalmic rabbit (an American Ophthalmological Society thesis).
Edward, Transactions of the American Ophthalmological Society 2011
7jsjA / Q86YT5 Structure of the nact-pf2 complex (see paper)
43% identity, 85% coverage
- Ligands: (2r)-2-[2-(4-tert-butylphenyl)ethyl]-2-hydroxybutanedioic acid; sodium ion (7jsjA)
A2VD10 Solute carrier family 13 (Sodium-dependent dicarboxylate transporter), member 3 from Rattus norvegicus
NP_074057 Na(+)/dicarboxylate cotransporter 3 from Rattus norvegicus
38% identity, 81% coverage
S13A3_HUMAN / Q8WWT9 Na(+)/dicarboxylate cotransporter 3; NaDC-3; hNaDC3; Na(+)-coupled carboxylate transporter 3; NaC3; Sodium-dependent high-affinity dicarboxylate transporter 2; Solute carrier family 13 member 3; SLC13A3 from Homo sapiens (Human) (see 8 papers)
TC 2.A.47.1.15 / Q8WWT9 Solute carrier family 13 member 3 (Na+/dicarboxylate cotransporter 3) (NaDC-3) (hNaDC3) (Sodium-dependent high-affinity dicarboxylate transporter 2) from Homo sapiens (see 6 papers)
37% identity, 84% coverage
- function: High-affinity sodium-dicarboxylate cotransporter that accepts a range of substrates with 4-6 carbon atoms, such as the citric acid cycle intermediates succinate and alpha-ketoglutarate (2-oxoglutarate), as well as other compounds including N-acetyl-L-aspartate (PubMed:10794676, PubMed:10992006, PubMed:15561973, PubMed:17356845, PubMed:17426067, PubMed:24247155, PubMed:30635937). Transports the dicarboxylate into the cell with a probable stoichiometry of 3 Na(+) for 1 divalent dicarboxylate, rendering the process electrogenic (PubMed:10794676, PubMed:10992006). Can transport citrate in a Na(+)- dependent manner, recognizing the divalent form of citrate rather than the trivalent form which is normally found in blood (PubMed:10794676).
catalytic activity: succinate(out) + 3 Na(+)(out) = succinate(in) + 3 Na(+)(in) (RHEA:71919)
catalytic activity: 2-oxoglutarate(out) + 3 Na(+)(out) = 2-oxoglutarate(in) + 3 Na(+)(in) (RHEA:71939)
catalytic activity: N-acetyl-L-aspartate(out) + 3 Na(+)(out) = N-acetyl-L- aspartate(in) + 3 Na(+)(in) (RHEA:71947)
catalytic activity: glutarate(out) + 3 Na(+)(out) = glutarate(in) + 3 Na(+)(in) (RHEA:71955)
catalytic activity: fumarate(out) + 3 Na(+)(out) = fumarate(in) + 3 Na(+)(in) (RHEA:71931)
catalytic activity: malate(out) + 3 Na(+)(out) = malate(in) + 3 Na(+)(in) (RHEA:72295)
catalytic activity: 2,2-dimethylsuccinate(out) + 3 Na(+)(out) = 2,2- dimethylsuccinate(in) + 3 Na(+)(in) (RHEA:72287)
catalytic activity: 2,3-dimethylsuccinate(out) + 3 Na(+)(out) = 2,3- dimethylsuccinate(in) + 3 Na(+)(in) (RHEA:72291) - substrates: Dicarboxylates, Na+
- Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue.
Kozlova, Biology 2023 - “...Q5U4P2 canonic HepG2 cells NEDD4L-205 Q96PU5 canonic HepG2 cells NEDD4L-225 K7EKL1 predicted HepG2 cells SLC13A3-201 Q8WWT9 canonic HepG2 cells SLC13A3-205 C9J4A3 predicted...”
- Proteomics and Metabolomics Analysis Reveals the Toxicity of ZnO Quantum Dots on Human SMMC-7721 Cells.
Yang, International journal of nanomedicine 2023 - “...MGMT Down P16401 Histone H1.5 H15 Down A6NDN3 Golgin subfamily A member 6B GOG6B Down Q8WWT9 Solute carrier family 13 member 3 S13A3 Down Q9NZR1 Tropomodulin-2 TMOD2 Down Q9UPM8 AP-4 complex subunit epsilon-1 AP4E1 Down P04908 Histone H2A type 1-B/E H2A1B Down Q8N302 Angiogenic factor with...”
- Liver Graft Proteomics Reveals Potential Incipient Mechanisms behind Early Renal Dysfunction after Liver Transplantation
Norén, International journal of molecular sciences 2022 - “...structure Arginine and proline metabolism Q9UKK3 PARP4 Protein mono-ADP-ribosyltransferase PARP4 0.47 0.03 Cell death Apoptosis Q8WWT9 SLC13A3 Solute carrier family 13 member 3 0.42 0.02 Transport Sodium-coupled sulphate, di- and tri-carboxylate transporters ijms-23-11929-t003_Table 3 Table 3 The Suzuki histological criteria. Grade Congestion Vacuolization Necrosis 0 None...”
- Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Kopel, The Biochemical journal 2021 - “...affinity) NaDC1/NaC1 Succinate -Ketoglutarate Fumarate Malate Citrate Kidney (BBM) Intestine (BBM) 17q11.2 None SLC13A3 2.A.47.1.15 Q8WWT9 Na + /dicarboxylate cotransporter (high-affinity) NaDC3/NaC3 Succinate -Ketoglutarate Fumarate Malate Citrate Kidney (BBM) Liver (SM/BLM) Placenta (BBM) 20q13.12 None SLC13A4 2.A.47.1.14 Q9UKG4 Na + /sulfate cotransporter SUT1/NaS2 Sulfate Placenta (BBM)...”
- Periplocymarin Induced Colorectal Cancer Cells Apoptosis Via Impairing PI3K/AKT Pathway.
Cheng, Frontiers in oncology 2021 - “...Q9UBU7 Protein DBF4 homolog A DBF4 2.26 0.03 Q8IZ40 REST corepressor 2 RCOR2 2.25 0.00 Q8WWT9 Solute carrier family 13 member 3 SLC13A3 2.24 0.03 Q08AE8 Protein spire homolog 1 SPIRE1 2.19 0.01 Q9H9D4 Zinc finger protein 408 ZNF408 2.15 0.00 Q9UFH2 Dynein heavy chain 17,...”
- Two subgroups in systemic lupus erythematosus with features of antiphospholipid or Sjögren's syndrome differ in molecular signatures and treatment perspectives.
Idborg, Arthritis research & therapy 2019 - “...aPL+ SLE ITGB1 P05556 Integrin beta-1 Cell adhesion, host-virus interaction, integrin 1.90E 10 3.4 SLC13A3 Q8WWT9 Solute carrier family 13 member 3 Ion transport, sodium transport 2.20E 08 2.3 CERS5 Q8N5B7 Ceramide synthase 5 Lipid biosynthesis/metabolism, sphingolipid metabolism 2.70E 08 2.7 MSX2 P35548 Homeobox protein MSX-2...”
- THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...SLC13A1 SLC13A2 SLC13A3 SLC13A4 SLC13A5 HGNC, UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Common abreviation NaS1 NaC1 NaC3 NaS2 NaC2 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3 2 citric acid...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...NaS1 NaC1 NaC3 NaS2 NaC2 HGNC, UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3 2 citric acid , succinic acid citric acid , succinic...”
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S13A3_RAT / Q9Z0Z5 Na(+)/dicarboxylate cotransporter 3; NaDC-3; rNaDC3; Na(+)-coupled carboxylate transporter 3; NaC3; Sodium-dependent high-affinity dicarboxylate transporter 2; SDCT2; Solute carrier family 13 member 3 from Rattus norvegicus (Rat) (see 5 papers)
TC 2.A.47.1.4 / Q9Z0Z5 The basolateral intestinal and renal electrogenic, Na+-dependent high affinity (2-50µM) dicarboxylate:(Na+)3 cotransporter (NaDC-3) (substrate range similar to that of NDC-1 except that tricarboxylates are transported with very low affinity). Na+:succinate = 3:1. Also transports N-acetyl-L-aspartate, an abundant amino acid in the nervous system from Rattus norvegicus (Rat) (see 2 papers)
38% identity, 81% coverage
- function: High-affinity sodium-dicarboxylate cotransporter that accepts a range of substrates with 4-6 carbon atoms, such as the citric acid cycle intermediates succinate and alpha-ketoglutarate (2-oxoglutarate), as well as other compounds including N-acetyl-L-aspartate (PubMed:10207168, PubMed:10794676, PubMed:10992006, PubMed:12177002, PubMed:9920886). Transports the dicarboxylate into the cell with a probable stoichiometry of 3 Na(+) for 1 divalent dicarboxylate, rendering the process electrogenic (PubMed:10207168, PubMed:10992006, PubMed:9920886). Can transport citrate in a Na(+)-dependent manner, recognizing the divalent form of citrate rather than the trivalent form which is normally found in blood (PubMed:10207168).
catalytic activity: succinate(out) + 3 Na(+)(out) = succinate(in) + 3 Na(+)(in) (RHEA:71919)
catalytic activity: 2-oxoglutarate(out) + 3 Na(+)(out) = 2-oxoglutarate(in) + 3 Na(+)(in) (RHEA:71939)
catalytic activity: N-acetyl-L-aspartate(out) + 3 Na(+)(out) = N-acetyl-L- aspartate(in) + 3 Na(+)(in) (RHEA:71947)
catalytic activity: glutarate(out) + 3 Na(+)(out) = glutarate(in) + 3 Na(+)(in) (RHEA:71955)
catalytic activity: fumarate(out) + 3 Na(+)(out) = fumarate(in) + 3 Na(+)(in) (RHEA:71931)
catalytic activity: malate(out) + 3 Na(+)(out) = malate(in) + 3 Na(+)(in) (RHEA:72295)
catalytic activity: 2,2-dimethylsuccinate(out) + 3 Na(+)(out) = 2,2- dimethylsuccinate(in) + 3 Na(+)(in) (RHEA:72287)
catalytic activity: 2,3-dimethylsuccinate(out) + 3 Na(+)(out) = 2,3- dimethylsuccinate(in) + 3 Na(+)(in) (RHEA:72291) - substrates: Dicarboxylates, Na+
S13A2_RABIT / Q28615 Solute carrier family 13 member 2; Na(+)/dicarboxylate cotransporter 1; NaDC-1; Renal sodium/dicarboxylate cotransporter from Oryctolagus cuniculus (Rabbit) (see 2 papers)
NP_001171063 solute carrier family 13 member 2 from Oryctolagus cuniculus
38% identity, 83% coverage
- function: Low-affinity sodium-dicarboxylate cotransporter, that mediates the entry of citric acid cycle intermediates, such as succinate, citrate, fumarate and alpha-ketoglutarate (2-oxoglutarate) into the small intestine and renal proximal tubule (By similarity) (PubMed:28731330, PubMed:7890707). Transports the dicarboxylate into the cell with a probable stoichiometry of 3 Na(+) for 1 divalent dicarboxylate, rendering the process electrogenic (PubMed:28731330, PubMed:7890707). Citrate is transported in protonated form as a divalent anion, rather than the trivalent form which is normally found in blood (PubMed:28731330). Has a critical role in renal dicarboxylate transport (By similarity).
catalytic activity: succinate(out) + 3 Na(+)(out) = succinate(in) + 3 Na(+)(in) (RHEA:71919)
catalytic activity: fumarate(out) + 3 Na(+)(out) = fumarate(in) + 3 Na(+)(in) (RHEA:71931)
catalytic activity: 2-oxoglutarate(out) + 3 Na(+)(out) = 2-oxoglutarate(in) + 3 Na(+)(in) (RHEA:71939) - Mapping Functionally Important Residues in the Na+/Dicarboxylate Cotransporter, NaDC1.
Colas, Biochemistry 2017 (PubMed)- GeneRIF: Mapping Functionally Important Residues in the Na(+)/Dicarboxylate Cotransporter, NaDC1.
- Transmembrane helix 7 in the Na+/dicarboxylate cotransporter 1 is an outer helix that contains residues critical for function.
Pajor, Biochimica et biophysica acta 2011 - GeneRIF: Data show that NaDC1 F336C had increased transport activity due to an increased Vmax for succinate.
- Molecular and functional analysis of SDCT2, a novel rat sodium-dependent dicarboxylate transporter.
Chen, The Journal of clinical investigation 1999
S13A3_MOUSE / Q91Y63 Na(+)/dicarboxylate cotransporter 3; NaDC-3; mNaDC3; Na(+)-coupled carboxylate transporter 3; NaC3; Sodium-dependent high-affinity dicarboxylate transporter 2; Solute carrier family 13 member 3 from Mus musculus (Mouse) (see paper)
NP_473396 Na(+)/dicarboxylate cotransporter 3 from Mus musculus
37% identity, 80% coverage
- function: High-affinity sodium-dicarboxylate cotransporter that accepts a range of substrates with 4-6 carbon atoms, such as the citric acid cycle intermediates succinate and alpha-ketoglutarate (2-oxoglutarate), as well as other compounds including N-acetyl-L-aspartate (PubMed:11287335). Transports the dicarboxylate into the cell with a probable stoichiometry of 3 Na(+) for 1 divalent dicarboxylate, rendering the process electrogenic (PubMed:11287335). Can transport citrate in a Na(+)-dependent manner, recognizing the divalent form of citrate rather than the trivalent form which is normally found in blood (By similarity).
catalytic activity: succinate(out) + 3 Na(+)(out) = succinate(in) + 3 Na(+)(in) (RHEA:71919)
catalytic activity: 2-oxoglutarate(out) + 3 Na(+)(out) = 2-oxoglutarate(in) + 3 Na(+)(in) (RHEA:71939)
catalytic activity: N-acetyl-L-aspartate(out) + 3 Na(+)(out) = N-acetyl-L- aspartate(in) + 3 Na(+)(in) (RHEA:71947)
catalytic activity: fumarate(out) + 3 Na(+)(out) = fumarate(in) + 3 Na(+)(in) (RHEA:71931)
catalytic activity: glutarate(out) + 3 Na(+)(out) = glutarate(in) + 3 Na(+)(in) (RHEA:71955)
catalytic activity: 2,2-dimethylsuccinate(out) + 3 Na(+)(out) = 2,2- dimethylsuccinate(in) + 3 Na(+)(in) (RHEA:72287)
catalytic activity: 2,3-dimethylsuccinate(out) + 3 Na(+)(out) = 2,3- dimethylsuccinate(in) + 3 Na(+)(in) (RHEA:72291)
catalytic activity: malate(out) + 3 Na(+)(out) = malate(in) + 3 Na(+)(in) (RHEA:72295) - A slit-diaphragm-associated protein network for dynamic control of renal filtration.
Kocylowski, Nature communications 2022 - “...transporter-like protein 2 10 TMs Transporter MFSD1* Q9DC37 MFSD1 11 or 12 TMs Transporter S13A3* Q91Y63 Solute carrier family 13 member 3 11 TMs/1 IM Transporter S22AJ* Q8VCA0 Solute carrier family 22 member 19 11 TMs Transporter S6A19* Q9D687 Solute carrier family 6 member 19 12...”
- The proteome of mouse cerebral arteries
Badhwar, Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism 2014 (secret) - Astroglial conditional Slc13a3 knockout is therapeutic in murine Canavan leukodystrophy.
Hull, Annals of clinical and translational neurology 2024 - GeneRIF: Astroglial conditional Slc13a3 knockout is therapeutic in murine Canavan leukodystrophy.
- Inhibition of Slug effectively targets leukemia stem cells via the Slc13a3/ROS signaling pathway.
Zhang, Leukemia 2020 - GeneRIF: Genetic or pharmacological inhibition of SLUG or forced expression of Slc13a3 suppresses the growth of human AML cells.
- 3-Hydroxyglutaric acid is transported via the sodium-dependent dicarboxylate transporter NaDC3.
Stellmer, Journal of molecular medicine (Berlin, Germany) 2007 (PubMed)- GeneRIF: demonstrate the membrane translocation of 3OH-GA mediated by NaDC3 and the cis-inhibitory effect on OCT2-mediated transport of cations
8w6cA / Q13183 Cryoem structure of nadc1 with citrate (see paper)
41% identity, 86% coverage
- Ligands: sodium ion; cholesterol hemisuccinate (8w6cA)
S13A2_HUMAN / Q13183 Solute carrier family 13 member 2; Na(+)/dicarboxylate cotransporter 1; NaDC-1; Renal sodium/dicarboxylate cotransporter from Homo sapiens (Human) (see 4 papers)
TC 2.A.47.1.17 / Q13183 Solute carrier family 13 member 2 (Na /di- and tricarboxylate cotransporter 1) (NaDC-1) (Renal sodium/dicarboxylate cotransporter) from Homo sapiens (see 4 papers)
39% identity, 83% coverage
- function: Low-affinity sodium-dicarboxylate cotransporter, that mediates the entry of citric acid cycle intermediates, such as succinate, citrate, fumarate and alpha-ketoglutarate (2-oxoglutarate) into the small intestine and renal proximal tubule (PubMed:10894787, PubMed:8967342, PubMed:9668069). Transports the dicarboxylate into the cell with a probable stoichiometry of 3 Na(+) for 1 divalent dicarboxylate, rendering the process electrogenic (PubMed:10894787, PubMed:8967342, PubMed:9668069). Citrate is transported in protonated form as a divalent anion, rather than the trivalent form which is normally found in blood (PubMed:10894787). Has a critical role in renal dicarboxylate transport (By similarity).
catalytic activity: succinate(out) + 3 Na(+)(out) = succinate(in) + 3 Na(+)(in) (RHEA:71919)
catalytic activity: fumarate(out) + 3 Na(+)(out) = fumarate(in) + 3 Na(+)(in) (RHEA:71931)
catalytic activity: 2-oxoglutarate(out) + 3 Na(+)(out) = 2-oxoglutarate(in) + 3 Na(+)(in) (RHEA:71939) - substrates: Citrate, Dicarboxylates, Na+
tcdb comment: Transports citrate and other Krebs cycle intermediates across the apical membrane of kidney proximal tubules and small intestinal cells (Pajor and Sun 2010; Bergeron et al. 2013). Transmembrane helices 7 and 11 in NaDC1 contains residues critical for function (Pajor and Sun 2010; Pajor et al. 2011). The mouse ortholog can transport succinate and adipate, but the rabbit transporter transports only succinate. Multiple amino acids in TMSs 8, 9 and 10 contribute to the transport of adipate, and A504 plays an important role while TMSs 3 and 4 function in substrate recognitioin (Oshiro and Pajor 2006; Oshiro et al. 2006). Pajor and Randolph 2005 have provided evidence for large-scale changes in the structure of NaDC-1 during the transport cycle - Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
Chi, Science advances 2024 - “...The cDNAs of full-length human SLC13A1 (NP_071889.2, UniProtKB ID: Q9BZW2) and SLC13A2 (NP_003975.1, UniProtKB ID: Q13183) were cloned into the pCAG vector (Invitrogen) with an N-terminal FLAG tag, respectively. A nature variant I550V was detected in SLC13A2 sequence ( 12 ). The plasmids used to transfect...”
- Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Kopel, The Biochemical journal 2021 - “...Q9BZW2 Na + /sulfate cotransporter NaS1 Sulfate Thiosulfate Selenate Kidney (BBM) 7q31.31 None SLC13A2 2.A.47.1.17 Q13183 Na + /dicarboxylate cotransporter (low affinity) NaDC1/NaC1 Succinate -Ketoglutarate Fumarate Malate Citrate Kidney (BBM) Intestine (BBM) 17q11.2 None SLC13A3 2.A.47.1.15 Q8WWT9 Na + /dicarboxylate cotransporter (high-affinity) NaDC3/NaC3 Succinate -Ketoglutarate Fumarate...”
- THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...cotransporter Systematic nomenclature SLC13A1 SLC13A2 SLC13A3 SLC13A4 SLC13A5 HGNC, UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Common abreviation NaS1 NaC1 NaC3 NaS2 NaC2 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...SLC13A5 Common abreviation NaS1 NaC1 NaC3 NaS2 NaC2 HGNC, UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3 2 citric acid , succinic acid citric...”
