PaperBLAST

Full List of Papers Linked to NP_199417.1

PTR3_ARATH / Q9FNL7 Protein NRT1/ PTR FAMILY 5.2; AtNPF5.2; Peptide transporter PTR3-A; AtPTR3 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
TC 2.A.17.3.4 / Q9FNL7 Peptide transporter, PTR3-A (induced by histidine, leucine and phenylalanine in cotyledons and lower leaves; involved in stress tolerance in seeds during germination and in defense against virulent bacterial pathogens) from Arabidopsis thaliana (Mouse-ear cress) (see 4 papers)
PTR3-A / RF|NP_199417.1 peptide transporter PTR3-A from Arabidopsis thaliana (see paper)
NP_199417 peptide transporter 3 from Arabidopsis thaliana
AT5G46050 PTR3 (PEPTIDE TRANSPORTER 3); dipeptide transporter/ transporter/ tripeptide transporter from Arabidopsis thaliana

• function: Peptide transporter involved in stress tolerance in seeds during germination and in defense against virulent bacterial pathogens.
• substrates: peptides
• AtPTR3, a wound-induced peptide transporter needed for defence against virulent bacterial pathogens in Arabidopsis.
  Karim, Planta 2007 (PubMed)
  • GeneRIF: The function and expression regulation of PTR3 are reported.
• Structural and functional characterization of AtPTR3, a stress-induced peptide transporter of Arabidopsis.
  Karim, Journal of molecular modeling 2005 (PubMed)
  • GeneRIF: a strong induction of the AtPTR3 gene was obtained in the whole plant upon exposure to salt; results suggest that the AtPTR3 protein is involved in stress tolerance in seeds during germination.
• Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum
  Wang, Frontiers in plant science 2021
  • “...GO: 0009628 Response to salt stress 0.00014 Thhalv10023595m AT1G62380 1-aminocyclopropane-1-carboxylate oxidase 2 (ACO2) peptide Thhalv10000830m AT5G46050 Transporter 3 (PTR3) Thhalv10001865m AT3G09260 Glycosyl hydrolase superfamily protein (PYK10) Thhalv10003061m AT4G12720 MutT/nudix family protein (NUDT7) Thhalv10013480m AT5G03630 Pyridine nucleotide-disulfide oxidoreductase family protein (MDAR2) III Thhalv10021496m AT3G23180 HR-like lesion-inducing protein-like...”
• The Arabidopsis RLCK VI_A2 Kinase Controls Seedling and Plant Growth in Parallel with Gibberellin
  Valkai, International journal of molecular sciences 2020
  • “...1.60 0.001941 yes AT3G16180 AT3G16180 Major facilitator superfamily protein, NPF 1.1 a 1.79 0.001941 yes AT5G46050 PTR3 peptide transporter 3, NPF 5.2 a 0.55 0.001941 yes AT5G62680 GTR2 Major facilitator superfamily protein, NPF 2.11 c 0.65 0.031474 yes DEGs of DELLA Transcription Regulators *** AT1G14920 GAI...”
• Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus
  Wen, BMC genomics 2020
  • “...18 , 58 ] AtNPF5.1 At2g40460 NPF51 ABA/GA 1/3/4 /MeJA [ 18 ] AtNPF5.2 PTR3 At5g46050 NPF51 ABA/GA 1/3/4 [ 9 ]; di-peptides [ 60 ] SA; MeJA; ABA AtNPF5.3 At5g46040 NPF51 ABA [ 18 ] AtNPF5.5 At2g38100 NPF52 NO 3 [ 61 ] AtNPF5.6 At2g37900...”
• Transcriptome analysis reveals key roles of AtLBR-2 in LPS-induced defense responses in plants
  Iizasa, BMC genomics 2017
  • “...[ 55 ] AT4G12480 Early Arabidopsis aluminum induced 1 (pEARLI 1)* 2.334243 [ 56 ] AT5G46050 Peptide transporter 3 (PTR3)* 2.322650 [ 57 ] AT3G28580 P-loop containing nucleoside triphosphate hydrolases superfamily protein 2.314015 AT3G50480 Homolog of RPW8 4 (HR4)* 2.311148 [ 10 ] AT2G26400 Acireductone dioxygenase...”
• Biology in the Dry Seed: Transcriptome Changes Associated with Dry Seed Dormancy and Dormancy Loss in the Arabidopsis GA-Insensitive sleepy1-2 Mutant
  Nelson, Frontiers in plant science 2017
  • “...LTP4 4.40 At4g02380 LEA5 2.34 At1g21630 EF hand family 1.65 2.77 2.95 At1g44575 NPQ4 0.89 At5g46050 PTR3 1.26 At5g54070 HSFA9 1.34 At4g09610 GASA2 1.29 At3g45970 EXPL1 1.01 At2g34740 A PP2C 0.97 At3g22490 A LEA 0.91 At5g45690 Unknown protein 0.83 At2g46240 BAG6 -2.13 -2.69 -3.19 At2g46250 Myosin...”
• Decreased glutathione reductase2 leads to early leaf senescence in Arabidopsis
  Ding, Journal of integrative plant biology 2016
  • “...7.340.9 AT3G26830 Phytoalexin deficient (PAD3) 2.25 5.661.4 AT4G12470 Azelaic acid induced 1 (AZI1) 2.62 7.651.1 AT5G46050 Peptide transporter PTR3A (PTR3) 2.27 8.051.5 AT5G64930 Regulator of pathogenesisrelated (HYS1) 2.66 6.001.7 AT3G57240 Beta1,3glucanase 3 (BG3) 4.58 7.921.2 Phytohormone pathway AT4G11890 Protein kinase family protein (ARCK1) 2.07 4.660.4 AT2G13810...”
• Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress
  Baldoni, Rice (New York, N.Y.) 2016
  • “...not yet well defined (Saier et al. 2006 ). This gene is similar to AtPTR3 (AT5G46050), whose expression is induced by salt stress and mechanical wounding and is regulated by jasmonic acid and salicylic acid (Karim et al. 2005 ; Karim et al. 2007 ). Another...”
• Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis
  Mata-Pérez, Frontiers in plant science 2015
  • “...associated with drought stress responses (Cheng et al., 2012 ), while peptide transporter 3 ( AT5G46050 ), involved in the response to wounding, was also repressed. Finally, another important group of down-regulated genes was activated in the response to cold and osmotic stress (16.36 and 8.73%,...”
  • “...XTH31 (AT3G44990), Arabidopsis thaliana xyloglucan endotransglycosylase/hydrolase 31; CHX17 (AT4G23700), Arabidopsis thaliana cation/H(+) antiporter 17; PTR3 (AT5G46050), Arabidopsis thaliana putative peptide transporter protein 3; CLV3 (AT2G27250), Arabidopsis thaliana protein CLAVATA 3; OZF1 (AT2G19810), Arabidopsis thaliana Oxidation-related Zinc Finger protein 1; HAC5 (AT3G12980), Arabidopsis thaliana histone acetyltransferase 5;...”
• The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress
  Thatcher, PloS one 2015
  • “...MSRB8 2.3 3.2E-03 methionine sulfoxide reductase B8 AT1G23730 BCA3 2.6 3.4E-03 beta carbonic anhydrase 3 AT5G46050 PTR3 2.4 3.5E-03 peptide transporter 3 AT3G43110 2.3 3.6E-03 Unknown AT2G40330 PYL6 2.4 4.3E-03 PYR1-like 6 AT5G52760 2.4 4.8E-03 Copper transport protein family AT1G15540 2.6 4.9E-03 2-oxoglutarate (2OG) and Fe(II)-dependent...”
• A dominant allele of Arabidopsis pectin-binding wall-associated kinase induces a stress response suppressed by MPK6 but not MPK3 mutations
  Kohorn, Molecular plant 2012
  • “...and 5'-GATGGCATGAGGAAGAGAGAAAC-3'; PTR3 (AT5G46050) 5'-ATCTTGGGTGCTTACGTTGGAG-3' and 5'-CCGAACTTTTTCGCAATTTTCCAC-3'; ESM1 (AT3G14210) 5'-CTTACTACGACGCCGGAAAC-3'...”
• Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana
  Chan, PLoS biology 2011
  • “...but not previously linked to GSL content. This network involved AtPTR3 (a putative peptide transporter, At5g46050 ) and DPL1 (a dihydrosphingosine lyase, At1g27980 ). T-DNA mutants in both genes appeared to be lethal as we could not identify homozygous progeny. However, comparison of the heterozygous progeny...”
• Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa L.)
  Zhao, BMC plant biology 2010
  • “...tissue throughout the plant, indicative of a role in long-distance transport [ 10 ]. AtPTR3 (At5g46050) was a salt stress and mechanical wounding inducible gene, JA and SA were both involved in regulation of it [ 12 , 13 ]. AtPTR5 (At5g01180) which mediated high-affinity transport...”
• AtPTR3, a wound-induced peptide transporter needed for defence against virulent bacterial pathogens in Arabidopsis
  Karim, Planta 2007 (PubMed)
  • “...Mutation in the wound-induced peptide transporter gene AtPTR3 (At5g46050) of Arabidopsis thaliana has been shown to aVect germination on media containing a high...”
  • “...we characterised the Arabidopsis peptide transporter gene AtPTR3 (At5g46050), identiWed due to GUS activity in a promoter trap line (Karim et al. 2005). In...”
• Enigma variations for peptides and their transporters in higher plants
  Waterworth, Annals of botany 2006
  • “...AT2G26690 AT2G37900 CHL1 AT1G12110 AT3G53960 AT1G62200 AT5G46050 PTR3 AT3G54450 AT5G46040 AT1G72120 AT3G01350 AT5G14940 III AT1G22570 AT1G72130 AT1G22540...”
  • “...(AT1G69850) and NTP2 (AT2G26690) in subfamily IV, PTR3 (AT5G46050) in subfamily III and PTR1 (AT3G54140) and PTR2 (AT2G02040) in subfamily II are indicated. in...”
• Structural and functional characterization of AtPTR3, a stress-induced peptide transporter of Arabidopsis
  Karim, Journal of molecular modeling 2005 (PubMed)
  • “...mutation in a PTR-type peptide transporter gene named At5g46050 in GenBank, here renamed AtPTR3. The gene and the deduced protein were characterized by...”
  • “...[42]. Mutant lines carrying a T-DNA inserted in At5g46050 in ecotype Columbia-0 was ordered from Salk Insertion Sequence Database (http:// signal.salk.edu). All...”

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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.