PaperBLAST
PaperBLAST Hits for NP_414592.1 DUF525 domain-containing protein ApaG (Escherichia coli str. K-12 substr. MG1655) (125 a.a., MINSPRVCIQ...)
Show query sequence
>NP_414592.1 DUF525 domain-containing protein ApaG (Escherichia coli str. K-12 substr. MG1655)
MINSPRVCIQVQSVYIEAQSSPDNERYVFAYTVTIRNLGRAPVQLLGRYWLITNGNGRET
EVQGEGVVGVQPLIAPGEEYQYTSGAIIETPLGTMQGHYEMIDENGVPFSIDIPVFRLAV
PTLIH
Running BLASTp...
Found 17 similar proteins in the literature:
ApaG / b0050 DUF525 domain-containing protein ApaG from Escherichia coli K-12 substr. MG1655 (see 5 papers)
NP_414592 DUF525 domain-containing protein ApaG from Escherichia coli str. K-12 substr. MG1655
P62672 Protein ApaG from Escherichia coli (strain K12)
b0050 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
S0049 hypothetical protein from Shigella flexneri 2a str. 2457T
ECs0055 hypothetical protein from Escherichia coli O157:H7 str. Sakai
DR76_RS13325 Co2+/Mg2+ efflux protein ApaG from Escherichia coli ATCC 25922
100% identity, 100% coverage
- Identification of bacterial factors involved in type 1 fimbria expression using an Escherichia coli K12 proteome chip
Chen, Molecular & cellular proteomics : MCP 2014 - “...NP_416335 NP_416680 NP_415195 NC_000913 NP_414786 NP_414592 NP_415912 NP_417164 NP_415785 NP_416249 NP_417399 NP_417573 NP_415468 NP_418508 NP_415858 NP_417776...”
- Knowns and Unknowns of Vitamin B6 Metabolism in Escherichia coli
Tramonti, EcoSal Plus 2021 (secret) - Functional genomics analysis of free fatty acid production under continuous phosphate limiting conditions
Youngquist, Journal of industrial microbiology & biotechnology 2017 - “...2 potassium translocating ATPase, subunit C b4111 proP 8.2 2.7 10 4 proline/glycine betaine transporter b0050 apaG 2.0 1.8 10 2 protein associated with Co2+ and Mg 2+ efflux Pentose phosphate b b1852 zwf 2.4 8.0 10 4 glucose-6-phosphate dehydrogenase b0767 pgl 2.0 4.8 10 2...”
- Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling
Li, BMC genomics 2013 - “...in at least one of our seven samples (Additional file 14 ), and 21 ( b0050, b0137, b1356, b1382, b1419, b1446, b1457, b1607, b1952, b1998, b3471, b3638, b3937, b4325, b4335, b4336, b4593, b4596, b4610, b4615 and b4620 ) of them were expressed in all the seven...”
- Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
King, Applied and environmental microbiology 2010 - “...b0884 ECs5321 ECs0206 ECs3395 ECs0055 ECs2569 b4361 b0210 b2529 b0050 b1859 bcsE (yhjS) yecJ yhcN yheO yaiZ ybeD ydcX yebG yohJ yieP rrmJ yiaU zntR xseA nudE...”
- Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
Jiménez, Genome biology 2003 - “...isomerase rRNA modification and chaperone b0049 Yes* COG0639 T Diadenosine tetraphosphatase rRNA modification and chaperone b0050 No COG2967 P Uncharacterized protein affecting Mg 2+ /Co 2+ transport rRNA modification and chaperone b0051 Yes** COG0030 J 6-m-2-A methyltransferase; put. 16S rRNA methyltransferase rRNA modification and chaperone b0052...”
- A functional update of the Escherichia coli K-12 genome
Serres, Genome biology 2001 - “...solvent tolerance b0201 rrsH n 16S rRNA b0001 ec_G0001 thrL l thr operon leader peptide b0050 ec_0078 apaG o Conserved protein b0081 ec_0123 mraZ o Conserved hypothetical protein b0005 ec_G0005 yaaX o Unknown CDS * Gene product type: c, carrier; e, enzyme; f, factor; h, extrachromosomal...”
- Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
Smulski, Journal of bacteriology 2001 - “...fimA fis fixX flgD b3256 b4015 b4016 b1623 b0111 b0050 b0564 b0469 b0908 b2601 b1704 b3433 b0930 b1597 b3734 b3731 b3732 b3736 b3572 b0778 b1270 b1661 b2155...”
- A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium
Wuyts, Applied microbiology and biotechnology 2015 - “...showed variation among 8 DT1 S . Typhimurium isolates (S0031, S0032, S0036, S0041, S0042, S0043, S0049 and S0050 in Data set S1), which were screened earlier to determine a positive control for the PCR with these markers. For each SNP marker, PCR amplicons were sequenced of...”
- Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
King, Applied and environmental microbiology 2010 - “...and metabolism ECs0969 ECs1601 b1129 b0884 ECs5321 ECs0206 ECs3395 ECs0055 ECs2569 b4361 b0210 b2529 b0050 b1859 bcsE (yhjS) yecJ yhcN yheO yaiZ ybeD ydcX yebG...”
- Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
Hussain, Scientific reports 2017 - “...Iron-enterobactin transporter membrane protein 1.87 0.01 DR76_RS23065 Ferrienterobactin ABC transporter periplasmic binding protein 1.80 0.01 DR76_RS13325 Cobalt transporter 1.54 0.01 DR76_RS12185 Fe3+ dicitrate ABC transporter permease 1.40 0.01 DR76_RS23085 Iron-enterobactin transporter ATP-binding protein 1.42 0.01 DR76_RS12180 Iron ABC transporter 1.24 0.01 DR76_RS12205 fecR Fec operon regulator...”
C5975_08880 Co2+/Mg2+ efflux protein ApaG from Cronobacter sakazakii
83% identity, 100% coverage
- Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains
Jang, Standards in genomic sciences 2018 - “...RND efflux (C5975_02520, Transporter), proteins associated with heavy metal efflux of nickel/cobalt (C5975_13445, RcnB), cobalt/magnesium (C5975_08880, ApaG), and manganese ions (C5975_18840, MntP), sugar efflux (C5975_13720, SetB), and multidrug resistance (MdtA, MdtH, MdtD). There were on average 513, 110, 1520 proteins that were annotated as integrases, transposases,...”
PA0591 hypothetical protein from Pseudomonas aeruginosa PAO1
52% identity, 95% coverage
- The Small RNAs PA2952.1 and PrrH as Regulators of Virulence, Motility, and Iron Metabolism in Pseudomonas aeruginosa
Coleman, Applied and environmental microbiology 2021 (secret) - Pseudomonas aeruginosa cells attached to a surface display a typical proteome early as 20 minutes of incubation
Crouzet, PloS one 2017 - “...difference in attachment ability compared to PAO1 control ( S8 Table ). 3 of them (PA0591, PA0950 and PA3675) presented an increase in the attachment capacity (ratio 1.5 to 1.6). For the others (PA0180, PA2235, PA2864, PA3160 and PA3435) there is a large decrease in attachment...”
- “...a flavodoxin and PA2864 encoding a protein of unknown function. Interestingly, for 3 mutant strains (PA0591, PA0950 and PA3675) a net increase in the attachment capacity was observed (ratio 1.5 to 1.6). No clear function is attributed to these genes but we can hypothesize that these...”
PP0400 apaG protein from Pseudomonas putida KT2440
51% identity, 98% coverage
PFLU5579 hypothetical protein from Pseudomonas fluorescens SBW25
45% identity, 98% coverage
FBX3_MOUSE / Q9DC63 F-box only protein 3 from Mus musculus (Mouse) (see paper)
NP_997598 F-box only protein 3 isoform 1 from Mus musculus
37% identity, 24% coverage
- function: Substrate recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex, SCF(FBXO3), which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity). Mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome (By similarity). In the presence of PML, HIPK2 ubiquitination still occurs, but degradation is prevented (By similarity). PML, HIPK2 and FBXO3 may act synergically to activate p53/TP53-dependent transactivation (By similarity). The SCF(FBXO3) also acts as a regulator of inflammation by mediating ubiquitination and degradation of FBXL2: specifically recognizes FBXL2 phosphorylated at 'Thr-404' and promotes its ubiquitination (PubMed:23542741).
subunit: Part of a SCF (SKP1-cullin-F-box) protein ligase complex SCF(FBXO3) consisting of FBXO3, SKP1, CUL1 and RBX1. Interacts with PML, interaction is direct and takes place either alone or within the SCF complex. - FBXO3 stabilizes USP4 and Twist1 to promote PI3K-mediated breast cancer metastasis.
Xu, PLoS biology 2023 - GeneRIF: FBXO3 stabilizes USP4 and Twist1 to promote PI3K-mediated breast cancer metastasis.
- E3 Ubiquitin Ligase FBXO3 Drives Neuroinflammation to Aggravate Cerebral Ischemia/Reperfusion Injury.
Gao, International journal of molecular sciences 2022 - GeneRIF: E3 Ubiquitin Ligase FBXO3 Drives Neuroinflammation to Aggravate Cerebral Ischemia/Reperfusion Injury.
- FBXO3 Protein Promotes Ubiquitylation and Transcriptional Activity of AIRE (Autoimmune Regulator).
Shao, The Journal of biological chemistry 2016 - GeneRIF: AIRE, which is phosphorylated on two specific residues near its N terminus, then binds to the F-box protein 3 (FBXO3) E3 ubiquitin ligase. In turn, this SCF(FBXO3) (SKP1-CUL1-F box) complex ubiquitylates AIRE, increases its binding to the positive transcription elongation factor b (P-TEFb), and potentiates its transcriptional activity.
- Tocotrienols Prevent the Decline of Learning Ability in High-Fat, High-Sucrose Diet-Fed C57BL/6 Mice
Kato, International journal of molecular sciences 2024 - “...Secretagogin 2.0 * 1.1 0.55 * Q810U5 Coiled-coil domain-containing protein 50 2.1 * 1.7 0.87 Q9DC63 F-box only protein 3 2.1 * 1.0 0.46 * Q80SY4 E3 ubiquitin-protein ligase MIB1 2.2 * 1.2 0.55 * Q64288 Olfactory marker protein 2.5 * 0.86 0.34 * Q61112 45...”
- Proteomic analysis reveals semaglutide impacts lipogenic protein expression in epididymal adipose tissue of obese mice.
Zhu, Frontiers in endocrinology 2023 - “...kDa heat shock protein ATPase homolog 2 Ahsa2 0.801091655 P41242 Megakaryocyte-associated tyrosine-protein kinase Matk 0.568717607 Q9DC63 F-box only protein 3 Fbxo3 0.722183075 P56375 Acylphosphatase-2 Acyp2 0.589639337 Q6TCG2 Membrane progesterone receptor epsilon Paqr9 0.620337924 Q6IME9 Keratin, type II cytoskeletal 72 Krt72 0.562148059 B1AZA5 Transmembrane protein 245 Tmem245...”
- Characterization and Proteomic-Transcriptomic Investigation of Monocarboxylate Transporter 6 Knockout Mice: Evidence of a Potential Role in Glucose and Lipid Metabolism
Jones, Molecular pharmacology 2019 (secret) - Amyloid Precursor Protein (APP) May Act as a Substrate and a Recognition Unit for CRL4CRBN and Stub1 E3 Ligases Facilitating Ubiquitination of Proteins Involved in Presynaptic Functions and Neurodegeneration
Del, The Journal of biological chemistry 2016 - “...Q8CH72 O08759 Q5U430 A2AN08 Q80TP3 Q9WUD1 Q3TCH7 A2A432 Q3U1J4 Q80T85 Q8N7N5 Q9DC63 Q8VDH1 A2RT62 Q8C7D2 64 179 483 42 103 20 55 72 101 213 572 308 35 88 111...”
- “...Usp9x Q3U1J4 Q8C7D2 Q9WUD1 Q3TCH7 P46935 Q7TQI3 P56399 Q02053 O88544 A2RT62 Q9DC63 Q9Z1K5 Q8N7N5 Q9QZM0 A2AN08 P70398 127 51 35 88 103 31 96 118 46 52 55 64 66...”
FBX3_HUMAN / Q9UK99 F-box only protein 3 from Homo sapiens (Human) (see 3 papers)
37% identity, 25% coverage
- function: Substrate recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex, SCF(FBXO3), which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:18809579, PubMed:26037928). Mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome (PubMed:18809579). In the presence of PML, HIPK2 ubiquitination still occurs, but degradation is prevented (PubMed:18809579). PML, HIPK2 and FBXO3 may act synergically to activate p53/TP53-dependent transactivation (PubMed:18809579). The SCF(FBXO3) also acts as a regulator of inflammation by mediating ubiquitination and degradation of FBXL2 in response to lipopolysaccharide (LPS) (PubMed:26037928). The SCF(FBXO3) complex specifically recognizes FBXL2 phosphorylated at 'Thr-404' and promotes its ubiquitination (By similarity).
subunit: Part of a SCF (SKP1-cullin-F-box) protein ligase complex SCF(FBXO3) consisting of FBXO3, SKP1, CUL1 and RBX1 (PubMed:18809579). Interacts with PML, interaction is direct and takes place either alone or within the SCF complex (PubMed:18809579).
subunit: (Microbial infection) Isoform 1 and 2 interact with Rift valley fever virus NSs; this interaction is important for GT2H1 degradation. - Multi-chaperone function modulation and association with cytoskeletal proteins are key features of the function of AIP in the pituitary gland.
Hernández-Ramírez, Oncotarget 2018 - “...) Co-F [ 105 ] P03372 Oestrogen receptor ( ESR1 ) Co-IP [ 106 ] Q9UK99 F-box only protein 3 ( FBXO3 ) Co-IP, AC-MS [ 7 ] P50395 Rab GDP dissociation inhibitor beta ( GDIB ) Co-F [ 107 ] Q14344 Guanine nucleotide-binding protein subunit...”
- “...ILGLLDTHLKTR KFPAGKVPAFEGDDGFCVFESNAIAYYVSNEELR 10 D4ABP9 FBX3_RAT F-box only protein 3 ( Fbxo3 ) 55.4 EEDLDAVEAQIGCKLPDDYR 91 Q9UK99 FBX3_HUMAN F-box only protein 3 ( FBXO3 ) 54.6 ITNAKGDVEEVQGPGVVGEFPIISPGR 11 Q99PF5 FUBP2_RAT Far upstream element-binding protein 2 ( Khsrp ) 74.2 KDAFADAVQR 98 Q92945 FUBP2_HUMAN Far upstream element-binding protein...”
- Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode.
Wang, Nature 2016 - “...Q96KQ7 Q8IX15 Q8WYB5 P19338 Q5H9L4 Q13029 P27797 Q9UER7 Q4LE39 Q9UPS6-2 P39687 P09429 Q9BT43 P17480 Q15911 Q9UK99 Q9Y4B6 Proline-, glutamic acid- and leucine-rich protein 1 Acidic leucine-rich nuclear phosphoprotein 32 family member B Myelin transcription factor 1-like protein Myelin transcription factor 1 Zinc finger and BTB domain-containing...”
- Virulence factor NSs of rift valley fever virus recruits the F-box protein FBXO3 to degrade subunit p62 of general transcription factor TFIIH.
Kainulainen, Journal of virology 2014 - Quantitative proteomics with siRNA screening identifies novel mechanisms of trastuzumab resistance in HER2 amplified breast cancers
Boyer, Molecular & cellular proteomics : MCP 2013 - “...factor Transmembrane protein 165 BT474 SILAC experiment Q6VVX0 Q9UK99 Q9Y6S9 Q8N3P4 Q59H77 CYP2R1 FBXO3 RPS6KL1 VPS8 CCT3 P81605 Q13268 Q15303 P02452 Q13332...”
- SUMOylation of the Forkhead transcription factor FOXL2 promotes its stabilization/activation through transient recruitment to PML bodies.
Georges, PloS one 2011 - “...P38398 + RNF6 Q9Y252 + RBCK1 Q9BYM8 + MDM2 Q00987 + E6AP Q05086 + FBX3/SCF Q9UK99 + CULLIN1 Q13616 + SKP1 P63208 + PLZF Q05516 + UBP7 Q93009 Enzymes involved in post-translational modifications of proteins and described as associated with PML Nuclear Bodies, according to Van...”
D4ABP9 F-box only protein 3 from Rattus norvegicus
37% identity, 24% coverage
XP_006234719 F-box only protein 3 isoform X2 from Rattus norvegicus
37% identity, 28% coverage
PDIP2_HUMAN / Q9Y2S7 Polymerase delta-interacting protein 2; 38 kDa DNA polymerase delta interaction protein; p38 from Homo sapiens (Human) (see 5 papers)
NP_056399 polymerase delta-interacting protein 2 isoform 1 from Homo sapiens
28% identity, 30% coverage
- function: Involved in DNA damage tolerance by regulating translesion synthesis (TLS) of templates carrying DNA damage lesions such as 8oxoG and abasic sites (PubMed:24191025). May act by stimulating activity of DNA polymerases involved in TLS, such as PRIMPOL and polymerase delta (POLD1) (PubMed:24191025, PubMed:26984527).
subunit: Interacts with PCNA and POLD2 (PubMed:12522211). Interacts with SSBP1 (PubMed:16428295). Interacts with PRIMPOL; leading to enhance DNA polymerase activity of PRIMPOL (PubMed:26984527). Interacts with POLH (PubMed:20554254). Interacts with POLD1; leading to stimulate DNA polymerase activity of POLD1 (PubMed:24191025). - Old Passengers as New Drivers: Chromosomal Passenger Proteins Engage in Translesion Synthesis
Falke, Cells 2024 - “...kinase (R/K-X1-3-S/T) [ 38 ]. Briefly, the sequence of human POLDIP2 was obtained from UniProt (Q9Y2S7) and analyzed using PhosphoPICK [ 39 ]. Two possible phosphorylation sites were identified at T216 and T5 ( Table S1 ). As the site scores were not very high, possible...”
- “...(POLDIP2: R2 = 0.99; MBP: R2 = 0.98). ( E ) Three-dimensional model of POLDIP2 (Q9Y2S7) from the AF2 database. ATR phosphorylation sites (S147, S150) are labeled, as well as possible Aurora B phosphorylation sites (T5, T216) according to PhosphoPICK. ( F ) Detail image of...”
- SRCAP is involved in porcine reproductive and respiratory syndrome virus activated Notch signaling pathway.
Ding, Journal of virology 2024 - “...0.045 Y box-binding protein 1; mediates pre-mRNA alternative splicing regulation; binds and stabilizes cytoplasmic mRNA Q9Y2S7 POLDIP2 6 18.5 42.03 7.33 0.026 Polymerase delta-interacting protein 2 O60869 EDF1 17 72.3 16.37 6.94 0.037 Endothelial differentiation-related factor 1; transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG...”
- Protective Effect of Dictyophora Polysaccharides on Sodium Arsenite-Induced Hepatotoxicity: A Proteomics Study.
Hu, Frontiers in pharmacology 2021 - “...chain transacylase E2 DBT P11182 1.33 0.75 1.01 DNA polymerase delta interacting protein 2 POLDIP2 Q9Y2S7 1.22 0.85 1.04 DnaJ homolog subfamily C member 9 DNAJC9 Q8WXX5 0.83 1.10 0.91 Dynein light chain roadblock-type 1 DYNLRB1 Q9NP97 1.08 0.78 0.85 ERO1-like protein alpha ERO1A Q96HE7 0.84...”