- The Concise Guide to PHARMACOLOGY 2013/14: transporters
Alexander, British journal of pharmacology 2013 - “...SLC13A3 SLC13A4 SLC13A5 Common abbreviation NaS1 NaC1 NaC3 NaS2 NaC2 HGNC, UniProt SLC13A1, Q9BZW2 SLC13A2, Q13183 SLC13A3, Q8WWT9 SLC13A4, Q9UKG4 SLC13A5, Q86YT5 Endogenous substrates SeO42-, S2O32-, SO42- citric acid, succinic acid citric acid, succinic acid SO42- citric acid, pyruvic acid Stoichiometry 3 Na + : 1...”
- Molecular and functional analysis of SDCT2, a novel rat sodium-dependent dicarboxylate transporter.
Chen, The Journal of clinical investigation 1999
S13A5_MOUSE / Q67BT3 Na(+)/citrate cotransporter; NaCT; Sodium-coupled citrate transporter; Sodium-dependent citrate transporter; Solute carrier family 13 member 5 from Mus musculus (Mouse) (see 5 papers)
40% identity, 85% coverage
- function: High-affinity sodium/citrate cotransporter that mediates citrate entry into cells, which is a critical participant of biochemical pathways (PubMed:14656221, PubMed:26324167, PubMed:35448538). May function in various metabolic processes in which citrate has a critical role such as energy production (Krebs cycle), fatty acid synthesis, cholesterol synthesis, glycolysis, and gluconeogenesis (PubMed:12826022). Transports citrate into the cell in a Na(+)-dependent manner, recognizing the trivalent form of citrate (physiological pH) rather than the divalent form (PubMed:12826022, PubMed:14656221, PubMed:26324167). Can recognizes succinate as a substrate, but its affinity for succinate is several fold lower than for citrate (PubMed:14656221, PubMed:26324167). The stoichiometry is probably 4 Na(+) for each carboxylate, irrespective of whether the translocated substrate is divalent or trivalent, rendering the process electrogenic (PubMed:14656221, PubMed:26324167). Involved in the regulation of citrate levels in the brain (PubMed:32682952).
catalytic activity: citrate(out) + 4 Na(+)(out) = citrate(in) + 4 Na(+)(in) (RHEA:65664)
subunit: Homodimer.
disruption phenotype: Mice show increased propensity for epileptic seizures, proepileptogenic neuronal excitability changes in the hippocampus, and significant citrate level alterations in the CSF and brain tissue (PubMed:32682952). Null mice show perturbations in fatty acids, bile acids, and energy metabolites in liver, serum, and brain (PubMed:35448538). - Functional analysis of a species-specific inhibitor selective for human Na+-coupled citrate transporter (NaCT/SLC13A5/mINDY).
Higuchi, The Biochemical journal 2020 - “...software. Homology modeling The primary sequence alignments of human and mouse NaCT (accession numbers Q86YT5, Q67BT3, respectively) were performed using PROMALS3D [ 21 ]. Based on the resulting primary sequence alignment, homology models of human and mouse NaCT were computed using the MODELLER program [ 22...”
- Retinoic Acid Regulates Immune Responses by Promoting IL-22 and Modulating S100 Proteins in Viral Hepatitis
Jie, Journal of immunology (Baltimore, Md. : 1950) 2017 - “...0.585 Q3KPB0 Olfactory receptor OS=Mus musculus GN=Olfr616 PE=2 SV=1 - [Q3KPB0_MOUSE] 0.455 0.552 0.558 0.676 Q67BT3 Solute carrier family 13 member 5 OS=Mus musculus GN=Slc13a5 PE=2 SV=1 - [S13A5_MOUSE] 0.485 0.626 0.563 0.671 P14069 Protein S100-A6 OS=Mus musculus GN=S100a6 PE=1 SV=3 - [S10A6_MOUSE] 0.509 0.457 0.557...”
XP_006246664 Na(+)/citrate cotransporter isoform X1 from Rattus norvegicus
38% identity, 79% coverage
- Arylhydrocarbon receptor-dependent mIndy (Slc13a5) induction as possible contributor to benzo[a]pyrene-induced lipid accumulation in hepatocytes.
Neuschäfer-Rube, Toxicology 2015 (PubMed)- GeneRIF: This study thus identified the Slc13a5 as an AhR target gene
- Prevention of diet-induced hepatic steatosis and hepatic insulin resistance by second generation antisense oligonucleotides targeted to the longevity gene mIndy (Slc13a5).
Pesta, Aging 2015 - GeneRIF: These data suggest that inducible liver-selective reduction of mIndy in rats is able to ameliorate hepatic steatosis and insulin resistance, conditions occurring with high calorie diets and during aging.
- The mammalian INDY homolog is induced by CREB in a rat model of type 2 diabetes.
Neuschäfer-Rube, Diabetes 2014 - GeneRIF: suggest that mIndy is a CREB-dependent glucagon target gene that is induced in fasting and in type 2 diabetes
- Expression and functional features of NaCT, a sodium-coupled citrate transporter, in human and rat livers and cell lines.
Gopal, American journal of physiology. Gastrointestinal and liver physiology 2007 (PubMed)- GeneRIF: Expression and function of NaCT in a cell line and in primary hepatocytes from rat liver.
- Structure, function, and expression pattern of a novel sodium-coupled citrate transporter (NaCT) cloned from mammalian brain.
Inoue, The Journal of biological chemistry 2002 (PubMed)- GeneRIF: NaCT is expressed in liver, testis and brain in rat and shows preference for citrate over dicarboxylates; it may play a role in cellular utilization of citrate in blood for the synthesis of fatty acids and cholesterol and for the generation of energy
S13A5_RAT / Q8CJ44 Na(+)/citrate cotransporter; NaCT; Sodium-coupled citrate transporter; Sodium-dependent citrate transporter; Solute carrier family 13 member 5 from Rattus norvegicus (Rat) (see 3 papers)
38% identity, 84% coverage
- function: High-affinity sodium/citrate cotransporter that mediates citrate entry into cells, which is a critical participant of biochemical pathways (PubMed:12177002, PubMed:12826022, PubMed:14656221). May function in various metabolic processes in which citrate has a critical role such as energy production (Krebs cycle), fatty acid synthesis, cholesterol synthesis, glycolysis, and gluconeogenesis (By similarity). Transports citrate into the cell in a Na(+)-dependent manner, recognizing the trivalent form of citrate (physiological pH) rather than the divalent form (PubMed:12177002, PubMed:12826022, PubMed:14656221). Can recognize succinate as a substrate, but its affinity for succinate is several fold lower than for citrate (PubMed:12177002, PubMed:14656221). The stoichiometry is probably 4 Na(+) for each carboxylate, irrespective of whether the translocated substrate is divalent or trivalent, rendering the process electrogenic (PubMed:12177002, PubMed:14656221). Involved in the regulation of citrate levels in the brain (By similarity).
catalytic activity: citrate(out) + 4 Na(+)(out) = citrate(in) + 4 Na(+)(in) (RHEA:65664)
subunit: Homodimer.
TC 2.A.47.1.5 / Q9W7I2 Basolateral Na+: di- and tricarboxylate (succinate cis-aconitate, citrate, etc.) cotransporter, fNaDC-3 from Pseudopleuronecta americanus (Winter flounder) (see paper)
33% identity, 85% coverage
- substrates: Dicarboxylates, Na+, Tricarboxylates
NP_001271439 Na(+)/citrate cotransporter isoform d from Homo sapiens
40% identity, 78% coverage
- Novel Homozygous Variants of SLC13A5 Expand the Functional Heterogeneity of a Homogeneous Syndrome of Early Infantile Epileptic Encephalopathy.
Alsemari, Pediatric neurology 2024 (PubMed)- GeneRIF: Novel Homozygous Variants of SLC13A5 Expand the Functional Heterogeneity of a Homogeneous Syndrome of Early Infantile Epileptic Encephalopathy.
- The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse.
Fernandez-Fuente, Communications biology 2023 - GeneRIF: The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse.
- Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Kopel, The Biochemical journal 2021 - GeneRIF: Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
- Structure and inhibition mechanism of the human citrate transporter NaCT.
Sauer, Nature 2021 - GeneRIF: Structure and inhibition mechanism of the human citrate transporter NaCT.
- A novel homozygous SLC13A5 whole-gene deletion generated by Alu/Alu-mediated rearrangement in an Iraqi family with epileptic encephalopathy.
Duan, American journal of medical genetics. Part A 2021 - GeneRIF: A novel homozygous SLC13A5 whole-gene deletion generated by Alu/Alu-mediated rearrangement in an Iraqi family with epileptic encephalopathy.
- Regulation on Citrate Influx and Metabolism through Inhibiting SLC13A5 and ACLY: A Novel Mechanism Mediating the Therapeutic Effects of Curcumin on NAFLD.
Sun, Journal of agricultural and food chemistry 2021 (PubMed)- GeneRIF: Regulation on Citrate Influx and Metabolism through Inhibiting SLC13A5 and ACLY: A Novel Mechanism Mediating the Therapeutic Effects of Curcumin on NAFLD.
- NaCT/SLC13A5 facilitates citrate import and metabolism under nutrient-limited conditions.
Kumar, Cell reports 2021 - GeneRIF: NaCT/SLC13A5 facilitates citrate import and metabolism under nutrient-limited conditions.
- A dynamic anchor domain in slc13 transporters controls metabolite transport.
Khamaysi, The Journal of biological chemistry 2020 - GeneRIF: A dynamic anchor domain in slc13 transporters controls metabolite transport.
- More
NP_001180269 Na(+)/dicarboxylate cotransporter 3 isoform d from Homo sapiens
36% identity, 84% coverage
- SLC13A3 is a major effector downstream of activated β-catenin in liver cancer pathogenesis.
Zhao, Nature communications 2024 - GeneRIF: SLC13A3 is a major effector downstream of activated beta-catenin in liver cancer pathogenesis.
- Association of Single Nucleotide Polymorphisms in KCNA10 and SLC13A3 Genes with the Susceptibility to Chronic Kidney Disease of Unknown Etiology in Central Indian Patients.
Kumari, Biochemical genetics 2023 (PubMed)- GeneRIF: Association of Single Nucleotide Polymorphisms in KCNA10 and SLC13A3 Genes with the Susceptibility to Chronic Kidney Disease of Unknown Etiology in Central Indian Patients.
- Structural and functional implications of SLC13A3 and SLC9A6 mutations: an in silico approach to understanding intellectual disability.
Hussain, BMC neurology 2023 - GeneRIF: Structural and functional implications of SLC13A3 and SLC9A6 mutations: an in silico approach to understanding intellectual disability.
- Distribution of organic anion transporters NaDC3 and OAT1-3 along the human nephron.
Breljak, American journal of physiology. Renal physiology 2016 (PubMed)- GeneRIF: NaDC3-related immunostaining was detected in the basolateral membrane of proximal tubules and in the basolateral membrane and/or luminal membrane of principal cells in connecting segments and collecting ducts
- An integrative study of the genetic, social and environmental determinants of chronic kidney disease characterized by tubulointerstitial damages in the North Central Region of Sri Lanka.
Nanayakkara, Journal of occupational health 2014 (PubMed)- GeneRIF: In a study addressing genetic, social, and environmental contributors of chronic kidney disease with tubulointerstitial damages in Sri Lanka, SNP rs6066043 of SLC13A3 was found attributable risk of 50%.
- Transporters involved in renal excretion of N-carbamoylglutamate, an orphan drug to treat inborn n-acetylglutamate synthase deficiency.
Schwob, American journal of physiology. Renal physiology 2014 (PubMed)- GeneRIF: OAT1 and NaDC3 in the basolateral membrane and OAT4 in the luminal membrane of proximal tubule cells are responsible for the avid renal secretion of N-carbamoylglutamate.
- Glutathione is a low-affinity substrate of the human sodium-dependent dicarboxylate transporter.
Schorbach, Nephron. Physiology 2013 (PubMed)- GeneRIF: study concludes NaDC3 present at the basolateral membrane of proximal tubule cells mediates sodium-dependent glutathione (GSH) uptake; the kinetic data show that NaDC3 is a low-affinity GSH transporter
- Differential interaction of dicarboxylates with human sodium-dicarboxylate cotransporter 3 and organic anion transporters 1 and 3.
Kaufhold, American journal of physiology. Renal physiology 2011 (PubMed)- GeneRIF: The data 1) reveal alpha-ketoglutarate as a common high-affinity substrate of NaDC3, OAT1, and OAT3
- More
8y5wA / Q9BZW2 Human nas1 intermediate state 2 (see paper)
35% identity, 86% coverage
- Ligands: sulfate ion; sodium ion (8y5wA)
8w6nB / Q9BZW2 Nas1 with sulfate in in/out state (see paper)
36% identity, 86% coverage
- Ligand: sulfate ion (8w6nB)
S13A1_MOUSE / Q9JHI4 Solute carrier family 13 member 1; NaSi-1; Renal sodium/sulfate cotransporter; Na(+)/sulfate cotransporter from Mus musculus (Mouse) (see paper)
NP_062354 solute carrier family 13 member 1 from Mus musculus
32% identity, 88% coverage
- function: Sodium:sulfate symporter that mediates sulfate reabsorption in the kidney and small intestine (PubMed:10766815). Can also mediate the transport of selenate and thiosulfate (By similarity).
catalytic activity: sulfate(out) + 3 Na(+)(out) = sulfate(in) + 3 Na(+)(in) (RHEA:71951)
catalytic activity: selenate(out) + 3 Na(+)(out) = selenate(in) + 3 Na(+)(in) (RHEA:72079)
catalytic activity: thiosulfate(out) + 3 Na(+)(out) = thiosulfate(in) + 3 Na(+)(in) (RHEA:72323) - Fetal loss and hyposulfataemia in pregnant NaS1 transporter null mice.
Dawson, The Journal of reproduction and development 2011 (PubMed)- GeneRIF: NaS1 is essential to maintain high maternal and fetal sulfate levels, which is important for maintaining pregnancy, placental development and normal birth weight
- Enhanced tumor growth in the NaS1 sulfate transporter null mouse.
Dawson, Cancer science 2010 - GeneRIF: Enhanced tumor growth in the NaS1 sulfate transporter null mouse.
- Kidney transcriptome reveals altered steroid homeostasis in NaS1 sulfate transporter null mice.
Dawson, The Journal of steroid biochemistry and molecular biology 2008 (PubMed)- GeneRIF: NaS1 is essential for maintaining a normal metabolic state in the kidney and that loss of NaS1 function leads to reduced circulating steroid levels and increased urinary steroid excretion.
- Hyperserotonaemia and reduced brain serotonin levels in NaS1 sulphate transporter null mice.
Lee, Neuroreport 2007 (PubMed)- GeneRIF: Our data indicate that decreased circulating SO4 concentrations modulate 5-HT neurotransmitter and receptor levels, in a manner consistent with the behavioural phenotypes of Nas1 mice.
- Transcriptional profile reveals altered hepatic lipid and cholesterol metabolism in hyposulfatemic NaS1 null mice.
Dawson, Physiological genomics 2006 (PubMed)- GeneRIF: NaS1 has a role in lipid and cholesterol metabolism
- Impaired memory and olfactory performance in NaSi-1 sulphate transporter deficient mice.
Dawson, Behavioural brain research 2005 (PubMed)- GeneRIF: Wild-type mice showed a significant decrease in time to locate a hidden food reward over four trials after overnight fasting while Nas1-/- mice did not change their performance.
- Hyposulfatemia, growth retardation, reduced fertility, and seizures in mice lacking a functional NaSi-1 gene.
Dawson, Proceedings of the National Academy of Sciences of the United States of America 2003 - GeneRIF: NaSi-1 is essential for maintaining sulfate homeostasis, and its expression is necessary for a wide range of physiological functions
- Regulation of the mouse Nas1 promoter by vitamin D and thyroid hormone.
Dawson, Pflugers Archiv : European journal of physiology 2002 (PubMed)- GeneRIF: 1,25-(OH)(2)D(3)- and T(3)-responsive element was identified within the Nas1 promoter.
- More
NP_001254976 Sodium-dependent high-affinity dicarboxylate transporter 2 from Caenorhabditis elegans
31% identity, 93% coverage
S13A1_RAT / Q07782 Solute carrier family 13 member 1; NaSi-1; Renal sodium/sulfate cotransporter; Na(+)/sulfate cotransporter from Rattus norvegicus (Rat) (see 5 papers)
TC 2.A.47.1.2 / Q07782 Renal sodium:sulfate cotransporter (Ssc, NaSi-1 or Nas1) (also transports tungstate, molybdate, thiosulfate and selenate) from Rattus norvegicus (Rat) (see 2 papers)
Slc13a1 / RF|NP_113839.1 solute carrier family 13 member 1 from Rattus norvegicus (see paper)
NP_113839 solute carrier family 13 member 1 from Rattus norvegicus
33% identity, 83% coverage
S13A1_HUMAN / Q9BZW2 Solute carrier family 13 member 1; Renal sodium/sulfate cotransporter; Na(+)/sulfate cotransporter; hNaSi-1 from Homo sapiens (Human) (see paper)
TC 2.A.47.1.16 / Q9BZW2 Solute carrier family 13 member 1 (Renal and intestinal sodium/sulfate cotransporter) (Na+/sulfate cotransporter) (hNaSi-1). Also transports thiosulfate and selenium. It is inhibited by many di- and tri-valent organic and inorganic anions from Homo sapiens (see 2 papers)
33% identity, 83% coverage
- function: Sodium:sulfate symporter that mediates sulfate reabsorption in the kidney and small intestine (PubMed:11161786). Can also mediate the transport of selenate and thiosulfate (By similarity).
catalytic activity: sulfate(out) + 3 Na(+)(out) = sulfate(in) + 3 Na(+)(in) (RHEA:71951)
catalytic activity: selenate(out) + 3 Na(+)(out) = selenate(in) + 3 Na(+)(in) (RHEA:72079)
catalytic activity: thiosulfate(out) + 3 Na(+)(out) = thiosulfate(in) + 3 Na(+)(in) (RHEA:72323) - substrates: Na+, Selenium, Sfulate, Thiosulfate, anions
- Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
Chi, Science advances 2024 - “...AND METHODS Protein expression and purification The cDNAs of full-length human SLC13A1 (NP_071889.2, UniProtKB ID: Q9BZW2) and SLC13A2 (NP_003975.1, UniProtKB ID: Q13183) were cloned into the pCAG vector (Invitrogen) with an N-terminal FLAG tag, respectively. A nature variant I550V was detected in SLC13A2 sequence ( 12...”
- Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Kopel, The Biochemical journal 2021 - “...TCDB ID UniProt ID Common name(s) Substrates Tissue expression Chromosome location Disease connection SLC13A1 2.A.47.1.16 Q9BZW2 Na + /sulfate cotransporter NaS1 Sulfate Thiosulfate Selenate Kidney (BBM) 7q31.31 None SLC13A2 2.A.47.1.17 Q13183 Na + /dicarboxylate cotransporter (low affinity) NaDC1/NaC1 Succinate -Ketoglutarate Fumarate Malate Citrate Kidney (BBM) Intestine...”
- “...by its amino acid sequence ID according to the UniProt database for protein sequences (e.g. Q9BZW2). Every member of the SLC13 family functions as an electrogenic transporter, meaning that their transport function is associated with membrane depolarization. Since all of them are coupled to Na +...”
- Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2.
Barker, PloS one 2020 - “...LRP2 0.8671 7.59E-27 6694 P98164 Low-density lipoprotein receptor-related protein 2 kidney SLC13A1 0.8667 8.5E-27 10916 Q9BZW2 Solute carrier family 13 member 1 secondary carrier transporter (PC00258) kidney UGT3A1 0.8608 4.52E-26 26625 Q6NUS8 UDP-glucuronosyltransferase 3A1 kidney SLC27A2 0.8535 3.26E-25 10996 O14975 Very long-chain acyl-CoA synthetase secondary carrier...”
- THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...Na + /citrate cotransporter Systematic nomenclature SLC13A1 SLC13A2 SLC13A3 SLC13A4 SLC13A5 HGNC, UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Common abreviation NaS1 NaC1 NaC3 NaS2 NaC2 Endogenous substrates SeO 4 2 , SO 4 2 , S...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...SLC13A2 SLC13A3 SLC13A4 SLC13A5 Common abreviation NaS1 NaC1 NaC3 NaS2 NaC2 HGNC, UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3 2 citric acid ,...”
- The Concise Guide to PHARMACOLOGY 2013/14: transporters
Alexander, British journal of pharmacology 2013 - “...SLC13A1 SLC13A2 SLC13A3 SLC13A4 SLC13A5 Common abbreviation NaS1 NaC1 NaC3 NaS2 NaC2 HGNC, UniProt SLC13A1, Q9BZW2 SLC13A2, Q13183 SLC13A3, Q8WWT9 SLC13A4, Q9UKG4 SLC13A5, Q86YT5 Endogenous substrates SeO42-, S2O32-, SO42- citric acid, succinic acid citric acid, succinic acid SO42- citric acid, pyruvic acid Stoichiometry 3 Na +...”
XP_539548 solute carrier family 13 member 1 from Canis lupus familiaris
33% identity, 83% coverage
TC 2.A.47.1.19 / Q6PE27 Solute carrier family 13, Slc13a1; Sodium/sulfate symporter, member 1, NaS1 of 583 aas and 14 TMSs from Danio rerio
34% identity, 88% coverage
- substrates: Na+, Sulfate
tcdb comment: Na+-sulfate cotransport is inhibited by thiosulfate, selenate, molybdate and tungstate (Markovich et al. 2008)
SSP0875 putative sodium:sulfate symporter from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
35% identity, 78% coverage
BN4_10586 SLC13 family permease from Pseudodesulfovibrio piezophilus C1TLV30
33% identity, 90% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...majority of the sequences in clade B (TOL2_29810, HRM2_07790, DP0767, DP0768, Asulf_01109, Desgi_0931, DesafDRAFT_1589, DesafDRAFT_2725, BN4_10586, Desal_0726) and all sequences in group C i , the sulfate transporter (YP_003577054) from R. capsulatus has a proline (P) at position 258 ( Figures 5 , 6 ). Similarly,...”
HRM2_07790 predicted Na(+)-dicarboxylate cotransporter (solute carrier family 13 protein) from Desulfobacterium autotrophicum HRM2
37% identity, 85% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...Even though, G258 is conserved in the majority of the sequences in clade B (TOL2_29810, HRM2_07790, DP0767, DP0768, Asulf_01109, Desgi_0931, DesafDRAFT_1589, DesafDRAFT_2725, BN4_10586, Desal_0726) and all sequences in group C i , the sulfate transporter (YP_003577054) from R. capsulatus has a proline (P) at position 258...”
- “...al., 2017 ). There was no significant change in the expression of another two DASS (HRM2_07790, HRM2_38270) and one SulP (HRM2_33490) family transporters between low and high sulfate grown cells ( Tarpgaard et al., 2017 ). No expression was detected for the SulP encoding gene HRM2_13280...”
Q2FMC1 Anion transporter from Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1)
34% identity, 85% coverage
8zl2A / Q9VVT2 Cryo-em structure of the drosophila indy (dids-bound asymmetric, ph 6)
33% identity, 91% coverage
- Ligand: 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid (8zl2A)
8w6hB / Q9BZW2 Nas1 with sulfate - in/in state (see paper)
35% identity, 86% coverage
- Ligands: sulfate ion; sodium ion; cholesterol (8w6hB)
INDY1_DROME / Q9VVT2 Protein I'm not dead yet; INDY transporter protein; drIndy from Drosophila melanogaster (Fruit fly) (see 3 papers)
TC 2.A.47.1.10 / Q9VVT2 Cation-independent, electroneutral tri- and di-carboxylate transporter with a preference for tricarboxylates, Indy (I'm not dead yet) [When Indy is mutated flies live about twice as long as wild type] from Drosophila melanogaster (Fruit fly) (see 7 papers)
Indy / RF|NP_730363.2 protein I'm not dead yet from Drosophila melanogaster (see paper)
NP_730363 I'm not dead yet, isoform B from Drosophila melanogaster
33% identity, 87% coverage
- function: Cation-independent electroneutral transporter (not associated with membrane depolarization) of a variety of tricarboxylic and dicarboxylic acid-cycle intermediates. There is also small, but detectable, transport of monocarboxylics. Transport is through the epithelium of the gut and across the plasma membranes of organs involved in intermediary metabolism and storage. Affinity for substrates is citrate > succinate > pyruvate. Fumarate, a- ketoglutarate, and glutarate are also transported, but not lactate. Transport mechanism that is not coupled to Na(+), K(+), or Cl(-). Function is shown in Xenopus oocytes and human retinal pigment epithelial (HRPE) cell lines.
- substrates: Dicarboxylates, Tricarboxylates
- Indy gene variation in natural populations confers fitness advantage and life span extension through transposon insertion.
Zhu, Aging 2014 - GeneRIF: Evolution reaffirms that the mechanism of heterozygote advantage has acted upon the Indy gene to assure increased reproductive fitness and, coincidentally, longer life span through regulatory transposon mutagenesis.
- Increased mitochondrial biogenesis preserves intestinal stem cell homeostasis and contributes to longevity in Indy mutant flies.
Rogers, Aging 2014 - GeneRIF: Our data suggest INDY may be a physiological regulator that modulates intermediary metabolism in response to changes in nutrient availability and organismal needs by modulating dPGC-1.
- Long-lived Indy induces reduced mitochondrial reactive oxygen species production and oxidative damage.
Neretti, Proceedings of the National Academy of Sciences of the United States of America 2009 - GeneRIF: Long-lived Indy induces reduced mitochondrial reactive oxygen species production and oxidative damage
- Long-lived Indy and calorie restriction interact to extend life span.
Wang, Proceedings of the National Academy of Sciences of the United States of America 2009 - GeneRIF: Study concludes that Indy and calorie restriction (CR) interact to affect longevity and that a decrease in Indy may induce a CR-like status that confers life span extension.
- No influence of Indy on lifespan in Drosophila after correction for genetic and cytoplasmic background effects.
Toivonen, PLoS genetics 2007 - GeneRIF: Does not influence lifespan in Drosophila after correction for genetic and cytoplasmic background effects.
- The life-extending gene Indy encodes an exchanger for Krebs-cycle intermediates.
Knauf, The Biochemical journal 2006 - GeneRIF: the transporter encoded by the life-extending gene Indy is a disulphonic stilbene-sensitive, sodium-independent anion exchanger that is capable of exchanging pairs of dicarboxylates and citrate across the plasma membrane
- Conditional tradeoffs between aging and organismal performance of Indy long-lived mutant flies.
Marden, Proceedings of the National Academy of Sciences of the United States of America 2003 - GeneRIF: Indy mutation causes a decrease in the slope of the mortality curve consistent with a slowing in the rate of aging without a concomitant reduction in resting metabolic rate, flight velocity, or age-specific fecundity.
- Functional identity of Drosophila melanogaster Indy as a cation-independent, electroneutral transporter for tricarboxylic acid-cycle intermediates.
Inoue, The Biochemical journal 2002 - GeneRIF: drIndy is a cation-independent electroneutral transporter for a variety of tricarboxylic acid-cycle intermediates, with preference for citrate compared with succinate.
- More
- Drosophila INDY and Mammalian INDY: Major Differences in Transport Mechanism and Structural Features despite Mostly Similar Biological Functions
Jaramillo-Martinez, Metabolites 2021 - “...SNT/V motifs are shown in red boxes. The accession numbers for the protein sequences are Q9VVT2 for Drosophila INDY and Q86YT5 for human INDY. Figure 4 Inward-facing models for Drosophila INDY and human INDY (NaCT). ( A ) The 3D model for Drosophila INDY, created with...”
ZPR_0364 sodium:sulfate symporter from Zunongwangia profunda SM-A87
36% identity, 83% coverage
XP_017170016 Na(+)/citrate cotransporter isoform X2 from Mus musculus
38% identity, 79% coverage
- Nervous System Deletion of Mammalian INDY in Mice Mimics Dietary Restriction-Induced Memory Enhancement.
Fan, The journals of gerontology. Series A, Biological sciences and medical sciences 2021 (PubMed)- GeneRIF: Nervous System Deletion of Mammalian INDY in Mice Mimics Dietary Restriction-Induced Memory Enhancement.
- The longevity gene mIndy (I'm Not Dead, Yet) affects blood pressure through sympathoadrenal mechanisms.
Willmes, JCI insight 2021 - GeneRIF: The longevity gene mIndy (I'm Not Dead, Yet) affects blood pressure through sympathoadrenal mechanisms.
- Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Kopel, The Biochemical journal 2021 - GeneRIF: Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
- Disruption of the sodium-dependent citrate transporter SLC13A5 in mice causes alterations in brain citrate levels and neuronal network excitability in the hippocampus.
Henke, Neurobiology of disease 2020 (PubMed)- GeneRIF: Disruption of the sodium-dependent citrate transporter SLC13A5 in mice causes alterations in brain citrate levels and neuronal network excitability in the hippocampus.
- Defective enamel and bone development in sodium-dependent citrate transporter (NaCT) Slc13a5 deficient mice.
Irizarry, PloS one 2017 - GeneRIF: The findings revealed the potentially important role of citrate and Slc13a5 in the development and function of teeth and bone.
- Deletion of the mammalian INDY homolog mimics aspects of dietary restriction and protects against adiposity and insulin resistance in mice.
Birkenfeld, Cell metabolism 2011 - GeneRIF: Our studies demonstrate a profound effect of mIndy on mammalian energy metabolism.
- Functional characterization of Na+ -coupled citrate transporter NaC2/NaCT expressed in primary cultures of neurons from mouse cerebral cortex.
Wada, Brain research 2006 (PubMed)- GeneRIF: Na+ -coupled di/tricarboxylate transport system expressed in neurons as NaC2/NaCT, which can transport the tricarboxylate citrate as well as dicarboxylates such as succinate, alpha-ketoglutarate, and malate.
- Functional features and genomic organization of mouse NaCT, a sodium-coupled transporter for tricarboxylic acid cycle intermediates.
Inoue, The Biochemical journal 2004 - GeneRIF: Molecular cloning and transport properties of NaCT.
Smp_170080 sodium/dicarboxylate cotransporter-related from Schistosoma mansoni
34% identity, 24% coverage
SDCS_STAAM / Q99SX1 Sodium-dependent dicarboxylate transporter SdcS; Na(+)/dicarboxylate symporter from Staphylococcus aureus (strain Mu50 / ATCC 700699) (see 2 papers)
SAOUHSC_02137 sodium-dependent transporter (huNaDC-1), putative from Staphylococcus aureus subsp. aureus NCTC 8325
Q2FWY4 Sodium-dependent dicarboxylate transporter SdcS from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SA1732 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV1916 similar to sodium-dependent transporter from Staphylococcus aureus subsp. aureus Mu50
SACOL1979 sodium-dependent transporter from Staphylococcus aureus subsp. aureus COL
34% identity, 83% coverage
- function: Mediates the transport of the dicarboxylates fumarate, malate, and succinate across the cytoplasmic membrane via a Na(+)- electrochemical gradient. Transports 2 Na(+) for each dicarboxylate.
- Spontaneous formation of MXene-oxidized sono/chemo-dynamic sonosensitizer/nanocatalyst for antibacteria and bone-tissue regeneration
Yu, Journal of nanobiotechnology 2023 - “...genes were upregulated, which were related to carbohydrate metabolism. In addition, the expression of genes (SAOUHSC_02137, SAOUHSC_01990 and SAOUHSC_01991) associated with cell membrane transport proteins was decreased. Importantly, the expression of genes (rpsS, inf-3, mutL, rplC and rpmG) associated with protein synthesis was also reduced. This...”
- Lysogenization of Staphylococcus aureus RN450 by phages ϕ11 and ϕ80α leads to the activation of the SigB regulon
Fernández, Scientific reports 2018 - “...SAOUHSC_01945 0.46 0.41 SAOUHSC_01949 0.48 0.36 SAOUHSC_01950 0.46 0.32 SAOUHSC_01951 0.48 0.31 SAOUHSC_01952 0.48 0.30 SAOUHSC_02137 sdcS 2.15 3.17 Up SAOUHSC_02163 0.19 0.08 SAOUHSC_02240 0.31 0.11 SAOUHSC_02260* hld 0.40 0.04 SAOUHSC_02261* agrB 0.50 0.17 SAOUHSC_02265 0.50 0.20 SAOUHSC_02266 0.45 0.24 SAOUHSC_02387 3.30 11.15 Up SAOUHSC_02400 3.31...”
- Antimicrobial Activity and Mechanism of Action of Dracocephalum moldavica L. Extracts Against Clinical Isolates of Staphylococcus aureus
Yu, Frontiers in microbiology 2019 - “...system permease TcyB 5.57 0.000234 Q2FW99 PTS system mannitol-specific transporter subunit IIB MtlA 4.88 0.00 Q2FWY4 DASS family divalent anion:sodium (Na+) symporter SdcS 4.68 0.000325 Q2G0Z5 FMN reductase NfrA 4.38 0.002173 Q2FYG9 Chorismate synthase AroC 3.62 0.000482 Table 3 Top 20 decreased expressed proteins in D....”
- Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
Scherr, Infection and immunity 2013 - “...SA1516 SA2517 SA1221 SA1919 SA1060 SA0550 SA2203 SA0004 SA1732 SA1939 SA0305 SA0980 SA2407 SA1803 SA0028 SA0567 SA1393 SA1997 SA1632 SA2297 SA1638 SA2290 SA1622...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...DNA processing protein sa_c1643s1381_at * 3.4 2.5 2.5 SA1357 thermonuclease sa_c3053s2604_a_at * 2.4 2.5 30 SA1732 replication initiation and membrane attachment protein Signal transduction sa_c1996s1713_a_at 2.9 2.5 15 arlS SA1450 sensor histidine kinase sa_c6155s5336_a_at * 4.4 2.5 2.5 lytS SA0245 sensor histidine kinase sa_c8186s7165_a_at 3.0 2.5...”
- “...factor protein RarA sa_c2977s2534_a_at 2.3 2.5 2.5 SA1711 DNA-3-methyladenine glycosylase sa_c3053s2604_a_at * 4.0 2.5 2.5 SA1732 replication initiation and membrane attachment protein sa_c3611s3091_at 2.5 2.5 2.5 SA1900 DNA repair exonuclease sa_c4309s3661_a_at 7.6 2.5 2.5 SA2072 ATP dependent DNA helicase sa_c5962s10062cv_s_at 2.4 2.5 2.5 SA2499 putative helicase...”
- Functional characterization of a Na(+)-coupled dicarboxylate carrier protein from Staphylococcus aureus
Hall, Journal of bacteriology 2005 - “...Cloning. The sdcS gene (GenBank accession number BA000017; locus SAV1916) was amplified from S. aureus genomic DNA (ATCC 700699D) by PCR and cloned into plasmid...”
- “...search resulted in the identification of the putative SAV1916 gene from S. aureus (strain Mu50), whose protein product is approximately 35% identical in...”
- Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung
Chaffin, PloS one 2012 - “...to glucarate transporters and sucrose-specific PTS transporter protein SACOL0178. Transcription of Na + /dicarboxylate symporter, SACOL1979, was lower by 7.3 and 2.4 fold after 30 in vivo compared to stationary phase and fresh LB conditions. Nucleosides, purines and pyrimidines transport Four of six genes for transport...”
TC 2.A.47.1.11 / Q2FFH9 The Na+ (or Li+):dicarboxylate (2:1) symporter, SdcS (catalyzes succinate:succinate antiport as well as electroneutral symport in reconstituted proteoliposomes from Staphylococcus aureus (strain USA300) (see paper)
SAUSA300_1897 sodium-dependent transporter from Staphylococcus aureus subsp. aureus USA300_FPR3757
USA300HOU_1918 DASS family divalent anion:sodium (Na+) symporter from Staphylococcus aureus subsp. aureus USA300_TCH1516
34% identity, 83% coverage
- substrates: Dicarboxylates, Fumarate, Li+, Na+, Succinate, malate
tcdb comment: Transports succinate, malate and fumarate with similar affiinities (7 μM, 8 μM and 15 μM, respectively), but aspartate and α-ketoglutarate with very low affinities (Hall and Pajor 2005; Hall and Pajor 2007) - Differential gene expression in Staphylococcus aureus exposed to Orange II and Sudan III azo dyes
Pan, Journal of industrial microbiology & biotechnology 2015 - “...CCGCCATTGCTTTCTCTTT SAUSA300_1679 (acsA) SAUSA300_1005 SAUSA300_1897 SAUSA300_0619 SAUSA300_0545 (azo1) Table 3Summary of differentially expressed...”
- “...1.61 SAUSA300_1673 I SAUSA300_2176 SAUSA300_1005 P P SAUSA300_1897 SAUSA300_0619 SAUSA300_1899 Poorly characterized SAUSA300_1700 SAUSA300_2268 P P Q 13 R R...”
- Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification
Bianco, Frontiers in cellular and infection microbiology 2023 - “..., intergenic (2727910) intergenic (201647), USA300HOU_1266 (1352385), ebh (1483188), engA (1544604), comEC (1700414), USA300HOU_1715 (1839546), USA300HOU_1918 (2063960), intergenic (2262458), lacE (2329451), USA300HOU_2279 (2414655), USA300HOU_2654 (2811819) galE (148897) , intergenic (191588) , pbuX (437253) , USA300HOU_0421 (445172) , USA300HOU_042 1 (445217) , set21 (452762) , thiD (638407)...”
ZPR_4168 sodium:sulfate symporter from Zunongwangia profunda SM-A87
36% identity, 83% coverage
UH47_00550 SLC13 family permease from Staphylococcus pseudintermedius
34% identity, 87% coverage
TDT_ARATH / Q8LG88 Tonoplast dicarboxylate transporter; AttDT; Sodium-dicarboxylate cotransporter-like; AtSDAT; Vacuolar malate transporter from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
TC 2.A.47.1.6 / Q8LG88 The tonoplast dicarboxylate (malate) transporter, AtDCT (see 3 papers)
TDT / GB|BAA96091.1 tonoplast dicarboxylate transporter from Arabidopsis thaliana (see paper)
AT5G47560 TDT (TONOPLAST DICARBOXYLATE TRANSPORTER); malate transmembrane transporter/ sodium:dicarboxylate symporter from Arabidopsis thaliana
NP_199567 tonoplast dicarboxylate transporter from Arabidopsis thaliana
34% identity, 78% coverage
- function: Putative carrier protein indirectly involved in the uptake of malate and fumarate to the vacuole, probably by regulating the energization across the tonoplast. Uptake of malate to vacuoles is inhibited by citrate and by the uncoupler carbonyl-cyanide m- chlorophenylhydrazone, but seems to be not affected by sodium. Critical for pH homeostasis.
- substrates: Citrate, malate
tcdb comment: The ortholog (70% identity) in tomatos increases the malate while decreasing the citrate concentrations, influencing flavor (Liu et al. 2017) - Nucleotide Imbalance, Provoked by Downregulation of Aspartate Transcarbamoylase Impairs Cold Acclimation in Arabidopsis
Bellin, Molecules (Basel, Switzerland) 2023 - “...1.85 0.49 0.39 TP H 2 O AT3G18440 ALMT9 1.40 0.92 0.71 0.86 TP malate AT5G47560 TDT 1.82 0.96 2.45 1.47 TP malate AT1G20840 TST1 0.84 1.50 1.10 0.89 0.66 TP monosaccharide AT4G35300 TST2 2.94 2.61 1.07 1.22 TP mono-, disaccharide molecules-28-01585-t003_Table 3 Table 3 DEGs...”
- Transcriptome analysis of Arabidopsis reveals freezing-tolerance related genes induced by root endophytic fungus Piriformospora indica
Jiang, Physiology and molecular biology of plants : an international journal of functional plant biology 2021 - “...6d, Table S7). Seven DEGs (AT5G17850, AT3G53720, AT5G47560, AT3G17630, AT2G38170, AT3G06370, AT5G17860) encode sodium exchanger proteins, two DEGs (AT4G35090...”
