PaperBLAST

Full List of Papers Linked to VIMSS10085628

PTR25_ARATH / Q9C7U1 Protein NRT1/ PTR FAMILY 5.12; AtNPF5.12 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G72140 proton-dependent oligopeptide transport (POT) family protein from Arabidopsis thaliana
NP_177359 Major facilitator superfamily protein from Arabidopsis thaliana

• PIN2-mediated self-organizing transient auxin flow contributes to auxin maxima at the tip of Arabidopsis cotyledons
  Pérez-Henríquez, Nature communications 2025
  • “...silicoanalysis The sequence spanning from +1346bp until transcription start site (TSS) of the TOB1 gene (AT1G72140) was analyzed using promoter analysis tool PlantRegMap. Additionally, the sequence extending +1000bp upstream the TSS was examined using PSCAN, http://159.149.160.88/pscan , a widely used promoter analysis tool. The PINs and...”
• Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum
  Dölfors, Journal of experimental botany 2024
  • “...). When analysing the transcript levels of these potential candidates, the nitrate peptide transporter AtNPF5.12 (At1g72140) was non-responsive in Sei-0 at 2 dpi and down-regulated in Can-0 ( Fig. 1C ), indicating that this gene might contribute to the differential V. longisporum response observed in the...”
  • “...the 1001 Genomes database revealed a short indel (9 nt) in the promoter sequence of At1g72140 in Sei-0 at position Chr1:27141089. We believe this is the main reason why Sei-0 exhibits a resistant phenotype compared with Col-0 and Can-0. Furthermore, Col-0 harbors an SNP in exon...”
• Transcriptomic analysis reveals the functions of H₂S as a gasotransmitter independently of Cys in Arabidopsis
  Fang, Frontiers in plant science 2023
  • “...treatment AT1G09070 , AT1G19180 , AT1G22190 , AT1G25400 , AT1G25560 , AT1G32920 , AT1G66180 , AT1G72140 , AT1G73500 , AT1G76650 , AT2G27080 , AT2G27830 , AT3G20370 , AT3G49570 , AT3G50800 , AT4G23870 , AT4G32480 , AT4G37260 , AT5G07580 , AT5G14730 , AT5G24660 , AT5G26220 , AT5G26260...”
• The Root-Colonizing Endophyte Piriformospora indica Supports Nitrogen-Starved Arabidopsis thaliana Seedlings with Nitrogen Metabolites
  Scholz, International journal of molecular sciences 2023
  • “...x x Nitrate (NPF family) NPF5.6 At2g37900 x x 3.57 x Nitrate (NPF family) NPF5.12 At1g72140 2.03 x x x Nitrate (NPF family) NPF5.14/NRT1.15 At1g72120 x 1.83 x x Nitrate (NPF family) NPF6.2/NRT1.4 At2g26690 x x 2.11 1.61 Ammonium (AMT family) AMT13 At3g24300 x 2.42 x...”
• Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis
  Xu, Biomolecules 2021
  • “...in plants [ 180 ]. Notably, several nitrate transporters belong to the CRGs, including NPF5.12 (AT1G72140), which mediates nitrate uptake in a pH-dependent manner and acts as vacuolar nitrate efflux transporters [ 181 ], NPF7.2/NRT1.8 (AT4G21680) functioning to remove nitrate from xylem vessels [ 182 ],...”
  • “...Ca 2+ AtCNGC2 (AT5G15410), CAX7 (AT5G17860), CSC1-like proteins (AT1G10090; AT1G62320) K + AtKUP7 Nitrate NPF5.12 (AT1G72140), NPF7.2/NRT1.8 (AT4G21680), NRT2.6 (AT3G45060), NPF2.7/NAXT1(AT3G45650), CLC-b (AT3G27170) Sugar SWEET16 (AT3G16690), HKL1 (AT1G50460), PMT6/PLT6 (AT4G36670) Lipid MIOX2 (AT2G19800), ITPK3 (AT4G08170), SFH14 (AT5G56160) Light BG1 (AT5G12050), ERD7 (AT2G17840), KNAT4 (AT5G11060), DFL2 (AT4G03400),...”
• Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives
  Cantila, International journal of molecular sciences 2020
  • “...BnaA02g15610D RLK AT1G71870 Protein DETOXIFICATION 54/MATE efflux fam_prot [ 70 , 76 ] BnaA02g15810D RLK AT1G72140 Protein NRT1/PTR FAMILY 5.12/proton-dependent oligopeptide transport (POT) fam_prot [ 70 , 76 ] BnaA02g15820D RLK AT1G72150 Patellin-1/transporter [ 70 , 76 ] BnaA02g15890D RLK AT1G72290.1 (CDS) Cysteine protease inhibitor WSCP...”
• TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture
  Michniewicz, Developmental cell 2019
  • “...transmembrane domain 8 ( Figures 1E and 1F ). We obtained insertional alleles defective in At1g72140 ( Figure 1D ) and found that these, like our missense allele, displayed mild resistance to the long-chain auxins IBA and 2,4-DB and wild-type sensitivity to the active auxins IAA...”
  • “...in isolate PS173. Because these insertional alleles displayed similar phenotypes as the missense allele in At1g72140 removed from the pen3 - 4 background ( Figure 1G ), we named this gene TRANSPORTER OF IBA1 (TOB1). We named the original missense allele tob1 - 1 and the...”
• Tonoplast-localized nitrate uptake transporters involved in vacuolar nitrate efflux and reallocation in Arabidopsis
  He, Scientific reports 2017
  • “...the Arabidopsis Genome Initiative or GenBank/EMBL databases under the following accession numbers: NPF5.11 (At1g72130), NPF5.12 (At1g72140), NPF5.16 (At1g22550), NRT1.8 (At4g21680), CHL1 (At1g12110), SAND (At2g28390), Actin2 (At3g18780). Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Acknowledgements We thank...”
• QTL analysis of the developmental response to L-glutamate in Arabidopsis roots and its genotype-by-environment interactions
  Walch-Liu, Journal of experimental botany 2017
  • “...NRT1 nitrate transceptor: At1g72120 ( NRT1.15/AtNPF5.14 ), At1g72125 ( NRT1.16/AtNPF5. 13), At1g72130 ( AtNPF5.11 ), At1g72140 ( AtNPF5.12 ). The NPF family in Arabidopsis has 53 members belonging to 8 subfamilies and between them they transport a diverse range of substrates, including peptides and hormones, in...”
• Transcriptomic Profiling Analysis of Arabidopsis thaliana Treated with Exogenous Myo-Inositol
  Ye, PloS one 2016
  • “...1 (AT1G08090), PT1 (AT5G43350), GPT2 , EMB1513 (AT2G37920), ABCG6 , proton-dependent oligopeptide transport family protein (AT1G72140), and carbohydrate transmembrane transporter (AT2G18590) ( S5 Table ) encode proteins involved in intracellular and intercellular transport. These genes were associated with the absorption of nitrate [ 73 ] and...”
• Transcriptomic Analysis of Soil-Grown Arabidopsis thaliana Roots and Shoots in Response to a Drought Stress
  Rasheed, Frontiers in plant science 2016
  • “...diverse gene families such as major facilitator super family (MFS) transporters [ AT1G08900, AT1G30560, AT1G33440, AT1G72140, AT1G80530, AT2G26690, AT2G34355, AT3G20460, AT3G45680, AT3G47960, AT4G19450, STP8 (AT5G26250), AT5G27350 , and AT5G62680 ], MATE efflux transporters ( AT1G71140, AT5G17700, AT5G19700 , and AT5G38030 ), microRNA genes [ MIR156b (...”
• Shoot chloride exclusion and salt tolerance in grapevine is associated with differential ion transporter expression in roots
  Henderson, BMC plant biology 2014
  • “...NG11_7897_10153 VIT_14s0066g02020 GSVIVT01032550001 AT5G14940 0.64 3.31E-07 Proton-dependent oligopeptide transport (POT) family protein NG11_35177_1429 VIT_18s0041g00670 GSVIVT01026058001 AT1G72140 0.89 7.91E-14 Proton-dependent oligopeptide transport (POT) family protein NG11_25530_14040 VIT_04s0008g03580 GSVIVT01035643001 AT1G22550 1.11 2.21E-24 Nitrate transporter 1.11 NG11_31776_20297 VIT_16s0050g01860 GSVIVT01028789001 AT5G24030 0.54 4.61E-05 SLAH3 (SLAC1 Homologue 3) CUST_21950_56777 VIT_07s0191g00070 GSVIVT01003419001...”
• Natural variation identifies multiple loci controlling petal shape and size in Arabidopsis thaliana
  Abraham, PloS one 2013
  • “...3.43 9 Decrease AT1G43560 AT1G31730 AT1G43780 1147 SEUSS CL-W2 Width 1 2.73 7 Decrease AT1G80580 AT1G72140 AT1G81020 1269 PIN1, CLV1 CL-L1 Length 2 5.4 12 Increase AT2G13990 AT2G13590 AT2G14870 185 CL-L2 Length 2 5.65 17 Increase AT2G18940 AT2G17090 AT2G23910 1008 ULT2 CL-A1 Area 2 6.1 21...”
• A temporal precedence based clustering method for gene expression microarray data
  Krishna, BMC bioinformatics 2010
  • “...AT5G59220, AT4G25100, AT3G58810, AT4G14630, AT3G53620, AT5G11520, AT3G27300, AT1G42970, AT5G43280, AT4G27430, AT1G49300, AT2G39460, AT2G37040, AT3G01480, AT5G24550, AT1G72140, AT5G62790, AT1G25540, AT1G02860, AT4G38970, AT2G43130, AT3G52960, AT3G01220, AT2G43750 Simple network statistics We computed certain network statistics to confirm that our network is not a randomly generated network and has the...”
• Nitrogen affects cluster root formation and expression of putative peptide transporters
  Paungfoo-Lonhienne, Journal of experimental botany 2009
  • “...). HaPTR5 shared the highest similarity with HaPTR12 (72% identity), Arabidopsis At1g22540 (60% identity), and At1g72140 and At1g72130 (51% identity, each). The two latter genes are expressed to a higher level in root than in shoot of Arabidopsis ( Tsay et al. , 2007 ), but...”
• A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture
  Jaquinod, Molecular & cellular proteomics : MCP 2007
  • “...66 5 At1g22570 62,897 9.1 12 44 POT 2d Transp. NF NF At1g72140 61,347 8.2 12 34 POT 2d Transp. NF NF At2g02040 64,380 5.5 10 567 (19) 807 POT 2d Transp. 103 7...”
• TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture.
  Michniewicz, Developmental cell 2019
  • GeneRIF: TOB1 is a transporter of the auxin precursor IBA. TOB1 localizes to the vacuolar membrane and regulates root system architecture. [TOB1]
• Tonoplast-localized nitrate uptake transporters involved in vacuolar nitrate efflux and reallocation in Arabidopsis.
  He, Scientific reports 2017
  • GeneRIF: At1g72140 (NPF5.12) is involved in the nitrate from vacuoles into cytosol, thus serving as important player to modulate nitrate allocation between roots and shoots.

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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.