PaperBLAST

PaperBLAST Hits for sp|B1V955|RS6_PHYAS Small ribosomal subunit protein bS6 OS=Phytoplasma australiense OX=59748 GN=rpsF PE=3 SV=1 (93 a.a., MKKYEIMYIL...)

Show query sequence

>sp|B1V955|RS6_PHYAS Small ribosomal subunit protein bS6 OS=Phytoplasma australiense OX=59748 GN=rpsF PE=3 SV=1
MKKYEIMYILRPNLDNNEVKKINDHLESVFSKKPSTILEKKEIGLKDLAYPINNHKKGYY
YWFITQTDNEAVLEFNRIVKITEEVIRFIIIKE

Running BLASTp...

Found 56 similar proteins in the literature:

C6ZDG4 Small ribosomal subunit protein bS6 from Staphylococcus xylosus
WP_017723387 30S ribosomal protein S6 from Staphylococcus xylosus
43% identity, 92% coverage

• Azithromycin Inhibits Biofilm Formation by Staphylococcus xylosus and Affects Histidine Biosynthesis Pathway
  Ding, Frontiers in pharmacology 2018
  • “...protein S18 1.11 A0A060MQE3 30S ribosomal protein S11 1.10 C6ZDI5 30S ribosomal protein S1 1.02 C6ZDG4 30S ribosomal protein S6 0.94 A0A060MLE4 30S ribosomal protein S15 0.88 A0A060MFY5 30S ribosomal protein S14 0.84 Table 4 Primers used for real-time PCR in this study. Name Sequence (53)...”
• Proteome Response of Staphylococcus xylosus DSM 20266T to Anaerobiosis and Nitrite Exposure
  Quintieri, Frontiers in microbiology 2018
  • “...n.d. 97 WP_029377923 Amino acid metabolism Glycine C -acetyltransferase Kbl 1.26 0.50 0.93 1.79 6 WP_017723387 Translation 30S ribosomal protein S6 RpsF 1.09 0.34 0.50 1.46 21 WP_042363303 Translation 50S ribosomal protein L10 RplJ 0.97 0.42 0.63 1.52 167 WP_029377464 Transcription Transcription termination protein NusA NusA...”

RS6_BACSU / P21468 Small ribosomal subunit protein bS6; 30S ribosomal protein S6; BS9 from Bacillus subtilis (strain 168) (see 2 papers)
8cduT / P21468 Rnase r bound to a 30s degradation intermediate (main state) (see paper)
BSU40910 30S ribosomal protein S6 from Bacillus subtilis subsp. subtilis str. 168
NP_391971 ribosomal protein S6 (BS9) from Bacillus subtilis subsp. subtilis str. 168
40% identity, 98% coverage

• function: Binds together with bS18 to 16S ribosomal RNA.
  subunit: Part of the 30S ribosomal subunit.
• Ligand: rna (8cduT)
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU28860 BSU01400 BSU16490 BSU01220 BSU29660 BSU01330 BSU40910 BSU01110 BSU01300 BSU01500 BSU01150 BSU01420 BSU01100 BSU01410 BSU01290 BSU16680 BSU15990...”
• Bacterial RNA motif in the 5' UTR of rpsF interacts with an S6:S18 complex.
  Fu, RNA (New York, N.Y.) 2014
  • GeneRIF: rpsF, ssbA, and rpsR are cotranscribed from S6 operon in Bacillus subtilis.
• Microwave supported hydrolysis prepares Bacillus spores for proteomic analysis
  Chen, International journal of mass spectrometry 2019
  • “...B 3494.9 3494.3 ARSTNKLAVPGAESALDQMKYEIAQEFGVQLGA Q81KU1 Small, acid-soluble spore protein B Bacillus subtilis 1480.7 1480.9 DIIRHIVVKEEE P21468 30S ribosomal protein S6 3115.7 3115.5 TILKAKPAAAKGVYVKNVAVTSTMGPGVKVD Q06797 50S ribosomal protein L1 3000.7 2999.9 TILKAKPAAAKGVYVKNVAV TSTMGPGVKV Q06797 50S ribosomal protein L1 1822.1 1822.1 VSEAVALVKKTNTAKFD Q06797 50S ribosomal protein L1 1707.0...”

SERP0044 ribosomal protein S6 from Staphylococcus epidermidis RP62A
39% identity, 95% coverage

• Concentration-Dependent Global Quantitative Proteome Response of Staphylococcus epidermidis RP62A Biofilms to Subinhibitory Tigecycline
  Sung, Cells 2022
  • “...J Arginine--tRNA ligase 1000.00 4.25 55.70 SERP0405 murB fig|176279.9.peg.385 M UDP-N-acetylenolpyruvoylglucosamine reductase 0.00 0.00 1000.00 SERP0044 rpsF fig|176279.9.peg.43 J 30S ribosomal protein S6 1.81 1.09 1.09 SERP0046 rpsR fig|176279.9.peg.45 J 30S ribosomal protein S18 0.00 0.00 1000.00 SERP0518 dltA fig|176279.9.peg.496 Q D-alanine--D-alanyl carrier protein ligase 0.00...”
• Staphylococcus epidermidis SrrAB regulates bacterial growth and biofilm formation differently under oxic and microaerobic conditions
  Wu, Journal of bacteriology 2015
  • “...0.21 0.87 0.33 1.35 0.26 Protein synthesis SERP0044 SERP1832 SERP0186 SERP1807 SERP1818 SERP1822 SERP1828 SERP1831 SERP1821 SERP1824 SERP1815 SERP1826 SERP1820...”

lmo0044 ribosomal protein S6 from Listeria monocytogenes EGD-e
Q725C0 Small ribosomal subunit protein bS6 from Listeria monocytogenes serotype 4b (strain F2365)
38% identity, 95% coverage

• SecA2 Associates with Translating Ribosomes and Contributes to the Secretion of Potent IFN-β Inducing RNAs
  Teubner, International journal of molecular sciences 2022
  • “...chaperone CopZ Function unknown 0.52 0.64 lmo1364 cspL Cold shock protein CspA Transcription 0.47 0.61 lmo0044 rpsF 30S ribosomal protein S6 Translation 0.47 0.61 lmo2608 rpsM 30S ribosomal protein S13 Translation 0.39 0.51 lmo2068 * groEL 60 kDa chaperonin Posttranslational modification. protein turnover. chaperones 0.40 0.50...”
• Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
  Gray, Scientific reports 2021
  • “...LSU ribosomal protein L18p (L5e) lmo2613 fig|1639.4024.peg.282 3.57 rplO J LSU ribosomal protein L15p (L27Ae) lmo0044 fig|1639.4024.peg.808 4.46 rpsF J SSU ribosomal protein S6p *FDR <0.01 log 2 fold change. # Time point. Table 3 ST101 pathways overexpressed in differentially* expressed genes at 24 and 48h...”
• Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenes
  Hu, Applied and environmental microbiology 2007
  • “...2017 by University of California, Berkeley lmo0001 lmo0044 lmo0045 lmo0046 lmo0223 lmo0248 lmo0249 lmo0726 lmo0727 lmo1059 lmo1268 lmo1469 lmo1468 lmo1523...”
• Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
  Srivastava, International journal of peptide research and therapeutics 2021
  • “...0.737 Non-allergen 123 Q71WX8 1.06 Non-allergen 124 Q71WF0 2.159 Non-allergen 125 Q71WN0 1.611 Non-allergen 126 Q725C0 0.638 Non-allergen 127 Q71ZZ5 0.527 Non-allergen 128 Q71ZG8 0.898 Non-allergen 129 Q71ZJ0 1.318 Non-allergen 130 Q71XH4 1.281 Non-allergen 131 Q71WL5 0.848 Non-allergen 132 Q720A8 0.628 Non-allergen 133 Q721Y1 0.988 Non-allergen...”

UH47_03310 30S ribosomal protein S6 from Staphylococcus pseudintermedius
38% identity, 95% coverage

• Carprofen-induced depletion of proton motive force reverses TetK-mediated doxycycline resistance in methicillin-resistant Staphylococcus pseudintermedius
  Magnowska, Scientific reports 2019
  • “...50S ribosomal protein L10 rplJ 2.1 translation UH47_00175 50S ribosomal protein L7/L12 rplL 0.8 translation UH47_03310 30S ribosomal protein S6 rpsF 0.8 translation UH47_05280 50S ribosomal protein L19 0.7 translation UH47_07890 30S ribosomal protein S5 0.8 translation UH47_11830 50S ribosomal protein L25 rplY 1.5 translation UH47_03525...”

8uu8f / A0A7X0WKH5 8uu8f (see paper)
37% identity, 97% coverage

• Ligand: rna (8uu8f)

NP_835129 SSU ribosomal protein S6P from Bacillus cereus ATCC 14579
BC_5476 30S ribosomal protein S6 from Bacillus cereus ATCC 14579
38% identity, 97% coverage

• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...TerD BC_0443 NP_830282 tellurium resistance protein N N 2,7 0,00 0,97 0,064 Translation RpsF BC_5476 NP_835129 30 S ribosomal protein S6 N N 2,3 0,01 2,32 0,073 RpsG BC_0126 NP_830007 30 S ribosomal protein S7 N N 0,566 0,2 1,8 0,01 RpsH BC_0145 NP_830025 30 S...”
• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...0,02 TerD BC_0443 NP_830282 tellurium resistance protein N N 2,7 0,00 0,97 0,064 Translation RpsF BC_5476 NP_835129 30 S ribosomal protein S6 N N 2,3 0,01 2,32 0,073 RpsG BC_0126 NP_830007 30 S ribosomal protein S7 N N 0,566 0,2 1,8 0,01 RpsH BC_0145 NP_830025 30...”

7bgdf / Q2G113 Staphylococcus aureus 30s ribosomal subunit in presence of spermidine (body only)
36% identity, 97% coverage

• Ligand: rna (7bgdf)

Q6GJV3 Small ribosomal subunit protein bS6 from Staphylococcus aureus (strain MRSA252)
Q2FJP8 Small ribosomal subunit protein bS6 from Staphylococcus aureus (strain USA300)
SA0352 30S ribosomal protein S6 from Staphylococcus aureus subsp. aureus N315
SAV0365 30S ribosomal protein S6 from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_00348 ribosomal protein S6 from Staphylococcus aureus subsp. aureus NCTC 8325
SACOL0437 30S ribosomal protein S6 from Staphylococcus aureus subsp. aureus COL
EKM74_RS10450, USA300HOU_RS01935 30S ribosomal protein S6 from Staphylococcus aureus
36% identity, 95% coverage

• Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
  Hiltunen, Microorganisms 2019
  • “...Q6GEI9 30S ribosomal protein S4 Q6GFY8 30S ribosomal protein S5 Q6GEK0 30S ribosomal protein S6 Q6GJV3 30S ribosomal protein S7 Q6GJC2 30S ribosomal protein S8 Q6GEJ7 30S ribosomal protein S9 Q6GEL8 50S ribosomal protein L1 Q6GJD0 50S ribosomal protein L10 Q6GJC9 50S ribosomal protein L11 Q6GJD1...”
• The Spl Serine Proteases Modulate Staphylococcus aureus Protein Production and Virulence in a Rabbit Model of Pneumonia
  Paharik, mSphere 2016
  • “...0.0000026 Q2FEP2 ( RL2_STAA3 ) 50S ribosomal protein L2 RplB Housekeeping, translation 6.00 0.67 0.0002 Q2FJP8 ( RS6_STAA3 ) 30S ribosomal protein s6 RpsF Housekeeping, translation 11.67 1.00 0.000000033 Q2FE84 ( Q2FE84_STAA3 ) Amino acid ABC transporter, amino acid-binding protein SAUSA300_2359 Membrane transporter 33.33 22.00 0.005...”
• sarA-mediated repression of protease production plays a key role in the pathogenesis of Staphylococcus aureus USA300 isolates
  Zielinska, Molecular microbiology 2012
  • “...lukF-PV Panton-Valentine leukocidin, 41 586 591 Q2FIH8 35 kDa lukS-PV Panton-Valentine leukocidin, 31 471 468 Q2FJP8 37 kDa hlgB Gamma-hemolysin component B 15 63 62 Q2FKN3 19 kDa isaB Immunodominant staphylococcal antigen B 6 28 39 Q2FHP4 37 kDa lukD Leukotoxin LukD 3 17 32 Surface...”
• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...rplA 50S ribosomal protein L1 6.1 Translation SA2031 rpsE 30S ribosomal protein S5 8.3 Translation SA0352 rpsF 30S ribosomal protein S6 5.7 Translation SA0497 rplJ 50S ribosomal protein L10 6.5 Translation SA0495 rplK 50S ribosomal protein L11 6.2 Translation SA2017 rplM 50S ribosomal protein L13 9.0...”
• Daptomycin resistance mechanisms in clinically derived Staphylococcus aureus strains assessed by a combined transcriptomics and proteomics approach
  Fischer, The Journal of antimicrobial chemotherapy 2011
  • “...TufA LysRS ProRS SA2048 SA2025 SA1099 SA2041 SAS052 SA2031 SA0352 SA0504 SA0498 SA0506 SA0475 SA1106 SA1528 Asp23 CodY SA1984 SA1098 SA0269 A number of pivotal...”
• The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
  Sharma-Kuinkel, Journal of bacteriology 2009
  • “...SACOL2214 SACOL0591 SACOL2226 SACOL1292 SACOL2230 SACOL2235 SACOL1642 SA0352 SACOL2225 SACOL0590 SACOL0593 SACOL1727 SACOL0958 rplE rplF rplJ rplM rplN rplO...”
• Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives
  Roberts, Journal of bacteriology 2006
  • “...SA0459 SA1067 SA2039 SA2030 SAS042 SAS047 SA1308 SA2031 SA0352 SA0352 SA0504 SA2034 SA2024 SA0503 SA2025 SAS079 SA2038 SA1414 SA0506 SA0506 SA0506 SA0502...”
• Borosilicate bioactive glass synergizing low-dose antibiotic loaded implants to combat bacteria through ATP disruption and oxidative stress to sequentially achieve osseointegration
  Fan, Bioactive materials 2025
  • “...mechanism in S. aureus . Fig. 5 a also indicates that ribosome-related genes, such as SAV0365 , SACOL0584 , SA0497 , and MW0495 , in the B/PMMA group were significantly upregulated in S. aureus . This implies an increased protein expression in response to a destructive...”
• Genome-wide CRISPRi screens for high-throughput fitness quantification and identification of determinants for dalbavancin susceptibility in Staphylococcus aureus
  Liu, mSystems 2024
  • “...n.t. SAOUHSC_01252 rnjB Ribonuclease J2 1.7 0.00436 n.t. SAOUHSC_02740 _02740 Drug transporter 1.5 0.02159 n.t. SAOUHSC_00348 rpsF;ssb;rpsR Ribosomal; ssDNA-bind; ribosomal 2.2 0.04321 0.045 b SAOUHSC_02459 _02459 Unknown 1.3 0.04388 n.t. SAOUHSC_02860 mvaS HMG-CoA synthase 2.2 0.00016 0.06 SAOUHSC_01501 ebpS Cell surface elastin binding protein 2.2 2.52E...”
• Genome-wide CRISPRi screens reveal the essentialome and determinants for susceptibility to dalbavancin inStaphylococcus aureus
  Liu, 2023
• Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin
  Sierra, Nucleic acids research 2020
  • “...[167/UACUUA] n/a rpmH SAOUHSC_03055 50S ribosomal protein L34 [12/UACUUA] Structural constituent of ribosome [GO:0003735] rpsF SAOUHSC_00348 30S ribosomal protein S6 [6/AACAUA] [22/UACAUC] Structural constituent of ribosome [GO:0003735] fusA SAOUHSC_00529 Elongation factor G 2/UACAUG[] [829/UACUUA] GTPase activity [GO:0003924] SAOUHSC_01091 SAOUHSC_01091 SpoU rRNA Methylase family protein [665/UACCUA] []186/UACUUA...”
• Host-inherent variability influences the transcriptional response of Staphylococcus aureus during in vivo infection
  Thänert, Nature communications 2017
  • “...Hypothetical SAOUHSC_00741 nrdI Ribonucleotide reductase stimulatory protein SAOUHSC_01942 splA Serine protease SplA SAOUHSC_00083 sbnI Hypothetical SAOUHSC_00348 rpsF 30S ribosomal protein S6 SAOUHSC_00436 gltD Glutamate synthase subunit beta SAOUHSC_00051 plc 1-phosphatidylinositol phosphodiesterase SAOUHSC_00411.2 psma2 Alpha phenol soluble modulin SAOUHSC_01121 hla Alpha-hemolysin SAOUHSC_00272 Hypothetical SAOUHSC_00801 secG Preprotein translocase...”
• Mode-of-action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus
  Menzel, Antimicrobial agents and chemotherapy 2011
  • “...LexA-regulated genes; upregulated ORFs SACOL0436 SACOL0437 SACOL0823 SACOL0824 SACOL1304 SACOL1374 SACOL1375 SACOL1381 SACOL1382 SACOL1400 SACOL1401 SACOL1986...”
• Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
  Peng, International journal of molecular sciences 2022
  • “...ribosomal protein L9 EKM74_RS07590 114.58 17.68 1144.54 138.16 3.320336 rpmH ; 50S ribosomal protein L34 EKM74_RS10450 236.72 37.3 7542.84 237.11 4.993827 rpsF ; 30S ribosomal protein S6 EKM74_RS10460 55.84 4.69 531.48 99.45 3.250636 rpsR ; 30S ribosomal protein S18 EKM74_RS11530 51.86 16.74 493.86 62.28 3.251456 rpmG...”
• Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA
  Xu, Frontiers in microbiology 2016
  • “...Orotidine-5'-phosphate decarboxylase USA300HOU_RS04905 oppF1 1.58 1.92E-02 Oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein USA300HOU_RS01935 rpsF 1.56 2.29E-02 Ribosomal protein S6 USA300HOU_RS04620 dltA 1.55 2.45E-02 Long-chain-fatty-acidCoA ligase USA300HOU_RS07105 dapA 1.52 4.99E-02 dihydrodipicolinate synthase USA300HOU_RS04635 dltD 1.51 3.00E-02 D-alanine transfer protein DltD USA300HOU_RS07190 1.51 4.86E-02 Nitric-oxide...”

3r3tA / Q81JI2 Crystal structure of 30s ribosomal protein s from bacillus anthracis
38% identity, 98% coverage

• Ligand: calcium ion (3r3tA)

HCW_02210 30S ribosomal protein S6 from Helicobacter cetorum MIT 00-7128
38% identity, 63% coverage

• Sequence divergence and conservation in genomes of Helicobacter cetorum strains from a dolphin and a whale
  Kersulyte, PloS one 2013
  • “...82% None HCD_08395 HEL3870 147 hypothetical HCW_04215, 97% None HCD_08400 HEL3869 340 hypothetical HCW_04205, 92%; HCW_02210, 75% in aa 182299 (127 aa protein) None HCD_08430 HEL3058 812 OMP, HomB, pfam01856 HCW_08600, 54%; HCW_07955, 39%; HCD_03000, 79%; HCD_00325, 47%; HCD_01285, 31% Many, 33% in aa 216812 HCD_08520...”

HP1246 ribosomal protein S6 (rps6) from Helicobacter pylori 26695
37% identity, 65% coverage

• High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins
  Loh, Infection and immunity 2018
  • “...HPB8_786 HP1435 HP1320 HP1319 HP1317 HP1309 HP1286 HP1254 HP1246 HP1245 HP1244 HP1192 HP1163 HP1100 HP0389 HP0549 HP0565 HP0588 0.59 0.60 0.56 0.67 0.68 0.53...”
  • “...in 26695/ J99 genome HP1435 HP1317 HP1426 HP1286 HP1246 HP1245 HP1100 HP0389 HP1412 jhp1408 HP0565 HP0601 HP0630 HP0642 HP0696 HP0731 HP0751 HP0802 HP0809...”
• Lack of stage-specific proteins in coccoid Helicobacter pylori cells
  Bumann, Infection and immunity 2004
  • “...HP0010 HP0109 HP1205 HP0072 HP0561 HP1563 HP1563 HP0390 HP1246 ureA/ureB groEL groEL dnaK tufB ureA fabG tsaA tsaA tagD rps6 Urease alpha subunit/urease beta...”

5myjAF / A2RNZ4 of 70S ribosome from Lactococcus lactis (see paper)
LLNZ_12790 30S ribosomal protein S6 from Lactococcus cremoris subsp. cremoris NZ9000
llmg_2475 30S ribosomal protein S6 from Lactococcus lactis subsp. cremoris MG1363
35% identity, 95% coverage

• Ligand: rna (5myjAF)
• Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
  Gupta, Scientific reports 2020
  • “...16 LLNZ_13155 50S ribosomal protein L13 Translation 17 LLNZ_12245 30S ribosomal protein S14 Translation 18 LLNZ_12790 30S ribosomal protein S6 Translation 19 LLNZ_02805 4-oxalocrotonate tautomerase Benzoate degradation 20 LLNZ_07675 50S ribosomal protein L27 Translation 21 LLNZ_07685 50S ribosomal protein L21 Translation 22 LLNZ_01065 50S ribosomal protein...”
• Mechanisms of Acetoin Toxicity and Adaptive Responses in an Acetoin-Producing Species, Lactococcus lactis
  Cesselin, Applied and environmental microbiology 2021
  • “...*RplI ribosomal protein or RplO Down llmg_2371 or 2366 *RplE ribosomal protein or RplF Down llmg_2475 RpsF (a) 30S ribosomal protein S6 Down llmg_2475 RpsF (b) 30S ribosomal protein S6 Down llmg_2557 RpsG 30S ribosomal protein S7 Down llmg_2284 Frr ribosome recycling factor Down llmg_2429 Tsf...”

P0DE96 Small ribosomal subunit protein bS6 from Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)
34% identity, 96% coverage

• The cytolytic activity of vaginolysin strictly depends on cholesterol and is potentiated by human CD59
  Zilnyte, Toxins 2015
  • “...PFO, perfringolysin; SLO, streptolysin O. UniProt accession numbers: VLY, B2ZUI3; ILY, Q9LCB8; PLY, Q04IN8; SLO, P0DE96; PFO, P0C2E9. Other sequence sources are as follows: INY, ZP_05744302 (NCBI); LLY [ 30 ]. The rationale for proline substitutions was based on the fact that proline lacks the NH-group...”

Q8EKV4 Small ribosomal subunit protein bS6 from Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831)
33% identity, 98% coverage

• Heat shock response in Lactobacillus plantarum
  De, Applied and environmental microbiology 2004 (secret)

Cj1070 30S ribosomal protein S6 from Campylobacter jejuni subsp. jejuni NCTC 11168
35% identity, 74% coverage

• Despite Shared Geography, Campylobacter Isolated from Surface Water Are Genetically Distinct from Campylobacter Isolated from Chickens
  Meinersmann, Microbiology spectrum 2023
  • “...CAMP1231 (Cj1313, pseH , N -acetyltransferase specific for PseC product, UDP-4-amino-4,6-dideoxy-beta- l -AltNAc), and CAMP1808 (Cj1070, rpsF , 30S ribosomal protein S6). Only one isolate (C3I6 from the chicken outgroup, rep21_1_rep(pWBG758) GQ900396 [97% identity] and rep 7a_20_Sep203(pSE1228p02) AE015931 [97% identity]) showed evidence of known plasmids by...”
  • “...differentiation of both water subpopulations from both chicken subpopulations. One was CAMP1808 (also known as Cj1070, 30S ribosomal protein S6). It is difficult to offer any explanation beyond chance for this result, but it is possible that alleles for the subpopulations allowed for better expression of...”
• Application of protein purification methods for the enrichment of a cytotoxin from Campylobacter jejuni
  Gatsos, BMC microbiology 2012
  • “...Proteolysis Cytoplasm 68 3 1 2 39 c 3 c 3 c 5 c A1W057 (Cj1070) 30S ribosomal protein S6 Translation Cytoplasm 226 8 1 8 A1W0G5 (Cj1181c) Elongation factor Ts (tsf) Protein biosynthesis Cytoplasm 201 5 2 10 A1W0K3 (Cj1220) 10 kDa chaperonin (groS) Protein...”
• Culture of Campylobacter jejuni with sodium deoxycholate induces virulence gene expression
  Malik-Kale, Journal of bacteriology 2008
  • “...Cj0987c Cj0989 Cj1006c Cj1028c Cj1038 Cj1053c Cj1056c Cj1070 Cj1071 Cj1079 Cj1103 Cj1180c Cj1181c Cj1191c Cj1201 Cj1204c Cj1212c Cj1217c Cj1223c Cj1224 Cj1242...”

A1W057 Small ribosomal subunit protein bS6 from Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176)
35% identity, 74% coverage

• Application of protein purification methods for the enrichment of a cytotoxin from Campylobacter jejuni
  Gatsos, BMC microbiology 2012
  • “...protein Proteolysis Cytoplasm 68 3 1 2 39 c 3 c 3 c 5 c A1W057 (Cj1070) 30S ribosomal protein S6 Translation Cytoplasm 226 8 1 8 A1W0G5 (Cj1181c) Elongation factor Ts (tsf) Protein biosynthesis Cytoplasm 201 5 2 10 A1W0K3 (Cj1220) 10 kDa chaperonin (groS)...”

SSA_0437 30S ribosomal protein S6, putative from Streptococcus sanguinis SK36
32% identity, 96% coverage

• Involvement of signal peptidase I in Streptococcus sanguinis biofilm formation
  Aynapudi, Microbiology (Reading, England) 2017
  • “...factor IF-2 No SSA_1043 12.99 5.47 Homoserine dehydrogenase No SSA_0636 14.5 6.01 N-(5-phosphoribosyl)anthranilate isomerase No SSA_0437 14.64 23.25 30S ribosomal protein S6 No SSA_0522 48.94 10.91 Putative ethanolamine utilization protein EutM1 No *Score provided by Progenesis software. By default, a score >5 indicates a statistically significant...”

lp_0009 ribosomal protein S6 from Lactobacillus plantarum WCFS1
Q890K2 Small ribosomal subunit protein bS6 from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
32% identity, 92% coverage

• Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts
  Santamaría, Frontiers in microbiology 2019
  • “...( Figure 2 ). Nine of these genes coding for the corresponding ribosomal proteins ( lp_0009 [RPLS6], lp_1033 [RPL3], lp_1034 [RPL4], lp_1035 [RPL23], lp_1036 [RPL2], lp_1038 [RPLS19], lp_1039 [RPL22], lp_1045 [RPL14], lp_1053 [RPS5]), were down-regulated ( Supplementary Table S2 ). In addition, genes required to counter...”
• Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
  Esteban-Torres, Frontiers in microbiology 2017
  • “...RT-qPCR d lp_1880 Hypothetical protein 2.31 0.08 lp_0997 cspC Cold sock protein CspC 1.8 1.01 lp_0009 rpsF 30S ribosomal protein S6 1.48 0.68 lp_2755 Membrane protein 1.34 0.45 lp_2057 ldhD D-lactate dehydrogenase 1.14 0.38 lp_2368 atpF H(+)-transporting two-sector ATPase, B subunit 0.95 3.04 lp_1449 Cell surface...”
  • “...[RPL24], lp_1047 [RPL5], lp_1048 [RPS14], lp_1052 [RPL18], lp_1053 [RPS5], lp_1061 [RPS11]) and six upregulated ( lp_0009 [RPS6], lp_0512 [RPL31], lp_0737 [RPS30A], lp_1636 [RPS16], lp_1973 [RPS21], lp_2126 [RPS20]). In addition, genes coding for cell division proteins [ lp_0542 ( divIC , septum formation initiator) and lp_2272 (...”
• Heat shock response in Lactobacillus plantarum.
  De, Applied and environmental microbiology 2004 (no snippet)

HSISS4_01661 30S ribosomal protein S6 from Streptococcus salivarius
32% identity, 96% coverage

• A Genome-Wide CRISPR Interference Screen Reveals an StkP-Mediated Connection between Cell Wall Integrity and Competence in Streptococcus salivarius
  Knoops, mSystems 2022
  • “...Large subunit ribosomal protein 3.51 4.15 rpsU HSISS4_01396 Small subunit ribosomal protein 1.23 5.40 rpsF HSISS4_01661 Small subunit ribosomal protein 3.81 3.04 rpsE HSISS4_01806 Small subunit ribosomal protein 3.88 2.64 rpsS HSISS4_01819 Small subunit ribosomal protein 3.84 2.90 HSISS4_00271 Ribosomal protein 3.75 2.80 HSISS4_r00031 tRNA Met...”

SPD_1370 ribosomal protein S6 from Streptococcus pneumoniae D39
SP_1541 30S ribosomal protein S6 from Streptococcus pneumoniae TIGR4
32% identity, 96% coverage

• The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
  Yadav, PloS one 2015
  • “...translation release factor activity, codon specific -2.9 (0.03) SPD_1245 (rpsU) ribosomal protein S21 -1.6 (0.05) SPD_1370 (rpsF) ribosomal protein S6 -1.4 (0.03) SPD_0481 ribosomal protein L7A family protein Ribonucleoprotein,Ribosomal protein -1.7 (0.01) SPD_2033 (yfiA) ribosomal subunit interface protein -2.2 (0.006) Fatty acid biosynthetic process SPD_0380 (fabH)...”
• Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
  Jiménez-Munguía, PeerJ 2018
  • “...deacetylase 587 Cytoplasmic TS29 Decreased 4.2 0.03 SP_1128 Enolase 349 Cytoplasmic TS30 Decreased 4.1 0.04 SP_1541 30S ribosomal protein S6 114 Cytoplasmic TS31 Decreased 4.4 0.04 SP_1910 Uncharacterized protein 523 Cytoplasmic Notes. a For increased proteins, the FC was calculated as the treatment/control ratio; for decreased...”
• Copper Chaperone CupA and Zinc Control CopY Regulation of the Pneumococcal cop Operon
  Neubert, mSphere 2017
  • “...17 , 27 29 ). We also chose an unrelated pneumococcal promoter region upstream of SP_1541 as a negative control ( pSP_1541 ). CopY bound to pSP_0727 in a protein and DNA concentration-dependent manner ( Fig.2A ; Fig.S2A and B ). In contrast, no binding to...”
  • “...10 nM cop promoter ( SP_0727 promoter with FAM) or to 10nM negative control ( SP_1541 promoter with FAM). Curve fit to one-site binding (hyperbola) or linear line where no substrate-dependent increase in binding occurred. Data are representative of four individual experiments. Download FIGS4, TIF file,...”

RP039 30S RIBOSOMAL PROTEIN S6 (rpsF) from Rickettsia prowazekii str. Madrid E
36% identity, 76% coverage

• Differential proteomic analysis of Rickettsia prowazekii propagated in diverse host backgrounds
  Tucker, Applied and environmental microbiology 2011
  • “...ISE6 RP365 Enoyl-(acyl carrier protein) reductase SF21 RP039 RP137 RP576 RP653 30S ribosomal protein S6 50S ribosomal protein L1 Protein export...”

STER_1728, STER_RS08450 30S ribosomal protein S6 from Streptococcus thermophilus
32% identity, 96% coverage

• Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome
  Henry, Frontiers in microbiology 2019
  • “...Fus Elongation factor G YP_821097.1 WP_011226574.1 STER_1762 STER_RS08620 RpsF 30S Ribosomal protein S6 YP_821065.1 WP_011681624.1 STER_1728 STER_RS08450 RplA 50S Ribosomal protein L1 YP_821124.1 WP_002946412.1 STER_1797 STER_RS08780 Efp Elongation factor P YP_821054.1 WP_011227545.1 STER_1715 STER_RS08380 InfA Translation initiation factor IF-1 YP_821195.1 WP_001040189.1 STER_1885 STER_RS09235 RpmF 50S Ribosomal...”
  • “...Elongation factor G YP_821097.1 WP_011226574.1 STER_1762 STER_RS08620 RpsF 30S Ribosomal protein S6 YP_821065.1 WP_011681624.1 STER_1728 STER_RS08450 RplA 50S Ribosomal protein L1 YP_821124.1 WP_002946412.1 STER_1797 STER_RS08780 Efp Elongation factor P YP_821054.1 WP_011227545.1 STER_1715 STER_RS08380 InfA Translation initiation factor IF-1 YP_821195.1 WP_001040189.1 STER_1885 STER_RS09235 RpmF 50S Ribosomal protein...”