- Insights into the Role of Transcriptional Gene Silencing in Response to Herbicide-Treatments in Arabidopsis thaliana
Markus, International journal of molecular sciences 2021 - “...PROTEIN; no no no 12 AT1G70300 K+ UPTAKE PERMEASE 6 (KUP6); yes no no 13 AT5G47560 TONOPLAST DICARBOXYLATE TRANSPORTER (TDT); no no no 14 AT1G09180 SECRETION-ASSOCIATED RAS SUPER FAMILY 1 (SARA1A); no no no 15 AT1G03550 SECRETORY CARRIER MEMBRANE PROTEIN (SCAMP) FAMILY PROTEIN; yes yes yes...”
- Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism
Zhang, GigaScience 2020 - “...(Kaladp0073s0021, AT1G25480missed expression data), PPDK (Kaladp0076s0229, AT4G15530), PPDK-RP (Kaladp0010s0106, AT4G21210), NADP-ME (Kaladp0092s0166, AT1G79750), TDT (Kaladp0042s0251, AT5G47560). The expression of Kalancho genes was detected at dawn (2h before the light period) and dusk (2h before the dark period, i.e., 10h after light treatments). The expression data of...”
- High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements
Warman, PLoS genetics 2020 - “...tdsgR53C03 50.99% 7.46E-01 AT4G35550 WUSCHEL-related homeobox 13a Sperm Cell GRMZM2G099382 Zm00001d044109 singleton tdsgR106G12 49.33% 7.46E-01 AT5G47560 Tonoplast dicarboxylate transporter Sperm Cell GRMZM2G352898 Zm00001d048434 singleton tdsgR37A04 51.31% 7.46E-01 AT3G63240 Type IV inositol polyphosphate 5-phosphatase 7 *Beta expansins have proliferated in the maize genome, including by tandem duplication...”
- Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles
Gorshkov, Plants (Basel, Switzerland) 2019 - “...bZIP5 basic leucine-zipper 5 1.97 6.20 10 3 3.23 2.10 10 6 miR159 a Lus10027321 AT5G47560 TDT tonoplast dicarboxylate transporter 4.99 5.39 10 3 6.78 9.58 10 5 a Lus10031827 AT5G12930 3.86 1.89 10 19 3.31 2.65 10 14 a Lus10041729 AT5G25620 YUC6 Flavin-binding monooxygenase family...”
- Functional Conservation and Divergence of Soybean GmSTOP1 Members in Proton and Aluminum Tolerance
Wu, Frontiers in plant science 2018 - “...from plants grown in the low pH treatment, while expression levels of PMI (At2g45220), AtTDT (At5g47560), AtNADP-ME2 (At5g11670), and AtMATE (At1g51340) were quantified in Al treated samples. UBQ1 transcript levels were used as the internal standard. Data are expressed as means of four replicates. Asterisks indicate...”
- “...Al tolerance related genes included pectin methylesterase inhibitor superfamily protein ( PMI, At2g45220 ), AtTDT (At5g47560), NADP-ME2 (At5g11670), and AtMATE (At1g51340). In both GmSTOP1-1 and GmSTOP1-3 complemented lines, the expression of AtPMI, AtTDT, NADP-ME2 , and AtMATE were partially restored. Yet, in GmSTOP1-2 complemented lines, the...”
- 2-Hydroxy Acids in Plant Metabolism
Maurino, The arabidopsis book 2015 - “...contains a single copy gene encoding the tDT (At5g47560) (Emmerlich et al., 2003). Loss-of-function mutants of tDT exhibited no apparent phenotype, but contain...”
- More
- Purification and functional characterization of the vacuolar malate transporter tDT from Arabidopsis.
Frei, The Journal of biological chemistry 2018 - GeneRIF: tDT from Arabidopsis is the first member of the well-known and widely present SLC13 group of carrier proteins, exhibiting an antiport mode of transport
- Benign TdT-positive cells in pediatric and adult lymph nodes: a potential diagnostic pitfall.
Pizzi, Human pathology 2018 (PubMed)- GeneRIF: Small subsets of TdT-positive cells are a normal finding in the lymph nodes of both pediatric and adult patients, and their occurrence does not apparently correlate with any clinical-pathological parameter.
- Impaired Malate and Fumarate Accumulation Due to the Mutation of the Tonoplast Dicarboxylate Transporter Has Little Effects on Stomatal Behavior.
Medeiros, Plant physiology 2017 - GeneRIF: manipulation of the tonoplastic organic acid transporter impacted mitochondrial metabolism, while the overall stomatal and photosynthetic capacity were unaffected.
- Impaired pH homeostasis in Arabidopsis lacking the vacuolar dicarboxylate transporter and analysis of carboxylic acid transport across the tonoplast.
Hurth, Plant physiology 2005 - GeneRIF: AttDT is critical for regulation of pH homeostasis under certain conditions. [AttDT] [tonoplast dicarboxylate transporter]
- Molecular Regulation of Photosynthetic Carbon Assimilation in Oat Leaves Under Drought Stress
Xu, Plants (Basel, Switzerland) 2024 - “...9 B). A total of six differentially expressed genes encode four proteins, with Q8L7Z9 and Q8LG88 encoding malate transporters, Q9C5D3 being a metal ion channel protein, Q96282 a chloride channel protein, and Q94CK4 a calcium-dependent phospholipid binding protein. Analysis of the physiological processes and gene expression...”
- “...with metal ion and Cl ion transport were Dicarboxylate transporter 2 (Q8L7Z9), Tonoplast dicarboxylate transporter (Q8LG88), heavy-metal-associated isoprenylated plant protein (Q9C5D3), chloride channel protein (Q96282), and Annexin (Q94CK4). Through gene co-expression analysis combined with promoter region structural analysis, 11 transcription factors (from MYB , AP2/ERF ,...”
DP0767 related to Na/dicarboxylate cotransporter from Desulfotalea psychrophila LSv54
32% identity, 87% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...though, G258 is conserved in the majority of the sequences in clade B (TOL2_29810, HRM2_07790, DP0767, DP0768, Asulf_01109, Desgi_0931, DesafDRAFT_1589, DesafDRAFT_2725, BN4_10586, Desal_0726) and all sequences in group C i , the sulfate transporter (YP_003577054) from R. capsulatus has a proline (P) at position 258 (...”
TC 2.A.47.1.13 / Q65NC0 The Na+-coupled dicarboxylate (succinate; malate; fumarate) transporter, SdcL (transports aspartate, α-ketoglutarate and oxaloacetate with low affinity). Km for succinate, ~6 from Bacillus licheniformis (strain DSM 13 / ATCC 14580) (see 2 papers)
BL01772 SLC13 family permease from Bacillus licheniformis DSM 13 = ATCC 14580
33% identity, 80% coverage
- substrates: Alpha-ketoglutarate, Dicarboxylates, Fumarate, Na+, Oxaloacetate, Succinate, malate
tcdb comment: μM; Km for Na+, 0.9 mM; Na :substrate = 2:1 (Strickler et al., 2009) - Functional characterization of a Na(+)-coupled dicarboxylate transporter from Bacillus licheniformis
Strickler, Biochimica et biophysica acta 2009 - “...plasmid (pQE-80L/SdcL) encodes SdcL with an N-terminal mRGS(H) 6 GS amino acid extension and places BL01772 expression under control of a T5 promoter/lac operator element. 2.3 Preparation of washed cells The pQE-80L/SdcL construct was transformed into E. coli C41 cells. Overnight cultures of transformed E. coli...”
- “...cotransporter from human kidney (hNaDC1) as a query. The search resulted in identification of the BL01772 gene from Bacillus licheniformis , whose protein product is ~ 36% identical in sequence to hNaDC1. The gene encoding BL01772 was renamed sdcL (for s odium/ d icarboxylate s ymporter...”
Cp1002_0120 SLC13 family permease from Corynebacterium pseudotuberculosis 1002
35% identity, 84% coverage
LOC106410664 tonoplast dicarboxylate transporter from Brassica napus
34% identity, 78% coverage
Asulf_01109 SLC13 family permease from Archaeoglobus sulfaticallidus PM70-1
35% identity, 73% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...is conserved in the majority of the sequences in clade B (TOL2_29810, HRM2_07790, DP0767, DP0768, Asulf_01109, Desgi_0931, DesafDRAFT_1589, DesafDRAFT_2725, BN4_10586, Desal_0726) and all sequences in group C i , the sulfate transporter (YP_003577054) from R. capsulatus has a proline (P) at position 258 ( Figures 5...”
DIP0179 Putative membrane protein from Corynebacterium diphtheriae NCTC 13129
35% identity, 89% coverage
LOC119173491 LOW QUALITY PROTEIN: solute carrier family 13 member 2-like from Rhipicephalus microplus
28% identity, 87% coverage
cg0277 Sodium:sulfate symporter transmembrane component from Corynebacterium glutamicum ATCC 13032
35% identity, 79% coverage
- Identification and characterization of a bacterial transport system for the uptake of pyruvate, propionate, and acetate in Corynebacterium glutamicum
Jolkver, Journal of bacteriology 2009 - “...the same procedure, the genes cg0088, cg0144, cg0277, cg0683, cg0701, cg1419, cg1696, cg2425, cg2557, cg3371, and cg3403 were inactivated. For transcriptional...”
- Acetohydroxyacid synthase, a novel target for improvement of L-lysine production by Corynebacterium glutamicum
Blombach, Applied and environmental microbiology 2009 - “...heme oxygenase ABC-type cobalamin/Fe3-siderophore transport system Others cg0277 cg0503 cg0569 cg0607 cg0963 cg1043 cg1049 cg1085 cg1087 cg1090 cg1229 cg1279...”
- Identification and characterization of the dicarboxylate uptake system DccT in Corynebacterium glutamicum
Youn, Journal of bacteriology 2008 - “...DNA microarray analysis showed higher mRNA levels of cg0277, which subsequently was named dccT, in the mutants than in the wild type, and transcriptional...”
- “...were below 15%. NG, no significant growth occurred. cg0277 (dccT) cg0661 cg0809 cg0921 cg1012 cg1612 cg1786 cg2312 cg3146 cg3373 a preculture medium (Table 2...”
TC 2.A.47.1.12 / A4QAL6 The aerobic dicarboxylate (succinate (Km, 30 μM), fumarate (Km, 79 from Corynebacterium glutamicum (strain R) (see paper)
35% identity, 79% coverage
- substrates: Dicarboxylates, Fumarate, Succinate, malate, oxoaloacetate
tcdb comment: μM), malate (Km, 360 μM)) transporter, DcsT or DccT. Also transports oxaloacetate with low affinity (Ebbighausen et al. 1991; Teramoto et al., 2008; Youn et al. 2008Youn et al. 2008)
cur_1939 putative transporter from Corynebacterium urealyticum DSM 7109
34% identity, 79% coverage
CU7111_1861 SLC13 family permease from Corynebacterium urealyticum DSM 7111
34% identity, 79% coverage
LOC18780397 tonoplast dicarboxylate transporter from Prunus persica
31% identity, 80% coverage
- Transcriptome Analysis of Genes Involved in Cold Hardiness of Peach Tree (Prunus persica) Shoots during Cold Acclimation and Deacclimation
Yu, Genes 2020 - “...shoots, with the exception of the DEG encoding non-symbiotic hemoglobin (LOC18766910) and tonoplast dicarboxylate transporter (LOC18780397), which were higher in Odoroki than in Soomee during both periods ( Figure 6 ). 3.8. Selection of the DEGs Involved in the Cold Hardiness of Peach Tree Shoots The...”
- “...p < 0.05. LOC18766910, non-symbiotic hemoglobin ; LOC18768153, squalene monooxygenase ; LOC18769194, polygalacturonase inhibitor ; LOC18780397, tonoplast dicarboxylate transporter ; LOC18784088, late embryogenesis abundant protein 2 ; LOC18793247, extracellular ribonuclease LE ; LOC18768928, bidirectional sugar transporter SWEET1 ; LOC18785901, 14 kDa proline-rich protein DC2.15 ; LOC109947416,...”
HP0214 sodium-dependent transporter (huNaDC-1) from Helicobacter pylori 26695
33% identity, 79% coverage
CE0194 putative cotransporter from Corynebacterium efficiens YS-314
35% identity, 76% coverage
LOC8055864 tonoplast dicarboxylate transporter from Sorghum bicolor
31% identity, 80% coverage
Q5EC47 Sodium sulfate cotransporter-2 from Rattus norvegicus
35% identity, 53% coverage
- ITRAQ Based Proteomics Reveals the Potential Mechanism of Placental Injury Induced by Prenatal Stress.
Li, International journal of molecular sciences 2024 - “...Leukocyte elastase inhibitor A (Serpinb1a) Q5M7T5 Protein Serpinc1 (Serpinc1) P20961 Plasminogen activator inhibitor 1 (Serpine1) Q5EC47 Protein Slc13a4 (Slc13a4) A0A0G2K2S2 Solute carrier family 2, facilitated glucose transporter member 1 (Slc2a1) Q9EQ25 Sodium-coupled neutral amino acid transporter 4 (Slc38a4) Q794F9 4F2 cell-surface antigen heavy chain (Slc3a2) M0R6B7...”
NP_766480 solute carrier family 13 member 4 from Mus musculus
34% identity, 60% coverage
LOC8055193 tonoplast dicarboxylate transporter from Sorghum bicolor
30% identity, 75% coverage
S13A4_HUMAN / Q9UKG4 Solute carrier family 13 member 4; Na(+)/sulfate cotransporter SUT-1; NaS2 from Homo sapiens (Human) (see 2 papers)
TC 2.A.47.1.14 / Q9UKG4 solute carrier family 13 (sodium/sulfate symporters), member 4, NaS2 from Homo sapiens (see 5 papers)
NP_036582 solute carrier family 13 member 4 isoform 2 from Homo sapiens
33% identity, 59% coverage
- function: Sodium:sulfate symporter that mediates sulfate reabsorption in the high endothelial venules (HEV).
catalytic activity: sulfate(out) + 3 Na(+)(out) = sulfate(in) + 3 Na(+)(in) (RHEA:71951) - substrates: Na+, Selenate, Sulfate, Thiosulfate
tcdb comment: Transports anions such as sulfate, thiosulfate and selenate (Bergeron et al. 2013) - SLC13A4 Might Serve as a Prognostic Biomarker and be Correlated with Immune Infiltration into Head and Neck Squamous Cell Carcinoma.
Yang, Pathology oncology research : POR 2021 - GeneRIF: SLC13A4 Might Serve as a Prognostic Biomarker and be Correlated with Immune Infiltration into Head and Neck Squamous Cell Carcinoma.
- Molecular analysis of sequence and splice variants of the human SLC13A4 sulfate transporter.
Zhang, Molecular genetics and metabolism 2017 (PubMed)- GeneRIF: Study found that despite differential expression of the two SLC13A4 transcripts, no detectable functional difference in the cellular sorting or sulfate transporting was found. However, some variants can influence both mechanism in specific cell membranes. This is like to have clinical implications based on the consequences of impaired sulfate transport during pregnancy in rodent models.
- Human placental sulfate transporter mRNA profiling from term pregnancies identifies abundant SLC13A4 in syncytiotrophoblasts and SLC26A2 in cytotrophoblasts.
Simmons, Placenta 2013 (PubMed)- GeneRIF: SLC13A4 and SLC26A2 were the most abundant sulfate transporter mRNAs, which localized to syncytiotrophoblast and cytotrophoblast cells, respectively.
- Molecular analysis of the human SLC13A4 sulfate transporter gene promoter.
Jefferis, Biochemical and biophysical research communications 2013 (PubMed)- GeneRIF: To investigate the regulation of SLC13A4 gene expression, we analysed the transcriptional activity of the SLC13A4 5'-flanking region in the JEG-3 placental cell line using luciferase reporter assays.
- Functional characterization and genomic organization of the human Na(+)-sulfate cotransporter hNaS2 gene (SLC13A4).
Markovich, Biochemical and biophysical research communications 2005 (PubMed)- GeneRIF: Here, we characterized the functional properties of the human Na(+)-sulfate cotransporter (hNaS2), determined its tissue distribution, and identified its gene (SLC13A4) structure.
- Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Rose, Molecular medicine (Cambridge, Mass.) - GeneRIF: Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
- Blood Plasma Circulating DNA-Protein Complexes: Involvement in Carcinogenesis and Prospects for Liquid Biopsy of Breast Cancer.
Shefer, Journal of personalized medicine 2023 - “...Q99999 Q9BT49 Q9BY07 Q9BYE3 Q9H000 Q9H239 Q9H2G4 Q9H6E4 Q9H6Y7 Q9HCP0 Q9NS84 Q9NYL4 Q9NZE8 Q9NZU5 Q9P126 Q9UKG4 Q9ULL5 Q9UPG8 Q9UQ90 Q9Y3C8 Q9Y3M8 * Proteins that negatively regulate the process are marked with hatching. Legend: HF; BCP; universal. jpm-13-01691-t004_Table 4 Table 4 Potential proteomic markers of breast cancer...”
- Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147
Maimaris, International journal of molecular sciences 2021 - “...15377, 15294, 15291, 46873, 22890, 15077 B Solute carrier family 12 member 7 A,B,G,F,J SLC13A4 Q9UKG4 A 15296, 15373, 15294, 15370, 15291, 15081, 46873, 22890, 15077 B Solute carrier family 13 member 4 A,B,G,F,I,J,K SLC22A1 O15245 A 15296, 15373, 15377, 5277, 5330, 5334, 8513, 15294, 15370,...”
- Consequences of NaCT/SLC13A5/mINDY deficiency: good versus evil, separated only by the blood-brain barrier.
Kopel, The Biochemical journal 2021 - “...Succinate -Ketoglutarate Fumarate Malate Citrate Kidney (BBM) Liver (SM/BLM) Placenta (BBM) 20q13.12 None SLC13A4 2.A.47.1.14 Q9UKG4 Na + /sulfate cotransporter SUT1/NaS2 Sulfate Placenta (BBM) Testis Heart 7q33 None SLC13A5 2.A.47.1.9 Q86YT5 Na + /citrate cotransporter NaCT/NaC2 Citrate Succinate Pyruvate Liver (SM/BLM) Brain (neuron) Testis (germ cell)...”
- THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...SLC13A4 SLC13A5 HGNC, UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Common abreviation NaS1 NaC1 NaC3 NaS2 NaC2 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3 2 citric acid , succinic acid...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...NaS2 NaC2 HGNC, UniProt SLC13A1 , Q9BZW2 SLC13A2 , Q13183 SLC13A3 , Q8WWT9 SLC13A4 , Q9UKG4 SLC13A5 , Q86YT5 Endogenous substrates SeO 4 2 , SO 4 2 , S 2 O 3 2 citric acid , succinic acid citric acid , succinic acid SO 4...”
- The Concise Guide to PHARMACOLOGY 2013/14: transporters
Alexander, British journal of pharmacology 2013 - “...abbreviation NaS1 NaC1 NaC3 NaS2 NaC2 HGNC, UniProt SLC13A1, Q9BZW2 SLC13A2, Q13183 SLC13A3, Q8WWT9 SLC13A4, Q9UKG4 SLC13A5, Q86YT5 Endogenous substrates SeO42-, S2O32-, SO42- citric acid, succinic acid citric acid, succinic acid SO42- citric acid, pyruvic acid Stoichiometry 3 Na + : 1 SO 4 2- (in)...”
Desal_0726 anion transporter from Desulfovibrio salexigens DSM 2638
32% identity, 75% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...of the sequences in clade B (TOL2_29810, HRM2_07790, DP0767, DP0768, Asulf_01109, Desgi_0931, DesafDRAFT_1589, DesafDRAFT_2725, BN4_10586, Desal_0726) and all sequences in group C i , the sulfate transporter (YP_003577054) from R. capsulatus has a proline (P) at position 258 ( Figures 5 , 6 ). Similarly, mutation...”
LOC8064842 tonoplast dicarboxylate transporter from Sorghum bicolor
32% identity, 80% coverage
Q59HF0 Solute carrier family 13 (Sodium/sulfate symporters), member 4 variant (Fragment) from Homo sapiens
33% identity, 65% coverage
Pcar_2073 Na/dicarboxylate cotransporter-like protein from Pelobacter carbinolicus str. DSM 2380
32% identity, 90% coverage
GRMZM2G099382 tonoplast dicarboxylate transporter from Zea mays
30% identity, 80% coverage
Q7UUK9 Probable transporter from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
32% identity, 85% coverage
B6T0F4 Tonoplast dicarboxylate transporter from Zea mays
29% identity, 80% coverage
- Growth Stimulatory Effects and Genome-Wide Transcriptional Changes Produced by Protein Hydrolysates in Maize Seedlings.
Santi, Frontiers in plant science 2017 - “...GRMZM2G135291_T01 G3XDL3 Putative iron-phytosiderophore transporter 3.82 GRMZM2G180547_T01 Q53LH2 Amino acid carrier, putative, expressed 3.53 GRMZM2G099382_T01 B6T0F4 Tonoplast dicarboxylate transporter 3.30 GRMZM2G072071_T01 B6U4J2 ATP-binding cassette sub-family B member 10 2.76 GRMZM2G148060_T01 K7VD92 Putative ferroportin-domain family protein 2.70 GRMZM2G118507_T01 K7VD86 Uncharacterized protein 2.65 GRMZM2G024196_T01 Q7XKF4 Probable metal-nicotianamine transporter...”
IL2396 Na+/dicarboxylate symporter from Idiomarina loihiensis L2TR
32% identity, 79% coverage
Mflv_0935 anion transporter from Mycobacterium flavescens PYR-GCK
30% identity, 93% coverage
SSP0304 putative di- and tricarboxylate transporter from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
29% identity, 83% coverage
XP_011523756 solute carrier family 13 member 2 isoform X5 from Homo sapiens
33% identity, 54% coverage
- Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
Chi, Science advances 2024 - GeneRIF: Cryo-EM structures of the human NaS1 and NaDC1 transporters revealed the elevator transport and allosteric regulation mechanism.
- SLC26A6 and NADC‑1: Future direction of nephrolithiasis and calculus‑related hypertension research (Review).
Yang, Molecular medicine reports 2021 (PubMed)- GeneRIF: SLC26A6 and NADC1: Future direction of nephrolithiasis and calculusrelated hypertension research (Review).
- rs11567842 SNP in SLC13A2 gene associates with hypocitraturia in Thai patients with nephrolithiasis.
Udomsilp, Genes & genomics 2018 (PubMed)- GeneRIF: Homozygous GG of rs11567842 SNP in NaDC-1 gene was a protective genotype for hypocitraturia in kidney stone patients
- Evidence for epistatic interaction between VDR and SLC13A2 genes in the pathogenesis of hypocitraturia in recurrent calcium oxalate stone formers.
Rendina, Journal of nephrology 2017 (PubMed)- GeneRIF: Results point to an epistatic interaction between the VDR and the SLC13A2 alleles in the pathogenesis of idiopathic hypocitraturia in calcium-oxalate stone formers.
- Expression of sodium-dependent dicarboxylate transporter 1 (NaDC1/SLC13A2) in normal and neoplastic human kidney.
Lee, American journal of physiology. Renal physiology 2017 - GeneRIF: NaDC1 is present throughout the entire proximal tubule, but was not detected in kidney tumors.
- Mapping Functionally Important Residues in the Na+/Dicarboxylate Cotransporter, NaDC1.
Colas, Biochemistry 2017 (PubMed)- GeneRIF: Mapping Functionally Important Residues in the Na(+)/Dicarboxylate Cotransporter, NaDC1.
- Synthesis, maturation, and trafficking of human Na+-dicarboxylate cotransporter NaDC1 requires the chaperone activity of cyclophilin B.
Bergeron, The Journal of biological chemistry 2011 - GeneRIF: cyclophilin isoform B is likely responsible for down-regulation of carrier expression by CsA and that it does so via its chaperone activity on NaDC1 (by direct interaction) rather than its rotamase activity.
- L-type voltage-dependent calcium channel alpha subunit 1C is a novel candidate gene associated with secondary hyperparathyroidism: an application of haplotype-based analysis for multiple linked single nucleotide polymorphisms.
Yokoyama, Nephron. Clinical practice 2010 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- More
PMI_RS01070 SLC13 family permease from Proteus mirabilis HI4320
28% identity, 81% coverage
- Decreased biofilm formation in Proteus mirabilis after short-term exposure to a simulated microgravity environment
Wang, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2021 - “...1.51757779099496 Down 0.00028 Lglutathione S-transferase PMI_RS09365 grcA 384 1.7488696118053 Down 6.98E-05 Autonomous glycyl radical cofactor PMI_RS01070 1383 1.36339040837153 Down 6.35E-05 Solute carrier family PMI_RS18490 gpmB 648 1.46649446000024 Down 7.08E-05 Probable phosphoglycerate mutase PMI_RS13405 279 1.90346273574243 Down 0.00028 Ethanolamine utilization protein EutM PMI_RS03835 rmf 171 1.77234261558484 Down...”
HAPS_2130 DASS family sodium-coupled anion symporter from Glaesserella parasuis SH0165
29% identity, 84% coverage
- Transcriptome analysis of heat resistance regulated by quorum sensing system in Glaesserella parasuis
Zhang, Frontiers in microbiology 2022 - “..., HAPS_2254 , HAPS_1551 , and aspA genes were up-regulated, and htrA , acnB , HAPS_2130 , icd , ulaA , gltA , HAPS_1218 , and mlc genes were down-regulated in the luxS mutant strain compared with the wild type strain, which were the same as...”
VV1_2805 Di- and tricarboxylate transporter from Vibrio vulnificus CMCP6
27% identity, 85% coverage
VP1256 transporter, NadC family from Vibrio parahaemolyticus RIMD 2210633
28% identity, 85% coverage
- Bacteriostatic effects of benzyl isothiocyanate on Vibrio parahaemolyticus: Transcriptomic analysis and morphological verification
Liu, BMC biotechnology 2021 - “...VP1278 SpoOM-like protein 0.75022 1.68430 DOWN VP0407 rpsU 30S ribosomal protein S21 0.75017 0.47875 DOWN VP1256 NadC family protein 0.74166 0.02730 DOWN VP0180 slmA Nucleoid occlusion protein 0.73893 2.70710 DOWN Bacterial chemotaxis VP2248 fliG Flagellar motor switch protein G 0.79604 0.14531 DOWN VP1892 Methyl-accepting chemotaxis protein...”
- “...file 4 ). Three genes VP0295, VPA1128, and VPA1735 were upregulated, while eight genes VP1092, VP1256, VP1741, nhaB, VP2351, VP2545, VP2778, and VP2826 were downregulated in sodium ion transport of biological processes. They regulated multiple proteins related to sodium ion transport, such as sodium/sulfate symporter, acyl-CoA...”
APL_1254 hypothetical protein from Actinobacillus pleuropneumoniae L20
27% identity, 84% coverage
HI0608 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Q57486 Uncharacterized transporter HI_0608 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
28% identity, 85% coverage
- The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon
Whitby, BMC genomics 2009 - “...HI0026 Lipoate biosynthesis protein A lipA 3.19 2.00 ns HI0174 tRNA methyltransferase 2.36 2.08 1.93 HI0608 Conserved hypothetical protein ns -1.54 -1.49 HI0747 NADH dehydrogenase ndh ns ns ns HI0889 Serine methylase glyA 1.83 1.68 -1.09 HI0890 Dephospho CoA kinase coaE 2.50 3.48 ns HI1218 L-lactate...”
- “...from the operon comprising the ornithine decarboxylase and putrescine transporter (HI0591 and HI0592) and the HI0608 gene encoding a probable transport permease are negatively impacted by disruption of the arcA and cya genes compared to the wildtype strain and are also downregulated in response to FeHm...”
- The ArcA regulon and oxidative stress resistance in Haemophilus influenzae
Wong, Molecular microbiology 2007 - “...5.9 2.52E-09 6.2 4.67E-09 HI1444 5,10 methylenetetrahydrofolate reductase ( metF ) 5.6 4.91E-06 4.1 2.57E-05 HI0608 Conserved hypothetical protein 5.5 3.65E-10 8.3 1.81E-10 HI1727 Argininosuccinate synthetase ( argG ) 4.8 5.02E-07 4.8 3.56E-07 HI1728 Conserved hypothetical protein 3.5 1.54E-06 3.1 2.58E-05 HI1739.1 l -lactate dehydrogenase (...”
- Cloning of novel soluble gp130 and detection of its neutralizing autoantibodies in rheumatoid arthritis
Tanaka, The Journal of clinical investigation 2000 - “...protein (XMECNC), Haemophilus influenzae probable membrane protein HI0608 (I64080), Bacillus subtilis cheV protein (A55592); -NI-SF- in saimiriine herpesvirus 1...”
- Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter
Mancusso, Nature 2012 - “...may aid in the development of such agents. Methods Expression and purification A transporter protein (Q57486) from Haemophilus influenzae , a homolog of human NaDC-1 and Drosophila INDY, was expressed, purified and characterized using standard protocols 31 33 . The Haemophilus protein was then nominated to...”
Halsa_0628 SLC13 family permease from Halanaerobium hydrogeniformans
24% identity, 84% coverage
VC0338 transporter, putative from Vibrio cholerae O1 biovar eltor str. N16961
28% identity, 73% coverage
NGO0377 putative transport protein from Neisseria gonorrhoeae FA 1090
26% identity, 91% coverage
- Dual species transcriptomics reveals conserved metabolic and immunologic processes in interactions between human neutrophils and Neisseria gonorrhoeae
Potter, PLoS pathogens 2024 - “...2 -responsive genes that are also more abundant in PMN-exposed Gc encode nutrient acquisition proteins (NGO0377- citT and NGO1205- tdfJ ), metabolic proteins (NGO1931- gapC , NGO0798- glnD , NGO1247- pgsA , NGO1382- relA , NGO1671- coaE , and NGO2113- ppk ), phage associated ORFs (NGO0489-...”
- The MisR Response Regulator Is Necessary for Intrinsic Cationic Antimicrobial Peptide and Aminoglycoside Resistance in Neisseria gonorrhoeae
Kandler, Antimicrobial agents and chemotherapy 2016 - “...Start End Relative to start codon NGO0181(tatC) NGO0377 (nadC) NGO0399 (htpX) NGO0794/NGO0795 (bfrA/bfrB) NGO0978 (dsbD) NGO1046 (clpB) NGO1422 (grpE) 24.34...”
- A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur
Yu, PloS one 2014 - “...Repressed GAAAACAACGATACTTTTC NGO0302 hypothetical protein NE TTAATTAACTTTTGTTTTA NGO0304 phenylalanyl-tRNA synthetase beta subunit + NR CAAAAGAAAAACCGATTTT NGO0377 NadC family protein, transporter NE TACACTAAGTATCTTATTT NGO0436 putative 3-methyl-2-oxobutanoate hydroxymethyltransferase + Activated TATAATAAAATCAATTCTT NGO0641 type III restriction/modification system modification methylase + Repressed ACAATAAAGTTTCTTTATA NGO0711 3 alcohol dehydrogenase + 4 NE...”
- “...Fur protein ( Figure 1A ). The DSHs of predicted Fur boxes in NGO302 and NGO0377 promoter regions were only 1 nm (1.00.06 nm and 1.00.02 nm, respectively) when 800 nM Fur protein was added ( Figure 1A ), suggesting that these two predicted sequences did...”
- Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
Isabella, BMC genomics 2011 - “...component FarR glnQ NGO0374 -2.9 -11.1 ABC-type amino acid transporter, ATP-binding protein FarR, FNR citT NGO0377 -5.6 -9.1 Di- and tri-carboxylate transporters (inorganic ion transport) cysA NGO0445 -5.6 -9.1 ABC-type sulfate transporter, ATP-binding protein Lrp sbp NGO0877 -4.8 -25.0 ABC-related sulfate-binding protein NGO1290 -3.8 -3.3 Putative...”
- “...NGO0262 -4.5 -1.8 Transcription elongation factor NGO0373 -7.4 -2.5 Amino acid ABC transporter, permease protein NGO0377 -7.4 -150.4 Probable transmembrane transport protein cspA NGO0410 -3.6 3.2 Cold shock protein A NGO0492 7.7 1.8 Putative phage associated protein NGO0506 13.6 -3.2 Putative phage associated protein NGO0635 -4.2...”
VP2826 putative transporter from Vibrio parahaemolyticus RIMD 2210633
29% identity, 71% coverage
- Bacteriostatic effects of benzyl isothiocyanate on Vibrio parahaemolyticus: Transcriptomic analysis and morphological verification
Liu, BMC biotechnology 2021 - “...DOWN VPA1613 Hypothetical protein 0.7494 1.35230 DOWN VP1287 Hypothetical protein 0.7427 1.93820 UP Other genes VP2826 Transporter 0.81597 0.21954 DOWN VPA1006 LysR family transcriptional regulator 0.75038 0.97802 DOWN VP0653 dnaK Molecular chaperone DnaK 0.80187 0.02678 UP Besides, rpsU-encoded ribosomal protein S21 can affect the motility and...”
- “...regulates flagellar motor switch protein G (Table 2 ) and VP1892 regulates methyl-accepting chemotaxis protein. VP2826 and VPA1006 were down-regulated, regulating transporter and LysR family transcriptional regulator, respectively. According to the objective of present study, we focused on the antibacterial mechanism of BITC by screening differentially...”
NMB0792 transporter, NadC family from Neisseria meningitidis MC58
26% identity, 91% coverage
- HexR Controls Glucose-Responsive Genes and Central Carbon Metabolism in Neisseria meningitidis
Antunes, Journal of bacteriology 2015 - “...of 6 genes (zwf, edd, eda, hexR, ackA2, and NMB0792) were altered under both conditions, and consequently the deletion of hexR resulted in the upregulation or...”
- Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis
Huis, PloS one 2011 - “...using TargetRNA in the related strain MC58 [36] . This way, NMB0205 ( fur ), NMB0792 ( nadC ), NMB0810 (encoding a putative TetR family transcriptional regulator) and NMB1224, NMB1914, NMB2014, and NMB2110, all encoding hypothetical proteins, were identified as putative targets of this novel sRNA....”
VCA0025 / Q9KNE0 dicarboxylate:Na+ symporter from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (see 6 papers)
TC 2.A.47.5.2 / Q9KNE0 Dicarboxylate (succinate, fumarate, malate) transporter, vcINDY from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
VCA0025 transporter, NadC family from Vibrio cholerae O1 biovar eltor str. N16961
28% identity, 79% coverage
- substrates: Citrate, Fumarate, Li+, Na+, Succinate, glutamate, malate
tcdb comment: The 3-d structure is known to 3.2 Å resolution with citrate and Na+ bound (Mancusso et al. 2012). May also transport citrate and glutamate with low affinity. Can use Na+ or Li+ as the cotransported cation. MtrF (TC#2.A.68.1.2) and YdaH (TC# 2.A.68.1.4) have been shown to have similar 3-d folds as vcINDY (Vergara-Jaque et al. 2015), confirming the assignment of these two families to the same superfamily (Prakash et al. 2003) - Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae
Sepúlveda-Cisternas, Scientific reports 2018 - “...phosphorylase 1.713 VCA0014 malQ 4-alpha-glucanotransferase 1.698 VCA0015 hypothetical protein 1.630 VCA0016 14-alpha-glucan branching enzyme 1.642 VCA0025 transporter NadC family 1.244 VCA0053 ppnP purine nucleoside phosphorylase 1.062 VCA0087 hypothetical protein 1.004 VCA0139 hypothetical protein 1.146 1.236 VCA0180 pepT peptidase T 1.364 VCA0205 C4-dicarboxylate transporter anaerobic 1.170 1.136...”
- Quorum-sensing regulators control virulence gene expression in Vibrio cholerae
Zhu, Proceedings of the National Academy of Sciences of the United States of America 2002 - “...45.0 2.7 18.0 19.7 16.3 10.5 28.4 40.4 39.5 6.9 VCA0025 VC1318 VCA0687 VC1362 VC1854 6.3 4.5 3.6 4.9 5.5 VC0819 VCA0744 VCA0877 VCA0690 VCA0688 VCA0691 12.7 5.3...”
- Experimental determination and data-driven prediction of homotypic transmembrane domain interfaces.
Xiao, Computational and structural biotechnology journal 2020 - “...49 BCNG-1 (O60741, 5u6oA6) e ITMLSMIVG A TC YAMF VG H ATA LI 50 NadC (Q9KNE0, 5uldA9) WKEI Q KT ADWG ILLLFGGGLCL a Accession number (acc) from the UniProt database. The X-ray identification code (e.g.1orqC4) consists of the PDB accession (e.g.1orq), the protein chain (e.g.C), and...”
- A facile approach for the in vitro assembly of multimeric membrane transport proteins
Riederer, eLife 2018 - “...) GltPh 10.1038/nature03018 Uniprot ID: O59010 Gene ( Vibrio cholerae ) VcINDY 10.1038/nature11542 Uniprot ID: Q9KNE0 Gene ( Escherichia coli ) CLC-ec1 10.1085/jgp.200308935 Uniprot ID: P37019 Gene ( Staphylothermus marinus ) GltSm 10.1111/febs.12105 Uniprot ID: A3DPQ3 Recombinant DNA reagent pBCH/G4-GltPh 10.1038/nature03018 Recombinant DNA reagent pET-VcINDY 10.1038/nature11542...”
7t9gA / Q9KNE0 Structure of vcindy-na+ (see paper)
28% identity, 79% coverage
- Ligand: sodium ion (7t9gA)
VC_1314 SLC13 family permease from Vibrio cholerae O1 biovar El Tor str. N16961
29% identity, 74% coverage
- RavA-ViaA antibiotic response is linked to Cpx and Zra2 envelope stress systems in Vibrio cholerae
Krin, Microbiology spectrum 2023 - “...also down-regulates outer membrane proteins. In parallel, transcriptomic data in ravvia showed strong induction of VC_1314 and the VC_1315-VC_1316 operon which presents similarities with the Cpx and Zra two-component envelope stress response systems. In E. coli , ZraSR contributes to antibiotic resistance and is important for...”
- “...in ravvia compared to WT, in all conditions shown in Tables S2 to S4. The VC_1314 gene and the VC_1315-VC_1316 operon show 8- to 10-fold upregulation. VC_1315 presents 35% sequence identity which E. coli zraS gene. The ZraP regulator and ZraSR two-component membrane stress response system...”
VC1314 transporter, putative from Vibrio cholerae O1 biovar eltor str. N16961
28% identity, 74% coverage
Asuc_0020 anion transporter from Actinobacillus succinogenes 130Z
26% identity, 87% coverage
Asuc_1568 anion transporter from Actinobacillus succinogenes 130Z
27% identity, 83% coverage
- Asuc_0142 of Actinobacillus succinogenes 130Z is the l-aspartate/C4-dicarboxylate exchanger DcuA
Cho, Microbiology (Reading, England) 2023 - “...contains several other potential C4DC transporters such as Asuc_1999 (DcuE), Asuc_1063 (DcuC family), Asuc_0304 (SdcA), Asuc_1568 (DASS family), and Asuc_02700273 (TRAP family) in addition to Asuc_0142 [ 10 ]. Many C4DC transporters have broad substrate specificity and replace each other functionally when individual transporters are deleted...”
- Transcriptome analysis and anaerobic C4 -dicarboxylate transport in Actinobacillus succinogenes
Rhie, MicrobiologyOpen 2018 - “...Asuc_0304 ( DASS ), and Asuc_02700273 ( TRAP ), were constitutively expressed, whereas three others, Asuc_1568 ( DASS ), Asuc_1482 ( DASS ), and Asuc_0142 (Dcu), were differentially expressed during growth on fumarate. Transport assays under anaerobic conditions with [ 14 C]fumarate and [ 14 C]succinate...”
- “...anion:Na + symporter 282 78 268 44 1.914 .047 2.543 .009 0.062 .946 0.702 .454 Asuc_1568 Na + dependent dicarboxylate transporter 1201 223 289 98 2.433 .012 1.547 .101 2.009 .036 1.138 .224 The C 4 Dicarboxylate Uptake (Dcu) Family Asuc_0142 anaerobic C 4 dicarboxylate transporter...”
DND132_2125 SLC13 family permease from Pseudodesulfovibrio mercurii
28% identity, 80% coverage
4f35B / Q9KNE0 Crystal structure of a bacterial dicarboxylate/sodium symporter (see paper)
28% identity, 78% coverage
- Ligand: sodium ion (4f35B)
APL_1252 hypothetical protein from Actinobacillus pleuropneumoniae L20
25% identity, 79% coverage
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...APL_1856 APL_1856 Hypothetical protein 2.775 APL_1855 APL_1855 Hypothetical protein 2.763 APL_0443 APL_0443 Autotransporter adhesin 2.762 APL_1252 APL_1252 Hypothetical protein 2.739 APL_0134 APL_0134 Hypothetical protein 2.681 APL_0836 APL_0836 Putative transcriptional regulator 2.661 APL_1588 APL_1588 Predicted TRAP transporter solute receptor 2.464 APL_1491 APL_1491 Hypothetical protein 2.282 APL_0104 APL_0104...”
TC 2.A.47.5.1 / Q58086 Hypothetical Na+ cotransporter, Orfl from Methanococcus jannaschii (see paper)
27% identity, 87% coverage
Amuc_0221 anion transporter from Akkermansia muciniphila ATCC BAA-835
26% identity, 85% coverage
- Omics-based analysis of <i>Akkermansia muciniphila</i> cultivation in food-grade media
Geerlings, Microbiome research reports 2024 - “...transporters such as Major Facilitator Superfamily (MFS), biopolymer, anion and amino acid transporters (Amuc_1331, Amuc_0546, Amuc_0221 and Amuc_0037), as well as peptide, aliphatic sulfonate, nitrate/sulfonate/bicarbonate, cobalt and manganese ABC transporters (Amuc_0672, AMUC_1297, Amuc_0408, Amuc_1198, Amuc_1199, Amuc_0056, Amuc_1380 and Amuc_1186) with an increase > 5-fold. In addition,...”
C9J4A3 HCG2018530, isoform CRA_c from Homo sapiens
51% identity, 20% coverage
Daes_0041 SLC13 family permease from Pseudodesulfovibrio aespoeensis Aspo-2
26% identity, 80% coverage
YPO0759 Sodium:sulfate symporter-family protein from Yersinia pestis CO92
27% identity, 79% coverage
BN4_12301 SLC13 family permease from Pseudodesulfovibrio piezophilus C1TLV30
26% identity, 87% coverage
HRM2_38270 NadC2 from Desulfobacterium autotrophicum HRM2
26% identity, 77% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...2017 ). There was no significant change in the expression of another two DASS (HRM2_07790, HRM2_38270) and one SulP (HRM2_33490) family transporters between low and high sulfate grown cells ( Tarpgaard et al., 2017 ). No expression was detected for the SulP encoding gene HRM2_13280 (...”
- “...HRM2_38300 can be found in the C ii group on the DASS tree along with HRM2_38270 whose expression was not affected by changes in the sulfate concentration ( Figure 5 ). The low affinity HRM2_40290 transporter can be found among the C i group sequences (...”
TON_1664 cation transporter from Thermococcus onnurineus NA1
26% identity, 79% coverage
- Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis
Lee, Scientific reports 2016 - “...protein (TON_1544) and single- or multiple-base deletions/insertions in aminotransferase (TON_0982), hypothetical protein (TON_1548), cation transporter (TON_1664), metalloprotease (12bp inserted) (TON_1694), and alcohol dehydrogenase (338bp deleted) (TON_0544), as well as in the intergenic region (51bp deleted) between sodium/phosphate symporter (TON_1475) and pyruvate/ketoisovalerate ferredoxin oxidoreductase (TON_1476). A long...”
- “...and TON_1548 could not be predicted or understood at this moment and the role of TON_1664 encoding cation transporter in archaea is unclear yet and awaits further analysis. Epigenomic analysis revealed cytosine methylation at N4 sites in T. onnurineus NA1. N 4 -methylcytosine (m4C) has been...”
XP_013932315 Inorganic phosphate transporter PHO87 from Ogataea parapolymorpha DL-1
28% identity, 52% coverage
Desor_1742 SLC13 family permease from Desulfosporosinus orientis DSM 765
24% identity, 78% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...transport proteins ( Figures 3 , 9 ). In Desulfosporosinus orientis the DASS encoding gene Desor_1742 is located in close proximity to the sat and apr AB genes as well as a SulP (Desor_1738, see above) and a TSUP (Desor_1745) encoding gene ( Figure 9 )....”
- “...close proximity to the sat and apr AB genes ( Figure 9 ). Desgi_3715 and Desor_1742 are part of the C i group of DASS sequences characterized by the highly conserved G258 residue. Finally, Desaci_2328, a CysZ encoding gene from Desulfosporosinus acidiphilus , is located close...”
AO090003000920 No description from Aspergillus oryzae RIB40
24% identity, 51% coverage
TC 2.A.47.2.4 / Q4DX24 Contractile vacuole phosphate:Na+ symporter of 727 aas and 12 TMSs, Pho91 (Pho90; Pho87) from Trypanosoma cruzi (strain CL Brener)
24% identity, 67% coverage
- substrates: Na+, phosphate
tcdb comment: Has an N-terminal SPX domain and a C-terminal anion permease domain. Plays an indirect role in pyrophosphate and oligophosphate synthesis (Jimenez and Docampo 2015). Pyrophosphate stimulates the phosphate-sodium symporter of Trypanosoma brucei acidocalcisomes and Saccharomyces cerevisiae vacuoles (Potapenko et al. 2019)
YBH4_SCHPO / O59712 Uncharacterized transporter C3B8.04c from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPBC3B8.04c membrane transporter from Schizosaccharomyces pombe
27% identity, 52% coverage
- Regulation of inorganic polyphosphate is required for proper vacuolar proteolysis in fission yeast
Sawada, The Journal of biological chemistry 2021 - “...+ ( 42 ), SPBC1683.01, SPAC23D3.12, and SPCC2H8.02) and one encoding a low-affinity phosphate transporter (SPBC3B8.04c). Hereafter we designate SPBC1683.01, SPAC23D3.12, SPCC2H8.02, and SPBC3B8.04c as pho841 + , pho842 + , pho843 + , and plt1 + ( plt : p hosphate l ow-affinity t ransporter),...”
- Genomic binding profiling of the fission yeast stress-activated MAPK Sty1 and the bZIP transcriptional activator Atf1 in response to H2O2
Eshaghi, PloS one 2010 - “...186 SPCC830.08c Pcr1 ER membrane protein DP1/Yop1 13 199 SPAC4H3.08 Pcr1 3-hydroxyacyl-CoA dehydrogenase 14 216 SPBC3B8.04c Pcr1 membrane transporter Note: a, Responsive (Resp.) rank is based on the average level of transcriptional induction at 30, 60, and 120 min after H 2 O 2 stress in...”
PFJ30894_RS04475 SLC13 family permease from Phascolarctobacterium faecium
26% identity, 79% coverage
- Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron
Ikeyama, MicrobiologyOpen 2020 - “...in the expression levels. In the coculture, two genes encoding SLC13/DASS family transporters (PFJ30894_RS03075 and PFJ30894_RS04475) exhibited much larger TPM values compared to the monoculture. Furthermore, sodium/glutamate symporter (PFJ30894_RS00375), Glu/Leu/Phe/Val dehydrogenase (PFJ30894_RS04940), and a gene cluster consisting of PFJ30894_RS01150 (4Fe4S dicluster domaincontaining protein), PFJ30894_RS01155 (2oxoacid:acceptor oxidoreductase...”
- “...0 15.65 Genes for SLC13 family transporters PFJ30894_RS03075 + Citrate transporter K14445 253.98 2764.97 7569.79 PFJ30894_RS04475 + SLC13/DASS family transporter K14445 1135.71 996.63 3053.47 Genes involved in the glutamate metabolism PFJ30894_RS00375 Sodium/glutamate symporter K03312 439.74 955.46 2475.13 PFJ30894_RS01150 + 4Fe4S dicluster domaincontaining protein K00176 359.17 357.32...”
STM3356 putative cation transporter from Salmonella typhimurium LT2
STM14_4048 SLC13 family permease from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
23% identity, 79% coverage
- Salmonella enterica subsp. enterica serovar Paratyphi B from mute swan (Cygnus olor): complete genome sequence features point towards invasive variant potential
Lamparter, Microbiology resource announcements 2024 - “...using standard reagents (Sifin diagnostics GmbH Berlin, Germany); d T variant PCR screening targeting the STM3356 Start codon was done according to ( 2 , 3 ). For isolation of genomic DNA (gDNA), one colony of isolate 22-SA01722-0 was enriched in lysogeny broth for 18 hours...”
- “...to SPI-5, SPI-6*, SPI-9, SPI-11 to SPI-14, and SPI-16 10, 11, 12, 16, 17, 1925 STM3356 (locus tag Q1K22_RS02410) start codon sequence PGAP v6.5, visualization of genome annotation in Geneious Prime v2020.2.2 ATA ATA 3, 1921 Further genetic features associated with invasive disease phenotype ABRicate v1.0.1,...”
- Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures
Yuan, mSystems 2022 - “...( Fig.6e ) (see Text S1 [Note 3]). Among the seven genes in the iModulon, STM3356 is a putative cation transporter whose function is still unknown, but disruption of this gene can convert tartrate-fermenting phenotypes into tartrate-nonfermenting phenotypes for S. enterica serovar Paratyphi B dT+ (...”
- Prevalence and Molecular Characterization of Salmonella Isolated from Broiler Farms at the Tolima Region-Colombia
Rodríguez-Hernández, Animals : an open access journal from MDPI 2021 - “...2015 to 2016. Figure 3 PCR amplification of 290 bp of the putative cation transporter STM3356 gene identifying dT+ Salmonella isolated from broilers farms in Tolima, Colombia. MWGeneRuler 100 bp Plus DNA Ladder ((Thermo Fisher Scientific, Waltham, MA, USA); lanes 124: Salmonella Paratyphi B isolates from...”
- Whole-Genome Sequencing Analysis of Nontyphoidal Salmonella enterica of Chicken Meat and Human Origin Under Surveillance in Sri Lanka
Tay, Foodborne pathogens and disease 2019 - “...Paratyphi B cannot due to a single nucleotide change in the start codon of the STM3356 gene (Malorny et al. , 2003 ). Hence, when the draft genome of these four isolates were blasted against the STM3356 gene of Java strain NCTC5706 (GenBank accession number: LT571437.1),...”
- SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data
Zhang, Applied and environmental microbiology 2019 (secret) - Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java
Gand, Applied microbiology and biotechnology 2019 - “...from the marker SPAB_04460 found in our genomic study and from the primer 166 (gene STM3356 ) of the study of Malorny et al. ( 2003 ), respectively. For each marker, a SNP probe and a (wild-type) WT probe were designed by putting the specific nucleotide...”
- Pseudomonas stutzeri as an alternative host for membrane proteins
Sommer, Microbial cell factories 2017 - “...NT A. aeolicus Aq_031 DASS 15605634 + S. enterica STM3166 DASS 16421721 NT S. enterica STM3356 DASS 16421915 NT S. enterica STM0832 DMT 16419338 + ++ S. enterica STM3765 DMT 16422334 + + + S. enterica STM3746 ESS 16767031 + + + S. enterica STM2913 GntP...”
- Analysis of Two Complementary Single-Gene Deletion Mutant Libraries of Salmonella Typhimurium in Intraperitoneal Infection of BALB/c Mice
Silva-Valenzuela, Frontiers in microbiology 2015 - “...using competitive infections with the wild-type parental strain: STM0286 , STM0551 , STM2363 , and STM3356 . Two mutants, STM0286 and STM2363 , were then complemented in trans with a plasmid encoding an intact copy of the corresponding wild-type gene, and regained the ability to fully...”
- “...S1 ). Three are deletions of genes specific to Salmonella ( STM0286, STM0551 , and STM3356 ) and one gene is shared with E. coli ( STM2363 ) (Table 2 ). All are proximal to genes that when deleted also appeared to be under selection in...”
- More
- Analysis of Two Complementary Single-Gene Deletion Mutant Libraries of Salmonella Typhimurium in Intraperitoneal Infection of BALB/c Mice
Silva-Valenzuela, Frontiers in microbiology 2015 - “...protein required for colicin V production STM3356 1.4 0.1 1.8 0.0 1.5 0.1 0.9 0.6 STM14_4048 Putative cation transporter The data are presented as M-value (log 2 ratio of output to input) and FDR (false discovery rate). Red indicates that the mutant is under negative selection....”
Q1K22_RS02410 SLC13 family permease from Salmonella enterica subsp. enterica serovar Paratyphi B
23% identity, 84% coverage
- Salmonella enterica subsp. enterica serovar Paratyphi B from mute swan (Cygnus olor): complete genome sequence features point towards invasive variant potential
Lamparter, Microbiology resource announcements 2024 - “...SPI-9, SPI-11 to SPI-14, and SPI-16 10, 11, 12, 16, 17, 1925 STM3356 (locus tag Q1K22_RS02410) start codon sequence PGAP v6.5, visualization of genome annotation in Geneious Prime v2020.2.2 ATA ATA 3, 1921 Further genetic features associated with invasive disease phenotype ABRicate v1.0.1, db VFDB_all_setA, minicov:...”
STY3536 possible membrane transport protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
23% identity, 79% coverage
- Loss of function of metabolic traits in typhoidal <i>Salmonella</i> without apparent genome degradation
Machado, mBio 2024 - “...metabolic pathways that are degraded in one serovar but not in the other. For example, sty3536 , which codes for a putative tartrate transporter, which is critical for tartrate utilization, is clearly degraded in S . Paratyphi A but appears intact in S . Typhi. However,...”
- “...metabolize tartaric acid (Fig. S13). Comparison of the amino acid sequence of S . Typhi STY3536 with its homolog in S . Typhimurium, which can utilize tartaric acid, reveals the presence of one amino acid substitution that may lead to loss of function (Fig. S14). Furthermore,...”
PHO91_YEAST / P27514 Low-affinity phosphate transporter PHO91 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
P27514 ABC-type phosphate transporter (EC 7.3.2.1) from Saccharomyces cerevisiae (see paper)
TC 2.A.47.2.2 / P27514 Vacuolar low affinity phosphate transporter, Pho91 (Estrella et al., 2008) with 12 C-terminal TMSs and an N-terminal 360 hydrophilic region. Also transports selenite (Lazard et al., 2010). Pyrophosphate stimulates the phosphate-sodium symporter of Trypanosoma brucei (TC# 2.A.47.2.4) acidocalcisomes and Saccharomyces cerevisiae vacuoles (this protein) from Saccharomyces cerevisiae (Baker's yeast) (see 8 papers)
RF|NP_014410.1 uncharacterized transporter YNR013C from Saccharomyces cerevisiae (see paper)
NP_014410 Pho91p from Saccharomyces cerevisiae S288C
YNR013C Low-affinity phosphate transporter of the vacuolar membrane; deletion of pho84, pho87, pho89, pho90, and pho91 causes synthetic lethality; transcription independent of Pi and Pho4p activity; overexpression results in vigorous growth from Saccharomyces cerevisiae
25% identity, 49% coverage
- function: Vacuolar phosphate transporter that probably exports phosphate from the vacuolar lumen to the cytosol.
- substrates: Selenite, phosphate
- Regulation of plants' phosphate uptake in common mycorrhizal networks: Role of intraradical fungal phosphate transporters
Walder, Plant signaling & behavior 2016 - “...ScPho86 (NP_012418), ScPho87 (NP_009966), ScPho89 (NP_009855), ScPho91 (NP_014410) and FmPT1 (AAZ22389). We also provide GenBank accession numbers for sequences...”
- Pho91 Is a vacuolar phosphate transporter that regulates phosphate and polyphosphate metabolism in Saccharomyces cerevisiae.
Hürlimann, Molecular biology of the cell 2007 - GeneRIF: Pho91 serves as a vacuolar phosphate transporter that exports phosphate from the vacuolar lumen to the cytosol
- The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae
Trilisenko, Cells 2019 - “...Low-affinity inorganic phosphate transporter 0.14 0.36 0.26 YJL198W PHO90 Low-affinity phosphate transporter 0.40 0.99 0.02 YNR013C PHO91 Low-affinity vacuolar phosphate transporter 0.39 0.73 0.00 YDR281C PHM6 Putative transport protein 6.0 5.97 3.52 YOL084W PHM7 Putative transport protein 12.01 11.47 8.22...”
- Genome-Wide Identification of Host Genes Required for Toxicity of Bacterial Cytolethal Distending Toxin in a Yeast Model
Denmongkholchai, Frontiers in microbiology 2019 - “...ER; FLC3 has a paralog, FLC1, that arose from the whole genome duplication Ion transport YNR013C PHO91 Low-affinity vacuolar phosphate transporter; exports phosphate from the vacuolar lumen to the cytosol; regulates phosphate and polyphosphate metabolism; acts upstream of Pho81p in regulation of the PHO pathway; localizes...”
- Widespread Cumulative Influence of Small Effect Size Mutations on Yeast Quantitative Traits
Hua, Cell systems 2018 - “...YPL137C, YOR092W, YBR159W, YGL083W, YNL156C, YDL128W, YBR296C, YOR175C, YJL198W, YOL101C, YHL019C, YJL117W, YGR263C, YML059C, YOR214C, YNR013C, YOR087W, YJL192C, YGR177C, YBL102W, YPL195W, YLL052C, YLR390W-A, YDR264C, YOR299W, YMR152W, YLL055W, YDR424C, YBR287W, YEL040W, YNL125C, YHL003C, YBR283C, YDL121C, YHR045W, YNR075W, YOR377W, YHR039C, YGL010W, YCL025C, YNR044W, YLR050C, YOL137W, YOL107W, YDL018C, YDR307W,...”
- A Genetic Screen for Saccharomyces cerevisiae Mutants That Fail to Enter Quiescence
Li, G3 (Bethesda, Md.) 2015 - “...SEE1 Probable lysine methyltransferase involved in the dimethylation of eEF1A (Tef1p/Tef2p); role in vesicular transport YNR013C PHO91 Vacuolar phosphate transporter, exports phosphate from vacuole to cytosol, overexpression results in vigorous growth YMR077C (VPS20) 4,5 Subunit of ESCRTIII, the endosomal sorting complex required for transport of transmembrane...”
- Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins
Peris, BMC genomics 2012 - “...of the two copies of S. cerevisiae chromosome XIV from strain CECT 1990 (between loci YNR013C and YNR031C) (Additional file 3 : Figure S2). S. kudriavzevii gene content and Gene Ontology (GO) analyses Data obtained from all hybrids analyzed in this work as well as from...”
- High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome
Yu, BMC genomics 2012 - “...- - - - - - - - - - - - - 5.30 P YNR013C PHO91 A - - - - - - - - - - - - - - - - 6.27 Cu YPR124W CTR1 B - - - - - 5.60 -...”
- Disruption of 12 ORFs located on chromosomes IV, VII and XIV of Saccharomyces cerevisiae reveals two essential genes
Volckaert, Yeast (Chichester, England) 2003 (PubMed)- “...XIV (YNL006w, YNR004w, YNR007c, YNR008w, YNR009w and YNR013c). Disruptants were generated using the PCR-based short flanking homology (SFH) strategy in yeast...”
- “...1997) and YNL006w, YNR004w, YNR007c, YNR008w, YNR009w and YNR013c on chromosome XIV (Verhasselt et al., 1994). Features of these ORFs, as collected to date,...”
- Phosphate transport and sensing in Saccharomyces cerevisiae
Wykoff, Genetics 2001 - “...30% identity with PHO87, PHO90 (YJL198w) and PHO91 (YNR013c), using a highly expressed constitutive promoter (ADH1). These four proteins do not share...”
Dde_1252 Di- and tricarboxylate transporters from Desulfovibrio desulfuricans G20
25% identity, 80% coverage
- New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20
Keller, Applied and environmental microbiology 2014 - “...Cytoplasmic carbon metabolism enzymes Dde_1250 Dde_1251 Dde_1252 Dde_1253 Dde_1254 Dde_1255 Dde_1256 Dde_1257 Dde_1258 Dde_3028 Dde_3029 Dde_2933 Protein Enzyme...”
- “...were two genes of a predicted three-gene operon (Dde_1252 to Dde_1250) encoding a malatefumarate uptake transporter (or antiporter with succinate) and two...”
RO3G_06658 uncharacterized protein from Rhizopus delemar RA 99-880
27% identity, 55% coverage
- Identification of lncRNA and weighted gene coexpression network analysis of germinating Rhizopus delemar causing mucormycosis
Kalita, Mycology 2023 - “...coding for CAZymes, viz. RO3G_03340 (GH16_19, chitin -1,6-glucanosyl transferase), MSTRG.5422.2 (GH28, polygalacturonase), RO3G_09825 (GH46, chitosanase), RO3G_06658 (GH47, -mannosidase), RO3G_04895 and RO3G_01689 both coding for GT15 (glycolipid 2--mannosyltransferase). The protein-coding accessions having GO information after hypergeometric test and Hochberg FDR cut-off 0.05 were enriched for the functions...”
Asuc_0304 anion transporter from Actinobacillus succinogenes 130Z
24% identity, 84% coverage
- Asuc_0142 of Actinobacillus succinogenes 130Z is the l-aspartate/C4-dicarboxylate exchanger DcuA
Cho, Microbiology (Reading, England) 2023 - “...environment [ 10 ]. The bacteria encode several putative carboxylate transporters including the SdcA transporter (Asuc_0304) for the uptake of C4DCs under oxidative conditions [ 19 ]. Under anaerobic conditions, six different potential transporters for C4DCs are expressed [ 10 ], including two Dcu-type transporters. DcuE...”
- “...A. succinogenes contains several other potential C4DC transporters such as Asuc_1999 (DcuE), Asuc_1063 (DcuC family), Asuc_0304 (SdcA), Asuc_1568 (DASS family), and Asuc_02700273 (TRAP family) in addition to Asuc_0142 [ 10 ]. Many C4DC transporters have broad substrate specificity and replace each other functionally when individual transporters...”
- Transcriptome analysis and anaerobic C4 -dicarboxylate transport in Actinobacillus succinogenes
Rhie, MicrobiologyOpen 2018 - “...detail. A total of six transporters were considered potential fumarate transporters: three transporters, Asuc_1999 (Dcu), Asuc_0304 ( DASS ), and Asuc_02700273 ( TRAP ), were constitutively expressed, whereas three others, Asuc_1568 ( DASS ), Asuc_1482 ( DASS ), and Asuc_0142 (Dcu), were differentially expressed during growth...”
- “...anion:Na + symporter 29 11 39 18 1.368 .178 1.025 .286 0.451 .641 0.790 .428 Asuc_0304 Na + dependent C 4 dicarboxylate transporter 269 306 266 252 0.176 .849 0.068 .941 0.030 .974 0.228 .805 Asuc_1482 divalent anion:Na + symporter 282 78 268 44 1.914 .047...”
- A Na+-coupled C4-dicarboxylate transporter (Asuc_0304) and aerobic growth of Actinobacillus succinogenes on C4-dicarboxylates
Rhie, Microbiology (Reading, England) 2014 (PubMed)- “...transporter (Asuc_0304) and aerobic growth of Actinobacillus succinogenes on C4-dicarboxylates Mi Na Rhie,1 Hyo Eun Yoon,1 Hye Yun Oh,1 Sandra Zedler,2...”
- “...dicarboxylate transporter) family. From the cloned genes, Asuc_0304 of the DASS family protein was able to restore aerobic growth on C4-dicarboxylates...”
XP_013933495 putative transporter C3B8.04c from Ogataea parapolymorpha DL-1
23% identity, 56% coverage
APL_1253 putative sodium/sulphate transporter from Actinobacillus pleuropneumoniae L20
23% identity, 84% coverage
YP_001472104 sodium/sulphate symporter from Shewanella sediminis HAW-EB3
22% identity, 80% coverage
SERP0348 anion transporter family protein from Staphylococcus epidermidis RP62A
23% identity, 67% coverage
HD0866 possible sodium/sulphate transporter from Haemophilus ducreyi 35000HP
24% identity, 84% coverage
Pcar_0639 putative membrane transporter from Pelobacter carbinolicus str. DSM 2380
24% identity, 77% coverage
Dde_0326 Putative a membrane protein from Desulfovibrio desulfuricans G20
23% identity, 78% coverage
HRM2_38230 NadC1 from Desulfobacterium autotrophicum HRM2
26% identity, 77% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...At low sulfate concentration (<100 M) genes encoding for two DASS family putative sulfate transporters (HRM2_38230, HRM2_38300) were highly expressed ( Tarpgaard et al., 2017 ). There was no significant change in the expression of another two DASS (HRM2_07790, HRM2_38270) and one SulP (HRM2_33490) family transporters...”
- “...conservation with pairwise identity values ranging from 18 to 28%. The high affinity sulfate transporters HRM2_38230 and HRM2_38300 can be found in the C ii group on the DASS tree along with HRM2_38270 whose expression was not affected by changes in the sulfate concentration ( Figure...”
TRIATDRAFT_219095 uncharacterized protein from Trichoderma atroviride
24% identity, 53% coverage
PFJ30894_RS03075 SLC13 family permease from Phascolarctobacterium faecium
27% identity, 82% coverage
- Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron
Ikeyama, MicrobiologyOpen 2020 - “...significant changes in the expression levels. In the coculture, two genes encoding SLC13/DASS family transporters (PFJ30894_RS03075 and PFJ30894_RS04475) exhibited much larger TPM values compared to the monoculture. Furthermore, sodium/glutamate symporter (PFJ30894_RS00375), Glu/Leu/Phe/Val dehydrogenase (PFJ30894_RS04940), and a gene cluster consisting of PFJ30894_RS01150 (4Fe4S dicluster domaincontaining protein), PFJ30894_RS01155...”
- “...two genes encoding SLC13/DASS family transporter were observed in the coculture. One of the genes (PFJ30894_RS03075) is encoded consecutively with the gene cluster of the succinate pathway. The SLC13 transporter is part of the divalent anion:Na + symporter (DASS) family (Mulligan, Fitzgerald, Wang, & Mindell, 2014...”
BP0380 putative Sodium:sulfate symportert from Bordetella pertussis Tohama I
24% identity, 74% coverage
CNAG_02180, XP_012049822 phosphate transporter from Cryptococcus neoformans var. grubii H99
26% identity, 46% coverage
- Dysregulating PHO Signaling via the CDK Machinery Differentially Impacts Energy Metabolism, Calcineurin Signaling, and Virulence in Cryptococcus neoformans
Bowring, mBio 2023 - “...P i starvation ( 55 , 56 ). The closest homolog in C. neoformans is CNAG_02180 (Pho91), which encodes a low-affinity vacuolar phosphate transporter. However, the high-affinity transporters Pho84, Pho840, and Pho89 could also contribute to basal P i uptake under P i -replete conditions. Although...”
- IP7-SPX Domain Interaction Controls Fungal Virulence by Stabilizing Phosphate Signaling Machinery
Desmarini, mBio 2020 - “...Cryptococcus neoformans var. grubii H99 CnPho81 ( XP_012049680 ), CnSyg1 ( XP_012051471 ), CnPho91 ( XP_012049822 ) phosphate transporter, and CnVtc4 ( XP_012049426 ) vacuolar transporter chaperone 4; Saccharomyces cerevisiae ScPho81 (SGDID:S000003465), ScVtc4 (SGDID:S000003549), ScVtc2 (SGDID:S000001890), and ScVtc3 (SGDID:S000005940); Histoplasma capsulatum HcPho81 ( EEH08674 ); Pneumocystis...”
HRM2_40290 Na(+)-dependent di-and tricarboxylate transporter/sulfate-sodium-cotransporter from Desulfobacterium autotrophicum HRM2
22% identity, 81% coverage
- Anion transport as a target of adaption to perchlorate in sulfate-reducing communities
Stoeva, The ISME journal 2020 - “...transporter. The closest studied homolog of PclT, HRM2_40290 from Desulfobacterium autotrophicum HRM2, is a putative sulfate symporter expressed under high...”
- “...are tightly regulated [44]. PclT is homologous to HRM2_40290 from D. autotrophicum, which is expressed only in "high" sulfate (~15 mM). Collectively, our study...”
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...was preferentially expressed in the presence of excess sulfate (mM), while the DASS family transporter HRM2_40290 was preferentially expressed in the presence of less than 100 M sulfate ( Tarpgaard et al., 2017 ). Phylogenetic Analysis Based on phylogenetic analysis, DASS family proteins from the examined...”
- “...At high sulfate concentration (15 mM) the genes encoding a SulP (HRM2_40360) and a DASS (HRM2_40290) family sulfate transporters were highly expressed. HRM2_40360 and HRM2_40290 were also detected in the membrane protein-enriched fractions of Desulfobacterium autotrophicum cultures growing in excess of sulfate ( Drries et al.,...”
CC1G_08098 phosphate transporter from Coprinopsis cinerea okayama7#130
24% identity, 46% coverage
RSAU_000666 SLC13 family permease from Staphylococcus aureus subsp. aureus 6850
22% identity, 67% coverage
CG7309 uncharacterized protein from Drosophila melanogaster
20% identity, 90% coverage
- Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction
François, Nature communications 2023 - “...the three predicted citrate transporters (Fig. S 1h ), exclusively expressed in the male germline: CG7309 , CG33934 , and Im not dead yet 2 ( Indy- 2) 22 , 23 . Single downregulation of citrate transporter failed to affect male fertility (Figs. 1 e, g,...”
- “...acetylation could be determined by testis-specific factors. Interestingly, the three transmembrane citrate transporters, Indy-2 , CG7309 , and CG33934 , are not only expressed exclusively in the male germline but are restricted to the late steps of spermatogenesis (Fig. S 6h ). dNAA20 expression is also...”
- A behavioral screen for mediators of age-dependent TDP-43 neurodegeneration identifies SF2/SRSF1 among a group of potent suppressors in both neurons and glia
Azpurua, PLoS genetics 2021 - “...MED28 Mediator complex 32459 Y MED31 Mediator complex subunit 31 MED31 Mediator complex 34574 Y CG7309 - SCL13A1 Transmembrane transport 44653 N/A CG8034 - SCL16A1 Transmembrane transport 32340 N/A CG2186 - RMB33 RNA-binding 33750 Y CG30379 - GRINA / Lifeguard1 Ca2+ homeostasis 36679 Y CG9451 -...”
- Sex Differences in Intestinal Carbohydrate Metabolism Promote Food Intake and Sperm Maturation
Hudry, Cell 2019 - “...citrate import into the germline to control spermatogenesis and/or into neurons to control food intake; CG7309 and Indy-2 genes code for putative citrate transporters and have testis-specific expression ( Leader etal., 2018 ). In mammals, the Indy homolog NaCT is specifically expressed in testis, liver, and...”
SAR0743 putative sodium:sulfate symporter protein from Staphylococcus aureus subsp. aureus MRSA252
22% identity, 67% coverage
PHO90_YEAST / P39535 Low-affinity phosphate transporter PHO90 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
P39535 ABC-type phosphate transporter (EC 7.3.2.1) from Saccharomyces cerevisiae (see paper)
TC 2.A.47.2.3 / P39535 Low affinity phosphate transporters (881aas). Also transports selenite from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 6 papers)
NP_012337 SPX domain-containing inorganic phosphate transporter from Saccharomyces cerevisiae S288C
YJL198W Low-affinity phosphate transporter; deletion of pho84, pho87, pho89, pho90, and pho91 causes synthetic lethality; transcription independent of Pi and Pho4p activity; overexpression results in vigorous growth from Saccharomyces cerevisiae
21% identity, 48% coverage
- function: Low-affinity phosphate transporter involved in the control of cellular phosphate levels.
- substrates: Selenite, phosphate
- Complementary structures of the yeast phosphate transporter Pho90 provide insights into its transport mechanism.
Schneider, Structure (London, England : 1993) 2024 (PubMed)- GeneRIF: Complementary structures of the yeast phosphate transporter Pho90 provide insights into its transport mechanism.
- Differential roles for the low-affinity phosphate transporters Pho87 and Pho90 in Saccharomyces cerevisiae.
Ghillebert, The Biochemical journal 2011 (PubMed)- GeneRIF: Pho90 represent non-redundant P(i) transporters, which are tuned by the integration of multiple nutrient signalling mechanisms in order to adjust P(i)-transport capacity to the general nutritional status of the environment.
- The SPX domain of the yeast low-affinity phosphate transporter Pho90 regulates transport activity.
Hürlimann, EMBO reports 2009 - GeneRIF: SPX domain of Pho90 limits the phosphate-uptake velocity, suppresses phosphate efflux and affects the regulation of the phosphate signal transduction pathway.
- Identification of the Genetic Requirements for Zinc Tolerance and Toxicity in Saccharomyces cerevisiae
Zhao, G3 (Bethesda, Md.) 2020 - “...APS3 YLR262C YPT6 YCR037C PHO87 YGL095C VPS45 YJL154C VPS35 YLR268W SEC22 YDL100C GET3 YGR105W VMA21 YJL198W PHO90 YLR396C VPS33 YDR089W VTC5 YHL031C GOS1 YLR242C ARV1 YMR243C ZRC1 YDR186C SND1 YHR026W VMA16 YKL080W VMA5 YNL323W LEM3 YDR276C PMP3 YHR094C HXT1 YKL119C VPH2 YOR270C VPH1 YDR456W NHX1 YHR108W...”
- The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae
Trilisenko, Cells 2019 - “...regulated by Pho4p 3.52 0.18 4.37 YCR037C PHO87 Low-affinity inorganic phosphate transporter 0.14 0.36 0.26 YJL198W PHO90 Low-affinity phosphate transporter 0.40 0.99 0.02 YNR013C PHO91 Low-affinity vacuolar phosphate transporter 0.39 0.73 0.00 YDR281C PHM6 Putative transport protein 6.0 5.97 3.52 YOL084W PHM7 Putative transport protein 12.01...”
- Widespread Cumulative Influence of Small Effect Size Mutations on Yeast Quantitative Traits
Hua, Cell systems 2018 - “...YHR110W, YOR044W, YDL137W, YJL171C, YOR285W, YMR029C, YLR064W, YPL137C, YOR092W, YBR159W, YGL083W, YNL156C, YDL128W, YBR296C, YOR175C, YJL198W, YOL101C, YHL019C, YJL117W, YGR263C, YML059C, YOR214C, YNR013C, YOR087W, YJL192C, YGR177C, YBL102W, YPL195W, YLL052C, YLR390W-A, YDR264C, YOR299W, YMR152W, YLL055W, YDR424C, YBR287W, YEL040W, YNL125C, YHL003C, YBR283C, YDL121C, YHR045W, YNR075W, YOR377W, YHR039C, YGL010W,...”
- Chemogenomic Study of Carboplatin in Saccharomyces cerevisiae: Inhibition of the NEDDylation Process Overcomes Cellular Resistance Mediated by HuR and Cullin Proteins
de, PloS one 2015 - “...Yes YBL051C PIN4 Yes YDR494W RSM28 No YBL052C SAS3 Yes YJL159W HSP150 No YBL053W No YJL198W PHO90 Yes YBL054W TOD6 No YLR038C COX12 Yes YBL055C Yes YLR232W No YBR061C TRM7 Yes YMR121C RPL15B Yes YER041W YEN1 Yes YOL070C NBA1 No YHL027W RIM101 Yes YOL108C INO4 No...”
- Evolution of the MAT locus and its Ho endonuclease in yeast species
Butler, Proceedings of the National Academy of Sciences of the United States of America 2004 - “...including the duplicated gene pair YCR037C (PHO87) and YJL198W (PHO90) (46). In S. kluyveri, which separated from the S. cerevisiae lineage before genome...”
- Phosphate transport and sensing in Saccharomyces cerevisiae
Wykoff, Genetics 2001 - “...genes that have 30% identity with PHO87, PHO90 (YJL198w) and PHO91 (YNR013c), using a highly expressed constitutive promoter (ADH1). These four proteins do not...”
- New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis
Ogawa, Molecular biology of the cell 2000 - “...(Bun-ya et al., 1996), two proteins homologous to Pho87, Yjl198w and Ynr013, and Syg1 (Spain et al., 1995), a multi-copy suppressor for a GPA1 deletion. The...”
8r34A / P39535 Cryoem structure of the symmetric pho90 dimer from yeast with substrates. (see paper)
22% identity, 75% coverage
- Ligand: phosphate ion (8r34A)
SA0645 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV0690 putative TetR-family transcriptional regulator from Staphylococcus aureus subsp. aureus Mu50
22% identity, 67% coverage
- Bactericidal and anti-quorum sensing activity of repurposing drug Visomitin against <i>Staphylococcus aureus</i>
Wu, Virulence 2024 - “...2 2 4 SA1915 MSSA 2 4 2 4 SA1916 MSSA 2 4 2 2 SA0645 MRSA 2 2 2 2 82174 MRSA 2 8 2 2 82231 MRSA 2 2 2 2 S. epidermidis RP62A MSSE c 2 2 2 8 ATCC 12,228 MSSE 2...”
- Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
Bohn, Nucleic acids research 2010 - “...and opp4D (SA0851) encoding components of oligopeptide transport systems ( 72 ), (ii) SA1432 and SA0645 encoding putative manganese and anion transporters, respectively, (iii) sucC (SA1088) and sucD (SA1089) encoding the succinylCoA synthetase alpha and beta subunits, respectively, (iv) gcvP (SA1366) and gcvT (SA1367), encoding enzymes...”
- The Quorum Sensing Inhibitor Hamamelitannin Increases Antibiotic Susceptibility of Staphylococcus aureus Biofilms by Affecting Peptidoglycan Biosynthesis and eDNA Release
Brackman, Scientific reports 2016 - “...downregulated in biofilms after treatment. These included aadD , fmtC , norA , tcaB , SAV0690 ( tetR ) and genes encoding beta-lactamases (SAV1504 and SAV1815) and multidrug resistance proteins (SAV0726, SAV1761, SAV2462). Downregulation of the expression of these genes might, in addition to the above...”
SAOUHSC_00698 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
22% identity, 67% coverage
STM0765 putative cation transporter from Salmonella typhimurium LT2
23% identity, 80% coverage
PHO87 / P25360 low-affinity phosphate transporter PHO87 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 15 papers)
PHO87_YEAST / P25360 Inorganic phosphate transporter PHO87 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
P25360 ABC-type phosphate transporter (EC 7.3.2.1) from Saccharomyces cerevisiae (see paper)
TC 2.A.47.2.1 / P25360 Inorganic phosphate transporter, Pho87. Also transports selenite from Saccharomyces cerevisiae (Baker's yeast) (see 6 papers)
PHO87 / RF|NP_009966.2 inorganic phosphate transporter PHO87 from Saccharomyces cerevisiae
NP_009966 SPX domain-containing inorganic phosphate transporter from Saccharomyces cerevisiae S288C
YCR037C Low-affinity inorganic phosphate (Pi) transporter, involved in activation of PHO pathway; expression is independent of Pi concentration and Pho4p activity; contains 12 membrane-spanning segments from Saccharomyces cerevisiae
21% identity, 47% coverage
- function: Involved in the uptake of inorganic phosphate
- substrates: Selenite, phosphate
- Computational identification of ubiquitylation sites from protein sequences.
Tung, BMC bioinformatics 2008 - “...P38080 809 0.87 Q9Y6K9 35 0.96 P38261 147 0.89 P10592 54 0.87 P25694 6 0.96 P25360 846 0.89 P38080 792 0.87 P40087 325 0.95 P09936 195 0.88 P12866 129 0.86 Q08412 232 0.93 P10591 54 0.88 Q05911 460 0.86 P04629 609 0.91 Q06408 156 0.87 P40087...”
- Regulation of plants' phosphate uptake in common mycorrhizal networks: Role of intraradical fungal phosphate transporters
Walder, Plant signaling & behavior 2016 - “...GenBank: ScPho84 (NP_013583), ScPho86 (NP_012418), ScPho87 (NP_009966), ScPho89 (NP_009855), ScPho91 (NP_014410) and FmPT1 (AAZ22389). We also provide GenBank...”
