PaperBLAST

PaperBLAST Hits for sp|Q9HXH8|QUEA_PSEAE S-adenosylmethionine:tRNA ribosyltransferase-isomerase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=queA PE=3 SV=1 (347 a.a., MRVADFHFDL...)

Show query sequence

>sp|Q9HXH8|QUEA_PSEAE S-adenosylmethionine:tRNA ribosyltransferase-isomerase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=queA PE=3 SV=1
MRVADFHFDLPEALIARHPLPERRASRLLALDGPTGTLAHRQFADLLDYLRPGDLMVFNN
TRVIPARLFGQKESGGKLEVLVERVLDQHRVLAHIRASKAPKPGTRILVEGGGSAEMLQR
HDALFELAFAEPVLPLLERVGHMPLPPYIDRPDDAADRERYQTVYAQRAGAVAAPTAGLH
FDEALLEAIRAKGVDTAFVTLHVGAGTFQPVRVERIEDHVMHREWLEVGQDVVDAVSVCR
ARGGRVVAVGTTSVRSLESAARDGELKPFSGDTDIFIYPGRPFHVVDALVTNFHLPESTL
LMLVSAFAGYPETMAAYAAAVAQGYRFFSYGDAMFITRNPAPRGPED

Running BLASTp...

Found 54 similar proteins in the literature:

Q9HXH8 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
100% identity, 100% coverage

• 3-Benzyl-Hexahydro-Pyrrolo[1,2-a]Pyrazine-1,4-Dione Extracted From Exiguobacterium indicum Showed Anti-biofilm Activity Against Pseudomonas aeruginosa by Attenuating Quorum Sensing
  Singh, Frontiers in microbiology 2019
  • “...Q51481 -5.6 PA1077_flgB flgB flagellar basal-body rod protein FlgB Q9I4Q2 -5.23 PA3824_queA queA S-adenosylmethionine:trna ribosyltransferase-isomerase Q9HXH8 -5.15 PA5501_znuB znuB permease of ABC zinc transporter ZnuB Q9HT72 -4.97 PA2236 pslF hypothetical protein Q9I1N3 -4.76 PA1082_flgG flgG flagellar basal-body rod protein FlgG Q9I4P7 -4.75 PA4309_pctA pctA chemotactic transducer...”
• Increased Virulence of Bloodstream Over Peripheral Isolates of P. aeruginosa Identified Through Post-transcriptional Regulation of Virulence Factors
  Hickey, Frontiers in cellular and infection microbiology 2018
  • “...rpoN Transcriptional regulators 4.302 Q9HTW6 16 * Aminopeptidase P pepP Translation, post-translational modification, degradation 2.107 Q9HXH8 2 S-adenosylmethionine:trna ribosyltransferase-isomerase queA Translation, post-translational modification, degradation 2.910 Q9HT52 2 Probable short-chain dehydrogenase Putative enzymes 6.625 Hypothetical proteins (Lamont et al., 2002 ) Hypothetical, unclassified, unknown >1.5 Gene name...”

PSPTO_1412 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Pseudomonas syringae pv. tomato str. DC3000
86% identity, 98% coverage

• Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data
  Di, Statistical applications in genetics and molecular biology 2013
  • “...PSPTO_2667 4.32 0.64 PSPTO_2665 5.27 0.49 PSPTO_4462 5.06 0.22 PSPTO_4128 5.55 0.82 PSPTO_2664 4.38 1.00 PSPTO_1412 4.85 0.07...”

WP_090305582 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Pseudomonas linyingensis
87% identity, 99% coverage

• Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera
  Rudra, Frontiers in microbiology 2023
  • “...protein WP_090306967 Supplementary Figure S52 1 aa Ins 945 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA # WP_090305582 Supplementary Figure S53 2 aa Ins 145182 # Isolated exception present in some CSIs (#; see Supplementary Figures for details). $ The protein homologs were not found in some species....”

PP0832 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Pseudomonas putida KT2440
87% identity, 99% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

PS417_23250 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Pseudomonas simiae
85% identity, 100% coverage

• Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism
  Price, mSystems 2019
  • “...genes were as follows: PS417_08675, or moaA , which is involved in molybdenum cofactor biosynthesis; PS417_23250, or tsaA , which is involved in tRNA modification; and four regulatory or signaling genes, PS417_00445, PS417_07615, PS417_13295, and PS417_22670. Sequence analysis. Protein sequences were analyzed by using PaperBLAST (...”

SG0645 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Sodalis glossinidius str. 'morsitans'
73% identity, 97% coverage

• Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut
  Runyen-Janecky, PLoS neglected tropical diseases 2022
  • “...SG1909 thioredoxin 2 4.2 SG1845 conserved hypothetical protein 4.0 SG2279 30S ribosomal protein S10 4.0 SG0645 S-adenosylmethionine 4.0 SG0374 protein-export protein SecG 3.8 SG0466 pyruvate dehydrogenase complex repressor 3.7 SG1094 arginine ABC transporter permease component 3.5 SG0468 pyruvate dehydrogenase dihydrolipoyltransacetylase component 3.5 SG2277 50S ribosomal protein...”

TsaA / b0405 tRNA preQ₁³⁴ S-adenosylmethionine ribosyltransferase-isomerase (EC 2.4.99.17) from Escherichia coli K-12 substr. MG1655 (see 12 papers)
queA / P0A7F9 tRNA preQ₁³⁴ S-adenosylmethionine ribosyltransferase-isomerase (EC 2.4.99.17) from Escherichia coli (strain K12) (see 9 papers)
QUEA_ECOLI / P0A7F9 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Queuosine biosynthesis protein QueA; EC 2.4.99.17 from Escherichia coli (strain K12) (see 2 papers)
b0405 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Escherichia coli str. K-12 substr. MG1655
71% identity, 96% coverage

• function: Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)
  catalytic activity: 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L- methionine = epoxyqueuosine(34) in tRNA + adenine + L-methionine + 2 H(+) (RHEA:32155)
  subunit: Monomer
• Landscape-Scale Factors Affecting the Prevalence of Escherichia coli in Surface Soil Include Land Cover Type, Edge Interactions, and Soil pH
  Dusek, Applied and environmental microbiology 2018
  • “...Gene locus taga b1756 b3251 b0722 b1288 b0405 SNP positionb 156 342 60 504 57 Forward primer CCGTCTGGCTGTGGAAAATC GCCCGCGCGTTCTG CCTCCGCATTAGGACGCAAT...”
• Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification
  Miles, Proceedings of the National Academy of Sciences of the United States of America 2011
  • “...in extracted ion chromatograms of RNA from the QueA (b0405) deletion strain, the precursor to oQ, preQ1 nucleoside (mz 1/4 312), is clearly present (see Fig. 1...”
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...and transport psiF queA poxB agp potB potA narY narZ b0384 b0405 b0871 b1002 b1125 b1126 b1467 b1468 7.5 4.3 6.1 6.1 4.0 4.6 6.1 8.0 2.5 2.6 1.6 4.9 2.5 2.5...”
• Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
  Jiménez, Genome biology 2003
  • “...protein 1 b0172 Yes* COG0233 J1 Ribosome releasing factor operon? tRNA modification and protein export b0405 No COG0809 J S -adenosylmethionine:tRNA ribosyltransferase-isomerase tRNA modification and protein export b0406 No COG0343 J Queuine tRNA-ribosyltransferase tRNA modification and protein export b0407 No COG1862 N ORF, hypothetical protein tRNA...”

SEN0387 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
70% identity, 96% coverage

• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis
  Fong, Microbial genomics 2023
  • “...1.33 SEN0286 Transposase (fragment) D7795_00327 SEN0286 P125109_00326 STMMW_03133 Absent 1.24 queA S -Adenosylmethionine:tRNA ribosyltransferase-isomerase D7795_00442 SEN0387 P125109_00436 STMMW_04741 STM0404 1.26 tgt Queuine tRNA-ribosyltransferase tRNA-guanine transglycosylase D7795_00443 SEN0388 P125109_00437 STMMW_04751 STM0405 1.64 lipB Lipoate-protein ligase B (lipoate biosynthesis protein B) D7795_00703 SEN0604 P125109_00677 STMMW_07001 STM0635 4.97 phoL...”
• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis
  Fong, 2022

STM0404 S-adenosylmethionine-tRNA ribosyltransferase-isomerase from Salmonella typhimurium LT2
SEET0819_08985, STMMW_04741 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
70% identity, 96% coverage

• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis
  Fong, Microbial genomics 2023
  • “...(fragment) D7795_00327 SEN0286 P125109_00326 STMMW_03133 Absent 1.24 queA S -Adenosylmethionine:tRNA ribosyltransferase-isomerase D7795_00442 SEN0387 P125109_00436 STMMW_04741 STM0404 1.26 tgt Queuine tRNA-ribosyltransferase tRNA-guanine transglycosylase D7795_00443 SEN0388 P125109_00437 STMMW_04751 STM0405 1.64 lipB Lipoate-protein ligase B (lipoate biosynthesis protein B) D7795_00703 SEN0604 P125109_00677 STMMW_07001 STM0635 4.97 phoL PhoH-like ATP-binding protein...”
• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis
  Fong, 2022
• Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction
  Tang, Scientific reports 2017
  • “...coli. CTAG site in LT2 Gene_id Annotation 284175 STM0242 proline tRNA synthetase 459521 STM0403 & STM0404 intergenic region between yajB and queA 500950 STM0445 & STM0446 intergenic region between yajG and bolA 1280403 STM1196 & STM1197 intergenic region between acpP and fabF 1280562 STM1197 3-oxoacyl-[acyl-carrier-protein] synthase...”
• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis
  Fong, Microbial genomics 2023
  • “...Transposase (fragment) D7795_00327 SEN0286 P125109_00326 STMMW_03133 Absent 1.24 queA S -Adenosylmethionine:tRNA ribosyltransferase-isomerase D7795_00442 SEN0387 P125109_00436 STMMW_04741 STM0404 1.26 tgt Queuine tRNA-ribosyltransferase tRNA-guanine transglycosylase D7795_00443 SEN0388 P125109_00437 STMMW_04751 STM0405 1.64 lipB Lipoate-protein ligase B (lipoate biosynthesis protein B) D7795_00703 SEN0604 P125109_00677 STMMW_07001 STM0635 4.97 phoL PhoH-like ATP-binding...”
• Whole Genome DNA Sequence Analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks
  Wilson, PloS one 2016
  • “...Clade C4 1068806 CP007505 coding SEET0819_05080 360 AAT->AAA N->K N - lipoprotein 1935930 CP007505 coding SEET0819_08985 966 AAT->AAC N->N S + S-adenosylmethionine:tRNA ribosyltransferase-isomerase 3265625 CP007505 coding SEET0819_15515 211 GGG->AGG G->R N + hypothetical protein Node2 1001360 CP007505 coding SEET0819_04720 856 GCG->TCG A->S N + isocitrate dehydrogenase...”

t2459 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Salmonella enterica subsp. enterica serovar Typhi Ty2
70% identity, 96% coverage

• Molecular prophage typing of Staphylococcus aureus isolates from bovine mastitis
  Ko, Journal of veterinary science 2018
  • “...t002 (15.5%, 13/84), t084 (8.3%, 7/84), t034 (7.1%, 6/84), t304 (7.1%, 6/84), t164 (6.0%, 5/84), t2459 (2.4%, 2/84), t4050 (2.4%, 2/84), t2612 (1.2%, 1/84). Four isolates were classified into 4 UT variants, PMB 173-1 (11-10-21-17-172-24-34-22-25, UT1), PMB 188-1 (11-19-17-34-22-25-25-25, UT2), PMB 8-1 (26-17-34-34-34-34-33-34, UT3), PMB 8-2...”
  • “...t189, and t002), 9.1% (2/22; t034, t164, and t4050), and 4.5% (1/22; t084, t304, t2612, t2459, UT1, UT2, UT3, and UT4). The major RST10-2 was composed of 4 spa types including two major spa types, t127 and t189. Relatively high frequencies of t127 and t189 among...”
• Staphylococcus aureus Isolated From Retail Meat and Meat Products in China: Incidence, Antibiotic Resistance and Genetic Diversity
  Wu, Frontiers in microbiology 2018
  • “...spa types (No.) CC1 (133) ST1 (124) t127 (93), t4792 (7), t174 (2), t177 (2), t2459 (2), t286 (2), t3471 (2), t5500 (2), t2478 (1), t078 (1), t8619 (1), t286 (1), t13819 (1), t693 (1), t591 (1), t899 (1), t17635 * (1), t1908 (1), t9632 (1),...”

SENTW_0390 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Salmonella enterica subsp. enterica serovar Weltevreden str.
70% identity, 96% coverage

• Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
  Brankatschk, Microbial biotechnology 2014
  • “...fadA SENTW_4072 4.47 Small (beta) subunit of the fatty acid-oxidizing multienzyme complex Post-transcriptional modification queA SENTW_0390 11.26 Synthesis of queuine in tRNA trmD SENTW_2838 9.46 tRNA methyltransferase yhdG SENTW_3515 7.78 tRNA-dihydrourindine synthase B rpoA SENTW_3542 7.24 DNA-dependent RNA polymerase Carbohydrate metabolism aceB SENTW_4287 10.86 Malate synthase...”

NTHI0351 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Haemophilus influenzae 86-028NP
60% identity, 95% coverage

• Microevolution in response to transient heme-iron restriction enhances intracellular bacterial community development and persistence
  Hardison, PLoS pathogens 2018
  • “...generate a mutation in a putative sRNAencoding gene, sRNA121, located in the intergenic region between NTHI0351 and NTHI0353. sRNA 121 and approximately 1kb of flanking DNA was cloned into pGEM-T Easy. sRNA121 was then deleted and replaced by a cassette comprising a spectinomycin resistance gene and...”
• Transient Nutrient Deprivation Promotes Macropinocytosis-Dependent Intracellular Bacterial Community Development
  Hardison, mSphere 2018
  • “...770 NTHI1895 tehB Tellurite resistance protein Tellurite resistance methyltransferase TehB 5 4.5 0.0034 GI:100606 0856 NTHI0351 queA S -Adenosylmethionine:tRNA ribosyltransferase-isomerase tRNA preQ1(34) S -adenosylmethionine ribosyltransferase-isomerase QueA 4 3.1 0.003 GI:499591 591 NTHI1169 tbp2 Transferrin-binding protein 2 Transferrin-binding protein-like solute binding protein 8 3 0.0075 GI:501001 680...”

lpg2004 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
58% identity, 96% 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
  • “...(dsRNA-specific ribonuclease) (RNAse III, dsRNA) rnc 2.04 2.24 Lpg0609 alanyl tRNA synthetase alaS 1.16 2.57 Lpg2004 S-adenosylmethionine:tRNA ribosyltransferase-isomerase queA 1.96 2.09 Lpg2012 ribonuclease PH (RNAse PH) rph 2.33 2.62 Energy Metabolism Lpg2981 ATP synthase epsilon chain, ATP synthase F1 epsilon subunit atpC 2.25 2.74 Lpg2982 H+-transporting...”
• Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors
  Aurass, Molecular & cellular proteomics : MCP 2016
  • “...lpg1901 lpg1912 lpg1924 lpg1953 lpg1964 lpg1968 lpg1972 lpg2004 lpg2030 lpg2052 lpg2176 lpg2271 lpg2273 Molecular & Cellular Proteomics 15.1 lpg2298 lpg2328...”

PD0562 S-adenosylmethionine: tRNA ribosyltransferase-isomerase from Xylella fastidiosa Temecula1
59% identity, 97% coverage

• The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa
  Gouran, Scientific reports 2016
  • “...ribosome subunits (nine out of 10), transfer RNAs (43 out of 49), tRNA maturation queA (PD0562), elongation factor efp (PD1253), endoribunuclease ybeY (PD1781), and chaperone dnaJ (PD1279) to assist in protein folding, are all indicative of the increased cell division rate in X. fastidiosa prtA ....”

XF1314 S-adenosylmethionine: tRNA ribosyltransferase-isomerase from Xylella fastidiosa 9a5c
58% identity, 97% coverage

• In vitro Determination of Extracellular Proteins from Xylella fastidiosa
  Mendes, Frontiers in microbiology 2016
  • “...0.629 Phage-related protein 41.8 XF1704 XF1433 - No No 0.098 Phage-related protein, xfp3 36.5 XF1577 XF1314 - No No 0.538 Phage-related protein, xfp4 30.4 XF1649 XF1379 P76513 No No 0.065 Phosphoserine aminotransferase (PSAT) 39.6 XF2326 XF2012 Q9PB19 No No 0.163 PilA2 Tfp pilus assembly protein, 15.4...”

NMV_2048 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Neisseria meningitidis 8013
61% identity, 98% coverage

• The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq
  Heidrich, Nucleic acids research 2017
  • “...NMV_0019 ( pilE ) 8503 5.3 NMV_2115 2964 2.7 COG0483 G Metabolism NMV_1651 769 3.5 NMV_2048 ( queA ) 295 3.0 NMV_0526 192 1.9 COG2018 R Poorly characterized NMV_1509 ( pilX ) 126 1.6 NMV_0208 98 2.0 COG1192 D Cell cycle control, cell division, Inorganic ion...”

FTN_1234 S-adenosylmethionine:tRNA ribosyltransferase- isomerase from Francisella tularensis subsp. novicida U112
52% identity, 97% coverage

• Exploitation of host cell biology and evasion of immunity by francisella tularensis
  Asare, Frontiers in microbiology 2010
  • “...aroB 3-Dehydroquinate synthetase FTN_1222 kpsF Phosphosugar isomerase FTN_1231 gloA Lactoylglutathione lyase FTN_1233 Haloacid dehalogenase-like hydrolase FTN_1234 queA S-adenosylmethionine: tRNA ribosyltransferase-isomerase FTN_1333 tktA Transketolase I FTN_1415 Thioredoxin FTN_1417 manB Phosphomannomutase FTN_1421 wbtH Glutamine amidotransferase/asparagine synthase FTN_1428 wbtO Transferase FTN_1494 aceE Pyruvate dehydrogenase complex, E1 component, pyruvate dehydrogenase...”
  • “...methyltransferase FTN_1061 Acid phosphatase, HAD superfamily protein FTN_1222 kpsF Phosphosugar isomerase FTN_1231 gloA Lactoylglutathione lyase FTN_1234 queA S-adenosylmethionine: tRNA ribosyltransferase- isomerase FTN_1333 tktA Transketolase I FTN_1376 FTN_1418 manC FTN_1428 wbtO Transferase FTN_1494 aceE Pyruvate dehydrogenase complex, E1 component, pyruvate dehydrogenase FTN_1553 nudH dGTP pyrophosphohydrolase FTN_1597 prfC...”
• Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
  Asare, Environmental microbiology 2010
  • “...bifunctional NMN adenylyltransferase/Nudix hydrolase 7 tnfn1_pw060510p01q158 FTN_0988 prmA 50S ribosomal protein L11, methyltransferase 7 tnfn1_pw060510p02q144 FTN_1234 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase 6 Transcription/Translation tnfn1_pw060323p03q127 FTN_0567 tRNA synthetase class II (D, K and N) 2 tnfn1_pw060510p03q168 FTN_0598 tRNA-dihydrouridine synthase 3 tnfn1_pw060419p04q129 FTN_1290 mglA macrophage growth locus, protein A 3...”
  • “...Cytoplasmic tnfn1_pw060420p02q180 FTN_0483 77 Phagosomal tnfn1_pw060323p06q168 FTN_0545 68 Phagosomal tnfn1_pw060510p01q158 FTN_0988 prmA 78 Phagosomal tnfn1_pw060510p02q144 FTN_1234 queA 67 Phagosomal tnfn1_pw060418p04q172 FTN_1418 manC 68 Phagosomal tnfn1_pw060510p01q119 FTN_1428 wbtO 82 Phagosomal Transcription/Translation tnfn1_pw060510p03q168 FTN_0598 42 Cytoplasmic tnfn1_pw060419p04q129 FTN_1290 mglA 71 Phagosomal Type IV Pilin tnfn1_pw060418p02q167 FTN_1137 pilQ 66...”
• Molecular bases of proliferation of Francisella tularensis in arthropod vectors
  Asare, Environmental microbiology 2010
  • “...bifunctional NMN adenylyltransferase/Nudix hydrolase 7 tnfn1_pw060510p01q158 FTN_0988 prmA 50S ribosomal protein L11, methyltransferase 7 tnfn1_pw060510p02q144 FTN_1234 queA S-adenosylmethionine:tRNA ribosyltransferase- isomerase 6 Transcription/Translation tnfn1_pw060323p03q127 FTN_0567 tRNA synthetase class II (D, K and N) 2 tnfn1_pw060510p03q168 FTN_0598 tRNA-dihydrouridine synthase 3 tnfn1_pw060419p04q129 FTN_1290 mglA macrophage growth locus, protein A...”

WP_010930156 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Bordetella pertussis CHLA-11
59% identity, 99% coverage

• T cell reactivity to Bordetella pertussis is highly diverse regardless of childhood vaccination
  da, Cell host & microbe 2023
  • “...10 WP_010931507 547 Antioxidant protein (Peroxiredoxin) 0.79 15 WP_003813333.1 213 S-adenosylmethionine--tRNA ribosyltransferase-isomerase QueA 0.76 17.5 WP_010930156 347 DNA mismatch repair protein MutS 0.72 10 WP_010930434.1 883 AEC family transporter 0.71 12.5 WP_010931519.1 315 LysR family transcriptional regulator 0.62 12.5 WP_010929840.1 307 Key resources table REAGENT or...”

BCAL3303 putative queuosine S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Burkholderia cenocepacia J2315
55% identity, 97% coverage

• DNA Methylation Epigenetically Regulates Gene Expression in Burkholderia cenocepacia and Controls Biofilm Formation, Cell Aggregation, and Motility
  Vandenbussche, mSphere 2020
  • “...0.270 1.397 0.382 ArgF ornithine carbamoyltransferase BCAL2782 1.373 0.237 1.166 0.668 PdxH pyridoxamine 5-phosphate oxidase BCAL3303 1.048 0.845 1.093 0.071 QueA S -adenosylmethionine:tRNA ribosyltransferase-isomerase BCAM0820 2.621 0.004 2.253 0.002 Hybrid two-component system kinase-response regulator protein BCAM0941 1.240 0.448 1.761 0.050 gnd 6-phosphogluconate dehydrogenase BCAM1262 1.237 0.397...”

queA / Q183N9 S-adenosylmethionine--tRNA ribosyltransferase-isomerase (EC 2.4.99.17) from Clostridioides difficile (strain 630) (see paper)
49% identity, 97% coverage

CBO3069 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Clostridium botulinum A str. ATCC 3502
50% identity, 97% coverage

• Gene expression profiling of Clostridium botulinum under heat shock stress
  Liang, BioMed research international 2013
  • “...CBO3570, CBO0377, and CBO0043) and seven downregulated genes (CBO1840, CBO3520, CBO3465, CBO2101, CBO0400, CBO2645, and CBO3069). The corresponding primers (see Table S1 in supplementary Material available online at http://dx.doi.org/10.1155/2013/760904 ) were designed using Primer Premier software version 5 (PREMIER Biosoft International, Palo Alto, CA, USA). Two...”
  • “...and cellular physiology in C. botulinum ATCC 3502. Among them, valS (CBO3164, valyl-tRNA synthetase), queA (CBO3069, S-adenosylmethionine), and tyrR (CBO1204, tyrosyl-tRNA synthetase) were the three most significantly downregulated genes (by 12.1-, 9.2-, and 5.6-fold, resp.). In addition, gatB (CBO3265, aspartyl/glutamyl-tRNA amidotransferase subunit B1), gatA (CBO3266, glutamyl-tRNA...”

lmo1531 similar to S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Listeria monocytogenes EGD-e
49% identity, 97% coverage

• The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production
  Stasiewicz, Applied and environmental microbiology 2011
  • “...gene (lmo1339 gki) lmo1985 (ilvN), lmo2483 (hprK) lmo1531 (queA) Glutamine synthetase repressor gene lmo1298, putative ABC permease gene lmo1746 Transcriptional...”

WP_108306792 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Metalysinibacillus jejuensis
48% identity, 98% coverage

• Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures
  Gupta, Frontiers in microbiology 2019
  • “...transcriptional regulator WP_108306939 Supplementary Figure 25 1 aa del 82-136 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA WP_108306792 Supplementary Figure 26 1 aa del 91-136 DNA primase WP_108306840 Supplementary Figure 27 1 aa del 497-535 FMN reductase (NADPH) CEA04024 Supplementary Figure 28 1 aa del 162210 UvrABC system...”

SA1466 S-adenosylmethionine tRNA ribosyltransferase from Staphylococcus aureus subsp. aureus N315
SAR1720 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Staphylococcus aureus subsp. aureus MRSA252
47% identity, 97% coverage

• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...2.5 SA1464 hypothetical protein sa_c2054s1766_a_at 3.0 2.5 2.5 SA1465 hypothetical protein sa_c2058s1770_at 2.1 2.5 2.5 SA1466 hypothetical protein sa_c2063s1774_a_at 3.4 2.5 2.5 SA1467 hypothetical protein sa_c2066s1777_a_at * 36.6 2.5 ND SA1468 hypothetical protein sa_c2109s1814_a_at * 29.3 2.5 ND SA1481 hypothetical protein sa_c2120s1823_a_at * 13.1 2.5 2.5...”
• Staphylococcus aureus MazF specifically cleaves a pentad sequence, UACAU, which is unusually abundant in the mRNA for pathogenic adhesive factor SraP
  Zhu, Journal of bacteriology 2009
  • “...0.99931 0.99870 SA2447 SA0930 SA0062 SA0794 SA2252 SA1466 SA1222 SA0830 SA1626 SA0456 dltB opp-1D queA Truncated transposase spoVG Downloaded from...”
• Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
  Dunman, Journal of bacteriology 2001
  • “...SA0523 SA0666 SA1391 SA1123 SA2351 SA0016 SA1045 SAS093 SA1466 SA1844 SA1842 SA1843 SAS066 SA1516 SA0434 SA1120 SA1920 SA2079 SA2135 SA1214 SA0099 SA0100 SA2241...”
• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...2.51E-04 SAR0552 fus elongation factor G 2.10 2.09E-02 SAR1216 trmD putative tRNA (guanine-7-)-methyltransferase 2.33 4.84E-04 SAR1720 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase 2.11 1.68E-02 SAR2309 rpoA RNA polymerase alpha subunit 2.61 2.40E-03 Peptidoglycan Synthesis SAR0470 lysR family regulatory protein 2.20 1.07E-02 SAR1762 thrS threonyl-tRNA synthetase 2.77 9.07E-04 SAR1991 gatB...”
  • “...SAR1485 rpsA putative 30S ribosomal protein S1 2.91 4.91E-02 SAR1719 tgt queuine tRNA-ribosyltransferase 2.01 4.96E-02 SAR1720 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase 2.49 1.44E-02 SAR2309 rpoA DNA-directed RNA polymerase subunit alpha 2.44 9.73E-03 Peptidoglycan Synthesis SAR1048 purD putative phosphoribosylamineglycine ligase 3.98 2.08E-02 SAR1762 thrS threonyl-tRNA synthetase 2.51 1.51E-02 SAR2212...”

SAOUHSC_01749 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Staphylococcus aureus subsp. aureus NCTC 8325
47% identity, 97% coverage

• Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin
  Sierra, Nucleic acids research 2020
  • “...[310/UACUUA] translation elongation factor activity [GO:0003746] aspS SAOUHSC_01737 Aspartyl-tRNA synthetase [1362/UACAUC] Aspartyl-tRNA aminoacylation [GO:0006422] queA SAOUHSC_01749 S -adenosylmethionine:tRNA ribosyltransferase-isomerase [457/UACAUC] n/a valS SAOUHSC_01767 valyl-tRNA synthetase [229/UACUUA] Valyl-tRNA aminoacylation [GO:0006438] rpsD SAOUHSC_01829 30S ribosomal protein S4 [175/UACUUA] Structural constituent of ribosome [GO:0003735] leuS SAOUHSC_01875 Leucyl-tRNA synthetase [575/UACUUA]...”

K7H03_22040 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Bacillus thuringiensis
46% identity, 98% coverage

• Draft Genome Sequence of Bacillus thuringiensis ZZQ-130 with Multiple Pesticidal Genes, Isolated from Caka Salt Lake, China
  Zheng, Microbiology resource announcements 2022
  • “...) ( 9 ). Thirty-one pesticidal proteins, including five rank 4 (identity, >95%) cry genes (K7H03_22040, K7H03_22045, K7H03_22070, K7H03_22070, and K7H03_27130), one rank 4 vip gene (K7H03_22005), one rank 1 (identity, <45%) vpa ( V i p 2the a ctive component of the Vpa/Vpb binary toxin)...”

O32054 S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC 2.4.99.17) from Bacillus subtilis (see paper)
BSU27720 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Bacillus subtilis subsp. subtilis str. 168
47% identity, 97% coverage

• A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century
  Bremer, Microbial biotechnology 2023
  • “...yqeV, rimO, tmtB tRNA N(6)threonylcarbamoyladenosine (t(6)A) methylthiotransferase 2.8.4.5 BSU00530 pthA spoVC, pth peptidyltRNA hydrolase 3.1.1.29 BSU27720 queA _ Sadenosylmethionine tRNA ribosyltransferaseisomerase 2.4.99.17 BSU13720 queC ykvJ 7cyano7deazaguanine (preQ0) synthase 6.3.4.20 BSU13730 queD ykvK 6carboxy5,6,7,8tetrahydropterin synthase; queuosine biosynthesis 4.1.2.50 BSU13730 queE ykvL 7carboxy7deazaguanine synthase 4.3.99.3 BSU13750 queF ykvM...”

QUEA_THEMA / Q9WZ44 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Queuosine biosynthesis protein QueA; EC 2.4.99.17 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
Q9WZ44 S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC 2.4.99.17) from Thermotoga maritima (see paper)
TM0574 S-adenosylmethionine tRNA ribosyltransferase from Thermotoga maritima MSB8
48% identity, 97% coverage

• function: Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA).
  catalytic activity: 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L- methionine = epoxyqueuosine(34) in tRNA + adenine + L-methionine + 2 H(+) (RHEA:32155)
  subunit: Monomer.
• Diffraction study of protein crystals grown in cryoloops and micromounts
  Berger, Journal of applied crystallography 2010
  • “...Thermotoga maritima protein TM0449 (JCSG), T. maritima proteins TM0574 (JCSG), TM0559 (JCSG) and TM1389 (JCSG), an intein protein (New England Biolabs), and...”
  • “...(e) Plate-like crystals of TM1389. ( f ) Crystals of TM0574. (g) Crystals of the intein protein. (h) Crystals of TM0559. (i) Crystals of RNase. ( j) Crystals of...”

QUEA_STRGC / A8AYK5 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Queuosine biosynthesis protein QueA; EC 2.4.99.17 from Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288) (see paper)
48% identity, 97% coverage

• function: Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA) (By similarity). Seems to have a role in modulation of ADS (arginine deiminase system) gene expression, perhaps exerting a negative effect on the translation of arc regulatory proteins.
  catalytic activity: 7-aminomethyl-7-carbaguanosine(34) in tRNA + S-adenosyl-L- methionine = epoxyqueuosine(34) in tRNA + adenine + L-methionine + 2 H(+) (RHEA:32155)
  subunit: Monomer.
  disruption phenotype: The arcA transcript in QueA-deficient strains is 14-fold more abundant than in the wild-type strain. However, no significant difference in arginine deiminase (AD) activity (encoded by arcA) is detected between the wild-type and QueA-deficient strains. The growth rate of a QueA-deficient strain does not differ significantly from that of the wild-type strain, but the QueA-deficient strain does not compete well with the wild-type during serial passage.

lp_2285 S-adenosylmethionine tRNA ribosyltransferase-isomerase from Lactobacillus plantarum WCFS1
46% identity, 97% coverage

• Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Quorum Sensing Molecule N-3-Oxododecanoyl Homoserine Lactone
  Spangler, Frontiers in microbiology 2019
  • “...0.65 0.3 0.82 PRSA1_LACPL lp_1452 prtM1 Peptidyl-prolyl isomerase 0.168 0.144 0.158 0.44 0.3 0.21 QUEA_LACPL lp_2285 queA SAM:tRNA ribosyltransferase-isomerase 0.148 0.276 -0.18 0.34 0.02 0.08 RL11_LACPL lp_0619 rplK 50S ribosomal protein L11 0.027 0.675 -0.58 0.34 0.29 1.51 RL17_LACPL lp_1063 rplQ 50S ribosomal protein L17 0.102...”
• Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs
  Wels, Microbial biotechnology 2011
  • “...( lexA ) transcription repressor of the SOS regulon Regulatory functions 4.2e08 0.79 1064 a lp_2285 ( queA ) Sadenosylmethionine tRNA ribosyltransferaseisomerase Protein synthesis 1.0e08 0.73 lp_2286 ( ruvB ) Holliday junction DNA helicase RuvB DNA metabolism lp_2287 ( ruvA ) Holliday junction DNA helicase RuvA...”

TDE2451 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Treponema denticola ATCC 35405
47% identity, 97% coverage

• Localization and pathogenic role of the cysteine protease dentipain in Treponema denticola
  Miyai-Murai, Molecular oral microbiology 2023
  • “...ATP-binding protein 2.25 TDE0806 hypothetical protein 2.18 TDE1618 hypothetical protein 2.17 TDE2752 hypothetical protein 2.13 TDE2451 S-adenosylmethioninetRNA ribosyltransferase-isomerase 2.09 TDE0345 methyl-accepting chemotaxis protein DmcB 2.07 TDE2372 hypothetical protein 2.04 TDE2373 precorrin-6Y C5,15-methyltransferase 2.04 TDE0346 protease PrtB 2.02 TDE0934 co-chaperonin GroES 2.01 TDE1175 chaperonin GroEL 2.00...”

Tery_0731 S-adenosylmethionine--tRNA-ribosyltransferase-isomerase from Trichodesmium erythraeum IMS101
45% identity, 90% coverage

• Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume
  Hilton, The ISME journal 2015
  • “...FHA domain containing protein), queA (Tery_0731, S-adenosylmethionine-transfer RNA-ribosyltransferase isomerase) and psbA (Tery_4763, photosystem II protein...”
  • “...encodes an S-adenosylmethionine-transfer RNAribosyltransferase isomerase (queA, Tery_0731) were found mostly at the transitional station, and also mapped to...”

SPy1400 putative S-adenosylmethionine-tRNA ribosyltransferase-isomerase from Streptococcus pyogenes M1 GAS
46% identity, 97% coverage

• Novel Tyrosine Kinase-Mediated Phosphorylation With Dual Specificity Plays a Key Role in the Modulation of Streptococcus pyogenes Physiology and Virulence
  Kant, Frontiers in microbiology 2021
  • “...3.26911 0.00201 0.019124 Spy1399 - PTS system galactose-specific transporter subunit IIC 3.5653 11.8376 0.00233 0.021278 Spy1400 - PTS system galactose-specific transporter subunit IIB 3.4328 10.7988 0.00331 0.027264 Spy1401 - PTS system galactose-specific transporter subunit IIA 3.2836 9.73783 0.00752 0.048447 Spy1542 scrA PTS system sucrose-specific transporter subunit...”
  • “...14.0335 0.00194 0.01875 Spy1399 PTS-IIC PTS system galactose-specific transporter subunit IIC 3.5653 11.8376 0.00233 0.021278 Spy1400 PTS-IIC PTS system galactose-specific transporter subunit IIB 3.4328 10.7988 0.00331 0.027264 Spy1401 PTS-IIA PTS system galactose-specific transporter subunit IIA 3.2836 9.73783 0.00752 0.048447 Spy1402 lacR.1 Lactose phosphotransferase system repressor 1.5411...”
• Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms
  Freiberg, mSystems 2016
  • “...4.39 4.46 4.47 2.95 2.89 2.88 2.51 2.44 2.43 PTS, galactose-specific IIC component G H Spy1400 4.61 5.81 5.78 3.16 1.97 2 2.61 1.44 PTS, galactose-specific IIB component G H Spy1401 4.3 4.48 5.03 3.34 3.16 2.6 2.2 2.02 1.47 PTS, galactose-specific IIA component G, T...”
  • “...Q Spy1388 nagA 2.03 2.01 1.18 1.86 1.85 1.02 1.75 1.74 0.91 N-Acetylglucosamine-6-phosphate deacetylase G Spy1400 2.92 3.08 2.54 3.59 3.75 3.2 2.05 2.21 1.66 PTS, galactose-specific IIB component G Spy1587 udp 4.14 4.05 2.56 2.35 2.26 2.39 2.3 Uridine phosphorylase F Spy1635 lacD2 3.63 3.68...”

SMc01207 PROBABLE S-ADENOSYLMETHIONINE:TRNA RIBOSYLTRANSFERASE-ISOMERASE(QUEUOSINE BIOSYNTHESIS PROTEIN QUEA) from Sinorhizobium meliloti 1021
48% identity, 94% coverage

• Queuosine biosynthesis is required for sinorhizobium meliloti-induced cytoskeletal modifications on HeLa Cells and symbiosis with Medicago truncatula
  Marchetti, PloS one 2013
  • “...to this pathway ( Fig. 4 ) we identified queF (SMc02723), tgt (SMc01206) and queA (SMc01207) genes on the S. meliloti main chromosome. These genes were individually inactivated and corresponding mutants triggered reduced HeLa cell deformations 48 hpi in regular HeLa culture medium (DMEM) containing 10%...”

RSP_2971 S-adenosylmethionine tRNA ribosyltransferase-isomerase from Rhodobacter sphaeroides 2.4.1
50% identity, 97% coverage

• Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
  Dufour, PLoS genetics 2012
  • “...peptides, and glycopeptides RSP_0686, RSP_1490 Protein folding and stabilization RSP_1219 tRNA and rRNA base modification RSP_2971 Unknown function Unknown function RSP_0151, RSP_0152, RSP_0269, RSP_0423, RSP_0557, RSP_0799, RSP_0896, RSP_1591, RSP_1956, RSP_1985, RSP_2225, RSP_2268, RSP_3075, RSP_3076, RSP_3089, RSP_3310, RSP_3329, RSP_4144, RSP_4209 Summary of the functional annotations of members...”

AS87_02265 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Riemerella anatipestifer Yb2
42% identity, 96% coverage

• Deletion of AS87_03730 gene changed the bacterial virulence and gene expression of Riemerella anatipestifer
  Wang, Scientific reports 2016
  • “...Unknown 1.55 AS87_05160 30S ribosomal protein S10 Cytoplasmic COG0051 J 1.55 AS87_04930 glycosyltransferase Cytoplasmic 1.29 AS87_02265 S-adenosylmethionine tRNA ribosyltransferase Cytoplasmic COG0809 J 1.09 AS87_03335 hypothetical protein Unknown 0.61 AS87_05990 hypothetical protein Unknown COG1002 V 0.51 AS87_03730 (mutated gene) acyl-protein synthetase Cytoplasmic 0.01 Functional categories: (1) Information...”

RJP_0222 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Rickettsia japonica YH
39% identity, 93% coverage

• Complete genomic DNA sequence of the East Asian spotted fever disease agent Rickettsia japonica
  Matsutani, PloS one 2013
  • “...family exonuclease RJP_0891 114 RPE-4 RPE-4 RPE-4 RPE-6 ND ND DNA polymerase III subunit alpha RJP_0222 115 RPE-4 RPE-4 RPE-4 RPE-7 ND ND tRNA ribosyltransferase-isomerase RJP_0300 90 RPE-6 RPE-6 RPE-6 RPE-7 ND ND NADH dehydrogenase subunit N RJP_0790 192 RPE-4 RPE-4 RPE-4 RPE-7 ND ND proline/betaine...”

MC1_01595 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA from Rickettsia parkeri str. Portsmouth
39% identity, 93% coverage

• A streamlined method for transposon mutagenesis of Rickettsia parkeri yields numerous mutations that impact infection
  Lamason, PloS one 2018
  • “...interchange protein dsbA Sp36 230327 MC1_01215 Prolyl endopeptidase Sp37 637085 MC1_03670 Hypothetical protein Sp38 292360292361 MC1_01595 S-adenosylmethionine:tRNA ribosyltransferase-isomerase Sp39 912985 MC1_05235 Hypothetical protein (RARP-2) Sp40 1279632 Intergenic n/a Sp41 995818 Intergenic n/a Sp42 372020 MC1_02055 ** GTP-binding protein LepA Sp43 651603651604 MC1_03735 ADP, ATP carrier protein...”

R7BMR5 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Eggerthella sp. CAG:368
45% identity, 60% coverage

• Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics
  Zallot, ACS chemical biology 2017
  • “...the DUF208 and QueA encoding genes were identified in an Eggerthella species (see Uniprot ID R7BMR5 as an example), reinforcing the link between DUF208 and the Q biosynthesis pathway. To analyze the phylogenetic distribution of TGT, QueA, DUF208, and QueG families in eubacterial genomes, the Phylogenetic...”

O51053 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)
38% identity, 98% coverage

• MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.
  Cruveiller, Nucleic acids research 2005
  • “...to the C-terminal part of a protein named QUEA_BORBU in the SWISSPROT databank (Accession no. O51053), annotated as a putative S -adenosylmethionine:tRNA ribosyl transferase-isomerase ( Figure 2B ). The BB0021 gene, located next to BOBURS0021 and transcribed in the same strand, has been annotated with an...”

Cla_0662 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Campylobacter lari RM2100
38% identity, 97% coverage

• Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress
  Riedel, Frontiers in microbiology 2020
  • “...30S ribosomal protein S12 J Cla_0451 0.70 0.034 CCO0588 0.61 0.022 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase J Cla_0662 0.73 0.018 CCO1379 0.71 0.041 Endoribonuclease L-PSP J Cla_0277 1.24 0.000 CCO1499 0.87 0.002 cmeD* Outer membrane component of efflux system M Cla_0986 0.81 0.008 CCO1098 0.66 0.036 flgI Flagellar...”

PG1540 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Porphyromonas gingivalis W83
38% identity, 96% coverage

• Adaptation of Porphyromonas gingivalis to microaerophilic conditions involves increased consumption of formate and reduced utilization of lactate
  Lewis, Microbiology (Reading, England) 2009
  • “...PG0720 PG0993 PG1501 PG1505 PG0017 PG0620 PG0273 PG1540 PG1089 PG0740 PG1036 PG1638 0.701519 0.689485 0.687504 0.670898 0.666572 0.644826 0.641523 0.637839...”
• Role of oxyR in the oral anaerobe Porphyromonas gingivalis
  Diaz, Journal of bacteriology 2006
  • “...PG0619 PG0421 PG1545 PG1286 PG0275 PG1321 PG1116 PG0686 PG1540 PG1124 PG0257 PG0888 PG1089 PG1960 PG0385 PG0707 PG1076 PG0037 PG0595 PG2117 PG1134 PG1108 PG0594...”

PGN_0569 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Porphyromonas gingivalis ATCC 33277
38% identity, 96% coverage

• Insights into Dynamic Polymicrobial Synergy Revealed by Time-Coursed RNA-Seq
  Hendrickson, Frontiers in microbiology 2017
  • “...PGN_1988 PGN_0380 PGN_1461 PGN_1906 hagC PGN_1376 PGN_1480 PGN_0739 PGN_1402 PGN_1904 hagB PGN_1340 PGN_0972 TPR motif PGN_0569 PGN_2050 PGN_0185 fimE PGN_1903 PGN_0172 PGN_1423 PGN_1673 PGN_0580 PGN_1413 PGN_0380 PGN_1145 PGN_1053 PGN_0180 fimA PGN_1507 PGN_0388 PGN_0972 TPR motif Figure 3 Differential expression of fimA locus genes ( PGN_0180 -...”
  • “...Fe-Mn 1.13 0.04 1.03 1.33 1.76 PGN_0567 prtC , collagenase 0.84 0.90 0.88 0.52 0.14 PGN_0569 S-adenosylmethionine: tRNA ribosyltransferase-isomerase 0.58 0.03 1.21 1.44 1.85 PGN_0604 ferritin 0.60 0.04 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 ,...”
• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
  Hendrickson, BMC microbiology 2009
  • “...Levels (3) PGN_0209 PGN_0360 PGN_0137 PGN_0278 PGN_0266 PGN_0278 PGN_0365 PGN_0517 PGN_0281 PGN_0366 PGN_1157 PGN_0543 PGN_0570 PGN_0569 PGN_0981 PGN_0819 PGN_0962 PGN_1711 PGN_1883 PGN_0987 PGN_1218 PGN_1229 PGN_1381 PGN_1805 PGN_1969 PGN_2045 PGN_2060 Proteins are listed by ORF number in the same manner as in Table 3. Transcription machinery Most...”

CCO1379 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Campylobacter coli RM2228
37% identity, 97% coverage

• Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress
  Riedel, Frontiers in microbiology 2020
  • “...S12 J Cla_0451 0.70 0.034 CCO0588 0.61 0.022 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase J Cla_0662 0.73 0.018 CCO1379 0.71 0.041 Endoribonuclease L-PSP J Cla_0277 1.24 0.000 CCO1499 0.87 0.002 cmeD* