PaperBLAST

Full List of Papers Linked to VIMSS10081723

PTR14_ARATH / Q9LQL2 Protein NRT1/ PTR FAMILY 7.3; AtNPF7.3; Nitrate transporter 1.5 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
TC 2.A.17.3.19 / Q9LQL2 Nitrate transporter 1.5 from Arabidopsis thaliana (see 5 papers)
AT1G32450 NRT1.5 (NITRATE TRANSPORTER 1.5); nitrate transmembrane transporter/ transporter from Arabidopsis thaliana
NP_174523 nitrate transporter 1.5 from Arabidopsis thaliana

• function: Low-affinity proton-dependent bidirectional nitrate transporter. Involved in nitrate loading into xylem and not in nitrate uptake. Not involved in histidine or dipeptides transport.
  disruption phenotype: No visible phenotype when grown under normal conditions. Lower nitrate concentration in xylem sap. Decreased long- distance root-to-shoot transport of nitrate but not of sulfate or phosphate.
• substrates: nitrate
• Fine-Tuning of Arabidopsis thaliana Response to Endophytic Colonization by Gluconacetobacter diazotrophicus PAL5 Revealed by Transcriptomic Analysis
  Soares, Plants (Basel, Switzerland) 2024
  • “...uptake (nitrogen sources) and transport systems were identified in shoots and roots. The NRT1.5 gene (at1g32450), a member of the NRT1 family that encodes the low-affinity transport system (LAT), was induced in both shoot and root tissues. Shoots and roots also showed the induction of genes...”
• Overexpression of SLIM1 transcription factor accelerates vegetative development in Arabidopsis thaliana
  Apodiakou, Frontiers in plant science 2024
  • “...3 content in 35S::SLIM1 is only 5% of the levels at 30 DAS. Additionally, NRT1;5 (AT1G32450), an important long-distance root-to-shoot transporter ( Chen etal., 2021 ), and NRT1;7 (AT1G69870), a source-to-sink transporter ( Fan etal., 2009 ), are induced in 35S::SLIM1 at 44 DAS relative to...”
• The K⁺ transporter NPF7.3/NRT1.5 and the proton pump AHA2 contribute to K⁺ transport in Arabidopsis thaliana under K⁺ and NO₃^- deficiency
  Sena, Frontiers in plant science 2023
  • “...QIAfilter Plasmid Mega Kit (Qiagen). The Cub-NRT1.5 bait vector was constructed by amplifying the NRT1.5 (At1g32450) full-length coding sequence (CDS) including the stop codon on plasmid pcAcNRT1.5-9 ( Drechsler etal., 2015 ) with Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific) and inserting it into PstI-SacII-digested pBT3-N plasmid...”
• Dynamic transcriptome analysis unravels key regulatory genes of maize root growth and development in response to potassium deficiency
  Guo, Planta 2023
  • “...2.7 AT4G18290 KAT2 POTASSIUM CHANNEL PROTEIN (Hong et al. 2013 ) Zm00001d017666 1.3 1.1 1.1 AT1G32450 NRT1.5 NITRATE TRANSPORTER 1.5 (Hong et al. 2013 ) Zm00001d018918 1.8 AT4G32500 AKT5 K+TRANSPORTER 5 (Pilot et al. 2003 ) Zm00001d031923 AT5G51710 KEA K+EFFLUX ANTIPORTER (Ahn et al. 2004 )...”
• ARR17 controls dioecy in Populus by repressing B-class MADS-box gene expression
  Leite, Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2022
  • “...(ZP1) Potra2n18c32253 1.63 0.04113 Potri.018G113300 AT4G02050 sugar transporter protein 7 (STP7) Potra2n14c27869 1.54 0.041274 Potri.014G179400 AT1G32450 nitrate transporter 1.5 (NRT1.5) Figure 2 . PISTILLATA ( PI ) and UNUSUAL FLORAL ORGANS ( UFO ) are strongly upregulated in arr17 CRISPR mutants on day 20. Volcano plot...”
• Regulation of Nitrate (NO₃) Transporters and Glutamate Synthase-Encoding Genes under Drought Stress in Arabidopsis: The Regulatory Role of AtbZIP62 Transcription Factor
  Rolly, Plants (Basel, Switzerland) 2021
  • “...in response to drought stress (about a 94.2-fold change) in Col-0. Table 2 identified NRT1.5 (AT1G32450) and NRT1.7 (AT1G69870) as potential targets for AtNRT2.2 during NO 3 transport. Meanwhile, the expression of AtNRT2.1 showed a similar transcript accumulation pattern with Col-0 WT ( Figure 3 C),...”
  • “...seed germination. The uptake activity is not required for sensor function. [ 31 ] NRT1.5 AT1G32450 Protein NRT1/PTR FAMILY 7.3; Transmembrane nitrate transporter. Involved in xylem transport of nitrate from root to shoot. Induced in response to nitrate. Not involved in nitrate uptake. Belongs to the...”
• Differences in mineral accumulation and gene expression profiles between two metal hyperaccumulators, Noccaea japonica and Noccaea caerulescens ecotype Ganges, under excess nickel condition
  Enomoto, Plant signaling & behavior 2021 (secret)
• The Loss of Function of the NODULE INCEPTION-Like PROTEIN 7 Enhances Salt Stress Tolerance in Arabidopsis Seedlings
  Le, Frontiers in plant science 2021
  • “...), RD29A ( AT5G52310 ), NIA1 ( AT1G77760 ), NIA2 ( AT1G37130 ), NRT1.5 ( AT1G32450 ), NRT1.8 ( AT4G21680 ), NCED3 ( AT3G14440 ), BG1 ( AT3G57270 ), and BG2 ( AT3G57260 ), ACTIN2 ( AT3G18780 ). Statistical Analyses To obtain reliable results, each experiment...”
• Transcriptome analysis of Rafflesia cantleyi flower stages reveals insights into the regulation of senescence
  Mohd-Elias, Scientific reports 2021
  • “...Promote UN013404 ABC transporter AT5G06530 Unclear UN004449 Sugar transporter 14 AT5G26340 Unclear UN026074 Nitrate transporter AT1G32450 Unclear UN015723 Polyamine transporter AT1G31830 Unclear Redox regulation UN004263 Catalase (CAT) AT1G20630 Unclear UN012078 Superoxide dismutase (SOD) AT3G56350 Unclear UN037470 L-Ascorbate oxidase (ASO) AT1G76160 Unclear UN001999 Peroxidase A2 AT5G06720 Unclear...”
• Molecular Regulatory Networks for Improving Nitrogen Use Efficiency in Rice
  Hou, International journal of molecular sciences 2021
  • “...Arabidopsis Directing root growth in sensing external NO 3 concentration Uptake [ 50 ] AtNPF7.3/AtNRT1.5 AT1G32450 Arabidopsis Low NO 3 dependent K + translocation from root to shoot Transport [ 51 , 52 ] AtNRT1.11 AT1G52190 Arabidopsis Phloem-specific NO 3 transporter redistributing xylem-borne NO 3 to...”
• Evidence for thermosensitivity of the cotton (Gossypium hirsutum L.) immature fiber (im) mutant via hypersensitive stomatal activity
  Kim, PloS one 2021
  • “...AT1G05300 Zinc transporter 5 precursor 0.45 0.17 Ghir_D01G024110 AT1G23090 Sulfate transporter 91 0.43 0.01 Ghir_A13G001050 AT1G32450 Nitrate transporter 1.5 0.27 0.00 Abscisic acid response Ghir_D05G020680 AT4G25000 Alpha-amylase-like 0.04 0.08 Ghir_D13G021720 AT5G57050 Protein phosphatase 2C family protein 0.31 0.02 Ghir_A10G010940 AT2G33380 Caleosin-related family protein 0.33 0.03 Ghir_A13G020900...”
• Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus
  Wen, BMC genomics 2020
  • “...[ 19 ] IAA AtNPF7.2 NRT1.8 At4g21680 NPF7 NO 3 [ 53 ] AtNPF7.3 NRT1.5 At1g32450 NPF7 NO 3 [ 53 ]; K + [ 23 ] AtNPF8.1 PTR1 At3g54140 NPF8 di-peptides [ 13 , 14 ]; MeJA [ 18 ] AtNPF8.2 PTR5 At5g01180 NPF8 di-peptides...”
• Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data
  Tu, Frontiers in genetics 2020
  • “...identified here are critical for plant development. For example, Sobic.004G276200 is a homolog of AtNRT1.5 (AT1G32450) that regulates root architecture and leaf senescence through nitrate response and root-to-shoot nitrate transport and potassium translocation ( Meng et al., 2015 ; Zheng et al., 2016 ). Sobic.006G016700 is...”
• A curated list of genes that affect the plant ionome
  Whitt, Plant direct 2020
  • “...etal.( 2013 ) A. thaliana AT1G31885 NIP3;1 As Shoots Xu etal.( 2015 ) A. thaliana AT1G32450 AtNRT1.5/ AtNPF7.3 K, NO3 Shoots, Roots Li etal.( 2017 ) A. thaliana AT1G36370 AtMSA1 S, Se Shoots Huang, etal.( 2016 ) A. thaliana AT1G56160 myb72 Fe, Cd, Zn, Co, Mo...”
• Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed
  Shahzad, Nature communications 2020
  • “...NRPD1a ), AT4G11130 ( RDR2 ), AT2G26650 ( AKT1 ), AT1G30270 ( CIPK23 ), and AT1G32450 ( NRT1 . 5 / NPF7 . 3 ). Reporting summary Further information on research design is available in the Nature Research Reporting Summary linked to this article. Supplementary information...”
• Cytokinin-regulated targets of Cytokinin Response Factor 6 are involved in potassium transport
  Hughes, Plant direct 2020
  • “...Increased AT3G02850 Stelar K+ Outward Rectifier SKOR K+ transport/homeostasis 0.3872 0.032512 0.6207 0.13213 1.6029 Increased AT1G32450 Nitrate Transporter 1.5 NRT1.5 K+ transport/homeostasis, Nitrate transport 0.4822 0.004754 0.7577 0.08566 1.5713 Increased AT1G01580 Ferric Reduction Oxidase 2 FRO2 Iron uptake 0.2160 0.000411 0.2742 0.00166 1.2691 Similar AT2G30766 FeUptakeInducing...”
• Lateral Transport of Organic and Inorganic Solutes
  Aubry, Plants (Basel, Switzerland) 2019
  • “...Phloem/xylem parenchyma, endodermis Immuno-electron microscopy and promoter GUS fusion At/[ 99 , 100 ] NRT1.5/NPF7.3 At1g32450 Potassium and nitrate transporter Root Pericycle In situ hybridization At/[ 101 ] PHO1 At3g23430 Inorganic phosphate exporter Root Stele, xylem-pole, endodermis Promoter GUS fusion At/[ 102 ] PHO1;H1 At1g68740 Inorganic...”
• Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita
  Medina, BMC genomics 2018
  • “...name chr1:1050634110,507,511 down At1g29980 Protein of unknown function 1.1 0.8863 BOMZH2 0.9127 BOMZH2 chr1:1172163111,721,864 up At1g32450 Transmembrane nitrate transporter 1.0 0.9526 ATREP4 chr1:1354431313,545,488 down At1g36180 acetyl-CoA carboxylase 2 acetyl-CoA carboxylase 2 (ACC2) 0.8 0.8685 ATHATN1 0.7852 VANDAL16 chr1:94121109,412,695 up At1g27100 Actin cross-linking protein 1.2 0.8485 AtSB2...”
  • “...maintenance organization of cell files or cell morphology in conductive elements, a xylem nitrate transporter (AT1G32450), a protein involved in oxidative stress (methionine sulfoxide reductase B5, AT4G04830), a 20S proteasome subunit (AT2G05840), a tetraspanin (AT2G23810), a protein similar to beta-glucosidase (AT3G60140) and a protein of unknown...”
• The Expected and Unexpected Roles of Nitrate Transporters in Plant Abiotic Stress Resistance and Their Regulation
  Zhang, International journal of molecular sciences 2018
  • “...Arabidopsis thaliana Polyamine resistance is increased in npf6.4 mutants [ 25 ] AtNPF7.3 / AtNRT1.5 At1g32450 Arabidopsis thaliana Downregulated by cadmium, salt stress, and knockout mutants show enhanced tolerance to abiotic stress; Suppress leaf senescence under nitrate deficiency and repress leaf chlorosis and growth retard when...”
• Nitrate Uptake Affects Cell Wall Synthesis and Modeling
  Landi, Frontiers in plant science 2017
  • “...http://atted.jp (Aoki et al., 2016 ). In detail, six low affinity nitrate transporters (At1g12110, At1g69850, At1g32450, At1g27080, At1g69870, At4g21680), two major facilitator super family proteins (At1g52190, At3g16180), seven high affinity nitrate transporters (At1g08090, At1g08100, At5g60780, At5g60770, At1g12940, At3g45060, At5g14570), and six ammonium transporters (At4g13510, At1g64780, At1g64780,...”
  • “...LOW AFFINITY NITRATE TRANSPORTER A. THALIANA AMMONIUM TRANSPORTER At1g12110 NT 1.1. At1g69850 NT 1.2 . At1G32450 NT 1.5 At1G27080 NT 1.6 At1g69870 NT 1.7 . At4g21680 NT 1.8 . At4g13510 AMT 1.1 At1g64780 AMT 1.2 At4g28700 AMT 1.4 At2g38290 AMT 2 Guard cellslateral roots Roots hairs...”
• Phosphate starvation induces DNA methylation in the vicinity of cis-acting elements known to regulate the expression of phosphate-responsive genes
  Yong-Villalobos, Plant signaling & behavior 2016
  • “...Pi-methDEGs are shown. Locus ID AT1G20840 AT1G32450 AT2G13540 AT4G35090 AT5G01180 AT1G47960 AT1G74590 AT2G16430 AT4G37670 AT5G22300 AT2G26760 AT3G02850...”
• A Functional EXXEK Motif is Essential for Proton Coupling and Active Glucosinolate Transport by NPF2.11
  Jørgensen, Plant & cell physiology 2015
  • “...reported ( Sun et al. 2014 ). These belong to the NAXT and NRT1.5 subclades (At1g32450, At4g21680 and At5g19640), which appear to encode nitrate transporters ( Segonzac et al. 2007 , Lin et al. 2008 , Li et al. 2010 ). Among the NPF transporters and...”
• Abiotic Stresses Downregulate Key Genes Involved in Nitrogen Uptake and Assimilation in Brassica juncea L
  Goel, PloS one 2015
  • “...membrane AT2G26690 AtNPF6.2/ NRT1/PTR family 6.2 1003 BjNRT1.5 KT119582 69.49 5.7 1860 620 Plasma membrane AT1G32450 AtNPF7.3/ nitrate transporter 1.5 1113 BjNRT1.7 KT119583 68.70 8.95 1866 622 Plasma membrane AT1G69870 AtNPF2.13/ nitrate transporter 1.7 987 BjNRT1.8 KT119584 64.72 6.22 1749 583 Plasma membrane AT4G21680 AtNPF7.2,/nitrate transporter...”
• Complex phylogeny and gene expression patterns of members of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) in wheat
  Buchner, Journal of experimental botany 2014
  • “...AtNPF6.4 At3g21670 BdNPF6.7 Bradi3g47010 OsNPF6.7 OsNPF6.6 Os02g35830 Loc_Os04g39030 AtNPF6.2 At2g26690 BdNPF6.2 Bradi2g41060 OsNPF6.2 Loc_Os01g37590 AtNPF7.3 At1g32450 BdNPF7.10 BdNPF7.11 Bradi3g52096 Bradi3g53380 OsNPF7.9 OsNPF7.10 OsNPF7.11 Loc_Os02g46460 Loc_Os06g21900 Loc_Os02g48570 AtNPF2.12 At1g27080 N/A N/A N/A N/A AtNPF2.13 At1g69870 BdNPF2.6 Bradi2g58470 OsNPF2.5 Loc_Os01g68510 AtNPF7.2 At4g21680 N/A N/A N/A N/A AtNPF2.9A At1g18880...”
• Function of Arabidopsis CPL1 in cadmium responses
  Aksoy, Plant signaling & behavior 2013
  • “...1 0.96 ( 0.32) 0.66 ( 0.21) 0.57 ( 0.23) AT1G32450 NITRATE TRANSPORTER 1.5 (NTR1.5) 1 1.22 ( 0.22) 0.68 ( 0.27) 0.53 ( 0.06) AT4G21680 NITRATE TRANSPORTER 1.8...”
