PaperBLAST

Full List of Papers Linked to NP_775118.1

KCNA1_RAT / P10499 Potassium voltage-gated channel subfamily A member 1; RBKI; RCK1; Voltage-gated potassium channel subunit Kv1.1 from Rattus norvegicus (Rat) (see 20 papers)
NP_775118 potassium voltage-gated channel subfamily A member 1 from Rattus norvegicus

• function: Voltage-gated potassium channel that mediates transmembrane potassium transport in excitable membranes, primarily in the brain and the central nervous system, but also in the kidney. Contributes to the regulation of the membrane potential and nerve signaling, and prevents neuronal hyperexcitability (PubMed:12177193, PubMed:17855588, PubMed:22206926). Forms tetrameric potassium-selective channels through which potassium ions pass in accordance with their electrochemical gradient (PubMed:23725331). The channel alternates between opened and closed conformations in response to the voltage difference across the membrane (PubMed:2539643). Can form functional homotetrameric channels and heterotetrameric channels that contain variable proportions of KCNA1, KCNA2, KCNA4, KCNA5, KCNA6, KCNA7, and possibly other family members as well; channel properties depend on the type of alpha subunits that are part of the channel (PubMed:10896669, PubMed:12177193, PubMed:2348860, PubMed:23725331). Channel properties are modulated by cytoplasmic beta subunits that regulate the subcellular location of the alpha subunits and promote rapid inactivation of delayed rectifier potassium channels (PubMed:10896669, PubMed:12114518). In vivo, membranes probably contain a mixture of heteromeric potassium channel complexes, making it difficult to assign currents observed in intact tissues to any particular potassium channel family member. Homotetrameric KCNA1 forms a delayed-rectifier potassium channel that opens in response to membrane depolarization, followed by slow spontaneous channel closure (PubMed:12681381, PubMed:22206926, PubMed:2348860, PubMed:23725331, PubMed:8038169). In contrast, a heterotetrameric channel formed by KCNA1 and KCNA4 shows rapid inactivation (PubMed:2348860). Regulates neuronal excitability in hippocampus, especially in mossy fibers and medial perforant path axons, preventing neuronal hyperexcitability. Response to toxins that are selective for KCNA1, respectively for KCNA2, suggests that heteromeric potassium channels composed of both KCNA1 and KCNA2 play a role in pacemaking and regulate the output of deep cerebellar nuclear neurons (PubMed:12177193, PubMed:23318870). May function as down-stream effector for G protein-coupled receptors and inhibit GABAergic inputs to basolateral amygdala neurons (PubMed:16306173). May contribute to the regulation of neurotransmitter release, such as gamma-aminobutyric acid (GABA) release (PubMed:17869444). Plays a role in regulating the generation of action potentials and preventing hyperexcitability in myelinated axons of the vagus nerve, and thereby contributes to the regulation of heart contraction (By similarity). Required for normal neuromuscular responses (PubMed:22206926). Regulates the frequency of neuronal action potential firing in response to mechanical stimuli, and plays a role in the perception of pain caused by mechanical stimuli, but does not play a role in the perception of pain due to heat stimuli (By similarity). Required for normal responses to auditory stimuli and precise location of sound sources, but not for sound perception (By similarity). The use of toxins that block specific channels suggest that it contributes to the regulation of the axonal release of the neurotransmitter dopamine (By similarity). Required for normal postnatal brain development and normal proliferation of neuronal precursor cells in the brain (By similarity). Plays a role in the reabsorption of Mg(2+) in the distal convoluted tubules in the kidney and in magnesium ion homeostasis, probably via its effect on the membrane potential (By similarity).
  catalytic activity: K(+)(in) = K(+)(out) (RHEA:29463)
  subunit: Homotetramer and heterotetramer with other channel-forming alpha subunits, such as KCNA2, KCNA4, KCNA5, KCNA6 and KCNA7 (PubMed:10884227, PubMed:10896669). Channel activity is regulated by interaction with the beta subunits KCNAB1 and KCNAB2 (PubMed:12114518, PubMed:9334400). Identified in a complex with KCNA2 and KCNAB2 (PubMed:10884227, PubMed:10896669, PubMed:11086297, PubMed:23318870). Interacts (via C-terminus) with the PDZ domains of DLG1, DLG2 and DLG4. Interacts with LGI1 within a complex containing LGI1, KCNA4 and KCNAB1. Interacts (via cytoplasmic N-terminal domain) with KCNRG; this inhibits channel activity (By similarity). Interacts with ANK3; this inhibits channel activity (By similarity). Interacts (via N-terminus) with STX1A; this promotes channel inactivation (PubMed:12114518). Interacts (via N-terminus) with the heterodimer formed by GNB1 and GNG2; this promotes channel inactivation (PubMed:12114518). Can interact simultaneously with STX1A and the heterodimer formed by GNB1 and GNG2 (PubMed:12114518). Interacts with ADAM11 (By similarity).
• MiR-21-5p alleviates trigeminal neuralgia in rats through down-regulation of voltage-gated potassium channel Kv1.1.
  Zhou, Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences 2024
  • GeneRIF: MiR-21-5p alleviates trigeminal neuralgia in rats through down-regulation of voltage-gated potassium channel Kv1.1.
• Key role for Kv11.1 (ether-a-go-go related gene) channels in rat bladder contractility.
  Barrese, Physiological reports 2023
  • GeneRIF: Key role for Kv11.1 (ether-a-go-go related gene) channels in rat bladder contractility.
• Ion Channel Modeling beyond State of the Art: A Comparison with a System Theory-Based Model of the Shaker-Related Voltage-Gated Potassium Channel Kv1.1.
  Langthaler, Cells 2022
  • GeneRIF: Ion Channel Modeling beyond State of the Art: A Comparison with a System Theory-Based Model of the Shaker-Related Voltage-Gated Potassium Channel Kv1.1.
• Rapamycin reveals an mTOR-independent repression of Kv1.1 expression during epileptogenesis.
  Sosanya, Neurobiology of disease 2015 (PubMed)
  • GeneRIF: This stuidy demonstrated that kainic-acid induced status epilepticus there are two phases of Kv1.1 repression: (1) an initial mTOR-dependent repression of Kv1.1 that is followed by (2) a miR-129-5p persistent reduction of Kv1.1.
• Complex N-Glycans Influence the Spatial Arrangement of Voltage Gated Potassium Channels in Membranes of Neuronal-Derived Cells.
  Hall, PloS one 2015
  • GeneRIF: Our findings provide direct evidence that N-glycans of Kv3.1 splice variants contribute to the placement of these glycoproteins in the plasma membrane of neuronal-derived cells while those of Kv1.1 were absent.
• Hydrogen sulfide increases excitability through suppression of sustained potassium channel currents of rat trigeminal ganglion neurons.
  Feng, Molecular pain 2013
  • GeneRIF: Endogenous H2S generating enzyme cystathionine-beta-synthetase was co-localized well with Kv1.1 and Kv1.4 in trigeminal ganglion neurons.
• Pharmacological characteristics of Kv1.1- and Kv1.2-containing channels are influenced by the stoichiometry and positioning of their α subunits.
  Al-Sabi, The Biochemical journal 2013 (PubMed)
  • GeneRIF: This study supports the possibility of alpha subunits being precisely arranged in Kv1 channels, rather than being randomly assembled.
• Degradation of high affinity HuD targets releases Kv1.1 mRNA from miR-129 repression by mTORC1.
  Sosanya, The Journal of cell biology 2013
  • GeneRIF: Overexpression of miR-129 represses Kv1.1 mRNA translation when mTORC1 kinase is inhibited.
• Kcna1-mutant rats dominantly display myokymia, neuromyotonia and spontaneous epileptic seizures.
  Ishida, Brain research 2012 (PubMed)
  • GeneRIF: This study demonistrated that Kcna1-mutant rats dominantly display myokymia, neuromyotonia and spontaneous epileptic seizures.
• Electro-pharmacological profile of a mitochondrial inner membrane big-potassium channel from rat brain.
  Fahanik-Babaei, Biochimica et biophysica acta 2011 (PubMed)
  • GeneRIF: Electro-pharmacological profile of a mitochondrial inner membrane big-potassium channel from rat brain
• RNA editing of Kv1.1 channels may account for reduced ictogenic potential of 4-aminopyridine in chronic epileptic rats.
  Streit, Epilepsia 2011 (PubMed)
  • GeneRIF: Our data suggest that altered Kv1.1(I400V) RNA editing contributes to the reduced ictogenic potential of 4-AP in chronic epileptic rats.
• Evidence for presence and functional effects of Kv1.1 channels in β-cells: general survey and results from mceph/mceph mice.
  Ma, PloS one 2011
  • GeneRIF: Kv1.1 channels are expressed in the beta-cells of several species
• In vitro and intrathecal siRNA mediated K(V)1.1 knock-down in primary sensory neurons.
  Baker, Molecular and cellular neurosciences 2011
  • GeneRIF: Our study provides evidence that K(V)1.1 contributes to the control of peripheral sensory nerve excitability
• Kv1.1 and Kv1.3 channels contribute to the degeneration of retinal ganglion cells after optic nerve transection in vivo.
  Koeberle, Cell death and differentiation 2010 (PubMed)
  • GeneRIF: Kv1.1 potassium channels apparently contribute to cell-autonomous death of retinal ganglion cells through different components of the apoptotic machinery.
• Arrangement of Kv1 alpha subunits dictates sensitivity to tetraethylammonium.
  Al-Sabi, The Journal of general physiology 2010
  • GeneRIF: Kv1.1 or 1.2 homomers and their concatenated forms between the pairs of adjacently and diagonally arranged heterotetramers show differential sensitivity to tetraethylammonium.
• Kv1.1 expression in microglia regulates production and release of proinflammatory cytokines, endothelins and nitric oxide.
  Wu, Neuroscience 2009 (PubMed)
  • GeneRIF: This study has revealed the specific expression of Kv1.1 in microglia AND was localized in the microglia in the rat brain between postnatal day 1 and day 10 then progressively reduced with age and was hardly detected at day 14 and day 21 in microglia.
• Contribution of Kv channel subunits to glutamate-induced apoptosis in cultured rat hippocampal neurons.
  Shen, Journal of neuroscience research 2009 (PubMed)
  • GeneRIF: alterations of Kv1.1 and Kv2.1 might contribute to glutamate-induced toxicity in hippocampal neurons
• Expression and localization of Kv1 potassium channels in rat dorsal and ventral spinal roots.
  Utsunomiya, Experimental neurology 2008 (PubMed)
  • GeneRIF: The numbers of Kv1.1 channel are higher in DRs than VRs.
• Functional coupling between the Kv1.1 channel and aldoketoreductase Kvbeta1.
  Pan, The Journal of biological chemistry 2008
  • GeneRIF: cofactor oxidation by Kvbeta1 is regulated by membrane potential, presumably via voltage-dependent structural changes in Kv1.1 channels
• Kv 1.1 is associated with neuronal apoptosis and modulated by protein kinase C in the rat cerebellar granule cell.
  Hu, Journal of neurochemistry 2008 (PubMed)
  • GeneRIF: In the rat cerebellar granule cell the protein kinase C pathway promotes neuronal apoptosis through an increase in the levels of expression of Kv1.1 alpha subunit.
• Manipulation of the potassium channel Kv1.1 and its effect on neuronal excitability in rat sensory neurons.
  Chi, Journal of neurophysiology 2007 (PubMed)
  • GeneRIF: Kv1.1 plays an important role in limiting AP firing and that siRNA may be a useful approach to establish the role of specific ion channels in the absence of selective antagonists.
• Mu opioid receptor activation inhibits GABAergic inputs to basolateral amygdala neurons through Kv1.1/1.2 channels.
  Finnegan, Journal of neurophysiology 2006 (PubMed)
  • GeneRIF: study shows that activation of presynaptic mu opioid receptors primarily attenuates GABAergic synaptic inputs to central nucleus of the amygdala-projecting neurons in the basolateral amygdala through a signaling mechanism involving Kv1.1 & Kv1.2 channels
• Involvement of Kv1.1 and Nav1.5 in proliferation of gastric epithelial cells.
  Wu, Journal of cellular physiology 2006 (PubMed)
  • GeneRIF: Kv1.1 is expressed in gastric epithelial cells and function as growth modulators.
• Two opposing roles of 4-AP-sensitive K+ current in initiation and invasion of spikes in rat mesencephalic trigeminal neurons.
  Saito, Journal of neurophysiology 2006 (PubMed)
  • GeneRIF: Consistent with these findings, strong immunoreactivities for Kv1.1 and Kv1.6, among 4-AP-sensitive and low-voltage-activated Kv1 family examined, were detected in the soma but not in the stem axon of MTN neurons.
• Activity- and mTOR-dependent suppression of Kv1.1 channel mRNA translation in dendrites.
  Raab-Graham, Science (New York, N.Y.) 2006 (PubMed)
  • GeneRIF: inhibition of mTOR increased Kv1.1 in hippocampal neurons & promoted Kv1.1 surface expression on dendrites without altering its axonal expression; synaptic excitation may cause local suppression of dendritic Kv1 channels by reducing their local synthesis
• Age-related changes in the distribution of Kv1.1 and Kv3.1 in rat cochlear nuclei.
  Jung, Neurological research 2005 (PubMed)
  • GeneRIF: Age-related changes in the distribution of Kv1.1 in auditory neuron rat cochlear nuclei.
• Developmental regulation and adult maintenance of potassium channel proteins (Kv 1.1 and Kv 1.2) in the cochlear nucleus of the rat.
  Caminos, Brain research 2005 (PubMed)
  • GeneRIF: Kv 1.1 was found in cochlear nucleus neuronal cell bodies at birth and postnatal day 21 through adulthood, labeling for potassium channel was in axonal processes, whereas the number of cell bodies labeled for Kv 1.1 decreased.
• Kv1.1 and Kv1.3 channels contribute to the delayed-rectifying K+ conductance in rat choroid plexus epithelial cells.
  Speake, American journal of physiology. Cell physiology 2004 (PubMed)
  • GeneRIF: Kv1.1 and Kv1.3 channels make a significant contribution to K+ efflux at the apical membrane of the choroid plexus.
• Glycosylation affects rat Kv1.1 potassium channel gating by a combined surface potential and cooperative subunit interaction mechanism.
  Watanabe, The Journal of physiology 2003
  • GeneRIF: N-glycosylation affected gating properties both by altering surface potential sensed by the channel's activation gating machinery and by modifying conformational changes regulating cooperative subunit interactions during activation and inactivation
• KCNE4 is an inhibitory subunit to Kv1.1 and Kv1.3 potassium channels.
  Grunnet, Biophysical journal 2003
  • GeneRIF: KCNE4 beta-subunit has a drastic inhibitory effect on currents generated by Kv1.1 and Kv1.3 potassium channels
• Kv1 potassium channel C-terminus constant HRETE region: arginine substitution affects surface protein level and conductance level of subfamily members differentially.
  Zhu, Molecular membrane biology (PubMed)
  • GeneRIF: Here we investigated the role of a highly conserved cytoplasmic C-terminal charged region of five amino acids (HRETE) of the S6 transmembrane domain in the protein and conductance expression of Kv1.1, Kv1.2, and Kv1.4 channels.
• Blockade of T-lymphocyte KCa3.1 and Kv1.3 channels as novel immunosuppression strategy to prevent kidney allograft rejection.
  Grgic, Transplantation proceedings
  • GeneRIF: Selective blockade of T-lymphocyte K(Ca)3.1 and K(v)1.3 channels may represent a novel alternative therapy for prevention of kidney allograft rejection.
• Episodic ataxia type 1 mutations differentially affect neuronal excitability and transmitter release.
  Heeroma, Disease models & mechanisms
  • GeneRIF: mutations in KCNA1 increase neurotransmitter release in episodic ataxia type 1
• Intracellular hemin is a potent inhibitor of the voltage-gated potassium channel Kv10.1.
  Sahoo, Scientific reports 2022
  • “...49 ( KCNH 2-S620T, here referred to as Kv11.1-ni), Kcna 1 (rat Kv1.1, acc. no. P10499), and KCNA 5 (human Kv1.5, acc. no. P22460). Kv10.1 channel mutant constructs C541A, H543A, H552V, and 2190 were prepared by using overlap-extension mutagenesis as described previously 26 . We also...”
• Investigating the Neurotoxic Impacts of Arsenic and the Neuroprotective Effects of Dictyophora Polysaccharide Using SWATH-MS-Based Proteomics.
  Zhang, Molecules (Basel, Switzerland) 2022
  • “...D3ZBP3 2.11 a 0.44 a 0.94 40 Potassium voltage-gated channel subfamily A member 1 Kcna1 P10499 2.30 a 0.53 a 1.21 41 Hydroxymethylbilane hydrolyase [cyclizing] Uros Q5XIF2 2.41 a 0.62 a 1.51 42 Long-chain-fatty-acid--CoA ligase 3 Acsl3 Q63151 2.50 a 0.63 a 1.57 43 Uridine-cytidine kinase...”
• Impact of intracellular hemin on N-type inactivation of voltage-gated K⁺ channels
  Coburger, Pflugers Archiv : European journal of physiology 2020
  • “...Kv1.2, Kv1.3 (KCNAB1, Q14722), Kv3.1 (KCNAB3, O43448), and DPP6a from Homo sapiens and Kv1.1 (Kcna1, P10499) and Kv4.2 (Kcnd2, Q63881) from Rattus norvegicus were subcloned into pcDNA3.1. Accession numbers refer to the UniProt database. Mutations were generated using the QuikChange Site-Directed Mutagenesis Kit (Agilent, Waldbronn, Germany)...”
• Membrane Protein Identification in Rodent Brain Tissue Samples and Acute Brain Slices
  Joost, Cells 2019
  • “...7 7 6 Ion Channels Q9Z2L0 Voltage-dependent anion-selective channel protein 1 0 9 12 11 P10499 Potassium voltage-gated channel subfamily A member 1 6 4 1 1 P25122 Potassium voltage-gated channel subfamily C member 1 7 4 3 3 P04775 Sodium channel protein type 2 subunit...”
• Identification and characterization of the BRI2 interactome in the brain
  Martins, Scientific reports 2018
  • “...Atp2b2 Plasma membrane calcium-transporting ATPase 2 CC Q64568 Atp2b3 Plasma membrane calcium-transporting ATPase 3 HP P10499 Kcna1 Potassium voltage-gated channel subfamily A member 1 CC Q6MG82 Prrt1 Proline-rich transmembrane protein 1 HP O88778 Bsn Protein bassoon CC, CB P63319 Prkcg Protein kinase C gamma type CC,...”
• Localization of Kv1.3 channels in presynaptic terminals of brainstem auditory neurons.
  Gazula, The Journal of comparative neurology 2010
  • “...440-4HK-42 Synthetic peptide amino acids 458476 C terminus of rat Kv 1.1 (EEDMNNSIAHYRQANIRTG; accession number P10499) NeuroMab 1: 100 Kv 1.2 Ms 75-008 clone K14/16 413-7RR-30 Antibody produced against bacterially-expressed GST-fusion protein corresponding to amino acids 428499 of rat heart Kv 1.2 Epitope mapped to within...”

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.