PaperBLAST

PaperBLAST Hits for D4A9G3 Tumor necrosis factor alpha-induced protein 8 (Rattus norvegicus) (212 a.a., MSVAVVPAAV...)

Show query sequence

>D4A9G3 Tumor necrosis factor alpha-induced protein 8 (Rattus norvegicus)
MSVAVVPAAVHPDSMLSEAEEPREVATDVFNSKNLAVQAQKKILGKMVSKSIATTLIDDT
SSEVLDELYRVTKEYTQNKKEAEKVIKNLIKTVIKLAVLHRNNQFNQDELALMEKFKRKV
HQLAMTVVSFHQVEYTFDRNVLSRLLNECRELLHDIIQRHLTAKSHGRVNNVFDHFSDCD
FLAALYNPFGKFKPHLQKLCDGINKMLDEENI

Running BLASTp...

Found 19 similar proteins in the literature:

D4A9G3 Tumor necrosis factor alpha-induced protein 8 from Rattus norvegicus
100% identity, 100% coverage

• Proteome profiling of different rat brain regions reveals the modulatory effect of prolonged maternal separation on proteins involved in cell death-related processes
  Drastichova, Biological research 2021
  • “...expression of Bcl-2 and Bcl-X L and the level of caspase-3 [ 129 131 ] D4A9G3 A0A0G2K2P3 Tnfaip8 TNF- induced protein 8 N S F Tnfaip8 can suppress TNF-mediated apoptosis by inhibiting TNF-induced caspase-8 activity [ 69 ] F1M5H6 D4A6A8 A0A0G2KB61 Tp53bp2 Tumor protein p53-binding protein...”
  • “...phosphorylating of Bad on Ser112 and inhibition of caspase-3 and PARP cleavage [ 153 ] D4A9G3 A0A0G2K2P3 Tnfaip8 TNF- induced protein 8 C C C N Tnfaip8 can suppress TNF-mediated apoptosis by inhibiting TNF-induced caspase-8 activity [ 69 ] C protein detected only in samples of...”

Q921Z5 Tumor necrosis factor alpha-induced protein 8 from Mus musculus
98% identity, 93% coverage

• A preliminary X-ray study of murine Tnfaip8/Oxi-α.
  Lee, International journal of molecular sciences 2014
  • “...forward strand and 5-GTTCTTCTCCTTTGCGCCCCTACAGCTGGCCGAACAGCCAAC-3 for the reverse strand. The gene harboring murine Tnfaip8/Oxi- (UniProt ID: Q921Z5) was amplified by PCR using 80 ng of the plasmid-cDNA [ 3 ] and 50 M of primers with Deep Vent Polymerase (New England Biolabs, Inc., Beverly, MA, USA). The...”

TFIP8_HUMAN / O95379 Tumor necrosis factor alpha-induced protein 8; TNF alpha-induced protein 8; Head and neck tumor and metastasis-related protein; MDC-3.13; NF-kappa-B-inducible DED-containing protein; NDED; SCC-S2; TNF-induced protein GG2-1 from Homo sapiens (Human) (see 4 papers)
NP_055165 tumor necrosis factor alpha-induced protein 8 isoform a from Homo sapiens
93% identity, 93% coverage

• function: Acts as a negative mediator of apoptosis and may play a role in tumor progression. Suppresses the TNF-mediated apoptosis by inhibiting caspase-8 activity but not the processing of procaspase-8, subsequently resulting in inhibition of BID cleavage and caspase-3 activation.
• The genomic environment around the Aromatase gene: evolutionary insights
  Castro, BMC evolutionary biology 2005
  • “...intestinalis SSC-S2 ENSANGP00000018260 A. gambiae CG4091 AAF47048 D. melanogaster ci0100140958 (scaffold 92) C. intestinalis A NP_055165 H. sapiens ENSMUSP00000034810 M. musculus ENSGALP00000007631 G. gallus ENSXETP00000044865 X. tropicalis B NP_078851 H. sapiens NP_081482 M. musculus ENSXETP00000017843 X. tropicalis SINFRUP00000149825 F. rubripes GSTENT00011674001 T. nigroviridis C NP_997264 H....”
• Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets.
  Qiu, Clinical proteomics 2023
  • “...b5 type B CYB5B_HUMAN 0.44319756 0.038741469 Q01813 PFKP ATP-dependent 6-phosphofructokinase, platelet type PFKAP_HUMAN 0.445046286 0.030080123 O95379 TNFAIP8 Tumor necrosis factor alpha-induced protein 8 TFIP8_HUMAN 0.456239147 0.003659428 Q8WXF7 ATL1 Atlastin-1 ATLA1_HUMAN 0.4730972 0.001434618 P54920 NAPA Alpha-soluble NSF attachment protein SNAA_HUMAN 0.497840334 0.013526283 Q9NUU6 OTULINL Inactive ubiquitin thioesterase...”
• Blood Proteome Profiling Reveals Biomarkers and Pathway Alterations in Fragile X PM at Risk for Developing FXTAS.
  Zafarullah, International journal of molecular sciences 2023
  • “...C-terminal-binding protein 1 44 Q6DD87 ZNF787 0.52 12.84 0.000149 0.007156 Zinc finger protein 787 45 O95379 TNFAIP8 0.6 13.02 0.000156 0.007156 Tumor necrosis factor alpha-induced protein 8 46 P56279 TCL1A 1.27 13.06 0.000158 0.007156 T-cell leukemia/lymphoma protein 1A 47 Q9H9G7; Q9HCK5; Q9UL18 AGO3; AGO4; AGO1 1.58...”
• PCSK9 Confers Inflammatory Properties to Extracellular Vesicles Released by Vascular Smooth Muscle Cells.
  Greco, International journal of molecular sciences 2022
  • “...5 1.63 Q15050 Ribosome biogenesis regulatory protein homolog 2 2 11.53 2.63 10 6 1.61 O95379 Tumour necrosis factor alpha-induced protein 8 2 2 11.95 0.000177 1.60 P07948 Tyrosine-protein kinase Lyn 3 2 19.58 7.27 10 9 1.58 P31150 Rab GDP dissociation inhibitor alpha 12 4...”
• FYCO1 Increase and Effect of Arimoclomol-Treatment in Human VCP-Pathology.
  Guettsches, Biomedicines 2022
  • “...P02794 Ferritin heavy chain 3.32 0.000 stores iron in a soluble, nontoxic, readily available form O95379 Tumor necrosis factor alphainduced protein 8 3.23 0.004 suppresses the TNFmediated apoptosis by inhibiting caspase8 activity Q8IYM9 E3 ubiquitinprotein ligase TRIM22 2.97 0.003 interferoninduced antiviral protein with E3 ubiquitinprotein ligase...”
• Death Processes in Bovine Theca and Granulosa Cells Modelled and Analysed Using a Systems Biology Approach.
  McEvoy, International journal of molecular sciences 2021
  • “...PRDM5 P55212 CASP6 Q92731 ESR2 O60936 NOL3 P04637 TP53 O95382 MAP3K6 Q13625 TP53BP2 Q96HF1 SFRP2 O95379 TNFAIP8 O75509 TNFRSF21 P49675 STAR O95831 AIFM1 P10721 KIT Q6P589 TNFAIP8L2 Q9UEE5 STK17A O15551 CLDN3 P55210 CASP7 Q9ULY5 CLEC4E P35222 CTNNB1 Q13158 FADD Q8NB16 MLKL Q9NQS1 AVEN Q8WUM4 PDCD6IP P10415...”
• Characterization of Odontogenic Differentiation from Human Dental Pulp Stem Cells Using TMT-Based Proteomic Analysis.
  Xiao, BioMed research international 2020
  • “...CIC Protein capicua homolog 0.684228 0.046815763 Q9H305 CDIP1 Cell death-inducing p53-target protein 1 0.685535 0.041525227 O95379 TNFAIP8 Tumor necrosis factor alpha-induced protein 8 0.689731 0.00960706 # Protein codes from the UniProt database ( http://www.uniprot.org ). FC=fold change. Table 3 The proteins with interaction degrees greater than...”
• Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls.
  Berge, Clinical proteomics 2019
  • “...Replication protein A 14kDa subunit RPA3 0.016781 0.2976 23.4742 0.16891 24.72695 0.38956 86.8 7 0.8 O95379 Tumor necrosis factor alpha-induced protein 8 TNFAIP8 0.016869 0.2251 22.0409 0.1305 23.8998 0.38972 40.4 5 0.8 Q9NY12 H/ACA ribonucleoprotein complex subunit 1 GAR1 0.01728 0.2208 27.6053 0.18001 28.7912 0.21825 29...”
• In-depth PtdIns(3,4,5)P3 signalosome analysis identifies DAPP1 as a negative regulator of GPVI-driven platelet function.
  Durrant, Blood advances 2017
  • “...11 11 2 No O00160 MYO1F Unconventional myosin-If 1.84e+6 13.4 8.3 8 8 2 No O95379 TNFAIP8 Tumor necrosis factor induced protein 8 1.12e+6 0.9 4.0 1 1 2 No Q8WVP5 TNFAIP8L1 Tumor necrosis factor induced protein 8like protein 1/TIPE1 3.18e+5 4.1 14.3 2 2 2...”

XP_006254771 tumor necrosis factor alpha-induced protein 8 isoform X3 from Rattus norvegicus
99% identity, 89% coverage

• MiR-379 relieves myocardial injury after acute myocardial infarction by regulating tumor necrosis factor-α-induced protein 8.
  Dai, Panminerva medica 2022 (PubMed)
  • GeneRIF: MiR-379 relieves myocardial injury after acute myocardial infarction by regulating tumor necrosis factor-alpha-induced protein 8.
• Expression and regulation of a novel identified TNFAIP8 family is associated with diabetic nephropathy.
  Zhang, Biochimica et biophysica acta 2010 (PubMed)
  • GeneRIF: Findings demonstrate that TNFAIP8 is one of critical components of a signal transduction pathway that links mesangial cell proliferation to diabetic renal injury.

NP_001171230 tumor necrosis factor alpha-induced protein 8 isoform 2 from Mus musculus
98% identity, 89% coverage

• TNFAIP8 protein functions as a tumor suppressor in inflammation-associated colorectal tumorigenesis.
  Lou, Cell death & disease 2022
  • GeneRIF: TNFAIP8 protein functions as a tumor suppressor in inflammation-associated colorectal tumorigenesis.
• TNFAIP8 Regulates Intestinal Epithelial Cell Differentiation and May Alter Terminal Differentiation of Secretory Progenitors.
  Hood, Cells 2021
  • GeneRIF: TNFAIP8 Regulates Intestinal Epithelial Cell Differentiation and May Alter Terminal Differentiation of Secretory Progenitors.
• Decoupling tumor cell metastasis from growth by cellular pilot protein TNFAIP8.
  Li, Oncogene 2021
  • GeneRIF: Decoupling tumor cell metastasis from growth by cellular pilot protein TNFAIP8.
• TNFAIP8 Deficiency Exacerbates Acute Graft Versus Host Disease in a Murine Model of Allogeneic Hematopoietic Cell Transplantation.
  Kumari, Transplantation 2020
  • GeneRIF: TNFAIP8 Deficiency Exacerbates Acute Graft Versus Host Disease in a Murine Model of Allogeneic Hematopoietic Cell Transplantation.
• The TIPE Molecular Pilot That Directs Lymphocyte Migration in Health and Inflammation.
  Sun, Scientific reports 2020
  • GeneRIF: The TIPE Molecular Pilot That Directs Lymphocyte Migration in Health and Inflammation.
• TNFAIP8 controls murine intestinal stem cell homeostasis and regeneration by regulating microbiome-induced Akt signaling.
  Goldsmith, Nature communications 2020
  • GeneRIF: TNFAIP8 controls murine intestinal stem cell homeostasis and regeneration by regulating microbiome-induced Akt signaling.
• TNFAIP8 influences the motor function in mice after spinal cord injury (SCI) through meditating inflammation dependent on AKT.
  Xue, Biochemical and biophysical research communications 2020 (PubMed)
  • GeneRIF: TNFAIP8 influences the motor function in mice after spinal cord injury (SCI) through meditating inflammation dependent on AKT.
• Effect of tumor necrosis factor-α-induced protein 8 on the immune response of CD4+ T lymphocytes in mice following acute insult.
  Yu, Molecular medicine reports 2018 (PubMed)
  • GeneRIF: TNFAIP8 expression following CLP may be associated with the pathogenesis of immune dysfunction in splenic T lymphocytes in mice.
• More

5jxdA / Q921Z5 Crystal structure of murine tnfaip8 c165s mutant (see paper)
98% identity, 88% coverage

• Ligand: [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (5jxdA)

NP_001273746 tumor necrosis factor alpha-induced protein 8 isoform d from Homo sapiens
94% identity, 78% coverage

• Tumor Necrosis Factor α-Induced Protein 8-Like 1 Binds to Protein Arginine Methyltransferase 1 to Suppress the Methylation of Signal Transducer and Activator of Transcription 3 and Cell Growth in Oral Squamous Cell Carcinoma.
  Liu, The American journal of pathology 2024 (PubMed)
  • GeneRIF: Tumor Necrosis Factor alpha-Induced Protein 8-Like 1 Binds to Protein Arginine Methyltransferase 1 to Suppress the Methylation of Signal Transducer and Activator of Transcription 3 and Cell Growth in Oral Squamous Cell Carcinoma.
• Kidney tubular epithelial cells control interstitial fibroblast fate by releasing TNFAIP8-encapsulated exosomes.
  Liu, Cell death & disease 2023
  • GeneRIF: Kidney tubular epithelial cells control interstitial fibroblast fate by releasing TNFAIP8-encapsulated exosomes.
• Synovial fluid exosome-derived miR-182-5p alleviates osteoarthritis by downregulating TNFAIP8 and promoting autophagy through LC3 signaling.
  Ji, International immunopharmacology 2023 (PubMed)
  • GeneRIF: Synovial fluid exosome-derived miR-182-5p alleviates osteoarthritis by downregulating TNFAIP8 and promoting autophagy through LC3 signaling.
• TNFAIP8 drives metabolic reprogramming to promote prostate cancer cell proliferation.
  Niture, The international journal of biochemistry & cell biology 2021
  • GeneRIF: TNFAIP8 drives metabolic reprogramming to promote prostate cancer cell proliferation.
• Proteomic Analysis of Plasma sEVs Reveals That TNFAIP8 Is a New Biomarker of Cell Proliferation in Diabetic Retinopathy.
  Xiao, Journal of proteome research 2021 (PubMed)
  • GeneRIF: Proteomic Analysis of Plasma sEVs Reveals That TNFAIP8 Is a New Biomarker of Cell Proliferation in Diabetic Retinopathy.
• TNFAIP8 regulates gastric cancer growth via mTOR-Akt-ULK1 pathway and autophagy signals.
  Chen, Journal of cellular and molecular medicine 2021
  • GeneRIF: TNFAIP8 regulates gastric cancer growth via mTOR-Akt-ULK1 pathway and autophagy signals.
• Current research status of TNFAIP8 in tumours and other inflammatory conditions (Review).
  Hua, International journal of oncology 2021 (PubMed)
  • GeneRIF: Current research status of TNFAIP8 in tumours and other inflammatory conditions (Review).
• Decoupling tumor cell metastasis from growth by cellular pilot protein TNFAIP8.
  Li, Oncogene 2021
  • GeneRIF: Decoupling tumor cell metastasis from growth by cellular pilot protein TNFAIP8.
• More

NP_956626 tumor necrosis factor alpha-induced protein 8-like protein 1 from Danio rerio
68% identity, 87% coverage

• Structural insight into TIPE1 functioning as a lipid transfer protein.
  Cao, Journal of biomolecular structure & dynamics 2023 (PubMed)
  • GeneRIF: Structural insight into TIPE1 functioning as a lipid transfer protein.

TP8L3_HUMAN / Q5GJ75 Tumor necrosis factor alpha-induced protein 8-like protein 3; TNF alpha-induced protein 8-like protein 3; TNFAIP8-like protein 3 from Homo sapiens (Human) (see 2 papers)
NP_997264 tumor necrosis factor alpha-induced protein 8-like protein 3 isoform 1 from Homo sapiens
57% identity, 72% coverage

• function: Acts as a lipid transfer protein. Preferentially captures and shuttles two lipid second messengers, i.e., phosphatidylinositol 4,5- bisphosphate and phosphatidylinositol 3,4,5-trisphosphate and increases their levels in the plasma membrane. Additionally, may also function as a lipid-presenting protein to enhance the activity of the PI3K-AKT and MEK-ERK pathways. May act as a regulator of tumorigenesis through its activation of phospholipid signaling.
• The Tnfaip8-PE complex is a novel upstream effector in the anti-autophagic action of insulin
  Kim, Scientific reports 2017
  • “...), NP_078851 for TIPE2 from Homo sapiens (hTIPE2), NP_001028707 for TIPE3 from Mus musculus (mTIPE3), NP_997264 for TIPE3 from Homo sapiens (hTIPE3). Figure 4 Structural comparison of ( a ) mTnfaip8, ( b ) hTIPE2 and ( c ) hTIPE3. The surface of the protein is...”
• The genomic environment around the Aromatase gene: evolutionary insights
  Castro, BMC evolutionary biology 2005
  • “...Fr Fugu rubripes ; Tn Tetraodon nigroviridis . SSC-S2 The ORF identified in Ensembl as NP_997264 (FLJ41287 protein), presents significant sequence similarity to three other GenBank entries. One of those is a novel tumor necrosis factor- inducible gene, SSC-S2 [ 25 ], which maps to HSA5....”
  • “...(figure 2 ). These are annotated as follows: AP4-E1 [GenBank: NP_031373 ], FLJ41287 (SSC-2SC) [GenBank: NP_997264 ], Collomin [GenBank: NP_861454 ], DMXL2 [GenBank: NP_056078 ], SCGIII [GenBank: NP_037375 ], MGC35274 [GenBank: NP_699205 ], TMOD2 [GenBank: NP_055363 ], and TMOD3 [GenBank: NP_055362 ] (figure 2 ). In...”
• Death Processes in Bovine Theca and Granulosa Cells Modelled and Analysed Using a Systems Biology Approach.
  McEvoy, International journal of molecular sciences 2021
  • “...MLKL Q9NQS1 AVEN Q8WUM4 PDCD6IP P10415 BCL2 Q9UMX3 BOK Q96IZ0 PAWR Q6ZN16 MAP3K15 Q6ZMQ8 AATK Q5GJ75 TNFAIP8L3 P58012 FOXL2 O15304 SIVA1 Q03169 TNFAIP2 P49662 CASP4 Q99683 MAP3K5 P14060 HSD3B1 Q19T08 ECSCR ijms-22-04888-t0A2_Table A2 Table A2 Genes with the highest degree (number of edges) (selected from the...”
• Ulcerative colitis: functional analysis of the in-depth proteome.
  Schniers, Clinical proteomics 2019
  • “...Sulfate transporter SLC26A2 P50443 18.52 0.26 Tumor necrosis factor alpha-induced protein 8-like protein 3 TNFAIP8L3 Q5GJ75 5.42 0.29 Carbonic anhydrase 2 HEL-76;CA2 V9HW21 12.09 0.30 Selenium-binding protein 1 HEL-S-134P;SELENBP1 V9HWG1 15.36 0.33 cAMP-dependent protein kinase inhibitor beta PKIB Q5T0Z6 7.57 0.34 Chloride anion exchanger SLC26A3;DKFZp686P10213 P40879...”

TP8L3_MOUSE / Q3TBL6 Tumor necrosis factor alpha-induced protein 8-like protein 3; TNF alpha-induced protein 8-like protein 3; TNFAIP8-like protein 3 from Mus musculus (Mouse) (see 2 papers)
NP_001028707 tumor necrosis factor alpha-induced protein 8-like protein 3 from Mus musculus
56% identity, 92% coverage

• function: Acts as a lipid transfer protein. Preferentially captures and shuttles two lipid second messengers, i.e., phosphatidylinositol 4,5- bisphosphate and phosphatidylinositol 3,4,5-trisphosphate and increases their levels in the plasma membrane. Additionally, may also function as a lipid-presenting protein to enhance the activity of the PI3K-AKT and MEK-ERK pathways. May act as a regulator of tumorigenesis through its activation of phospholipid signaling.
  disruption phenotype: Deficient mice develop normally during the first 3 months of life under pathogen-free conditions. However, following subcutaneous injection of the carcinogen 3-methylcholanthrene, deficient mice exhibit markedly delayed skin tumor onset and reduced tumor size compared with wild-type mice.
• The Tnfaip8-PE complex is a novel upstream effector in the anti-autophagic action of insulin
  Kim, Scientific reports 2017
  • “...(hTIPE1), EDL38778 for mTIPE2 ( Mus musculus ), NP_078851 for TIPE2 from Homo sapiens (hTIPE2), NP_001028707 for TIPE3 from Mus musculus (mTIPE3), NP_997264 for TIPE3 from Homo sapiens (hTIPE3). Figure 4 Structural comparison of ( a ) mTnfaip8, ( b ) hTIPE2 and ( c )...”
• Identical expression profiling of human and murine TIPE3 protein reveals links to its functions.
  Cui, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society 2015
  • GeneRIF: Tnfaip8l3 expression was almost identical in most organs from human and mice. Tnfaip8l3 is a cytoplasmic protein expressed preferentially in epithelial-derived cells with secretory functions.

8gynA / Q7SZE8 Zebrafish tipe1 strucutre in complex with pe (see paper)
71% identity, 74% coverage

• Ligand: [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (8gynA)

TP8L1_HUMAN / Q8WVP5 Tumor necrosis factor alpha-induced protein 8-like protein 1; TIPE1; TNF alpha-induced protein 8-like protein 1; TNFAIP8-like protein 1; Oxidative stress-regulated gene-beta; Oxy-beta from Homo sapiens (Human) (see 2 papers)
NP_001161414 tumor necrosis factor alpha-induced protein 8-like protein 1 from Homo sapiens
NP_689575 tumor necrosis factor alpha-induced protein 8-like protein 1 from Homo sapiens
XP_011525982 tumor necrosis factor alpha-induced protein 8-like protein 1 isoform X1 from Homo sapiens
56% identity, 87% coverage

• function: Acts as a negative regulator of mTOR activity.
  subunit: Interacts with FBXW5; TNFAIP8L1 competes with TSC2 to bind FBXW5 increasing TSC2 stability by preventing its ubiquitination.
• The Tnfaip8-PE complex is a novel upstream effector in the anti-autophagic action of insulin
  Kim, Scientific reports 2017
  • “...(mTnfaip8), AAH07014 for Tnfaip8 from Homo sapiens (hTnfaip8), BC032199.1 for TIPE1 from Mus musculus (mTIPE1), NP_001161414 for TIPE1 from Homo sapiens (hTIPE1), EDL38778 for mTIPE2 ( Mus musculus ), NP_078851 for TIPE2 from Homo sapiens (hTIPE2), NP_001028707 for TIPE3 from Mus musculus (mTIPE3), NP_997264 for TIPE3...”
• The genomic environment around the Aromatase gene: evolutionary insights
  Castro, BMC evolutionary biology 2005
  • “...G. gallus ENSXETP00000044865 X. tropicalis SINFRUT00000165316 annotated as pseudogene F. rubripes GSTENT00018057001 T. nigroviridis D NP_689575 H. sapiens ENSMUSP00000076961 M. musculus ENSGALP00000006772 G. gallus SINFRUP00000156999 F. rubripes GSTENT00028868001 T. nigroviridis Colmedin CG6867 NP_573262 D. melanogaster COF-2 AY494975 C. elegans unc-122 AY494976 C. elegans COL1 NP_861454 H....”
• In-depth PtdIns(3,4,5)P3 signalosome analysis identifies DAPP1 as a negative regulator of GPVI-driven platelet function.
  Durrant, Blood advances 2017
  • “...O95379 TNFAIP8 Tumor necrosis factor induced protein 8 1.12e+6 0.9 4.0 1 1 2 No Q8WVP5 TNFAIP8L1 Tumor necrosis factor induced protein 8like protein 1/TIPE1 3.18e+5 4.1 14.3 2 2 2 No Q9BPZ7 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1/SIN1 2.93e+5 0.9 2.1 1 1...”
• TIPE1 inhibits the growth of Ewing's sarcoma cells by suppressing Wnt/β-catenin signaling.
  Wang, Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico 2023 (PubMed)
  • GeneRIF: TIPE1 inhibits the growth of Ewing's sarcoma cells by suppressing Wnt/beta-catenin signaling.
• A pan-cancer analysis of TNFAIP8L1 in human tumors.
  Sun, Medicine 2023
  • GeneRIF: A pan-cancer analysis of TNFAIP8L1 in human tumors.
• Phosphoinositide-Binding Protein TIPE1 Promotes Alternative Activation of Macrophages and Tumor Progression via PIP3/Akt/TGFβ Axis.
  Cheng, Cancer research 2022 (PubMed)
  • GeneRIF: Phosphoinositide-Binding Protein TIPE1 Promotes Alternative Activation of Macrophages and Tumor Progression via PIP3/Akt/TGFbeta Axis.
• TIPE1 inhibits osteosarcoma tumorigenesis and progression by regulating PRMT1 mediated STAT3 arginine methylation.
  Yang, Cell death & disease 2022
  • GeneRIF: TIPE1 inhibits osteosarcoma tumorigenesis and progression by regulating PRMT1 mediated STAT3 arginine methylation.
• TNF-α-Induce Protein 8-Like 1 Inhibits Hepatic Steatosis, Inflammation, and Fibrosis by Suppressing Polyubiquitination of Apoptosis Signal-Regulating Kinase 1.
  Wu, Hepatology (Baltimore, Md.) 2021 (PubMed)
  • GeneRIF: TNF-alpha-Induce Protein 8-Like 1 Inhibits Hepatic Steatosis, Inflammation, and Fibrosis by Suppressing Polyubiquitination of Apoptosis Signal-Regulating Kinase 1.
• Human tumor necrosis factor alpha-induced protein eight-like 1 exhibited potent anti-tumor effect through modulation of proliferation, survival, migration and invasion of lung cancer cells.
  Bordoloi, Molecular and cellular biochemistry 2021 (PubMed)
  • GeneRIF: Human tumor necrosis factor alpha-induced protein eight-like 1 exhibited potent anti-tumor effect through modulation of proliferation, survival, migration and invasion of lung cancer cells.
• TIPE1 impairs stemness maintenance in colorectal cancer through directly targeting β-catenin.
  Ye, Carcinogenesis 2020 (PubMed)
  • GeneRIF: TIPE1 impairs stemness maintenance in colorectal cancer through directly targeting beta-catenin.
• TIPE1 accelerates atherogenesis by inducing endothelial dysfunction in response to oxidative stress.
  Shao, Biochimica et biophysica acta. Molecular basis of disease 2020 (PubMed)
  • GeneRIF: Excessive ROS induced by the overexpression of TIPE1 in endothelial cells accelerated the process of atherogenesis.
• More

TP8L1_MOUSE / Q8K288 Tumor necrosis factor alpha-induced protein 8-like protein 1; TIPE1; TNF alpha-induced protein 8-like protein 1; TNFAIP8-like protein 1; Oxidative stress regulated gene-beta; Oxy-beta from Mus musculus (Mouse) (see 3 papers)
NP_079842 tumor necrosis factor alpha-induced protein 8-like protein 1 from Mus musculus
56% identity, 87% coverage

• function: Acts as a negative regulator of mTOR activity.
  subunit: Interacts with FBXW5; TNFAIP8L1 competes with TSC2 to bind FBXW5 increasing TSC2 stability by preventing its ubiquitination.
• TIPE1 limits virus replication by disrupting PKM2/ HIF-1α/ glycolysis feedback loop.
  Ren, Free radical biology & medicine 2024 (PubMed)
  • GeneRIF: TIPE1 limits virus replication by disrupting PKM2/ HIF-1alpha/ glycolysis feedback loop.
• TIPE1 promotes liver regeneration by enhancing ROS-FoxO1 axis mediated autophagy.
  Zhang, The FEBS journal 2023 (PubMed)
  • GeneRIF: TIPE1 promotes liver regeneration by enhancing ROS-FoxO1 axis mediated autophagy.
• Epithelial TIPE1 Protein Guards against Colitis by Inhibiting TNF-α-Mediated Inflammation.
  Lou, Journal of immunology (Baltimore, Md. : 1950) 2023 (PubMed)
  • GeneRIF: Epithelial TIPE1 Protein Guards against Colitis by Inhibiting TNF-alpha-Mediated Inflammation.
• TNF-α-Induce Protein 8-Like 1 Inhibits Hepatic Steatosis, Inflammation, and Fibrosis by Suppressing Polyubiquitination of Apoptosis Signal-Regulating Kinase 1.
  Wu, Hepatology (Baltimore, Md.) 2021 (PubMed)
  • GeneRIF: TNF-alpha-Induce Protein 8-Like 1 Inhibits Hepatic Steatosis, Inflammation, and Fibrosis by Suppressing Polyubiquitination of Apoptosis Signal-Regulating Kinase 1.
• TIPE1 induces apoptosis by negatively regulating Rac1 activation in hepatocellular carcinoma cells.
  Zhang, Oncogene 2015 (PubMed)
  • GeneRIF: TIPE1 induced apoptosis in HCC cells by negatively regulating Rac1 pathway
• The expression of TIPE1 in murine tissues and human cell lines.
  Cui, Molecular immunology 2011 (PubMed)
  • GeneRIF: TIPE1(TNFAIP8-like 1)protein was detected in a variety of tissues such as neurons, brain, hepatocytes, germ cells of female and male reproductive organs, muscular tissues and cells of epithelial origin it was not expressed in mature T or B lymphocytes

TP8L2_HUMAN / Q6P589 Tumor necrosis factor alpha-induced protein 8-like protein 2; TIPE2; TNF alpha-induced protein 8-like protein 2; TNFAIP8-like protein 2; Inflammation factor protein 20 from Homo sapiens (Human) (see 4 papers)
NP_078851 tumor necrosis factor alpha-induced protein 8-like protein 2 from Homo sapiens
56% identity, 86% coverage

• function: Acts as a negative regulator of innate and adaptive immunity by maintaining immune homeostasis (PubMed:27043859). Plays a regulatory role in the Toll-like signaling pathway by determining the strength of LPS-induced signaling and gene expression (PubMed:32188758). Inhibits TCR-mediated T-cell activation and negatively regulate T-cell function to prevent hyperresponsiveness (By similarity). Inhibits also autolysosome formation via negatively modulating MTOR activation by interacting with RAC1 and promoting the disassociation of the RAC1-MTOR complex (PubMed:32460619). Plays an essential role in NK-cell biology by acting as a checkpoint and displaying an expression pattern correlating with NK-cell maturation process and by negatively regulating NK-cell maturation and antitumor immunity (By similarity). Mechanistically, suppresses IL-15-triggered mTOR activity in NK-cells (By similarity).
  subunit: May interact with CASP8; however, such result is unclear since PubMed:19079267 could not reproduce the interaction with CASP8. Interacts with RAC1 (PubMed:32460619).
• Proteomic profiling of oleamide-mediated polarization in a primary human monocyte-derived tumor-associated macrophages (TAMs) model: a functional analysis
  Wisitpongpun, PeerJ 2024
  • “...Q8TBX8 Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma 2.694 0.007376605 P04839 Cytochrome b-245 heavy chain 2.688 0.00097136 Q6P589 Tumor necrosis factor alpha-induced protein 8-like protein 2 (TIPE2) 2.581 3.62855E06 Q16678 Cytochrome P450 1B1 2.449 0.000127442 Q14410 Glycerol kinase 2 (GK 2) 2.440 0.000376778 Identification and prediction of target...”
• Zika Virus Infection of Sertoli Cells Alters Protein Expression Involved in Activated Immune and Antiviral Response Pathways, Carbohydrate Metabolism and Cardiovascular Disease
  Rashid, Viruses 2022
  • “...10 1 Q8TDJ6 DMXL2 DmX-like protein 2 2.21 1.1 10 3 3.02 1.9 10 4 Q6P589 TNFAIP8L2 Tumor necrosis factor alpha-induced protein 8-like protein 2 2.20 1.9 10 4 2.59 6.9 10 4 1.13 2.2 10 1 P18464 HLA-B HLA class I histocompatibility antigen, B-51 alpha...”
• Death Processes in Bovine Theca and Granulosa Cells Modelled and Analysed Using a Systems Biology Approach.
  McEvoy, International journal of molecular sciences 2021
  • “...MAP3K6 Q13625 TP53BP2 Q96HF1 SFRP2 O95379 TNFAIP8 O75509 TNFRSF21 P49675 STAR O95831 AIFM1 P10721 KIT Q6P589 TNFAIP8L2 Q9UEE5 STK17A O15551 CLDN3 P55210 CASP7 Q9ULY5 CLEC4E P35222 CTNNB1 Q13158 FADD Q8NB16 MLKL Q9NQS1 AVEN Q8WUM4 PDCD6IP P10415 BCL2 Q9UMX3 BOK Q96IZ0 PAWR Q6ZN16 MAP3K15 Q6ZMQ8 AATK Q5GJ75...”
• Tumor Necrosis Factor-α-Induced Protein-8-like 2 Transfected Adipose-Derived Stem Cells Regulated the Dysfunction of Monocrotaline Pyrrole-Induced Pulmonary Arterial Smooth Muscle Cells and Pulmonary Arterial Endothelial Cells.
  Li, Journal of cardiovascular pharmacology 2024 (PubMed)
  • GeneRIF: Tumor Necrosis Factor-alpha-Induced Protein-8-like 2 Transfected Adipose-Derived Stem Cells Regulated the Dysfunction of Monocrotaline Pyrrole-Induced Pulmonary Arterial Smooth Muscle Cells and Pulmonary Arterial Endothelial Cells.
• The deubiquitinase OTUD1 deubiquitinates TIPE2 and plays a protective role in sepsis-induced lung injury by targeting TAK1-mediated MAPK and NF-κB signaling.
  Ming, Biochemical pharmacology 2024 (PubMed)
  • GeneRIF: The deubiquitinase OTUD1 deubiquitinates TIPE2 and plays a protective role in sepsis-induced lung injury by targeting TAK1-mediated MAPK and NF-kappaB signaling.
• TIPE2 inhibits the migration and invasion of epithelial ovarian cancer cells by targeting Smad2 to reverse TGF-β1-induced EMT.
  Tang, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2024 (PubMed)
  • GeneRIF: TIPE2 inhibits the migration and invasion of epithelial ovarian cancer cells by targeting Smad2 to reverse TGF-beta1-induced EMT.
• TIPE2 acts as a tumor suppressor and correlates with tumor microenvironment immunity in epithelial ovarian cancer.
  Xu, Aging 2023
  • GeneRIF: TIPE2 acts as a tumor suppressor and correlates with tumor microenvironment immunity in epithelial ovarian cancer.
• TIPE2 sensitizes breast cancer cells to paclitaxel by suppressing drug-induced autophagy and cancer stem cell properties.
  Hu, Human cell 2023 (PubMed)
  • GeneRIF: TIPE2 sensitizes breast cancer cells to paclitaxel by suppressing drug-induced autophagy and cancer stem cell properties.
• TIPE2 regulates the response of BV2 cells to lipopolysaccharide by the crosstalk between PI3K/AKT signaling and microglia M1/M2 polarization.
  Gao, International immunopharmacology 2023 (PubMed)
  • GeneRIF: TIPE2 regulates the response of BV2 cells to lipopolysaccharide by the crosstalk between PI3K/AKT signaling and microglia M1/M2 polarization.
• Research progress of TIPE2 in immune-related diseases.
  Gao, International immunopharmacology 2023 (PubMed)
  • GeneRIF: Research progress of TIPE2 in immune-related diseases.
• TIPE2 ameliorates neuroinflammation and cognitive impairment in sepsis-associated encephalopathy through regulating RhoA/ROCK2-NF-κB signaling pathway.
  Yuan, Biochemical pharmacology 2023 (PubMed)
  • GeneRIF: TIPE2 ameliorates neuroinflammation and cognitive impairment in sepsis-associated encephalopathy through regulating RhoA/ROCK2-NF-kappaB signaling pathway.
• More

XP_013852617 tumor necrosis factor alpha-induced protein 8-like protein 2 isoform X1 from Sus scrofa
55% identity, 86% coverage

• Characterization and transcriptional regulation analysis of the porcine TNFAIP8L2 gene.
  Li, Molecular genetics and genomics : MGG 2010 (PubMed)
  • GeneRIF: Findings provide an important basis for further understanding of porcine TNFAIP8L2 regulation and function in swine.

Q3ZBK5 Tumor necrosis factor alpha-induced protein 8-like protein 2 from Bos taurus
54% identity, 86% coverage

• Comparative proteome analysis revealed the differences in response to both Mycobacterium tuberculosis and Mycobacterium bovis infection of bovine alveolar macrophages.
  Cai, Frontiers in cellular and infection microbiology 2023
  • “...b-245 chaperone 1 1.552 0.034538 mitochondria Q3T100 Microsomal glutathione S-transferase 3 1.838 0.004157 plasma membrane Q3ZBK5 Tumour necrosis factor alpha-induced protein 8-like protein 2 2.805 0.013505 cytoplasm Q6L708 Claudin-1 1.564 0.011168 plasma membrane Q8HXK9 Apoptosis-associated speck-like protein containing a CARD 1.531 0.007273 cytoplasm Q95123 Succinate dehydrogenase...”

TP8L2_MOUSE / Q9D8Y7 Tumor necrosis factor alpha-induced protein 8-like protein 2; TIPE2; TNF alpha-induced protein 8-like protein 2; TNFAIP8-like protein 2 from Mus musculus (Mouse) (see 2 papers)
NP_081482 tumor necrosis factor alpha-induced protein 8-like protein 2 from Mus musculus
XP_006502103 tumor necrosis factor alpha-induced protein 8-like protein 2 isoform X1 from Mus musculus
55% identity, 86% coverage

• function: Acts as a negative regulator of innate and adaptive immunity by maintaining immune homeostasis. Plays a regulatory role in the Toll- like signaling pathway by determining the strength of LPS-induced signaling and gene expression (PubMed:18455983). Inhibits TCR-mediated T-cell activation and negatively regulate T-cell function to prevent hyperresponsiveness (By similarity). Inhibits also autolysosome formation via negatively modulating MTOR activation by interacting with RAC1 and promoting the disassociation of the RAC1-MTOR complex (PubMed:34524845). Plays an essential role in NK-cell biology by acting as a checkpoint and displaying an expression pattern correlating with NK-cell maturation process and by negatively regulating NK-cell maturation and antitumor immunity (By similarity). Mechanistically, suppresses IL-15-triggered mTOR activity in NK-cells (PubMed:34524845).
  subunit: May interact with CASP8; however, such result is unclear since could not reproduce the interaction with CASP8. Interacts with RAC1.
  disruption phenotype: When infected with lymphocytic choriomeningitis virus (LCMV), TIPE2-deficient mice exhibit significantly enhanced CD4(+) and CD8(+) T-cell immune responses compared with WT mice (PubMed:18455983). TIPE2-deficient NK-cells exhibit enhanced activation, cytotoxicity, and IFN-gamma production upon stimulation and enhanced response to IL-15 for maturation (PubMed:34524845).
• The genomic environment around the Aromatase gene: evolutionary insights
  Castro, BMC evolutionary biology 2005
  • “...H. sapiens ENSMUSP00000034810 M. musculus ENSGALP00000007631 G. gallus ENSXETP00000044865 X. tropicalis B NP_078851 H. sapiens NP_081482 M. musculus ENSXETP00000017843 X. tropicalis SINFRUP00000149825 F. rubripes GSTENT00011674001 T. nigroviridis C NP_997264 H. sapiens ENSMUSP00000034810 M. musculus ENSGALP00000007631 G. gallus ENSXETP00000044865 X. tropicalis SINFRUT00000165316 annotated as pseudogene F. rubripes...”
• TIPE2 gene transfer ameliorates aging-associated osteoarthritis in a progeria mouse model by reducing inflammation and cellular senescence.
  Guo, Molecular therapy : the journal of the American Society of Gene Therapy 2024
  • GeneRIF: TIPE2 gene transfer ameliorates aging-associated osteoarthritis in a progeria mouse model by reducing inflammation and cellular senescence.
• TIPE2 knockout reduces myocardial cell damage by inhibiting IFN-γ-mediated ferroptosis.
  Yang, Biochimica et biophysica acta. Molecular basis of disease 2023 (PubMed)
  • GeneRIF: TIPE2 knockout reduces myocardial cell damage by inhibiting IFN-gamma-mediated ferroptosis.
• TIPE2 Promotes Tumor Initiation But Inhibits Tumor Progression in Murine Colitis-Associated Colon Cancer.
  Etwebi, Inflammatory bowel diseases 2022
  • GeneRIF: TIPE2 Promotes Tumor Initiation But Inhibits Tumor Progression in Murine Colitis-Associated Colon Cancer.
• Tumor Necrosis Factor-α-Induced Protein 8-Like 2 Fosters Tumor-Associated Microbiota to Promote the Development of Colorectal Cancer.
  Lou, Cancer immunology research 2022 (PubMed)
  • GeneRIF: Tumor Necrosis Factor-alpha-Induced Protein 8-Like 2 Fosters Tumor-Associated Microbiota to Promote the Development of Colorectal Cancer.
• Tumor Necrosis Factor-α-Induced Protein 8-Like 2 Ameliorates Cardiac Hypertrophy by Targeting TLR4 in Macrophages.
  Yao, Oxidative medicine and cellular longevity 2022
  • GeneRIF: Tumor Necrosis Factor-alpha-Induced Protein 8-Like 2 Ameliorates Cardiac Hypertrophy by Targeting TLR4 in Macrophages.
• TIPE2 attenuates neuroinflammation and brain injury through Bcl-2/Bax/cleaved caspase-3 apoptotic pathways after intracerebral hemorrhage in mice.
  Xia, Brain research bulletin 2022 (PubMed)
  • GeneRIF: TIPE2 attenuates neuroinflammation and brain injury through Bcl-2/Bax/cleaved caspase-3 apoptotic pathways after intracerebral hemorrhage in mice.
• TNFAIP8L2/TIPE2 impairs autolysosome reformation via modulating the RAC1-MTORC1 axis.
  Li, Autophagy 2021
  • GeneRIF: TNFAIP8L2/TIPE2 impairs autolysosome reformation via modulating the RAC1-MTORC1 axis.
• Microarray gene expression profiling provides insights into functions of TIPE2 in HBV-related apoptosis.
  Cui, Molecular immunology 2021 (PubMed)
  • GeneRIF: Microarray gene expression profiling provides insights into functions of TIPE2 in HBV-related apoptosis.
• More

NP_001014061 tumor necrosis factor alpha-induced protein 8-like protein 2 from Rattus norvegicus
55% identity, 86% coverage

• TIPE2 regulates periodontal inflammation by inhibiting NF-κB p65 phosphorylation.
  DU, Journal of applied oral science : revista FOB 2023
  • GeneRIF: TIPE2 regulates periodontal inflammation by inhibiting NF-kappaB p65 phosphorylation.
• Exogenous TIPE2 Inhibit TAK1 to Improve Inflammation and Neuropathic Pain Induced by Sciatic Nerve Injury Through Inactivating NF-κB and JNK.
  Sun, Neurochemical research 2022
  • GeneRIF: Exogenous TIPE2 Inhibit TAK1 to Improve Inflammation and Neuropathic Pain Induced by Sciatic Nerve Injury Through Inactivating NF-kappaB and JNK.
• Expression and regulation of tumor necrosis factor-α-induced protein-8-like 2 is associated with acute lung injury induced by myocardial ischemia reperfusion in diabetic rats.
  Kong, Microvascular research 2020 (PubMed)
  • GeneRIF: Expression and regulation of tumor necrosis factor-alpha-induced protein-8-like 2 is associated with acute lung injury induced by myocardial ischemia reperfusion in diabetic rats.
• Tumor necrosis factor‑α‑induced protein‑8 like 2 regulates lipopolysaccharide‑induced rat rheumatoid arthritis immune responses and is associated with Rac activation and interferon regulatory factor 3 phosphorylation.
  Shi, Molecular medicine reports 2017 (PubMed)
  • GeneRIF: TIPE2 regulates lipopolysaccharide-induced rat rheumatoid arthritis immune responses and is associated with Rac1 activation and IRF3 phosphorylation.
• Protective effect of Xuebijing injection on D-galactosamine- and lipopolysaccharide-induced acute liver injury in rats through the regulation of p38 MAPK, MMP-9 and HO-1 expression by increasing TIPE2 expression.
  Liu, International journal of molecular medicine 2016
  • GeneRIF: Expression of tumor necrosis factor (TNF)alphainduced protein 8-like 2 (TIPE2), matrix metalloproteinase-9 (MMP-9) and heme oxygenase-1 (HO-1) and mitogen-activated protein kinase (MAPK) signaling was modulated by Xuebijing injection (XBJ).

TFP8L_DROME / Q7KVH9 Protein salivary glands marred; Tumor necrosis factor alpha-induced protein 8-like protein; TNF alpha-induced protein 8-like protein from Drosophila melanogaster (Fruit fly) (see paper)
43% identity, 89% coverage

• function: Important for modulating JNK signaling, cytoskeletal remodeling and autophagy in larval salivary glands (PubMed:25836674). During salivary gland development, involved in the positive regulation of the JNK signaling pathway, acting downstream of the TNF ligand egr and upstream of bsk (PubMed:25836674).
  subunit: Interacts with the Ste20-like MAP kinase msn.
  disruption phenotype: Viable and develops to adulthood (PubMed:25836674). However, pupal salivary glands are abnormal with large empty vacuole-like structures, tubulin disorganization, and reduced autophagy flux (PubMed:25836674). Salivary glands appear normal up to the wandering larval stage, but then exhibit a slight increase in overall length until in pupae 23 hours after puparium formation, salivary glands are significantly longer and wider (PubMed:25836674). Salivary gland histolysis occurs but appears to be delayed (PubMed:25836674). In salivary glands, bsk activation and thus JNK signaling appears to be disrupted as nuclear localization of bsk is absent in large areas of the salivary gland tissues (PubMed:25836674).

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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.