- Differential roles for the low-affinity phosphate transporters Pho87 and Pho90 in Saccharomyces cerevisiae.
Ghillebert, The Biochemical journal 2011 (PubMed)- GeneRIF: Pho87 and Pho90 represent non-redundant P(i) transporters, which are tuned by the integration of multiple nutrient signalling mechanisms in order to adjust P(i)-transport capacity to the general nutritional status of the environment.
- Ddi1p and Rad23p play a cooperative role as negative regulators in the PHO pathway in Saccharomyces cerevisiae.
Auesukaree, Biochemical and biophysical research communications 2008 (PubMed)- GeneRIF: However, our results revealed that Ddi1p and its associated protein Rad23p are not involved in the decrease in Pho81p level under high-phosphate condition.
- Tolerance to replication stress requires Dun1p kinase and activation of the electron transport chain
Nagar, Biochimica et biophysica acta. Molecular cell research 2023 - “...replication fork barrier (RFB), two sites within each repeat of the rDNA locus, and at YCR037C locus, where Pol2 pausing is exacerbated in rrm3 cells [ 43 , 57 ]. As expected, treatment of cells with 200 mM hydroxyurea resulted in an increased Pol2 occupancy on...”
- Identification of the Genetic Requirements for Zinc Tolerance and Toxicity in Saccharomyces cerevisiae
Zhao, G3 (Bethesda, Md.) 2020 - “...VMA2 YFL004W VTC2 YJL012C VTC4 YLR261C VPS63 YCL038C ATG22 YGL212W VAM7 YJL024C APS3 YLR262C YPT6 YCR037C PHO87 YGL095C VPS45 YJL154C VPS35 YLR268W SEC22 YDL100C GET3 YGR105W VMA21 YJL198W PHO90 YLR396C VPS33 YDR089W VTC5 YHL031C GOS1 YLR242C ARV1 YMR243C ZRC1 YDR186C SND1 YHR026W VMA16 YKL080W VMA5 YNL323W...”
- The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae
Trilisenko, Cells 2019 - “...YBR296C PHO89 Plasma membrane Na + /Pi cotransporter, transcription regulated by Pho4p 3.52 0.18 4.37 YCR037C PHO87 Low-affinity inorganic phosphate transporter 0.14 0.36 0.26 YJL198W PHO90 Low-affinity phosphate transporter 0.40 0.99 0.02 YNR013C PHO91 Low-affinity vacuolar phosphate transporter 0.39 0.73 0.00 YDR281C PHM6 Putative transport protein...”
- The role of the Parkinson's disease gene PARK9 in essential cellular pathways and the manganese homeostasis network in yeast
Chesi, PloS one 2012 - “...NEM1 YDR289C RTT103 YKL064W MNR2 YOR106W VAM3 YLR093C NYV1 YPL106C SSE1 YMR123W PKR1 YKL113C RAD27 YCR037C PHO87 YPR040W TIP41 YPL179W PPQ1 YDR126W SWF1 YDR435C PPM1 YHR180W YHR180W YJR033C RAV1 YJL053W PEP8 YKR028W SAP190 YIL054W YIL054W YBR231C SWC5 YIL040W APQ12 YER072W VTC1 YLL044W YLL044W YJL004C SYS1 YJR074W...”
- Transcriptomic profiling of the Saccharomyces cerevisiae response to quinine reveals a glucose limitation response attributable to drug-induced inhibition of glucose uptake
dos, Antimicrobial agents and chemotherapy 2009 - “...YCL025c YHR094c YMR011w YDR345c YHR092c YHR096c YJL214w YFL011w YKL217w YHL036w YML123c YCR037c YBR106w YBR296c YFL054c -- -- S R -- S -- S -- S R -- S R S R R...”
- Role of PUG1 in inducible porphyrin and heme transport in Saccharomyces cerevisiae
Protchenko, Eukaryotic cell 2008 - “...COS3 12 4 2.0 1.9 2.4 1.7 3.3 2.1 4.4 2.6 YDR038C YCR037C YGL006W ENA5 CCH1 PMC1 10 22 9 1.8 3.1 2.9 1.9 3.5 2.7 3.1 4.4 1.7 1.3 3.7 2.8 Na/Pi cotransporter...”
- A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae
Addinall, Genetics 2008 - “...YOR017W YLR191W YOL044W YAL055W YDR329C YGR133W YGR231C YJL117W YCR037C YGL023C [YML061C YDR466W YDL095W LAC1 LCB3 LEM3 LEU3 LHP1 LIA1 MCK1 MGR2 MLH2 MNI1 MNI2...”
- Evolution of the MAT locus and its Ho endonuclease in yeast species
Butler, Proceedings of the National Academy of Sciences of the United States of America 2004 - “...cerevisiae chromosome X, including the duplicated gene pair YCR037C (PHO87) and YJL198W (PHO90) (46). In S. kluyveri, which separated from the S. cerevisiae...”
- More
TC 2.A.47.4.2 / Q9HMC9 Antimonite resistance protein (inducible by both arsenite and antimonite) (see paper)
33% identity, 22% coverage
Dalk_2252 sodium/sulphate symporter from Desulfatibacillum alkenivorans AK-01
24% identity, 79% coverage
Q7UTC7 Sodium/sulfate symporter from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
27% identity, 22% coverage
TC 2.A.47.4.5 / Q9K7H7 Na+:SO4= symporter from Bacillus halodurans (see paper)
25% identity, 24% coverage
Q57048 Uncharacterized transporter HI_0020 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI0020 transport protein, putative from Haemophilus influenzae Rd KW20
24% identity, 77% coverage
STM3166 putative cation transporter from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
24% identity, 81% coverage
- Pseudomonas stutzeri as an alternative host for membrane proteins
Sommer, Microbial cell factories 2017 - “...A. aeolicus Aq_1330 DAACS 15606533 ++ NT A. aeolicus Aq_031 DASS 15605634 + S. enterica STM3166 DASS 16421721 NT S. enterica STM3356 DASS 16421915 NT S. enterica STM0832 DMT 16419338 + ++ S. enterica STM3765 DMT 16422334 + + + S. enterica STM3746 ESS 16767031 +...”
BGP_2612 sulfur deprivation response regulator from Beggiatoa sp. PS
29% identity, 23% coverage
DEFDS_2162 citrate transporter from Deferribacter desulfuricans SSM1
28% identity, 30% coverage
GSU0844 potassium uptake protein, Trk family from Geobacter sulfurreducens PCA
27% identity, 36% coverage
DP0768 related to Na/dicarboxylate cotransporter from Desulfotalea psychrophila LSv54
37% identity, 19% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...G258 is conserved in the majority of the sequences in clade B (TOL2_29810, HRM2_07790, DP0767, DP0768, Asulf_01109, Desgi_0931, DesafDRAFT_1589, DesafDRAFT_2725, BN4_10586, Desal_0726) and all sequences in group C i , the sulfate transporter (YP_003577054) from R. capsulatus has a proline (P) at position 258 ( Figures...”
Alvin_1981 Citrate transporter from Allochromatium vinosum DSM 180
28% identity, 22% coverage
c5038 Putative membrane-bound protein from Escherichia coli CFT073
22% identity, 93% coverage
- Transcriptomic and Metabolomic Profiling Reveals That KguR Broadly Impacts the Physiology of Uropathogenic Escherichia coli Under in vivo Relevant Conditions
Yang, Frontiers in microbiology 2021 - “...data ( Figure 1C ). As expected, target genes encoded on the KG island (except c5038 ) were dramatically downregulated in this experiment, indicating the credibility of this experiment. All DEGs were then subjected to KEGG pathway enrichment analysis. As shown in Figure 1D , the...”
- “...from three independent experiments are presented. (C) KguR binding sites in the promoter regions of c5038 and kguS . N stands for random nucleotides between the imperfect inverted repeats. (D,E) Binding of KguR protein to native and mutant promoters of c5038 (D) and kguS (E) ....”
- Structural basis for the reaction cycle of DASS dicarboxylate transporters
Sauer, eLife 2020 - “...the citrate transporter from Escherichia coli ; TtdT, the L-tartrate/succinate antiporter from Escherichia coli ; c5038 from Escherichia coli ; VcINDY, sodium-dependent dicarboxylate transporter from Vibrio cholerae ; SdcF and SdcL, sodium-dependent dicarboxylate transporters from Bacillus licheniformis ; SdcS, sodium-dependent dicarboxylate transporter from Staphyloccocus aureus ;...”
- Transcriptional Control of Dual Transporters Involved in α-Ketoglutarate Utilization Reveals Their Distinct Roles in Uropathogenic Escherichia coli
Cai, Frontiers in microbiology 2017 - “...horizontal gene transfer. Global anaerobic transcriptional regulators Fumarate and nitrate reduction (FNR) and ArcA induced c5038 expression in anaerobiosis, and C5038 played a major role in anaerobic growth on KG. KgtP was required for aerobic growth on KG, and its expression was repressed by FNR and...”
- FNR regulates expression of important virulence factors contributing to pathogenicity of uropathogenic Escherichia coli
Barbieri, Infection and immunity 2014 - “...island genes, including the -ketoglutarate transporter gene (c5038), the kinase gene, and the response regulator gene of the novel two-component signal...”
- “...reported that KguS/KguR directly regulates the transport gene c5038 (11); therefore, it is very likely that FNR indirectly regulates other pathogenicity island...”
- A novel two-component signaling system facilitates uropathogenic Escherichia coli's ability to exploit abundant host metabolites
Cai, PLoS pathogens 2013 - “...-KG to succinyl-CoA, which can be further transformed to succinate by succinyl-CoA synthetase [43] . c5038 is predicted to encode a putative dicarboxylate transporter with 13 transmembrane alpha-helices (TMHMM program [44] ), showing 49% similarity to citrate/succinate antiporter CitT, and c5039 encodes an enzyme belonging to...”
- “...of c5032 - 5039 to growth on -KG and induction of c5032 - lacZ or c5038 - lacZ expression by -KG. (A) In vitro growth of island gene mutants in M9 medium containing -KG as the sole carbon and energy source. Optical density of the CFT073...”
- Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli
Lloyd, Journal of bacteriology 2007 - “...J. BACTERIOL. TABLE 5--Continued Genea c5035 c5036 c5037 c5038 c5039 c5040 c5060 c5061 yddO c5078 yddQ yddR c5081 Putative periplasmic binding protein Putative...”
sll0640 sulfur deprivation response regulator from Synechocystis sp. PCC 6803
31% identity, 22% coverage
- Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002
Dahlgren, Photosynthesis research 2021 - “...A1231 None 4.34 OmpA/MotB outer membrane porin no homolog A0794 sac1 None 4.3 Sodium/sulfate symporter sll0640 Inner membrane (2, 4) A1405 nblS Both 4.17 2-component system sensor for light stress/nutrient stress sll0698 Thylakoid membrane (2, 4, 5, 6) A1088 ccs1 One 4.1 Cytochrome c biogenesis protein...”
- Iron deprivation in Synechocystis: inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profiling
Hernández-Prieto, G3 (Bethesda, Md.) 2012 - “...1.35 0.48 0.02 0.60 1.7610 6 0.99 slr0593-as1 2.09 1.95 0.94 0.04 1.09 9.6210 4 sll0640 Probable sodium/sulfate symporter 1.20 1.24 0.28 0.08 0.84 1.1810 7 0.99 sll0640-as4 1.91 1.99 0.32 0.09 0.98 4.2110 5 slr1293 Similar to phytoene dehydrogenase 1.27 1.65 0.16 0.36 0.16 2.7810...”
- Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
Zhang, BMC genomics 2008 - “...be necessary to study various mutants affecting S acclimation, including: (1) a mutant of the sll0640 gene, whose Chlamydomonas reinhardtii homologue sac1 ( s ulfur ac climation) is a putative sensor of S levels in the environment and is required for survival of S-deprived Chlamydomonas cells...”
- Nitrogen or sulfur starvation differentially affects phycobilisome degradation and expression of the nblA gene in Synechocystis strain PCC 6803
Richaud, Journal of bacteriology 2001 - “...sulfur-deprived cells in the light (7); a homologue (sll0640) present in Synechocystis strain PCC 6803 is of particular interest. (iii) NblR, identified in...”
cg2072 di-and tricarboxylate transporter from Corynebacterium glutamicum ATCC 13032
37% identity, 17% coverage
- Characterization of the dicarboxylate transporter DctA in Corynebacterium glutamicum
Youn, Journal of bacteriology 2009 - “...citrate (3); two DASS family transporters encoded by cg2072 and cg2243, in addition to DccT (40); and, besides DctA, two further DAACS-type transporters encoded...”
- Population Heterogeneity in Corynebacterium glutamicum ATCC 13032 caused by prophage CGP3
Frunzke, Journal of bacteriology 2008 - “...to cg2071) or adjacent to (cg1848 to cg1889 and cg2072 to cg2109) the CGP3 prophage region in the C. glutamicum genome, as determined by DNA microarray analysis...”
- “...genes located next to the CGP3 region (cg1849 to cg1979 and cg2072 to cg2109) were about the same in the WT and mutant (Fig. 1) (33). The vast majority of the...”
- Identification and characterization of the dicarboxylate uptake system DccT in Corynebacterium glutamicum
Youn, Journal of bacteriology 2008 - “...DAACS (cg2810, cg2870, cg3356)-, and three DASS (cg0277, cg2072, cg2243)type transporter-encoding genes have been annotated (27). In spite of the presence of...”
HRM2_38300 NadC3 from Desulfobacterium autotrophicum HRM2
26% identity, 22% coverage
- Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis
Marietou, Frontiers in microbiology 2018 - “...transporters was also observed in the sulfate reducer Desulfobacterium autotrophicum where the DASS family transporter HRM2_38300 was preferentially expressed in the presence of excess sulfate (mM), while the DASS family transporter HRM2_40290 was preferentially expressed in the presence of less than 100 M sulfate ( Tarpgaard...”
- “...had an alanine at position 260 with the exception of a fraction of sequences (Dbac_2041, HRM2_38300, TOL2_19410, Dole_1359, Dalk_2252) from group C ii where S260 is substituted by a proline (P) could suggest that in prokaryotic DASS-family sulfate transporters the amino acid at position 260 might...”
Asuc_0183 anion transporter from Actinobacillus succinogenes 130Z
24% identity, 75% coverage
Halsa_0709 SLC13 family permease from Halanaerobium hydrogeniformans
32% identity, 23% coverage
M9RBF1 Putative transport protein from Octadecabacter antarcticus 307
30% identity, 22% coverage
SMa1916 Conserved hypothetical protein from Sinorhizobium meliloti 1021
26% identity, 22% coverage
- Bacterial PerO Permeases Transport Sulfate and Related Oxyanions
Hoffmann, Journal of bacteriology 2017 - “...RSP_3330; S. meliloti perO1, SMc04179; S. meliloti perO2, SMa1916; A. tumefaciens perO, Atu4475; P. stutzeri perO, PST_0569; and D. shibae perO, Dshi_2766....”
- “...meliloti perO1, SMc04179), EcoRI (S. meliloti perO2, SMa1916), and BclI (A. tumefaciens perO, Atu4475). The resulting mutagenesis plasmids were transferred by...”
- Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid
Barnett, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...Also, we identified a sulfate uptake protein, SMA1916, which is 56% identical to the chromosomal protein SMC04179. Putative Calcium-Binding Proteins. SMA0060...”
PH1912 hypothetical protein from Pyrococcus horikoshii OT3
20% identity, 69% coverage
VP0295 putative sodium/sulfate symporter from Vibrio parahaemolyticus RIMD 2210633
26% identity, 26% coverage
- Bacteriostatic effects of benzyl isothiocyanate on Vibrio parahaemolyticus: Transcriptomic analysis and morphological verification
Liu, BMC biotechnology 2021 - “...small subunit, hypothetical protein and hypothetical protein, respectively (see Additional file 4 ). Three genes VP0295, VPA1128, and VPA1735 were upregulated, while eight genes VP1092, VP1256, VP1741, nhaB, VP2351, VP2545, VP2778, and VP2826 were downregulated in sodium ion transport of biological processes. They regulated multiple proteins...”
TK90_0502 TrkA-C domain protein from Thioalkalivibrio sp. K90mix
27% identity, 23% coverage
- Complete genome sequence of Thioalkalivibrio sp. K90mix
Muyzer, Standards in genomic sciences 2011 - “...we also searched for K + -transporters and found genes encoding the following transporters: TrkA-C (TK90_0502), TrkA-N (TK90_2266) and TrkH (TK90_2267) that are part of the potassium uptake system [ 47 ]. Chemotaxis and motility We found different genes encoding methyl-accepting chemotaxis sensory transducers (TK90_0580, TK90_0949,...”
RSP_0656 Probable sodium/sulphate symporter from Rhodobacter sphaeroides 2.4.1
27% identity, 22% coverage
- Bacterial PerO Permeases Transport Sulfate and Related Oxyanions
Hoffmann, Journal of bacteriology 2017 - “...R. capsulatus perO, Rcc00882; R. sphaeroides perO1, RSP_0656; R. sphaeroides perO2, RSP_3330; S. meliloti perO1, SMc04179; S. meliloti perO2, SMa1916; A....”
- “...genes given in parentheses: SalI (R. sphaeroides perO1, RSP_0656), PstI (R. sphaeroides perO2, RSP_3330), SphI (S. meliloti perO1, SMc04179), EcoRI (S. meliloti...”
IL2505 Na+/anion symporter from Idiomarina loihiensis L2TR
24% identity, 24% coverage
VSAL_I0422 SLC13 family permease from Aliivibrio salmonicida LFI1238
VSAL_I0422 ion transporter superfamily protein from Vibrio salmonicida LFI1238
27% identity, 22% coverage
- Construction of a fur null mutant and RNA-sequencing provide deeper global understanding of the Aliivibrio salmonicida Fur regulon
Thode, PeerJ 2017 - “...complementarities were found between RyhB and mRNAs of the fur , sodB , cysN and VSAL_I0422 genes. Other sRNAs with potential functions in iron homeostasis were identified. Conclusion The present work provides by far the most comprehensive and deepest understanding of the Fur regulon in A....”
- “...3.4 Metabolism VSAL_I0122 prlC oligopeptidase A 3.2 VSAL_I0421 cysN sulfate adenylyltransferase subunit 1 3.4 RyhB VSAL_I0422 ion transporter superfamily protein 3.8 RyhB VSAL_I0423 cysC adenylylsulfate kinase 4.0 VSAL_I1133 hisG ATP phosphoribosyltransferase 3.4 VSAL_I1769 nrdA ribonucleoside-diphosphate reductase 1 alpha chain 3.8 VSAL_I1857 queD queuosine biosynthesis protein 4.0...”
APL_1627 hypothetical protein from Actinobacillus pleuropneumoniae L20
29% identity, 25% coverage
VF_0322 divalent anion:sodium symporter family protein from Vibrio fischeri ES114
VF_0322 SLC13 family permease from Aliivibrio fischeri
26% identity, 23% coverage
- Vibrio fischeri imports and assimilates sulfate during symbiosis with Euprymna scolopes
Wasilko, Molecular microbiology 2021 - “...homolog (Accession: NC_006840.2; locus_tag: VF_0323) and 2) the V. fischeri YfbS homolog (Accession: NC_006840.2; locus_tag: VF_0322). For the species for which tBLASTn searches failed, genome assembly and annotation reports for those species ( www.ncbi.nlm.nih.gov/genome ) were searched for contigs/scaffolds with matching sequences. Results from searches performed...”
- “...- VF_0312 cysH PAPS reductase A subunit 3 - VF_0320 cysD Sulfate adenylyltransferase 1 - VF_0322 yfbS Divalent anion: sodium symporter family protein 2 - VF_0773 cobA Urophorphyrin-III C-methyltransferase 3 - VF_1008 yfcA Inner membrane protein 8 + VF_1531 VF_1531 Ferrochelatase 3 - VF_1893 cysK O...”
YPO2561 putative ion transport protein from Yersinia pestis CO92
25% identity, 27% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory