PaperBLAST

PaperBLAST Hits for TCDB::Q9HZ58 Probable L-glutamate/N-acetylglutamate uptake porter, GltS.  Involved in N-acetylglutamate catabolism as a carbon and nitrogen source (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)) (404 a.a., MPTLHLDALS...)

Show query sequence

>TCDB::Q9HZ58 Probable L-glutamate/N-acetylglutamate uptake porter, GltS.  Involved in N-acetylglutamate catabolism as a carbon and nitrogen source (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
MPTLHLDALSTTALALLLLALGSQLKKRSRWLTRLCVPSPVIAGFGFAFLVWLLRDRGWL
DIGLDTSLQTPLMVAFFTTVGLGGSLGLLRKGGKTLLVYLSACWALAILQNLIGVGSAGL
LGLDPLLGIMAGAVSLEGGFGAAAAFGPVAEGLGAQGATTVALASATFGMVAGGLLGSPV
ARWLIERNRLPVQAESDNRLEALGQQERRQHAAATLDGNLLLRLLTCVLLVMVLGFWLGD
ALEERLGLVLPSYVGAMFIAIVLRNLDDRLGWLRIPDHAVGTLGDVCLGIFLTMAMMSLK
FWELENLGLPLLGVLFIQVAVLLLLTIFVLFRLLGRNYDAAVLCAGFLGHGLGATPNAVA
NMGAVCEHYRVFSHKAFIIVPLCGAVLIDLVAIPAITWFINAFS

Running BLASTp...

Found 43 similar proteins in the literature:

TC 2.A.27.1.3 / Q9HZ58 Probable L-glutamate/N-acetylglutamate uptake porter, GltS.  Involved in N-acetylglutamate catabolism as a carbon and nitrogen source from Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
PA3176 sodium/glutamate symporter GltS from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage

• substrates: L-glutamate, N-acetylglutamate
• Utilization of L-glutamate as a preferred or sole nutrient in Pseudomonas aeruginosa PAO1 depends on genes encoding for the enhancer-binding protein AauR, the sigma factor RpoN and the transporter complex AatJQMP
  Lundgren, BMC microbiology 2021
  • “...for three putative glutamate transporters: the ABC-transporter complex AatJQMP (PA1339 PA13342), the sodium-glutamate symporter GltS (PA3176), and the proton-glutamate symporter GltP (PA5479). Deletion of the aatJ or aatQM genes in P. aeruginosa PAO1 significantly reduced the growth of this bacterium on L-glutamate as either the sole...”
• High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes
  Johnson, PLoS genetics 2008
  • “...protein ( HisP ) PA3000 PAK aromatic amino acid APC family transporter ( AroP1 ) PA3176 PA01 glutamate/sodium ion symporter ( GltS ) PA3560 PAK phosphotransferase system transporter fructose-specific IIBC component ( FruA ) PA3562 PAK phosphotransferase system transporter enzyme I ( FruI ) PA3597 PAK...”
  • “...N-Acetyl-L-Glutamic Acid N +/ PA1341 amino acid ABC transporter membrane protein L-Glutamic Acid -C +/ PA3176 glutamate/sodium ion symporter ( GltS ) N-Acetyl-L-Glutamic Acid - N +/ PA3560 phosphotransferase system transporter fructose-specific IIBC component ( FruA ) D-Fructose C - PA3562 phosphotransferase system transporter enzyme I...”
• Reverse engineering antibiotic sensitivity in a multidrug-resistant Pseudomonas aeruginosa isolate
  Struble, Antimicrobial agents and chemotherapy 2006
  • “...PA3146 PA3148 PA3149 PA3153 PA3157 PA3158 PA3159 PA3160 PA3176 PA3337 PA3514 PA3748 PA3753 PA4020 PA4501 PA4503 PA4514 PA4996 PA5265 Pae AF035937cds10 a Pae...”

PA14_23160 sodium/glutamate symporter from Pseudomonas aeruginosa UCBPP-PA14
99% identity, 100% coverage

• Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates
  Jeske, NPJ biofilms and microbiomes 2022
  • “...PA14_17640 potA 1.34 PA14_47930 1.10 PA14_37900 1.49 PA14_17930 glpD 1.27 PA14_47940 1.46 PA14_39650 cirA 3.77 PA14_23160 gltS 1.35 PA14_47960 1.09 PA14_39820 ufrA 1.43 PA14_23170 hutG 1.17 PA14_48000 1.29 PA14_55340 exbD2 1.52 PA14_23190 1.09 PA14_52810 dctM 1.06 PA14_55360 exbB2 1.06 PA14_26210 hisP 1.14 PA14_52820 dctQ 1.39 PA14_26220...”

DV527_RS02905 sodium/glutamate symporter from Staphylococcus saprophyticus
45% identity, 99% coverage

• Transcriptome Analysis of Halotolerant Staphylococcus saprophyticus Isolated from Korean Fermented Shrimp
  Jo, Foods (Basel, Switzerland) 2022
  • “...conditions. Furthermore, expression of almost all the genes encoding symporters and antiporters, except sodium/glutamate symporter (DV527_RS02905) and dicarboxylate/amino acid symporter (DV527_RS05020), was downregulated. The transporter mediating the uptake of dicarboxylate/amino acid is known for the uptake of succinate, fumarate, and l -malate in bacteria [ 28...”
  • “...1.75 2.42 0.67 DV527_RS07575 mscL Large conductance mechanosensitive channel protein MscL 1.98 4.73 2.75 Symporter DV527_RS02905 gltS Sodium/glutamate symporter 0.67 1.68 1.02 DV527_RS05020 Dicarboxylate/amino acid: cation symporter 0.47 2.04 1.57 DV527_RS04605 putP Sodium/proline symporter PutP 3.66 4.06 0.40 DV527_RS07535 Alanine:cation symporter family protein 0.49 1.72 1.23...”

SERP1935 sodium:glutamate symporter from Staphylococcus epidermidis RP62A
40% identity, 99% coverage

• Impact of the Staphylococcus epidermidis LytSR two-component regulatory system on murein hydrolase activity, pyruvate utilization and global transcriptional profile
  Zhu, BMC microbiology 2010
  • “...OppC 12.38 SERP0950 peptide ABC transporter, ATP-binding protein, putative 3.383 SERP1440 putP proline permease 2.124 SERP1935 gltS sodium:glutamate symporter 3.267 Inorganic ion transport and metabolism SERP0284 Na+/H+ antiporter, MnhD component, putative 3.294 SERP0287 Na+/H+ antiporter, MnhG component, putative 2.576 SERP0660 cobalt transport family protein 2.718 SERP1777...”

FN1801 Sodium/glutamate symport carrier protein from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
40% identity, 97% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...FN1398, FN1420, FN1432, FN1480, FN1525, FN1701, FN1734, FN1735, FN1737, FN1738, FN1739, FN1740, FN1741, FN1797, FN1798, FN1801, FN1811, FN1833, FN1834, FN1858, FN1860, FN1898, FN1989, FN2008, FN2009, FN2102, FN2105, FN2106. 2 Covers FN0130, FN0236, FN0450, FN0598, FN0658, FN0660, FN0695, FN0827, FN0828, FN1080, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354,...”
• Autoaggregation response of Fusobacterium nucleatum
  Merritt, Applied and environmental microbiology 2009
  • “...from glutathione (6). A putative sodium glutamate symporter (FN1801) was induced, as were several key genes of the butyrate fermentation pathway (FN0271 to...”
  • “...in genes related to sodium homeostasis. For example, FN1801 and FN1989 are both predicted sodium-dependent amino acid symporters, which increase the cytosolic...”

SA2135 hypothetical protein from Staphylococcus aureus subsp. aureus N315
41% identity, 99% coverage

• Transcriptional profiling analysis of the global regulator NorG, a GntR-like protein of Staphylococcus aureus
  Truong-Bolduc, Journal of bacteriology 2011
  • “...SA0516 SA1280 SA0871 SA0931 SA1184 SA1606 SA1607 SA1913 SA2135 SA0135 SA0237 SA0478 SA0517 SA1173 SA2553 SA1731 SA0172 SA0118 SA1952 SA1976 SA2386 SA0660 PTS...”
• 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
  • “...SA2515 gluconokinase sa_c6202s5382_a_at 3.2 2.5 15 lacA SA2570 galactoside O-acetyltransferase sa_c10479s10921_s_at 4.0 2.5 2.5 manA1 SA2135 mannose-6-phosphate isomerase sa_c6557s5724_a_at 5.9 2.5 ND manA2 SA2664 mannose-6-phosphate isomerase sa_c8176s7154_a_at 2.5 2.5 2.5 nagA SA0761 N-acetylglucosamine-6-phosphate deacetylase sa_c6517s5684_a_at 2.2 2.5 5 rbsK SA0253 ribokinase sa_c9971s8667_a_at 2.5 2.5 2.5 rpe...”
• Genome-wide transcriptional profiling of the response of Staphylococcus aureus to cryptotanshinone
  Feng, Journal of biomedicine & biotechnology 2009
  • “...ribA , isdA , modA , seo , SA1831, srtB , glpT , oppF , SA2135, msmX , opp-1F , dps , and SA0302). In general, there were positive correlations between microarray data and real-time RT-PCR data for all 13 genes ( Table 3 ). However,...”
  • “...(i.e., ribA , isdA , modA , seo , srtB , glpT , oppF , SA2135, msmX , opp-1F , and dps ), the levels of gene induction did not differ markedly between microarray data and real-time RT-PCR data. 4. Conclusion In summary, the presented antibacterial...”
• Overexpression of genes of the cell wall stimulon in clinical isolates of Staphylococcus aureus exhibiting vancomycin-intermediate- S. aureus-type resistance to vancomycin
  McAleese, Journal of bacteriology 2006
  • “...SA0178 SA0179 SA0180 SA0821 SA0822 SA1272 SA1674 SA1675 SA2135 SA2255 SA2425 SA2427 SA2428 SA0668 SA0199 SA0200 SA0847 SA2251 SA2252 SA2253 SA2254 SA0242 SA1718...”
• Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
  Dunman, Journal of bacteriology 2001
  • “...SA1842 SA1843 SAS066 SA1516 SA0434 SA1120 SA1920 SA2079 SA2135 SA1214 SA0099 SA0100 SA2241 SA0085 SA0174 SA0350 SA0453 SA0754 SA1037 SA1240 SA1275 SA1319 SA1388...”

SACOL2340 sodium:glutamate symporter from Staphylococcus aureus subsp. aureus COL
SAOUHSC_02622 sodium/glutamate symporter from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_2291 sodium/glutamate symporter from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_2246 sodium/glutamate symporter from Staphylococcus aureus subsp. aureus str. Newman
41% identity, 99% coverage

• Identification of Staphylococcus aureus Cellular Pathways Affected by the Stilbenoid Lead Drug SK-03-92 Using a Microarray
  Schwan, Antibiotics (Basel, Switzerland) 2017
  • “...to untreated cells [ 34 ]. Our microarray showed that a tetR -family transcriptional regulator, SACOL2340, and two genes that comprise a putative TCS in S. aureus annotated as MW2284 (14.1-fold downregulated) and MW2285 in strain MW2 (26.3-fold downregulated) were downregulated. A bioinformatic analysis of the...”
  • “...symporter Signaling/Regulation SACOL2360 14.1 LytTR family regulator protein SACOL2361 26.9 histidine kinase sensor membrane protein SACOL2340 2.2 transcriptional regulator TetR-family Cell Wall Associated SACOL0151 2.7 UDP- N -acetylglucosamine 2-epimerase Cap5P ( cap5P ) SACOL0247 3.2 holin-like protein LrgA ( lrgA ) SACOL0612 2.1 glycosyl transferase, group...”
• Glucose Augments Killing Efficiency of Daptomycin Challenged Staphylococcus aureus Persisters
  Prax, PloS one 2016
  • “...51 ] HG003 D6 Derivative of HG003 carrying SNP in SAOUHSC_00670 ( pitA ) and SAOUHSC_02622 ( gltS ). [ 48 ] USA300 NE39 ptsG - (phosphotransferase system, glucose-specific IIABC component) [ 47 ] USA300 NE172 ptsG - (phosphotransferase system, glucose-specific IIABC component) [ 47 ]...”
• Identification of the main glutamine and glutamate transporters in Staphylococcus aureus and their impact on c-di-AMP production
  Zeden, Molecular microbiology 2020
  • “...biological replicates were plotted against the Lglutamyl hydrazide concentration in the growth medium 2.5 GltS (SAUSA300_2291) is a glutamate transporter in S. aureus S. aureus does not only take up glutamine but also shows robust glutamate uptake (Figures 2 and 3 ). However, none of the...”
  • “...a high degree of similarity (52% identity) to the B. subtilis GltT protein. In addition, SAUSA300_2291 (from here on referred to as GltS) is annotated in UniProt ( www.uniprot.org ) as a potential glutamate transporter in S. aureus . To experimentally test if GltT or GltS...”
• Inactivation of the Ecs ABC transporter of Staphylococcus aureus attenuates virulence by altering composition and function of bacterial wall
  Jonsson, PloS one 2010
  • “...NWMN_2081 transporter 0.2 NWMN_2089 BCCT family osmoprotectant transporter 2.1 NWMN_2224 PTS system component 2.1 1.8 NWMN_2246 sodium/glutamate symporter 2.5 2.4 NWMN_2261 ABC transporter ATP-binding protein HtrB 2.2 NWMN_2268 L-lactate permease 3.0 NWMN_2279 PTS system sucrose-specific IIBC component 2.4 NWMN_2311 amino acid ABC transporter ATP-binding protein 2.0...”

ZP_02423775 hypothetical protein from Eubacterium siraeum DSM 15702
41% identity, 99% coverage

• Phylogenetic evidence for lateral gene transfer in the intestine of marine iguanas
  Nelson, PloS one 2010
  • “...Unresolved Faecalibacterium prausnitzii ZP_02090920 4.00E123 83 714 13 1370613840 46.7 Sodium/glutamate symporter Unresolved Eubacterium siraeum ZP_02423775 5.00E12 80 714 14 1379514877 56.7 Sodium/glutamate symporter Unresolved Eubacterium siraeum ZP_02423775 7.00E134 73 714 15 1489515938 61.3 Immunogenic protein Unresolved Coprococcus eutactus ZP_02205701 6.00E61 44 714 16 1621417023 57.9...”

PFJ30894_RS00375 sodium/glutamate symporter from Phascolarctobacterium faecium
40% identity, 99% coverage

• Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron
  Ikeyama, MicrobiologyOpen 2020
  • “...(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 subunit alpha), PFJ30894_RS01160 (2oxoacid:ferredoxin oxidoreductase subunit beta), and PFJ30894_RS01165 (pyruvate/ketoisovalerate oxidoreductase gamma subunit)...”
  • “...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 359.17 357.32 501.28 PFJ30894_RS01155 + 2oxoacid:acceptor oxidoreductase subunit alpha K00174 335.97 426.04 689.65 PFJ30894_RS01160 + 2oxoacid:ferredoxin oxidoreductase...”

HRAG_00091 sodium/glutamate symporter from Helicobacter bilis ATCC 43879
40% identity, 93% coverage

• Evidence for conserved function of γ-glutamyltranspeptidase in Helicobacter genus
  Rossi, PloS one 2012
  • “...supported by the presence in the H. bilis genome of a putative glutamate transporter gene (HRAG_00091; gltS ) showing 60% of amino acid identity with H. pylori GltS homologue [47] . Glutamate transporters gltS as well as ggt genes are missing in the EHS H. hepaticus...”

CD1746 sodium/glutamate symporter from Clostridium difficile 630
35% identity, 96% coverage

• Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile
  Saujet, PLoS genetics 2013
  • “...0.26 A CD1085-CD1086 CD1086 Putative peptidase, M20D family 0.26 CD1555 Putative amino acid permease 0.22 CD1746 gltC Sodium/glutamate symporter 0.20 E CD1259 brnQ-1 Branched chain amino acid transporter 0.39 CD2439 Diacylglycerol kinase/undecaprenol kinase 0.45 + CD1068 Polysaccharide biosynthesis protein 0.23 CD3257 Polysaccharide deacetylase 0.11 2.1 CD3248...”
  • “...E activated the expression of genes encoding peptidases (CD3652, CD1086, CD3521) or amino acids permeases (CD1746, CD1555 and CD1259). Moreover, the CD2833 and CD0760 genes encoding a Ca 2+ -transporting ATPase and a Ca 2+ /Na + antiporter, respectively, were downregulated in the sigE mutant. These...”

YPO0035 sodium/glutamate symport carrier protein from Yersinia pestis CO92
41% identity, 96% coverage

• Na+/H+ antiport is essential for Yersinia pestis virulence
  Minato, Infection and immunity 2013
  • “...and YPO2561); ESS, glutamate:Na symporter (YPO0035); GPH, glycoside-pentoside-hexuronide: cation symporter (YPO0995 and YPO1226); SSS, solute:sodium symporter...”

FN0793 Sodium/glutamate symport carrier protein from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
C4N14_08255 sodium/glutamate symporter from Fusobacterium nucleatum subsp. nucleatum ATCC 23726
36% identity, 100% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...FN0341, FN0352, FN0375, FN0376, FN0377, FN0397, FN0398, FN0399, FN0400, FN0450, FN0598, FN0658, FN0660, FN0685, FN0695, FN0793, FN0800, FN0801, FN0827, FN0828, FN1022, FN1080, FN1086, FN1135, FN1136, FN1166, FN1167, FN1187, FN1190, FN1198, FN1256, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354, FN1362, FN1363, FN1398, FN1420, FN1432, FN1480, FN1525, FN1701, FN1734,...”
  • “...FN0660, FN0695, FN0827, FN0828, FN1080, FN1301, FN1348, FN1349, FN1352, FN1353, FN1354, FN1701,FN2102. 3 Covers FN0660, FN0793, FN0800, FN0801, FN1187, FN1398, FN1432, FN1801. 4 Covers FN0192, FN0396, FN0397, FN0399, FN0400, FN0998, FN1111, FN1359, FN1362, FN1363, FN1523, FN1525. 5 Covers FN0308, FN0309, FN0310, FN0375, FN0376, FN0377. In contrast...”
• Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σ^E-dependent small RNA with unusual mRNA activation activity
  Ponath, mBio 2024
  • “...transport ( 33 ), three putative genes involved in amino acid transport (C4N14_05105, C4N14_08210, and C4N14_08255) as well as one sugar uptake-related gene (C4N14_03585). An operon encoding the RNase PH, a putative -ketoacyl-acyl-carrier-protein synthetase (C4N14_03815), and a co-factor synthetase (C4N14_03820) is also downregulated at both the...”

PMI2867 sodium/glutamate symport carrier protein from Proteus mirabilis HI4320
42% identity, 96% coverage

• Elucidating the genetic basis of crystalline biofilm formation in Proteus mirabilis
  Holling, Infection and immunity 2014
  • “...bcr Biofilm deficient NHSH1 PMI1608 ABBF1.1C8 NHSE5 PMI2867 PMI1551 DLD1A6 PMI2861 DLD1D11 STS8.1D7 PMI0696d PMI1479e glnE gltS lrp nirB Urease production...”

NMC0069 sodium/glutamate symport carrier protein from Neisseria meningitidis FAM18
37% identity, 99% coverage

• Description and nomenclature of Neisseria meningitidis capsule locus
  Harrison, Emerging infectious diseases 2013
  • “...protein (NMC0044 FAM18 genome annotation) and a gene encoding the sodium/glutamate symport carrier protein, gltS (NMC0069). PCR reactions were performed for isolates 29013, 707, 29031, 29043, 29046, 3608, 275, 388, 162, WUE171, WUE172, and WUE173 ( Table 1 ) by using the Expand Long Template PCR...”
  • “...at 68C for 20 min. Initial reactions used 1 of the following primer pairs: gltS (NMC0069) to tex (NMC0059) (primers gltS 5- CCGACCAAGCCGTATTGC + ATGATACTCGAAGGCGTGGTT-3 and tex 5- TGTCGAAGCCGTCCATAATCT + GCCCTGTCCAACAAGTTCGT-3) and tex to NMC0044 (primers tex 5- CGCCCGGTTCGTCATCC + TTGCTGCTGGTAGGCGAATCC -3 and NMC0044 5- CGGGCGAACACGGTAAT...”

NMB0085 sodium/glutamate symporter from Neisseria meningitidis MC58
37% identity, 99% coverage

• Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection
  Pandey, Nature communications 2018
  • “...(WT) 36 NEIS1795 NMC1795 Mafl immunity gene: type o2MGI-2 Unknown N. lactamica (WT) 291 NEIS0069 NMB0085 Sodium glutamate transport Unknown N. lactamica (WT) 291 NEIS0073 NMB0088 Outer membrane transport Unknown N. lactamica (WT) 291 NEIS1837 NMB0334 (pgi2) Glycolysis pathway enzyme Unknown N. lactamica (WT) 291 NEIS2437...”
• Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis
  Lau, Cell & bioscience 2011
  • “...- - - Sodium glutamate symport carrier protein gltS Sodium and glutamate uptake - CV1105 NMB0085 NGO1890 Proton glutamate symport protein - Hydrogen and glutamate uptake LHK_02672 CV1198 CV3409 - - Proline/betaine transproter proP Proline, glycine betaine and ectoine uptake LHK_02126 CV1299 CV2901 - - ABC-type...”
• Identification of a meningococcal L-glutamate ABC transporter operon essential for growth in low-sodium environments
  Monaco, Infection and immunity 2006
  • “...Indeed, a sodium/glutamate symporter (GltS), encoded by the ORF NMB0085, is annotated in the genome of the serogroup B MC58 strain (44). The operation of two...”

FPV33_RS00465 sodium/glutamate symporter from Klebsiella aerogenes
41% identity, 96% coverage

• Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions
  Chen, Frontiers in microbiology 2024
  • “...Bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD 1.08 FPV33_RS19735 proA Glutamate-5-semialdehyde dehydrogenase 1.01 FPV33_RS00465 gltS Sodium/glutamate symporter 1.14 FPV33_RS09905 gapA Glyceraldehyde-3-phosphate dehydrogenase 2.84 FPV33_RS06275 fdx ISC system 2Fe-2S type ferredoxin 1.75 FPV33_RS03960 ndoA Non-heme iron oxygenase ferredoxin subunit 2.69 Ammonia assimilation FPV33_RS06645 GAT1 Type...”

HI1530 glutamate permease (gltS) from Haemophilus influenzae Rd KW20
39% identity, 92% coverage

• Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae
  Gladitz, Nucleic acids research 2005
  • “...0 59.2 ABC transporter-ATP-binding protein HI1474 31 200 37.09 ET4 9.8 61.34 Glutamate permease (gltS) HI1530 38 404 31.2 HFDY 0 37.44 Gene = the gene number in the annotated H.influenzae Rd genome; %GC = the percentage of GC base pairs in the gene; = the...”

APL_0967 sodium/glutamate symport carrier protein from Actinobacillus pleuropneumoniae L20
36% identity, 99% coverage

• Biofilm formation by virulent and non-virulent strains of Haemophilus parasuis
  Bello-Ortí, Veterinary research 2014
  • “...HS372_01950 APL_1574 Putative hydrolase ydeN HS372_02244 APL_0254 Cytosol non-specific dipeptidase HS372_01281 APL_1230 Phosphoserine phosphatase HS372_01385 APL_0967 Glutamate permease HS372_01220 APL_0463 Putative phosphinothricin acetyltransferase YwnH HS372_01490 APL_0928 hypothetical protein HS372_01179 APL_1499 Threonine synthase HS372_02366 APL_0395 Sigma-E factor negative regulatory protein HS372_01208 APL_0895 Formate dehydrogenase-N subunit gamma HS372_01221...”
• Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus
  Tremblay, BMC genomics 2013
  • “...APL_0920 APL_1494 APL_1665 APL_2011 APL_2025 APL_2026 Down-regulated APL_0226 APL_0333 APL_0615 APL_0630 APL_0644 APL_0682 APL_0771 APL_0903 APL_0967 APL_0982 APL_1136 APL_1169 APL_1292 APL_1388 APL_1450 APL_1474 APL_1558 APL_1597 APL_1759 APL_1782 APL_1962 Interestingly, APL_1494, which encodes the fine tangled pili,was down-regulated in the drip-flow biofilm and in bacteria attached to...”
• Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
  Labrie, Veterinary research 2010
  • “...rnhA Ribonuclease HI 1.345 APL_0201 nusB Transcription antitermination protein NusB 1.457 Transport and binding proteins APL_0967 gltS Sodium/glutamate symport carrier protein 4.155 APL_0377 glpT Glycerol-3-phosphate transporter 3.247 APL_0064 dppA Periplasmic dipeptide transport protein 3.168 APL_0869 abgB Aminobenzoyl-glutamate utilization-like protein 3.004 APL_1857 merP Copper chaperone MerP 2.911...”

gltS / O26036 glutamate:Na⁺ symporter GltS from Helicobacter pylori (strain ATCC 700392 / 26695) (see 2 papers)
HP1506 glutamate permease (gltS) from Helicobacter pylori 26695
35% identity, 98% coverage

• Coupled amino acid deamidase-transport systems essential for Helicobacter pylori colonization
  Leduc, Infection and immunity 2010
  • “...Hp-AnsB), hp0724 (encoding Hp-DcuA), hp1118 (encoding Hp-GT), and hp1506 (encoding Hp-GltS) genes was performed in H. pylori strain 26695 or SS1. Deletions were...”
  • “...unknown sodium-dependent transporter (49). We found that gltS (hp1506), annotated to exhibit homology to Na/Glu symporters, is a good candidate for glutamate...”
• Global transposon mutagenesis and essential gene analysis of Helicobacter pylori
  Salama, Journal of bacteriology 2004
  • “...we also detected an insertion in the adjacent gene HP1506. Insertions in HP1506 were detected in several pools; thus, transposon insertion in this gene was the...”

GltC / b3653 glutamate:sodium symporter from Escherichia coli K-12 substr. MG1655
gltS / P0AER8 glutamate:sodium symporter from Escherichia coli (strain K12) (see 7 papers)
GLTS_ECOLI / P0AER8 Sodium/glutamate symporter; Glutamate permease from Escherichia coli (strain K12) (see 6 papers)
TC 2.A.27.1.1 / P0AER8 Glutamate:Na+ symporter (transports L- and D-glutamate, α-methylglutamate and homocysteate). Swapping the order of the two halves (repeat units) does not decrease activity from Escherichia coli (see 7 papers)
NP_418110 glutamate:sodium symporter from Escherichia coli str. K-12 substr. MG1655
b3653 glutamate transporter from Escherichia coli str. K-12 substr. MG1655
40% identity, 96% coverage

• function: Catalyzes the sodium-dependent, binding-protein-independent transport of glutamate.
• substrates: glutamate
• Membrane topology of the GltS Na+/glutamate permease of Escherichia coli.
  Szvetnik, FEMS microbiology letters 2007 (PubMed)
  • GeneRIF: This paper presents the membrane topology analysis of the GltS.
• Structure and function of prokaryotic glutamate transporters from Escherichia coli and Pyrococcus horikoshii.
  Raunser, Biochemistry 2006 (PubMed)
  • GeneRIF: Gel filtration indicates a reversible equilibrium of two oligomeric states in detergent solution that we identified as a trimer and hexamer by blue-native gel electrophoresis and cross-linking.
• Directed evolution of ionizing radiation resistance in Escherichia coli
  Harris, Journal of bacteriology 2009
  • “...clpX b0437 b0437/ b0438 b0438 Glutamate transport gltS b3653 Miscellaneous ylbEb yjgL yjgL b4572 b2453 b2453 CB1014 CB1015 CB1024 CB3000 CB1025 1943223 1943323...”
• Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis
  Løbner-Olesen, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...b2422 b2540 b2752 b2698 b2425 b1061 b0958 b1183 b1140 b2751 b3653 Raw 0.13A 0.23 0.25 0.44 0.27 0.46 0.44 0.32 0.29 0.29 0.31 0.33 0.34 0.61 0.44 0.42 0.39...”

PP0996 sodium-glutamate symporter from Pseudomonas putida KT2440
42% identity, 92% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

HBZC1_14360 sodium/glutamate symporter from Helicobacter bizzozeronii CIII-1
37% identity, 95% coverage

• Comparative genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans
  Schott, BMC genomics 2011
  • “...deamidase-transport systems of AnsB (HBZC1_05200 and HBZC1_12160) plus DcuA (HBZC1_00140) and GT (HBZC1_08080) plus GltS (HBZC1_14360) that contribute to periplasmic ammonia production in H. pylori and may have a possible role in the resistance to weakly acidic conditions and in the pathogenesis of gastritis [ 20...”

NGFG_01803 sodium/glutamate symporter from Neisseria gonorrhoeae MS11
38% identity, 93% coverage

• Transcriptional landscape and essential genes of Neisseria gonorrhoeae
  Remmele, Nucleic acids research 2014
  • “...and transcript annotations (dark green) on plus and minus strands were visualized. The non-essential genes NGFG_01803, NGFG_ 04088 and NGFG_01809 have dense TIS, while essential modification methylases HphIA (NGFG_04087) and HphIB (NGFG_01806) display very few insertions and thus constitute essential genes. The potential promoter region of...”
  • “...contrast, the genes upstream and downstream of the operon comprising NGFG_04087 and NGFG_01806, NGFG_01809 and NGFG_01803, display high TIS density which results in P -values of 1 and 0.99, respectively, thereby defining NGFG_01809 and NGFG_01803 as non-essential genes (Figure 5C ). Furthermore, all aminoacyl-tRNA synthetase genes...”

NGO1890 GltS from Neisseria gonorrhoeae FA 1090
38% identity, 93% coverage

• Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
  Isabella, BMC genomics 2011
  • “...FNR yaaJ NGO1787 -3.3 -4.3 Sodium/alanine symport protein NGO1807 -2.7 -3.8 Amino-acid symport protein gltS NGO1890 -3.1 -5.0 Sodium/glutamate symport protein MtrR NGO1954 -3.6 -6.3 Di- and tri-peptide permease, PRT2 sstT NGO1957 -4.5 -11.1 Sodium/serine symport protein glnM NGO2011 -6.7 -12.5 ABC-type amino acid transport system,...”
• Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis
  Lau, Cell & bioscience 2011
  • “...- - Sodium glutamate symport carrier protein gltS Sodium and glutamate uptake - CV1105 NMB0085 NGO1890 Proton glutamate symport protein - Hydrogen and glutamate uptake LHK_02672 CV1198 CV3409 - - Proline/betaine transproter proP Proline, glycine betaine and ectoine uptake LHK_02126 CV1299 CV2901 - - ABC-type proline/glycine...”
• MtrR modulates rpoH expression and levels of antimicrobial resistance in Neisseria gonorrhoeae
  Folster, Journal of bacteriology 2009
  • “...NGO1600 NGO1699 NGO1738 NGO1741 NGO1742 NGO1749 NGO1751 NGO1765 NGO1890 NGO2011 NGO2013 NGO2014 leuS NGO0018 potH rpoH NGO0302 bioA bioD pdxH NGO0756 brfB umpA...”

TC 2.A.27.1.2 / P73275 Glutamate:Na+ symporter (see paper)
slr1145 glutamate permease from Synechocystis sp. PCC 6803
35% identity, 99% coverage

• substrates: Na+, glutamate
• Sodium-dependent uptake of glutamate by novel ApGltS enhanced growth under salt stress of halotolerant cyanobacterium Aphanothece halophytica
  Boonburapong, Bioscience, biotechnology, and biochemistry 2012 (PubMed)
  • “...identity) to GltS from Synechocystis sp. PCC 6803 (slr1145) and Escherichia coli. The predicted ApGltS consisted of 476 amino acid residues with a molecular...”
  • “...(gltS) gene from A. halophytica Hitherto, SygltS (slr1145) of Synechocystis sp. PCC 6803 was the only known glutamate transporter in cyanobacteria.9)...”
• Identification of genes encoding amino acid permeases by inactivation of selected ORFs from the Synechocystis genomic sequence
  Quintero, Genome research 2001
  • “...in Synechocystis sp. strain PCC 6803. Glutamate Permeases ORF slr1145 of Synechocystis sp. strain PCC 6803 (Kaneko et al. 1996) would encode a protein with 42%...”
  • “...to E. coli GltS, we conclude that the ORF slr1145 product is a Na+-dependent glutamate transporter and that ORF slr1145 represents a Synechocystis sp. strain...”

VPA0035 sodium/glutamate symporter from Vibrio parahaemolyticus RIMD 2210633
36% identity, 93% coverage

• Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions
  Nydam, Frontiers in cellular and infection microbiology 2014
  • “...COG0548E 9.5 21.3 22.6 43.7 45.7 vp2910 Hypothetical protein COG4974L 2.0 4.8 6.7 11.6 15.1 vpa0035 Sodium/glutamate symporter COG0786E 7.0 1.3 1.7 3.0 3.5 vpa0639 Arginine transporter permease subunit ArtM COG4160E 40.5 90.1 113.9 124.2 57.8 vpa0669 Hypothetical protein 2.0 4.1 6.2 10.1 12.4 vpa0680 Arylsulfatase...”
  • “...the metabolism associated genes may have roles in arginine biosynthesis, including the sodium/glutamate symporter ( vpa0035 ), glutamate synthase subunits ( vp0481 , vp0483 ), N-acetylglutamate synthase ( vp2371 ), arginosuccinate lyase/N-acetylglutamate synthase ( vp2756 ), arginosuccinate synthase ( vp2757 ), and acetylglutamate kinase ( vp2758...”

ABO_1616 sodium/glutamate symport carrier protein from Alcanivorax borkumensis SK2
38% identity, 99% coverage

• Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis
  Schneiker, Nature biotechnology 2006
  • “...+ /alanine ( dagA , ABO_0618), Na + /sulfate (ABO_0929), Na + /glutamate (ABO_1478 and ABO_1616, see above) as well as several other Na + -dependent symporters (ABO_0344, ABO_1913, ABO_2155, ABO_2158, ABO_2678). The A. borkumensis SK2 genome encodes diverse and alternative systems for the uptake of...”
  • “...and in addition to the uptake systems for glutamate ( glt P, ABO_1478, glt S, ABO_1616) and choline/betaine (ABO_0232, ABO_0637 and ABO_0808), the A. borkumensis SK2 genome contains the genetic determinants for the biosynthesis of glutamate ( glt A, ABO_1501, glt B, ABO_2229, glt D, ABO_2228...”

t3773 glutamate permease from Salmonella enterica subsp. enterica serovar Typhi Ty2
41% identity, 96% coverage

• Context-dependent change in the fitness effect of (in)organic phosphate antiporter glpT during Salmonella Typhimurium infection
  Santamaria, Nature communications 2025 (no snippet)

STM3746 GltS family, glutamate transport protein from Salmonella typhimurium LT2
41% identity, 96% coverage

• Pseudomonas stutzeri as an alternative host for membrane proteins
  Sommer, Microbial cell factories 2017
  • “...STM0832 DMT 16419338 + ++ S. enterica STM3765 DMT 16422334 + + + S. enterica STM3746 ESS 16767031 + + + S. enterica STM2913 GntP 16421462 ++ NT S. enterica STM3512 GntP 16422071 + ++ S. enterica STM3541 GntP 16422100 + + S. enterica STM3801 GntP...”

YP_001675245 sodium/glutamate symporter from Shewanella halifaxensis HAW-EB4
35% identity, 96% coverage

• Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation
  Zhao, PloS one 2010
  • “...subunit, twin-Arginine translocation YP_001676082 + +/- Na + /solute symporter solute YP_001674780 + + glutamate YP_001675245 + + YP_001675528, 6399 + + YP_001476116, + + neurotransmitter YP_001675407, 6136 + Eexcitatory amino acid YP_001473092 + + proline YP_001674892 + YP001475470 + + dicarboxylate YP_001673007, 3467, 3772, 3827...”

YP_001675528 sodium/glutamate symporter from Shewanella halifaxensis HAW-EB4
36% identity, 96% coverage

• Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation
  Zhao, PloS one 2010
  • “...YP_001676082 + +/- Na + /solute symporter solute YP_001674780 + + glutamate YP_001675245 + + YP_001675528, 6399 + + YP_001476116, + + neurotransmitter YP_001675407, 6136 + Eexcitatory amino acid YP_001473092 + + proline YP_001674892 + YP001475470 + + dicarboxylate YP_001673007, 3467, 3772, 3827 + YP_001673866, 2587...”

PBPRA2089 Putative sodium/glutamate symporter from Photobacterium profundum SS9
35% identity, 95% coverage

• Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates
  Campanaro, BMC evolutionary biology 2008
  • “...were found to be down-regulated; 2 were down-regulated at 4C compared to 16C. Two genes, PBPRA2089 and PBPRA0281, were identified in the list from the systematic mutagenesis screening as responsible for piezosensitivity in SS9 mutants. Discussion Vibrionaceae and Shewanellaceae represent a significant portion of the culturable...”

DMO12_07344, HTZ92_1001 sodium/glutamate symporter from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
38% identity, 92% coverage

• Genome diversity of domesticated Acinetobacter baumannii ATCC 19606^T strains
  Artuso, Microbial genomics 2022
  • “...HTZ92_1002 ATPase AAA DMO12_07341 (300) 3977672 T ->TC* W9L 19/411/411 GO593_18950/FQU82_02560 HTZ92_1001 Sodium/glutamate symporter gltS DMO12_07344 (411) 3978830 A ->ATC 21L 20/382/382 GO593_18955/FQU82_02561 HTZ92_1000 Alpha-beta fold hydrolase DMO12_07347 (382) SNPs between ATCC 19606(M, H) and ATCC 19606(A ) Stop codon 711049 3389623 T ->A K337 403/345/403...”
  • “...->GA E45R 75/300/300 GO593_18945/FQU82_02559 HTZ92_1002 ATPase AAA DMO12_07341 (300) 3977672 T ->TC* W9L 19/411/411 GO593_18950/FQU82_02560 HTZ92_1001 Sodium/glutamate symporter gltS DMO12_07344 (411) 3978830 A ->ATC 21L 20/382/382 GO593_18955/FQU82_02561 HTZ92_1000 Alpha-beta fold hydrolase DMO12_07347 (382) SNPs between ATCC 19606(M, H) and ATCC 19606(A ) Stop codon 711049 3389623...”

SO2923 sodium/glutamate symporter from Shewanella oneidensis MR-1
36% identity, 96% coverage

• Cellular response of Shewanella oneidensis to strontium stress
  Brown, Applied and environmental microbiology 2006
  • “...possibly involved in osmotic stress protection (e.g., SO2923, which encodes a putative sodium/ glutamate symporter). The majority of differentially expressed...”
• Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions
  Liu, Journal of bacteriology 2005
  • “...in glutamate synthesis and a Na/glutamate symporter gene (SO2923) were upregulated in MR-1 by NaCl stress (Table 1S). Besides the primary response, a secondary...”

F898_02609 sodium/glutamate symporter from Acinetobacter courvalinii
37% identity, 99% coverage

• Proteomic and Systematic Functional Profiling Unveils Citral Targeting Antibiotic Resistance, Antioxidant Defense, and Biofilm-Associated Two-Component Systems of Acinetobacter baumannii To Encumber Biofilm and Virulence Traits
  Selvaraj, mSystems 2020
  • “...BchC F898_02608 2 8 8.71292 0.00691163 80,765 22.9 10 D0C713 Chlorophyll synthesis pathway protein BchC F898_02609 3 12 5.51743 0.00371512 212 33.3 4 D0C711 Cupin domain protein yhhW_3 4 18 4.34739 0.005373 2,941 9.4 6 D0C713 Chlorophyll synthesis pathway protein F962_01825 5 19 4.29623 1.80E04 3.47E+09...”

CV1105 sodium/glutamate symport carrier protein from Chromobacterium violaceum ATCC 12472
39% identity, 96% coverage

• Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis
  Lau, Cell & bioscience 2011
  • “...LHK_01612 - - - Sodium glutamate symport carrier protein gltS Sodium and glutamate uptake - CV1105 NMB0085 NGO1890 Proton glutamate symport protein - Hydrogen and glutamate uptake LHK_02672 CV1198 CV3409 - - Proline/betaine transproter proP Proline, glycine betaine and ectoine uptake LHK_02126 CV1299 CV2901 - -...”
• Identification of Burkholderia cenocepacia genes required for bacterial survival in vivo
  Hunt, Infection and immunity 2004
  • “...galU (Burkholderia pseudomallei); AAG24457 28D8 CV1105 (Chromobacterium violaceum); NP_900675 CV1105 (Chromobacterium violaceum); NP_900675 Bcep6477...”

VPA0031 sodium/glutamate symporter from Vibrio parahaemolyticus RIMD 2210633
34% identity, 96% coverage

• Transcriptome Analysis Reveals the Effect of Low NaCl Concentration on Osmotic Stress and Type III Secretion System in Vibrio parahaemolyticus
  Zhang, International journal of molecular sciences 2023
  • “...may be responsible for osmotic stress. Our RNA-seq results showed that five transporter genes ( VPA0031 , VP1229 , VPA0409 , VP2665 , and VP2043 ) were significantly downregulated, whereas only one gene ( VP1302 ) was significantly upregulated in the WT strain when cultured in...”
  • “...3% NaCl ( Figure 3 A). Then, the qRT-PCR results confirmed that two genes ( VPA0031 and VP2665 ) were downregulated under low-salinity conditions, and the low-salinity condition could also induce a higher expression of VP1302 ( Figure 3 A). In the present study, RNA-seq and...”

VIBR0546_06697 sodium/glutamate symporter from Vibrio brasiliensis LMG 20546
35% identity, 93% coverage

• Effects of NaCl Concentration on the Behavior of Vibrio brasiliensis and Transcriptome Analysis
  Hu, Foods (Basel, Switzerland) 2022
  • “...10 6 up VIBR0546_03992 putative salt-induced outer membrane protein 2.468 1.304 3.57 10 5 up VIBR0546_06697 sodium/glutamate symporter 2.705 1.435 1.36 10 4 up VIBR0546_12742 sodium/alanine symporter 2.326 1.218 2.10 10 4 up VIBR0546_12482 putative outer membrane protein 2.272 1.184 7.17 10 4 up VIBR0546_07217 outer...”

YP_001476116 sodium/glutamate symporter from Shewanella sediminis HAW-EB3
35% identity, 94% coverage

• Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation
  Zhao, PloS one 2010
  • “...+ /solute symporter solute YP_001674780 + + glutamate YP_001675245 + + YP_001675528, 6399 + + YP_001476116, + + neurotransmitter YP_001675407, 6136 + Eexcitatory amino acid YP_001473092 + + proline YP_001674892 + YP001475470 + + dicarboxylate YP_001673007, 3467, 3772, 3827 + YP_001673866, 2587 + + YP_001673465 +...”

SYNW0882 Sodium/glutamate symporter from Synechococcus sp. WH 8102
35% identity, 97% coverage

• Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
  Su, Nucleic acids research 2006
  • “...the type II alternative RNA polymerase factor SYNW2496 (RpoD) ( 56 ), the sodium/glutamate symporter SYNW0882 (GltS) ( 57 ), the porin SYNW2224 (Som) ( 16 ) and the molybdenum cofactor biosynthesis proteins SYNW2468 (MoaC) and SYNW2469 (MoeA) ( Table 2 ). Interestingly, some of the...”
  • “...on ammonium versus nitrate, including amt1 ( synw0253 ), nirA ( synw2477 ), gltS ( synw0882 ) apeF ( synw1074 ) and petF2 ( synw1274 ), etc. ( Table 2 ). These genes might be constitutively expressed at similar levels on ammonium and nitrate. We expect...”

BP0402 putative sodium/glutamate symport carrier protein from Bordetella pertussis Tohama I
Q7VSK9 Sodium/glutamate symporter from Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
33% identity, 95% coverage

• A new class of binding protein-dependent solute transporter exemplified by the TAXI-GltS system fromBordetella pertussis
  Jaques, 2024

SAMN05444581_1147 sodium/glutamate symporter from Methylocapsa palsarum
35% identity, 88% coverage

• Draft Genome Sequence of Methylocapsa palsarum NE2^T, an Obligate Methanotroph from Subarctic Soil
  Miroshnikov, Genome announcements 2017
  • “...biosynthesis of bacteriochlorophyll and carotenoids. Most of these photosynthesis-related genes are assembled in gene clusters (SAMN05444581_1147 to SAMN05444581_1149, SAMN05444581_11410 to SAMN05444581_11450). It remains to be seen if these genes are expressed under some certain environmental conditions. Accession number(s). The Methylocapsa palsarum NE2 T genome sequence was...”

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Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.