PaperBLAST

Full List of Papers Linked to VIMSS10096807

H2B7_ARATH / Q9LZT0 Histone H2B.7; HTB11 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G46030 HTB11; DNA binding from Arabidopsis thaliana
Q1H5F9 Histone H2B from Arabidopsis thaliana

• function: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling
  subunit: The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA
• Advances in biological functions and mechanisms of histone variants in plants
  Wu, Frontiers in genetics 2023
  • “...AT1G08170 Regulate seed development but not expressed in sperm cells H2B.9 AT3G45980 H2B.10 AT5G02570 H2B.11 AT3G46030 H3 H3.3 AT4G40030 HIRA Transcriptional activation Flowering time Zhao et al. (2021) ; Male Gametogenesis Ingouff et al. (2010) ; Cell proliferation and organogenesis Otero et al. (2016) AT4G40040 ATRX...”
• Histone variants and modifications during abiotic stress response
  Nunez-Vazquez, Frontiers in plant science 2022
  • “...H2B.10 Variant At5g02570, HTB10 Development of reproductive tissues ( Jiang etal., 2020a ) H2B.11 Variant At3g46030, HTB11 H3 H3.1 Canonical At5g65360, HTR1 CAF1 Transcriptional repression ( Stroud etal., 2012 ; Wollmann etal., 2012 ) At1g09200, HTR2 At3g27360, HTR3 At5g10400, HTR9 At5g10390, HTR13 H3.3 Variant At4g40030, HTR4...”
• New Insights into the Chloroplast Outer Membrane Proteome and Associated Targeting Pathways
  Fish, International journal of molecular sciences 2022
  • “...At3g16950 PDC E3 At3g19720 * ARC5 At3g25690 CHUP1 At3g25860 PDC E2 At3g26070 PAP/FBN3a At3g26740 CCL At3g46030 Histone H2B At3g46780 pTAC16 At3g49350 - At3g53560 TPR Protein At3g63520 * Carotenoid Cleaving Protein At4g00550 DGD2 At4g02482 Putative GTPase At4g02510 TOC159 At4g05050 UBQ11 At4g13550 * Putative Triglyceride Lipase At4g14430 Enoyl-CoA...”
• Comparative Analysis of Proteins Regulated during Cadmium Sulfide Quantum Dots Response in Arabidopsis thaliana Wild Type and Tolerant Mutants
  Gallo, Nanomaterials (Basel, Switzerland) 2021
  • “...treated wt and treated atnp 01: heat shock 70 kDa protein 3 (Hsp70-3), histone H2B.7 (At3g46030), L-ascorbate peroxidase 1 (Apx1), and filament-like plant protein 6 (Fpp6). Hsp70-3, in collaboration with other chaperone proteins, assists translocation of precursor proteins into organelles, facilitates folding of de novo synthesized...”
  • “...the degradation of damaged proteins undergoing stress conditions such as from Cd [ 46 ]; At3g46030 is a core component of the nucleosome [ 39 ]; Apx1 is a key component of the reactive oxygen species gene network, moreover, its synthesis can be induced by Cd...”
• Plant Histone HTB (H2B) Variants in Regulating Chromatin Structure and Function
  Khadka, Plants (Basel, Switzerland) 2020
  • “...classes. Class I contains HTB1(At1g07790), HTB2 (At5g22880), HTB3 (At2g28720), HTB4 (At5g59910), HTB9 (At3g45980), and HTB11 (At3g46030) and class II HTB5 (At2g37470), HTB6 (At3g53650), HTB7 (At3g09480), and HTB10 (At5g02570). Class I variants can be further divided into class I-A (H2B4, 9, and 11) and class I-B (HTB1,...”
• The evolution and functional divergence of the histone H2B family in plants
  Jiang, PLoS genetics 2020
  • “...S 314 HTB5 AT2G37470 S 83 HTB6 AT3G53650 S 223 HTB9 AT3G45980 S 110 HTB11 AT3G46030 S 75 Data from Cyclebase 3.0 (REF) To test the link between H2B.3 and the cell cycle further, we analysed the expression of the somatic H2Bs in a mutant background...”