• Nitrogen form-mediated ethylene signal regulates root-to-shoot K+ translocation via NRT1.5.
  Chen, Plant, cell & environment 2021 (PubMed)
  • GeneRIF: Nitrogen form-mediated ethylene signal regulates root-to-shoot K(+) translocation via NRT1.5.
• The Arabidopsis NRT1/PTR FAMILY protein NPF7.3/NRT1.5 is an indole-3-butyric acid transporter involved in root gravitropism.
  Watanabe, Proceedings of the National Academy of Sciences of the United States of America 2020
  • GeneRIF: The Arabidopsis NRT1/PTR FAMILY protein NPF7.3/NRT1.5 is an indole-3-butyric acid transporter involved in root gravitropism.
• Nitrate transporter NPF7.3/NRT1.5 plays an essential role in regulating phosphate deficiency responses in Arabidopsis.
  Cui, Biochemical and biophysical research communications 2019 (PubMed)
  • GeneRIF: The NPF7.3/NRT1.5 is an important component in the regulation of phosphate deficiency responses in Arabidopsis.
• The Transcription Factor MYB59 Regulates K+/NO3 - Translocation in the Arabidopsis Response to Low K+ Stress.
  Du, The Plant cell 2019
  • GeneRIF: These data demonstrate that MYB59 responds to low K(+) (LK) stress and directs root-to-shoot K(+)/NO3 (-) transport by regulating the expression of NPF7.3 in Arabidopsis roots.
• NRT1.5/NPF7.3 Functions as a Proton-Coupled H+/K+ Antiporter for K+ Loading into the Xylem in Arabidopsis.
  Li, The Plant cell 2017
  • GeneRIF: This study reveals that NRT1.5 plays a crucial role in K(+) translocation from root to shoot and is also involved in the coordination of potassium/nitrates distribution in plants.
• Arabidopsis NRT1.5 Mediates the Suppression of Nitrate Starvation-Induced Leaf Senescence by Modulating Foliar Potassium Level.
  Meng, Molecular plant 2016 (PubMed)
  • GeneRIF: NRT1.5 likely perceives nitrate starvation-derived signals to prevent leaf senescence by facilitating foliar potassium accumulation
• The Arabidopsis nitrate transporter NPF7.3/NRT1.5 is involved in lateral root development under potassium deprivation.
  Zheng, Plant signaling & behavior 2016
  • GeneRIF: a possible involvement of NPF7.3/NRT1.5 in auxin homeostasis in roots under potassium deprivation, is reported.
• Nitrate-Dependent Control of Shoot K Homeostasis by the Nitrate Transporter1/Peptide Transporter Family Member NPF7.3/NRT1.5 and the Stelar K+ Outward Rectifier SKOR in Arabidopsis.
  Drechsler, Plant physiology 2015
  • GeneRIF: Data show that nutritional conditions as a critical factor for the joint activity of Arabidopsis proteins SKOR and NPF7.3/NRT1.5 for shoot potassium (K) homeostasis.
• The Arabidopsis ethylene/jasmonic acid-NRT signaling module coordinates nitrate reallocation and the trade-off between growth and environmental adaptation.
  Zhang, The Plant cell 2014
  • GeneRIF: Data show that ethylene (ET) and jasmonic acid (JA)-nitrate transporters NRT1.8 and NRT1.5 signaling affect the crosstalk between stress-initiated nitrate allocation to roots (SINAR) and the environment.
• Arabidopsis NRT1.5 is another essential component in the regulation of nitrate reallocation and stress tolerance.
  Chen, Plant physiology 2012
  • GeneRIF: NRT1.5 is involved in nitrate allocation to roots and the consequent tolerance to several stresses.
• Mutation of the Arabidopsis NRT1.5 nitrate transporter causes defective root-to-shoot nitrate transport.
  Lin, The Plant cell 2008
  • GeneRIF: NRT1.5 participates in root xylem loading of nitrate but in addition to the pathway involving NRT1.5, another mechanism is responsible for xylem loading of nitrate. [NRT1.5]

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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.