PaperBLAST

Full List of Papers Linked to P17710

HXK1_MOUSE / P17710 Hexokinase-1; Hexokinase type I; HK I; Hexokinase, tumor isozyme; EC 2.7.1.1 from Mus musculus (Mouse) (see 5 papers)
P17710 hexokinase (EC 2.7.1.1) from Mus musculus (see paper)

• function: Catalyzes the phosphorylation of various hexoses, such as D- glucose, D-glucosamine, D-fructose, D-mannose and 2-deoxy-D-glucose, to hexose 6-phosphate (D-glucose 6-phosphate, D-glucosamine 6-phosphate, D-fructose 6-phosphate, D-mannose 6-phosphate and 2-deoxy-D-glucose 6- phosphate, respectively). Does not phosphorylate N-acetyl-D-glucosamine (By similarity). Mediates the initial step of glycolysis by catalyzing phosphorylation of D-glucose to D-glucose 6-phosphate (By similarity). Involved in innate immunity and inflammation by acting as a pattern recognition receptor for bacterial peptidoglycan. When released in the cytosol, N-acetyl-D-glucosamine component of bacterial peptidoglycan inhibits the hexokinase activity of HK1 and causes its dissociation from mitochondrial outer membrane, thereby activating the NLRP3 inflammasome (PubMed:27374331).
  catalytic activity: a D-hexose + ATP = a D-hexose 6-phosphate + ADP + H(+) (RHEA:22740)
  catalytic activity: D-fructose + ATP = D-fructose 6-phosphate + ADP + H(+) (RHEA:16125)
  catalytic activity: D-glucose + ATP = D-glucose 6-phosphate + ADP + H(+) (RHEA:17825)
  catalytic activity: D-mannose + ATP = D-mannose 6-phosphate + ADP + H(+) (RHEA:11028)
  catalytic activity: D-glucosamine + ATP = D-glucosamine 6-phosphate + ADP + H(+) (RHEA:10948)
  subunit: Monomer (By similarity). Interacts with RABL2/RABL2A; binds preferentially to GTP-bound RABL2 (PubMed:23055941). Interacts with VDAC1. The HK1-VDAC1 complex interacts with ATF2 (By similarity). Interacts (via N-terminal spermatogenic cell-specific region) with PFKM isoform 2 and isoform 3 (via C-terminus) (PubMed:19889946). Interacts with SMAD5 (By similarity).
• Proteomic reference map for sarcopenia research: mass spectrometric identification of key muscle proteins of organelles, cellular signaling, bioenergetic metabolism and molecular chaperoning
  Dowling, European journal of translational myology 2024
  • “...Protein name Gene Peptides Coverage (%) Molecular mass (kDa) (i) Glycolysis, gluconeogenesis and glycogen metabolism P17710 Hexokinase-1 Hk1 19 21.5 108.3 O08528 Hexokinase-2 Hk2 32 43.6 102.5 P47857 Phosphofructokinase, muscle Pfkm 32 54.6 85.3 P05064 Fructose-bisphosphate aldolase ALDOA Aldoa 37 89.3 39.4 P17751 Triosephosphate isomerase Tpi1...”
• Abnormal Regulation of Mitochondrial Sphingolipids during Aging and Alzheimer's Disease.
  Crivelli, ASN neuro 2024
  • “...of the following proteins: Q9D3D9, P02535, Q9DC61, P26645, Q99KE1, Q8VEM8, Q9Z1P6, P63040, Q91ZZ3, P19783, and P17710 which were analyzed for gene enrichment ( Figure 3B ). The main function of the individual proteins is reported in Supplementary Table 2 . The results of the analysis highlighted...”
• Proteomic Analysis Identifies Multiple Mechanisms of 5-Fluorouracil-Induced Gut Mucositis in Mice.
  Ivanov, Cancers 2024
  • “...Glutamate dehydrogenase 1, mitochondrial P26443 Glud1 2.0 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 P47856 Gfpt1 5.9 Hexokinase-1 P17710 Hk1 2.8 Hydroxymethylglutaryl-CoA synthase, mitochondrial P54869 Hmgcs2 8.6 Isocitrate dehydrogenase [NADP] cytoplasmic O88844 Idh1 2.5 Isocitrate dehydrogenase [NADP], mitochondrial P54071 Idh2 2.6 N-acetylneuraminic acid synthase (sialic acid synthase) Q99J77 Nans...”
• Micro-RNA and Proteomic Profiles of Plasma-Derived Exosomes from Irradiated Mice Reveal Molecular Changes Preventing Apoptosis in Neonatal Cerebellum.
  Pazzaglia, International journal of molecular sciences 2022
  • “...0.204 Q6ZWV3 60S ribosomal protein L10 Rpl10 0.210 P62267 40S ribosomal protein S23 Rps23 0.244 P17710 Hexokinase-1 Hk1 5.598 P19783 Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Cox4i1 6.534 Q64521 Glycerol-3-phosphate dehydrogenase, mitochondrial Gpd2 6.570 Q64314 Hematopoietic progenitor cell antigen CD34 Cd34 8.780 Q9Z126 Platelet...”
• Effects of semaglutide on vascular structure and proteomics in high-fat diet-induced obese mice.
  Yue, Frontiers in endocrinology 2022
  • “...regulatory subunit 1 Psmd1 0.8788 1.1211 Q8R0G9 Nuclear pore complex protein Nup133 Nup133 0.8849 1.1136 P17710 Hexokinase-1 Hk1 1.1147 0.9062 Q91VK4 Integral membrane protein 2C Itm2c 1.1441 0.8824 Q91WP0 Mannan-binding lectin serine protease 2 Masp2 1.1178 0.8794 Q921R8 Solute carrier family 41 member 3 Slc41a3 1.2734...”
• Search for Highly Divergent Tandem Repeats in Amino Acid Sequences
  Rudenko, International journal of molecular sciences 2021
  • “...Below, we present two examples of such sequences from Swiss-Prot. 1. Hexokinase-1 from Mus musculus (P17710; sequence length: 974 amino acids). The enzyme is the first in the glycolysis pathway, where it catalyzes the phosphorylation of hexoses; it consists of two sub-units and is ubiquitously expressed...”
  • “...Multiple alignment of 64-character repeats found in the sequence of Mus musculus hexokinase-1 (P17710). No. Sequence of a Period 1 NMIMMTN..MNK.KN.MTINKNK.NKMNKKNIKMNKKTKNTMKTI.KKKTK.KKNN.IMKKMKNK.NMTM.NNNKNNT 2 NTKITNK..TNK.KM.KNKNN.K..ITMKKTN.KKTINTMMMKMT.MMKKKKININ.IKN.M.N..NMKT.TKKKKNI 3 NMMIMKNKKTKK.TKKMKKNMKK.MMMKTITK.NKKKKKNTNKKN.NNNNK.ITTN.NNT.K.K..KKKK.NKNNKNI 4 NTTKMMK..TKK.TK.TTKMNNK.NNTIKKIK.TTKNKTTKMNTI.TMTKT.MKNK.NKK.M.N..KITM.NKNK.NI 5 NKTKKMK..K.K.KM..NKMTNK.KITKMKNK.TKKNMKMINNNT.KKKKTNTMTKKNNK.M.TKKNMKKKTKNMTTN 6 KNKNMKN..NKK.NI.MNKNKKKKNKKKKKNM.KMTNMKNKMKMN.NKKKT.K.NKI.M.N..MKNI.NMMIMMN 7 KMMKKKTNT.KM.IKKNTNK.NKMKKKN.KNKKKIMKKT.NMMNK.TTNK.NMI.M.K..NMNKKNTKM 8 MMKMNTN..TNK.KM.MTNNNMK.NKMNKKNIKMNKKTKNTMKTI.KKKTK.KKNN.IMK.K.K..KMKM.NKMMMNK 9 TNMNMKI..NKKKTK.NNKNKTT.KITMKKNN.KNTIKTINKKMKKMNKKK.ININ.IKN.M.N..NNKT.NKKKKNI 10 NMKIMKN..TNK.KM.TKKNKKMTKK.MMMTTITK.TKKKKKNTNKKN.NNNNK.ITTK.NNT.K.K..KKKK.NKNNKNI 11...”
• Proteomic Analysis of Cardiac Adaptation to Exercise by High Resolution Mass Spectrometry
  Al-Menhali, Frontiers in molecular biosciences 2021
  • “...mitochondrial Acadm 160.0 5.1 0.0170 Q924X2 Carnitine O-palmitoyltransferase 1, muscle isoform Cpt1b 46.2 3.9 0.0189 P17710 Hexokinase-1 Hk1 33.7 5.5 0.0198 P51881 ADP/ATP translocase 2 Slc25a5 585.8 63.6 0.0200 Q8BH80 Vesicle-associated membrane protein, associated protein B and C Vapb 367.4 41.3 0.0198 Q9D6J6 NADH dehydrogenase [ubiquinone]...”
• PAX2 promotes epithelial ovarian cancer progression involving fatty acid metabolic reprogramming.
  Feng, International journal of oncology 2020
  • “...Slc2a1, Glut-1, Glut1 Solute carrier family 2, facilitated glucose transporter member 1 0.86 - 0.3308 P17710 Hk1 Hexokinase-1 0.91 - 0.1620 O08528 Hk2 Hexokinase-2 0.83 - 0.2196 Q3TRM8 Hk3 Hexokinase-3 NA NA NA Q8VDL4 Adpgk ADP-dependent glucokinase 0.87 - 0.2782 P06745 Gpi Glucose-6-phosphate isomerase 1.05 -...”
• Slow-twitch skeletal muscle defects accompany cardiac dysfunction in transgenic mice with a mutation in the myosin regulatory light chain.
  Kazmierczak, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2019
• Bovine and murine models highlight novel roles for SLC25A46 in mitochondrial dynamics and metabolism, with implications for human and animal health
  Duchesne, PLoS genetics 2017
  • “...P17879 Heat shock 70 kDa protein 1B Hs71b Hspa1b 0,12045145 Down Heat shock protein b31.a1.a1 P17710 Isoform HK1 of Hexokinase-1 Hxk1 Hk1 0,12045145 Down Glucose transport c407.a1.a1 P29341 Polyadenylate-binding protein 1 Pabp1 Pabpc1 0,12045145 Down c176.a1.a1 Q02248 Catenin beta-1 Ctnb1 Ctnnb1 0,13406441 Down b31.a2.a1 P17710 Isoform...”
• Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition
  Mahadevan, eLife 2017
  • “...0.86 X X X GTF2I Q9ESZ8 1.5 0.89 X HELB Q6NVF4 1.5 0.89 X HK1 P17710 1.5 0.89 X X HMCN2 A2AJ76 1.5 0.89 X LGI3 Q8K406 1.5 0.89 X PC Q05920 1.5 0.89 X RAB3IP Q68EF0 1.5 0.89 X UQCR11 Q9CPX8 1.5 0.89 X ATP1A1...”
• Proteomic Analysis of Mitochondria-Enriched Fraction Isolated from the Frontal Cortex and Hippocampus of Apolipoprotein E Knockout Mice Treated with Alda-1, an Activator of Mitochondrial Aldehyde Dehydrogenase (ALDH2).
  Stachowicz, International journal of molecular sciences 2017
  • “...249 1.09 16 Heat shock cognate 71 kDa protein P63017 37 351 1.08 17 Hexokinase-1 P17710 33 246 1.07 18 Spectrin chain, non-erythrocytic 1 Q62261 72 351 1.07 19 ADP/ATP translocase 1 P48962 22 217 1.11 20 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit -1 P62874 12 134...”
• Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics.
  Hadley, eLife 2015
  • “...not enriched V-type proton ATPase 116 kDa subunit a Q9Z1G4 19 0.98 Detected, enriched Hexokinase-1 P17710 18 1.00 Detected, not enriched Heat shock protein HSP 90-alpha P07901 18 0.93 Detected, enriched Ubiquitin thioesterase OTUB1 Q7TQI3 18 0.85 Previously unreported Vesicle-fusing ATPase P46460 17 0.88 Previously unreported...”
• Proteomic characterization of a mouse model of familial Danish dementia.
  Vitale, Journal of biomedicine & biotechnology 2012
  • “...0.049 P28738 Kinesin heavy chain isoform 5C Kif5c 5.84/109 6 8 281 288 1.41 0.047 P17710 Hexokinase-1 Hk1 6.44/108 10 12 407 425 1.27 0.025 Q62108 Disks large homolog 4 Dlg4 5.56/80 3 4 116 890 1.51 0.043 P50516 V-type proton ATPase catalytic subunit A Atp6v1a...”
• Myelin proteomics: molecular anatomy of an insulating sheath.
  Jahn, Molecular neurobiology 2009
  • “...A1 P07901 Hsp90aa1 B,E Heat shock protein 90 kDa B1 P11499 Hsp90ab1 T,E Hexokinase 1 P17710 Hk1 T,E Hexokinase 2 O08528 Hk2 E Ig superfamily member 8, EWI-2 Q8R366 Igsf8 B,S,R,E Internexin , Neurofilament 66 kDa P46660 Ina W,B,V,R,T,E Junctional adhesion molecule C Q9D8B7 Jam3 S,E...”
• iTRAQ analysis of complex proteome alterations in 3xTgAD Alzheimer's mice: understanding the interface between physiology and disease.
  Martin, PloS one 2008
  • “...kinase B 1.77 COF2_MOUSE (P45591) Coflin 1.77 TPM3_MOUSE (P21107) Tropomyosin alpha 3 chain 1.75 HXK1_MOUSE (P17710) Hexokinase 1.75 AT1A4_MOUSE (Q9WV27) Na+/K+ ATPase chain 4 1.75 SYPH_MOUSE (Q62277) Synaptophysin (Major synaptic vesicle protein p38) (BM89 antigen) 1.75 1433E_MOUSE (P62259) 14-3-3 epsilon 1.74 Q8BWN0_MOUSE (Q8BWN0) Adult pancreas islet...”
• Proteomic mapping provides powerful insights into functional myelin biology.
  Taylor, Proceedings of the National Academy of Sciences of the United States of America 2004

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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.