• Emerging knowledge of the organelle outer membranes - research snapshots and an updated list of the chloroplast outer envelope proteins
  Inoue, Frontiers in plant science 2015
  • “...(x)(xi) At3g01280 VDAC1 (mito) (i) YES (x) At3g12580 Hsc70-4 (cytosol) (iv) At3g21865 PEX22 (peroxisome) (iv) At3g46030 histone H2B (nucleus) (iii) At3g63150 MIRO2 (mito) (iv) (x)(xi) At4g14430 enoyl-CoA isomerase (peroxisome) (iii) At4g16450 Complex I subunit (mito) (iii) At4g31780 MGD1 (IEM) (iii) YES At4g35000 APX3 (peroxisome) (iii)(iv) YES...”
• Defining the core proteome of the chloroplast envelope membranes
  Simm, Frontiers in plant science 2013
  • “...Organelles At1g27390 Tom20-2 Putative mitochondrial outer membrane translocase component 1 -Helical TM n.d./X 3 I At3g46030 HTB11 Putative H2B-type histone None X/n.d. 1 III At4g14430 ECHIb Putative enoyl-CoA hydratase/isomerase 1 -Helical TM X 1 III At4g35000 APX3 Putative peroxisomal ascorbate peroxidase 1 -Helical TM X 5...”
• Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants
  Du, Cell 2012
  • “...8 30.4 1863 25.7 At5g59910 At1g07790 H2B 1 At5g22880 79.6 16.6 42.2 4327 59.8 At3g45980 At3g46030 At5g10400 At1g09200 H3 1 At5g10390 63 21 52.9 3674 50.7 At5g65360 At3g27360 HTR12 At1g01370 2 2 25.3 90.3 1.2 At1g07820 At3g3730 At2g28740 H4 1 At5g59970 26 13 62.1 2028 28.0...”
• A unified phylogeny-based nomenclature for histone variants
  Talbert, Epigenetics & chromatin 2012
  • “...HTB7 H2B.7 " At1g08170 HTB8 H2B.8 " At3g45980 HTB9 H2B.9 " At5g02570 HTB10 H2B.10 " At3g46030 HTB11 H2B.11 " H3 Gene Protein Former name At5g65360 HTR1 H3.1 H3.1 At1g09200 HTR2 " " At3g27360 HTR3 " " At5g10400 HTR9 " " At5g10390 HTR13 " " At4g40030 HTR4...”
• Transcription profile analysis reveals that zygotic division results in uneven distribution of specific transcripts in apical/basal cells of tobacco
  Ma, PloS one 2011
  • “...histone H3 5.00E-71 NtAc 5 10 AT4G33865 40S ribosomal protein S29 3.00E-28 NtAc 6 9 AT3G46030 HTB11; DNA binding 1.00E-65 NtAc 7 9 AT3G12410 3-5 exonuclease/ nucleic acid binding 4.00E-58 NtAc 8 9 AT5G65360 histone H3 1.00E-70 NtAc 9 9 AT3G43810 calmodulin 9.00E-78 NtAc 10 8...”
  • “...Nt B c 13 7 AT3G52590 ubiquitin extension protein 4.00E-69 Nt B c 14 7 AT3G46030 HTB11; DNA binding 2.00E-65 Nt B c 15 7 No hit Nt B c 16 7 AT3G59540 60S ribosomal protein L38 1.00E-31 Nt B c 17 7 AT4G33865 40S ribosomal...”
• Transcriptional responses of winter barley to cold indicate nucleosome remodelling as a specific feature of crown tissues
  Janská, Functional & integrative genomics 2011
  • “...H3 (At5g10400, At5g10390) , H3.2 (At1g5600, At1g13370) , H4 (At5g59970) , HTB4 (At5g59910) , HTB11 (At3g46030) , HTA11 (At3g54560) and HTA12 (At5g02560) . Of these, H2A and HTA11 have been shown to be directly involved in the perception of temperature during nucleosome remodelling (Kumar and Wigge...”
• An iTRAQ-based proteomics approach to clarify the molecular physiology of somatic embryo development in Prince Rupprecht's larch (Larix principis-rupprechtii Mayr)
  Zhao, PloS one 2015
  • “...(Fragment) K7NMH3 1 0.359 7.194 2 Histone H4 A9NLQ1 1 1.110 2.457 4 Histone H2B Q1H5F9 1 0.541 11.364 2 Histone H4 Q6NR90 1 1 1.862 4 Histone H3 Q0WRA9 1 1.043 1.504 4 Histone H2A.6 Q9LD28 1 0.798 1 2 Other proteins d Ubiquitin-like protein...”

New Search

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.