SYNW2511 30S ribosomal protein S6 from Synechococcus sp. WH 8102
31% identity, 71% coverage

• Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
  Su, Nucleic acids research 2006
  • “...of the nitrate reductase NarB might be regulated by the ferredoxin-NADP reductase PetH (SYNW0751) and SYNW2511. The -factors RpoD (SYNW2496) and SigA (SYNW1783), which were down- and up-regulated by ammonium, respectively, are probably involved in the transcription of some genes that are down- or up-regulated by...”

FE46_RS04555 30S ribosomal protein S6 from Flavobacterium psychrophilum
FP1851 30S ribosomal protein S6 from Flavobacterium psychrophilum JIP02/86
33% identity, 81% coverage

• Dual RNA-Seq of Flavobacterium psychrophilum and Its Outer Membrane Vesicles Distinguishes Genes Associated with Susceptibility to Bacterial Cold-Water Disease in Rainbow Trout (Oncorhynchus mykiss)
  Chapagain, Pathogens (Basel, Switzerland) 2023
  • “...pyrophosphatase 29.61 FE46_RS12455 Copper resistance 28.99 FE46_RS11385 50S ribosomal L27 23.06 FE46_RS05880 3,4-Dihydroxy-2-butanone-4-phosphate synthase 22.28 FE46_RS04555 30S ribosomal S6 21.17 FE46_RS04560 30S ribosomal S18 19.11 FE46_RS02470 Ribosome assembly cofactor 16.53 FE46_RS05480 NAD(P) FAD-dependent oxidoreductase 158.95 FE46_RS10070 Cytochrome-c cbb3-type subunit I 149.66 FE46_RS08120 4Fe-4S dicluster domain-containing 125.13...”
• Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm
  Levipan, Frontiers in microbiology 2018
  • “...GO:0003735, GO:0019843, GO:0006412 3.37 FP1850 30S ribosomal protein S18 rpsR GO:0005840, GO:0003735, GO:0019843, GO:0006412 3.22 FP1851 30S ribosomal protein S6 rpsF GO:0005840, GO:0003735, GO:0019843, GO:0006412 4.21 FP1867 rRNA methyltransferase FP1867, FPSM_00933 GO:0003723, GO:0008173, GO:0001510, GO:0006396 4.12 FP2045 30S ribosomal protein S15 rpsO GO:0005840, GO:0003735, GO:0019843, GO:0006412...”

DVU0956 ribosomal protein S6 from Desulfovibrio vulgaris Hildenborough
26% identity, 91% coverage

• Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete
  Gao, Applied and environmental microbiology 2016
  • “...DVU1316 DVU0839 DVU0874 DVU1896 DVU1309 DVU1328 DVU1320 DVU0956 DVU1299 DVU1317 DVU2925 DVU2926 DVU2924 DVU2518 DVU1313 DVU1310 DVU1319 DVU0835 DVU1306 DVU2535...”

QBX69_00365 30S ribosomal protein S6 from Rickettsia rickettsii str. 'Sheila Smith'
35% identity, 76% coverage

• Core-genome guided novel therapeutic targets identification and chimeric vaccine designing against Rickettsia rickettsii
  Arshad, Scientific reports 2025
  • “...9 QBX69_05105 MULTISPECIES: Nucleotide exchange factor GrpE Cytoplasmic 10 QBX69_00180 DsbA family protein Cytoplasmic 11 QBX69_00365 30S ribosomal protein S6 Cytoplasmic 12 QBX69_00570 Cell cycle transcriptional regulator TrcR Cytoplasmic 13 QBX69_00635 Translation elongation factor Ts Cytoplasmic 14 QBX69_00715 ABC transporter permease Membrane 15 QBX69_00760 Ribosome biogenesis...”

LSEI_0009 Ribosomal protein S6 from Lactobacillus casei ATCC 334
31% identity, 92% coverage

• Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress
  Broadbent, Journal of bacteriology 2010
  • “...LSEI_1379 LSEI_1244 LSEI_1601 LSEI_1327 LSEI_1328 LSEI_1332 LSEI_0009 LSEI_1583 LSEI_1585 LSEI_1586 LSEI_1303 LSEI_1393 Fold change vs controlb Predicted...”

EF_0007 30S ribosomal protein S6 from Enterococcus faecalis V583
32% identity, 90% coverage

• The Enterococcus faecalis exoproteome: identification and temporal regulation by Fsr
  Shankar, PloS one 2012
  • “...RNA polymerase omega subunit, RpoZ (EF_3126) 11.53/5.36 6/35 51 2a 30S ribosomal protein S6, RpsF (EF_0007) 11.59/5.01 7/11 48 3a Dps Family protein (EF_3233) 17.93/4.56 6/11 33 4a Fumarate reductase subunit (EF_2556) 53.83/5.26 12/35 25 5a Alkyl hydroperoxide reductase, AhpC (EF_2739) 21.3/4.5 16/22 43 6a N-acetylmuramoyl-L-alanine...”

7nhkg / A0A1B4XKB6 7nhkg (see paper)
32% identity, 93% coverage

• Ligand: rna (7nhkg)

all4802 30S ribosomal protein S6 from Nostoc sp. PCC 7120
31% identity, 83% coverage

• The First Proteomics Study of Nostoc sp. PCC 7120 Exposed to Cyanotoxin BMAA under Nitrogen Starvation
  Koksharova, Toxins 2020
  • “...protein S10 all4336 genetic information processing 0.068 0.059 51 rpsF | 30S ribosomal protein S6 all4802 genetic information processing 1.27 0.06 52 rps7 | 30S ribosomal protein S7 all4339 genetic information processing 0.74 0.06 53 rplL | 50S ribosomal protein L7/L12 alr5303 genetic information processing 0.67...”

FN1657 SSU ribosomal protein S6P from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
30% identity, 89% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...FN1631, FN1632, FN1634, FN1635, FN1637, FN1638, FN1639, FN1640, FN1641, FN1642, FN1643, FN1644, FN1645, FN1646, FN1656, FN1657, FN1781, FN1828, FN1879, FN1979, FN2037, FN2038, FN2039, FN2040. 3 Covers FN0040, FN0054, FN0067, FN0069, FN0070, FN0110, FN0298, FN0299, FN0405, FN0466, FN0506, FN0611, FN0697, FN0753, FN0754, FN0755, FN1268, FN1340, FN1489, FN1517,...”

Teth39_2275 30S ribosomal protein S6 from Thermoanaerobacter ethanolicus ATCC 33223
34% identity, 97% coverage

• A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E
  Clarkson, Biotechnology for biofuels 2014
  • “...proteins Teth39_0365 2.00 Ribosomal protein L7/L12 0.020 Teth39_1753 2.01 RNA binding S1 domain protein 0.001 Teth39_2275 2.33 Ribosomal protein S6 0.006 Transporters Teth39_0231 2.85 Calcium translocating P-type ATPase, PMCA-type 0.001 Teth39_0278 2.82 Heavy metal translocating P-type ATPase 0.036 Teth39_0282 4.65 Copper translocating P-type ATPase 0.004 Teth39_1033...”

RS6_THET8 / Q5SLP8 Small ribosomal subunit protein bS6; 30S ribosomal protein S6; TS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
5a9zBJ / Q5SLP8 of Thermous thermophilus ribosome bound to BipA-GDPCP (see paper)
P23370 Small ribosomal subunit protein bS6 from Thermus thermophilus
27% identity, 91% coverage

• function: Located on the outer edge of the platform on the body of the 30S subunit
  subunit: Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein bS18. May make transient contacts with protein uL2 of the 50S subunit during translation
• Ligand: rna (5a9zBJ)
• Polyanions Cause Protein Destabilization Similar to That in Live Cells
  Sörensen, Biochemistry 2021
  • “...linkage. 16 In the control experiments, ribosomal protein S6 from Thermus thermophilus was used (UniProtKB Q5SLP8). In this variant, all K and R side chains were replaced with serine side chains, resulting in a very negative protein. 30 This research was funded by the Knut and...”
• Design of stable circular permutants of the GroEL chaperone apical domain
  Melnik, Cell communication and signaling : CCS 2024
  • “...the per-residue intrinsic disorder propensity of the ribosomal protein S6 from Thermus thermophiles (UniPrit ID: P23370). The circles denote the position of the sites of the designed breaks in the amino acid sequence. B Dependence of the changes in the global stability (G u ) of...”

K9TWE1 Small ribosomal subunit protein bS6 from Chroococcidiopsis thermalis (strain PCC 7203)
30% identity, 83% coverage

• Intact cell MALDI-TOF mass spectrometric analysis of Chroococcidiopsis cyanobacteria for classification purposes and identification of possible marker proteins
  Šebela, PloS one 2018
  • “...5.3 300.0 6 36.4 K9U8M9 Glutaredoxin 11989.1 11996.8 11858.0 11865.6 11867 6.7 122.3 2 10.7 K9TWE1 30S ribosomal protein S6 12204.2 12211.9 12073.1 12080.7 12077 4.9 347.6 8 65.4 K9TYF8 Photosystem I reaction center subunit IV 13392.0 13400.1 13260.9 13268.9 13267 9.4 1210.2 18 75.8 K9U057...”

Q31SC5 Small ribosomal subunit protein bS6 from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)
28% identity, 84% coverage

• Reconsidering Dogmas about the Growth of Bacterial Populations
  Ughy, Cells 2023
  • “...RecN DNA repair 10 10 Q31KL2 FtsQ 8 8 Q31PH9 rib. pseudouridine synth 8 9 Q31SC5 30S rib prot S6 3 3 Q31L22 50S rib. prot L18 3 4 Proteins characteristic only for the late stationary phase Q31NF6 Inorganic pyrophosphatase 7 16 Q31RU6 Ser-glyoxylate transaminase 5...”

D0R2Q2 Small ribosomal subunit protein bS6 from Lactobacillus johnsonii (strain FI9785)
31% identity, 92% coverage

• Identification of Genes Required for Glucan Exopolysaccharide Production in Lactobacillus johnsonii Suggests a Novel Biosynthesis Mechanism
  Mayer, Applied and environmental microbiology 2020
  • “...helicase pcrA 18 84 294 1.60 0.33 3.04 X DNA unwinding involved in DNA replication D0R2Q2 30S ribosomal protein S6 rpsF 9 12 255 1.60 0.33 3.03 X Translation D0R268 Putative secreted protein FI9785_210 21 102 323 1.55 0.34 2.93 X D0R3I4 Proline-tRNA ligase proS 16...”

LSA0007 30S Ribosomal protein S6 from Lactobacillus sakei subsp. sakei 23K
31% identity, 92% coverage

• Analysis of Lactobacillus sakei mutants selected after adaptation to the gastrointestinal tracts of axenic mice
  Chiaramonte, Applied and environmental microbiology 2010
  • “...response, two are ribosomal proteins with regulatory functions (LSA0007 and LSA1667), one is an ATPdependent H transporter (LSA1127), and one is a cysteinyl...”
  • “...LSA1033 Transcription-translation 30S ribosomal protein S6 (RpsF) LSA0007 50S ribosomal protein L10 (RplJ) LSA1667 Translation Cysteinyl tRNA synthase (CysS)...”

ECH_0308 ribosomal protein S6 from Ehrlichia chaffeensis str. Arkansas
29% identity, 85% coverage

• Ehrlichia chaffeensis transcriptome in mammalian and arthropod hosts reveals differential gene expression and post transcriptional regulation
  Kuriakose, PloS one 2011
  • “...40.Ribosomal protein S15 ECH_0727 4.6, 4.0 41.Ribosomal protein S19 ECH_0413 2.2, 2.5 42.Ribosomal protein S6 ECH_0308 2.6, 2.4 43.Ribosomal protein S8 ECH_0423 2.2, 2.1 Metabolism/Cellular Processes 44.ATP synthase F1, delta subunit ECH_0131 2.4, 2.5 45.Cell division protein FtsA ECH_1090 2.2, 2.1 46.Monovalent cation/proton antiporter, MrpF/PhaF subunit...”

F452_RS0105155 30S ribosomal protein S6 from Porphyromonas gulae DSM 15663
PGN_0639 30S ribosomal protein S6 from Porphyromonas gingivalis ATCC 33277
PG0595 ribosomal protein S6 from Porphyromonas gingivalis W83
27% identity, 79% coverage

• Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
  Lee, Journal of veterinary science 2019
  • “...30S ribosomal protein S16 6.79E-15 +2.42 * F452_RS0105395 50S ribosomal protein L25 1.61E-12 +2.25 * F452_RS0105155 30S ribosomal protein S6 6.09E-09 +1.90 * F452_RS0102635 30S ribosomal protein S12 2.01E-06 +1.69 * F452_RS0100485 50S ribosomal protein L13 1.57E-05 +1.63 * F452_RS0105160 30S ribosomal protein S18 4.00E-04 +1.52...”
• Synthesis of ppGpp impacts type IX secretion and biofilm matrix formation in Porphyromonas gingivalis
  Kim, NPJ biofilms and microbiomes 2020
  • “...PGN_0636 rpmE2 50S ribosomal protein L31 4.02 PGN_0637 htrA Heat shock-related protease htrA protein 1.93 PGN_0639 rpsF 30S ribosomal protein S6 1.77 PGN_0694 rpmH 50S ribosomal protein L34 2.09 PGN_0963 infC Translation initiation factor IF-3 2.10 PGN_0965 rplT 50S ribosomal protein L20 2.08 PGN_1580 rpsU 30S...”
• Insights into Dynamic Polymicrobial Synergy Revealed by Time-Coursed RNA-Seq
  Hendrickson, Frontiers in microbiology 2017
  • “...0.59 0.46 0.72 PGN_0638 rpoD , RNA polymerase sigma factor 0.76 0.21 0.55 0.54 0.56 PGN_0639 rpsF , 30S ribosomal protein S6 0.57 0.25 0.12 0.25 0.66 PGN_0660 ahpC , alkyl hydroperoxide reductase C subunit 1.12 0.54 1.30 1.75 1.14 PGN_0661 ahpF , alkyl hydroperoxide reductase...”
• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
  Hendrickson, BMC microbiology 2009
  • “...Unchanged (19) Decreased Levels (1) PGN_0035 PGN_0167 PGN_0640 PGN_0965 PGN_0394 PGN_0188 PGN_0279 PGN_1572 PGN_1589 PGN_0636 PGN_0639 PGN_1647 PGN_1648 PGN_0641 PGN_0964 PGN_1698 PGN_1844 PGN_1088 PGN_1219 PGN_1651 PGN_1852 PGN_1573 PGN_1575 PGN_1853 PGN_1854 PGN_1588 PGN_1590 PGN_1855 PGN_1861 PGN_1832 PGN_1840 PGN_1863 PGN_1868 PGN_1842 PGN_1843 PGN_1872 PGN_1890 PGN_1849 PGN_1850 PGN_1891 PGN_1856...”
• Role of oxyR in the oral anaerobe Porphyromonas gingivalis
  Diaz, Journal of bacteriology 2006
  • “...PG0257 PG0888 PG1089 PG1960 PG0385 PG0707 PG1076 PG0037 PG0595 PG2117 PG1134 PG1108 PG0594 PG0193 PG1542 PG0434 Alkyl hydroperoxide reductase, C subunit Dps...”

cg3308 30S ribosomal protein S6 from Corynebacterium glutamicum ATCC 13032
NCgl2881 30S ribosomal protein S6 from Corynebacterium glutamicum ATCC 13032
28% identity, 97% coverage

• Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
  Zhang, Scientific reports 2018
  • “...0.00 2259.05 4.1 12 NCgl2678 cg3073 sseA1 Thiosulfate sulfurtransferase 5.67/29868.54 1402.17 2611.50 3.4 14 NCgl2881 cg3308 rpsF 30S ribosomal protein S6 6.29/10958.78 3095.29 1181.77 NC 20 NCgl0187 cg0238 L-gulonolactone oxidase 5.68/53062.18 154.17 434.86 3.0 22 NCgl2620 cg3007 pvdS2 RNA polymerase sigma factor, putative 5.31/35304.59 0.00 1072.35...”
• Protein S-mycothiolation functions as redox-switch and thiol protection mechanism in Corynebacterium glutamicum under hypochlorite stress
  Chi, Antioxidants & redox signaling 2014
  • “...proteins Cg0601 RpsC 30S ribosomal protein Cys153cons. S3 Cg3308 RpsFb 30S ribosomal protein Cys67cons. S6 Cg0673 RplM 50S ribosomal protein Cys50 not cons. L13...”
• Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
  Brocker, Journal of bacteriology 2009
  • “...cg2380 cg0088 cg1376 cg1377 cg1379 cg1380 cg3226 cg3227 cg3308 cg0810 cg1628 cg1581 cg1582 cg1583 cg3026 cg3027 cg3028 cg3029 cg1156 cg1451 cg0576 cg2894 cg1364...”
• Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase
  Brockmann-Gretza, BMC genomics 2006
  • “...cg2429 0.52 glnA glutamine synthetase I E cg2942 0.48 Bacterial regulatory proteins, AsnC family K cg3308 0.65 rpsF 30S ribosomal protein S6 J cg3370 0.58 NADH-dependent flavin oxidoreductase C Genes under Rel-dependent, positive stringent control cg0414 1.66 wzz cell surface polysaccharide biosynthesis protein D cg0552 1.60...”
• Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
  Zhang, Scientific reports 2018
  • “...4.98/40789.73 0.00 2259.05 4.1 12 NCgl2678 cg3073 sseA1 Thiosulfate sulfurtransferase 5.67/29868.54 1402.17 2611.50 3.4 14 NCgl2881 cg3308 rpsF 30S ribosomal protein S6 6.29/10958.78 3095.29 1181.77 NC 20 NCgl0187 cg0238 L-gulonolactone oxidase 5.68/53062.18 154.17 434.86 3.0 22 NCgl2620 cg3007 pvdS2 RNA polymerase sigma factor, putative 5.31/35304.59 0.00...”
• Global Transcriptomic Analysis of the Response of Corynebacterium glutamicum to Vanillin
  Chen, PloS one 2016 (no snippet)
• Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
  Brocker, Journal of bacteriology 2009
  • “...NCgl1173 NCgl1174 NCgl1175 NCgl1176 NCgl2816 NCgl2817 NCgl2881 NCgl0676 NCgl1383 NCgl1341 NCgl1342 NCgl1343 NCgl2635 NCgl2636 NCgl2637 NCgl2638 NCgl0975...”

azo0718 RpsF protein from Azoarcus sp. BH72
29% identity, 72% coverage

• Environmental factors affecting the expression of pilAB as well as the proteome and transcriptome of the grass endophyte Azoarcus sp. strain BH72
  Hauberg-Lotte, PloS one 2012
  • “...the proteins that showed lower levels in the 2D-gels (encoded by azo0086 , azo0156 , azo0718 , azo0754 , azo1062 , azo1280 , azo2396 , azo3419 ) in samples with conditioned supernatant, the mRNA levels were reduced as well. However, some discrepancies between the two approaches...”

ZMO1225 30S ribosomal protein S6 from Zymomonas mobilis subsp. mobilis ZM4
26% identity, 74% coverage

• Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
  Yang, Biotechnology for biofuels 2018
  • “...(R97H) 11798701179870 ZMO1162 C to T (A94V) 12504541250454 Promoter of ZMO1223 ( fabD ) and ZMO1225 ( rpsF ) C to T 12623261262326 ZMO1236 ( adhA ) C to T (A153T) 12633771263378 Promoter of ZMO1236 ( adhA ) and downstream of ZMO1237 ( ldhA ) Missing...”
• Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses
  Yang, PloS one 2013
  • “...dehydrogenase gene (ZMO0367), 30S ribosomal protein S5 gene (ZMO0533), and 30S ribosomal protein S6 gene (ZMO1225) had higher expression levels with ethanol treatment (ca 2-fold change), however, the protein level decreased in ethanol treated cells (ca 1.5-fold to 2-fold change). Other example includes six genes such...”

CAC3724 Ribosomal protein S6 from Clostridium acetobutylicum ATCC 824
29% identity, 97% coverage

• Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum
  Tomas, Journal of bacteriology 2004
  • “...(Fig. 6C). Finally, several genes encoding ribosomal proteins (CAC3724 [two probes present on the array] and CAC3147 [Fig. 3B]) had lower expression in the...”

AH67_08045 30S ribosomal protein S6 from Bifidobacterium pseudolongum PV8-2
26% identity, 94% coverage

• The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions
  Vazquez-Gutierrez, BMC genomics 2017
  • “...AH68_09115 glutamyl-tRNA amidotransferase AH67_07920 AH68_09245 single-stranded DNA-binding protein AH67_08040 x AH68_09250 30S ribosomal protein S6 AH67_08045 AH68_09340 phosphoglycerol transferase AH67_08095 x AH68_09765 heat shock protein GrpE AH67_08330 x AH68_09770 molecular chaperone DnaK AH67_08335 x AH68_10135 sugar ABC transporter ATP-binding protein AH67_08590 a signal peptide predicted according...”

8p8vE / P75543 8p8vE (see paper)
27% identity, 41% coverage

• Ligand: rna (8p8vE)

lpg1592 30S ribosomal protein S6 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
27% identity, 80% coverage

• The LetA/S two-component system regulates transcriptomic changes that are essential for the culturability of Legionella pneumophila in water
  Mendis, Scientific reports 2018
  • “...Lpg0339 50S ribosomal protein L14 rplN 1.05 1.58 Lpg0341 50S ribosomal protein L5 1.18 1.74 Lpg1592 30S ribosomal protein S6 rpsF 3.92 3.25 Lpg1711 ribosome recycling factor (ribosome releasing factor) frr 1.34 2.09 Lpg1713 translation elongation factor Ts (EF-Ts) (ubiquitin associated domain:elongation factor Ts) tsf 2.51...”
• Transcriptomic changes of Legionella pneumophila in water
  Li, BMC genomics 2015
  • “...4.22 5.00 30S ribosomal protein S20 lpg2636 rpsT 3.86 4.43 6.92 30S ribosomal protein S6 lpg1592 rpsF 2.99 4.18 4.84 30S ribosomal protein S7 lpg0325 rpS7 2.43 3.36 3.89 50S ribosomal protein L15 lpg0348 rplO 1.76 3.37 3.21 50S ribosomal protein L16 lpg0336 rplP 2.49 3.73...”
• Identification of non-dot/icm suppressors of the Legionella pneumophila DeltadotL lethality phenotype
  Vincent, Journal of bacteriology 2006
  • “...the dotL suppressors lpg no.a Gene name lpg1591 lpg1592 lpg1593 lpg1594 lpg1595 lpg1596 lpg1439 lpg1438 lpg1437 lpg1436 lpg0604 lpg0605 lpg0606 lpg0607 lpg0608...”

CDR20291_3523 30S ribosomal protein S6 from Clostridium difficile R20291
CD3663 30S ribosomal protein S6 from Clostridium difficile 630
31% identity, 98% coverage

• Proteomic Signatures of Clostridium difficile Stressed with Metronidazole, Vancomycin, or Fidaxomicin
  Maaß, Cells 2018
  • “...x CDIF630erm_03585 Pgi CDR20291_3146 glucose-6-phosphate isomerase x CDIF630erm_02574 GuaB CDR20291_2224 IMP dehydrogenase x CDIF630erm_03992 RpsF CDR20291_3523 30S ribosomal protein S6 x CDIF630erm_00160 Adk CDR20291_0088 adenylate kinase x CDIF630erm_02772 LeuS CDR20291_2410 leucine-tRNA ligas x CDIF630erm_03872 LysS CDR20291_3389 lysine-tRNA ligase x CDIF630erm_00461 CDIF630erm_00461 CDR20291_0338 cobalt-dependent inorganic pyrophosphatase x...”
• Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile
  van, Antimicrobial agents and chemotherapy 2019
  • “...CD630DERM_23550 CD3175 CD0080A CD0072 CD3031 CD3663 CD0093 CD3206 CD3174 CD630DERM_32060 CD630DERM_31740 CD630DERM_31750 CD630DERM_00801 CD630DERM_00720...”

BL0416 30S ribosomal protein S6 from Bifidobacterium longum NCC2705
29% identity, 93% coverage

• Low-pH adaptation and the acid tolerance response of Bifidobacterium longum biotype longum
  Sánchez, Applied and environmental microbiology 2007
  • “...65 10 1.39E 19 3.23E 07 -- 1.82 2.29 1.53 frr rpsF BL1506 BL0416 15 82 1.51E 04 3.70E 04 2.59 8.80 -- -- BL1394 19 3.29E 03 5.92 -- nusA BL1615 57 4.42E 08 1.82...”

DR0098 ribosomal protein S6 from Deinococcus radiodurans R1
Q9RY52 Small ribosomal subunit protein bS6 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)
22% identity, 91% coverage

• The single-stranded DNA-binding protein of Deinococcus radiodurans
  Eggington, BMC microbiology 2004
  • “...gene encodes a contiguous ORF The region encompassing the ssb gene, which is flanked by DR0098, the ribosomal protein S6 gene and DR0101, the ribosomal protein S18 gene, was PCR amplified from genomic DNA and sequenced (Fig. 1 ). The genomic DNA was derived from the...”
  • “...different PCR primers and sequencing primers. In a direct approach, primers starting in the flanking DR0098 ribosomal protein S6 gene (5' CATCAAGGCTTCGGGCAAC 3') and the DR0101 ribosomal protein S18 gene (5' TTGCGTTCGCCGCTGTTTCC 3') were used to PCR amplify the ssb gene and flanking regions. Sequencing primers...”
• iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to ¹²C⁶⁺ heavy ion irradiation
  Gao, BMC microbiology 2022
  • “...could be categorized into a number of groups. Group 1 includes the translation regulation-related proteins Q9RY52 (RpsF), Q9RY49 (RplI), Q9RXJ3 (RpsQ), and Q9RST0 (RplL). Group 2 includes GPT binding-related proteins Q9RWN5 (FtsZ), Q9RXK5 (FusA) and Q9RV32 (BipA). Proteins Q9RWQ9 (GroEL) and Q9RY23 (DnaK), which control unfolded...”

YPTB0438 30S ribosomal protein S6 from Yersinia pseudotuberculosis IP 32953
A1JIS8 Small ribosomal subunit protein bS6 from Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
YPO3539 30S ribosomal protein S6 from Yersinia pestis CO92
25% identity, 71% coverage

• IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
  Miller, PLoS pathogens 2014
  • “...L7/L12 rplL 3.0 YPTB0404 10 kDa chaperonin groES 5.2 YPTB0405 60 kDa chaperonin groEL 5.7 YPTB0438 30S ribosomal protein S6 rpsF 2.2 YPTB0440 30S ribosomal protein S18 rpsR 2.2 YPTB0441 50S ribosomal protein L9 rplI 2.3 YPTB0464 50S ribosomal protein L21 rplU 2.3 YPTB0465 50S ribosomal...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPO3748 50S ribosomal protein L7/L12 0.58 (0.014) YPTB0408 (efp) YPO0354 elongation factor P 1.7 (0.018) YPTB0438 (rpsF) YPO3539 30S ribosomal protein S6 0.597 (0.018) 0.501 (0.003) YPTB0441 (rplI) YPO3536 50S ribosomal protein L9 0.476 (< 0.001) YPTB0464 (rplU) YPO3512 50S ribosomal protein L21 0.539 (0.006) YPTB0465...”
• Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach
  Liu, Molecular & cellular proteomics : MCP 2010
  • “...8 9 8 11 13 A1JHR2 A1JN60 A1JQX1a A1JS10 A1JS26 A1JK11 A1JS31 A1JIS8 65 57 32 93 92 31 31 31 131 131 131 131 NME NME NME NME AIJQX1 is not a complete...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...ribosomal protein L7/L12 0.58 (0.014) YPTB0408 (efp) YPO0354 elongation factor P 1.7 (0.018) YPTB0438 (rpsF) YPO3539 30S ribosomal protein S6 0.597 (0.018) 0.501 (0.003) YPTB0441 (rplI) YPO3536 50S ribosomal protein L9 0.476 (< 0.001) YPTB0464 (rplU) YPO3512 50S ribosomal protein L21 0.539 (0.006) YPTB0465 (rpmA) YPO3511...”

BAB1_0480 Ribosomal protein S6 from Brucella melitensis biovar Abortus 2308
25% identity, 62% coverage

• Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
  Roset, Scientific reports 2017
  • “...ID Gene Protein description Loc. b Signal peptide Mean ratio(I/C) SD Ratio Ribosomal proteins GI:82615467 BAB1_0480 rpsF 30S ribosomal protein S6 C NO 0.80 0.01 GI:82700001 BAB1_1184 rpsB 30S ribosomal protein S2 C NO 0.73 0.10 GI:82700063 BAB1_1251 rpsS 30S ribosomal protein S19 C NO 0.79...”

BR0455 30S ribosomal protein S6 from Brucella suis 1330
25% identity, 62% coverage

• Quantitative analysis of the Brucella suis proteome reveals metabolic adaptation to long-term nutrient starvation
  Al, BMC microbiology 2013
  • “...acid ABC transporter, periplasmic amino acid binding protein 37.2/5.3 1.31 0.00014 Protein metabolism Biosynthesis 1783 BR0455 ribosomal protein S6 17.1/8.0 1.69 0.0069 1980 BR0452 ribosomal protein L9 21.0/4.8 1.59 0.00041 Secretion 313 BR1945 preprotein translocase, SecA subunit 103.0/5.1 1.34 0.005 DNA / RNA metabolism Biosynthesis 221...”

Q5F925 Small ribosomal subunit protein bS6 from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
27% identity, 75% coverage

• Availability of iron ions impacts physicochemical properties and proteome of outer membrane vesicles released by Neisseria gonorrhoeae
  Płaczkiewicz, Scientific reports 2023
  • “...Translation Methionyl-tRNA formyltransferase Q5F5P7 J: Translation Cysteine-tRNA ligase Q5F5D6 J: Translation 30S ribosomal protein S6 Q5F925 J: Translation Peptide chain release factor 2 Q5F5H5 J: Translation Integration host factor beta subunit Q5F906 K: Transcription Putative RpiR-family transcriptional regulator Q5F8P9 K: Transcription Transcription termination factor rho Q5FA35...”

E3D771 Small ribosomal subunit protein bS6 from Gardnerella vaginalis (strain ATCC 14019 / 317)
28% identity, 69% coverage

• pH Stress Mediated Alteration in Protein Composition and Reduction in Cytotoxic Potential of Gardnerella vaginalis Membrane Vesicles
  Shishpal, Frontiers in microbiology 2021
  • “...monophosphate kinase) E3D7W7 3 Cellular energy homeostasis and adenine nucleotide metabolism. 30S ribosomal protein S6 E3D771 2 Translation 30S ribosomal protein S16 E3D753 4 Translation 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (BPG-dependent PGAM) E3D976 2 Glycolysis, moonlighting protein involved in plasminogen binding Uncharacterized protein * E3D7I4 2 Unknown 50S...”

EAMY_3145 30S ribosomal protein S6 from Erwinia amylovora CFBP1430
EAM_0448 30S ribosomal protein S6 from Erwinia amylovora ATCC 49946
25% identity, 70% coverage

• The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora
  Yang, BMC genomics 2020
  • “...rpsG , ribosomal protein S7 1.26 10.84 EAMY_0816 rpsP , ribosomal protein S16 1.22 9.43 EAMY_3145 rpsF , ribosomal protein S6 1.21 10.8 EAMY_3387 rpsJ , ribosomal protein S10 1.24 10.35 a Differentially expressed genes (DEGs) between the (p) ppGpp 0 mutant and WT at 3h...”
• Identification of novel virulence factors in Erwinia amylovora through temporal transcriptomic analysis of infected apple flowers under field conditions
  Schachterle, Molecular plant pathology 2022
  • “...Thiolperoxidase 6.8 waaL EAM_0086 Oantigen ligase 5.8 rpsJ EAM_3199 Ribosome small subunit protein 5.5 rpsF EAM_0448 Ribosome small subunit protein 5.2 cspC EAM_1967 Cold shock protein 5.0 iscS EAM_2492 Ironsulphur cluster formation and repair 4.7 EAM_1467 Putative nucleotidebinding protein 4.1 moaB EAM_1219 Molybdenum cofactor 3.0 EAM_1468...”

New Search

Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.