- Novel Mechanisms for Heme-dependent Degradation of ALAS1 Protein as a Component of Negative Feedback Regulation of Heme Biosynthesis
Kubota, The Journal of biological chemistry 2016 - “...Q9Y6Y0 Q9NZI8 Q9UHB6 P49006 O00264 Q99453 P30044 Q13310 Q9Y2S7 Q92841 Q15185 Q9P258 Q14257 P49458 O60749 Q9NYL9 Q13509 Q8NFA0 P62987 P16989 O15231 Heme-mediated...”
- Splicing factor 2-associated protein p32 participates in ribosome biogenesis by regulating the binding of Nop52 and fibrillarin to preribosome particles
Yoshikawa, Molecular & cellular proteomics : MCP 2011 - “...binding/replication/repair Q14683 SMC1A_HUMAN P12004 PCNA_HUMAN Q9Y2S7 PDIP2_HUMAN Q9UBB5 MBD2_HUMAN O00255 MEN1_HUMAN P78527 PRKDC_HUMAN P26358 DNMT1_HUMAN...”
- A unique arginine cluster in PolDIP2 enhances nucleotide binding and DNA synthesis by PrimPol
Kasho, Nucleic acids research 2021 - “...binding motif and a proximal Arg-cluster. The amino acid sequences aligned were: Homo sapiens PolDIP2 (NP_056399); Homo sapiens FBxo3 (XP_011518282.1); Labrenzia marina ApaG (POF34899.1); Rhodospirillaceae bacterium ApaG (HBC05999.1); Aestuariispira insulae ApaG (RED46168.1); Alphaproteobacteria bacterium ApaG (OLB70390.1); Escherichia coli ApaG (ART45711.1); Shewanella oneidensis MR-1 ApaG (AAN56626). Region...”
E9PT51 DNA polymerase delta interacting protein 2 from Rattus norvegicus
30% identity, 28% coverage
Q91VA6 Polymerase delta-interacting protein 2 from Mus musculus
NP_080665 polymerase delta-interacting protein 2 precursor from Mus musculus
30% identity, 28% coverage
- Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria
Gnad, Molecular & cellular proteomics : MCP 2010 - “...Q01279 Q60932 Q60932 Q02013 A2APH4 Q9WTQ5 P97315 Q924Z4 Q91VA6 Q8C064 P14602 Q03265 Q9Z1T1 O88587 Q9CQF4 P67778 Q9CRD0 Q63918 P53986 Tsfm Glud1 Pc Hars2 Sntb1...”
- Endothelial Poldip2 regulates sepsis-induced lung injury via Rho pathway activation.
Dolmatova, Cardiovascular research 2022 - GeneRIF: Endothelial Poldip2 regulates sepsis-induced lung injury via Rho pathway activation.
- Myeloid Poldip2 Contributes to the Development of Pulmonary Inflammation by Regulating Neutrophil Adhesion in a Murine Model of Acute Respiratory Distress Syndrome.
Ou, Journal of the American Heart Association 2022 - GeneRIF: Myeloid Poldip2 Contributes to the Development of Pulmonary Inflammation by Regulating Neutrophil Adhesion in a Murine Model of Acute Respiratory Distress Syndrome.
- Poldip2 controls leukocyte infiltration into the ischemic brain by regulating focal adhesion kinase-mediated VCAM-1 induction.
Eidson, Scientific reports 2021 - GeneRIF: Poldip2 controls leukocyte infiltration into the ischemic brain by regulating focal adhesion kinase-mediated VCAM-1 induction.
- Characterization of Poldip2 knockout mice: Avoiding incorrect gene targeting.
Lassègue, PloS one 2021 - GeneRIF: Characterization of Poldip2 knockout mice: Avoiding incorrect gene targeting.
- Mitochondrial Protein Poldip2 (Polymerase Delta Interacting Protein 2) Controls Vascular Smooth Muscle Differentiated Phenotype by O-Linked GlcNAc (N-Acetylglucosamine) Transferase-Dependent Inhibition of a Ubiquitin Proteasome System.
Paredes, Circulation research 2020 - GeneRIF: Preservation of the differentiated phenotype in Poldip2+/- mice inhibits neointima formation after injury. Poldip2 deficiency induces a highly differentiated phenotype in VSMCs through a mechanism that involves regulation of metabolism and proteostasis.
- Poldip2 mediates blood-brain barrier disruption and cerebral edema by inducing AQP4 polarity loss in mouse bacterial meningitis model.
Gao, CNS neuroscience & therapeutics 2020 - GeneRIF: Poldip2 mediates blood-brain barrier disruption and cerebral edema by inducing AQP4 polarity loss in mouse bacterial meningitis model.
- Poldip2 deficiency protects against lung edema and vascular inflammation in a model of acute respiratory distress syndrome.
Forrester, Clinical science (London, England : 1979) 2019 - GeneRIF: Heterozygous deletion of Poldip2 protects against lung edema and vascular inflammation in a model of acute respiratory distress syndrome.
- Hepatic deficiency of Poldip2 in type 2 diabetes dampens lipid and glucose homeostasis.
Jiang, Metabolism: clinical and experimental 2019 (PubMed)- GeneRIF: hepatic dysregulation of Poldip2 may contribute to diabetic dyslipidemia and hyperglycemia
- More
NP_001277074 polymerase delta-interacting protein 2 isoform 2 from Homo sapiens
30% identity, 30% coverage
- Metabolic regulation of the proteasome under hypoxia by Poldip2 controls fibrotic signaling in vascular smooth muscle cells.
Paredes, Free radical biology & medicine 2023 - GeneRIF: Metabolic regulation of the proteasome under hypoxia by Poldip2 controls fibrotic signaling in vascular smooth muscle cells.
- Knockout of AMD-associated gene POLDIP2 reduces mitochondrial superoxide in human retinal pigment epithelial cells.
Nguyen, Aging 2023 - GeneRIF: Knockout of AMD-associated gene POLDIP2 reduces mitochondrial superoxide in human retinal pigment epithelial cells.
- Endothelial Poldip2 regulates sepsis-induced lung injury via Rho pathway activation.
Dolmatova, Cardiovascular research 2022 - GeneRIF: Endothelial Poldip2 regulates sepsis-induced lung injury via Rho pathway activation.
- Poldip2/Nox4 Mediates Lipopolysaccharide-Induced Oxidative Stress and Inflammation in Human Lung Epithelial Cells.
Wang, Mediators of inflammation 2022 - GeneRIF: Poldip2/Nox4 Mediates Lipopolysaccharide-Induced Oxidative Stress and Inflammation in Human Lung Epithelial Cells.
- [PolDIP2 regulates mitochondrial functioning and cellular metabolism].
Andjongo, Medecine sciences : M/S 2021 (PubMed)- GeneRIF: [PolDIP2 regulates mitochondrial functioning and cellular metabolism].", trans "PolDIP2, une proteine cle de la regulation du fonctionnement mitochondrial et du metabolisme cellulaire.
- Crystal structure and molecular dynamics of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability.
Kulik, Protein science : a publication of the Protein Society 2021 - GeneRIF: Crystal structure and molecular dynamics of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability.
- Human Polymerase δ-Interacting Protein 2 (PolDIP2) Inhibits the Formation of Human Tau Oligomers and Fibrils.
Kasho, International journal of molecular sciences 2021 - GeneRIF: Human Polymerase delta-Interacting Protein 2 (PolDIP2) Inhibits the Formation of Human Tau Oligomers and Fibrils.
- Mitochondrial Protein Poldip2 (Polymerase Delta Interacting Protein 2) Controls Vascular Smooth Muscle Differentiated Phenotype by O-Linked GlcNAc (N-Acetylglucosamine) Transferase-Dependent Inhibition of a Ubiquitin Proteasome System.
Paredes, Circulation research 2020 - GeneRIF: Poldip2 deficiency in human aortic vascular smooth muscle in vitro induces the expression of the SRF , myocardin, and MRTFA and dramatically represses KLF4. Poldip2 deficiency upregulates the hexosamine biosynthetic pathway and OGT (O-linked N-acetylglucosamine transferase)-mediated protein O-GlcNAcylation. Poldip2 deficiency induces a highly differentiated phenotype in VSMCs by regulating metabolism and proteostasis.
- More
G3GTP7 Vitronectin from Cricetulus griseus
29% identity, 13% coverage
LOC105134419 F-box protein SKIP16-like from Populus euphratica
28% identity, 23% coverage
- Heterophylly Quantitative Trait Loci Respond to Salt Stress in the Desert Tree Populus euphratica
Fu, Frontiers in plant science 2021 - “...LOC105138604, LOC105129804, LOC105139638, LOC105121124) Kinase activity GO:0016301 0.0009 E3 ubiquitin-protein ligase SHPRH-like (LOC105107433), (LOC105142410, LOC105110458, LOC105134419) Ubiquitin ligase complex GO:0000151 0.0081 WD repeat-containing protein 48 (LOC105110458), (LOC105126665, LOC105126240, LOC105123276, LOC105124653, LOC105115456, LOC105131169, LOC105127854, LOC105110458, LOC105111425, LOC105109520, LOC105130122, LOC105117107, LOC105126350, LOC105112394, LOC105111615, LOC105142410, LOC105130009, LOC105129804, LOC105111272) Regulation...”
LOC100809876 F-box protein SKIP16-like from Glycine max
30% identity, 23% coverage
SKI16_ARATH / Q9LND7 F-box protein SKIP16; SKP1-interacting partner 16 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G06110 SKIP16 (SKP1/ASK-interacting protein 16); protein binding from Arabidopsis thaliana
27% identity, 27% coverage
- function: Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins.
subunit: Part of a SCF (ASK-cullin-F-box) protein ligase complex (By similarity). Interacts with SKP1A/ASK1, SKP1B/ASK2, ASK4, ASK11 and ASK13. - Identification and Validation of Reference Genes for RT-qPCR Analysis in Non-Heading Chinese Cabbage Flowers
Wang, Frontiers in plant science 2016 - “...) KU851930 AT3G13410 TAATAGCACCGTTGGAGTT/CACTGATGAGGATGAGAAGA 110 60.3/60.3 105.6 0.992 SKP1/Ask-interacting protein 16 ( SKIP16 ) KU851931 AT1G06110 CTCAACATCACTACTCCTCTC/AATGGCTAACACGCTTCA 124 61.1/61.1 97.5 0.996 Clathrin adaptor complex ( CAC ) KU851932 AT5G46630 CTGCTCCTTCGTCTACAT/AGTCCATAATCTCGTCTAACA 200 59.9/59.8 97.3 0.996 Protein phosphatase 2A ( PP2A ) KU851933 AT1G10430 ACCGTGGCTACTATTCAG/GCAGTAAGAGGAAGATAATCG 208 59.9/59.7 104.1...”
- Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR
Hu, BMC molecular biology 2009 - “...Glyma08g05480.1 CK768960 Gma.34482 AT1G58050 Nuclear helicase Unwinding of the DNA double-helix SKIP16 Glyma12g05510.1 CD397253 Gma.6079 AT1G06110 SKP1/Ask-Interacting Protein 16 Protein binding MTP Glyma03g29350.2 CF808703 Gma.7635 AT2G41790 Metalloprotease, Insulin degrading enzyme Protein degradation PEPKR1 Glyma10g38460.1 AW396185 Gma.23799 AT1G12580 Phosphoenolpyruvate Carboxylase-Related Kinase 1 Protein phosphorylation TIP41 Glyma20g26690.1 EV263725...”
- “...( At4G34270 ), HDC ( At1G58050 ) and UKN2 ( At4G33380 ); and SKIP16 ( At1G06110 ), MTP ( At2G41790 ), PEPKR1 ( At1G12580 ) and UKN1 ( At3G13410 ), which were identified as potential reference genes via a soybean microarray gene expression analysis [ 37...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.
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.
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.
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.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory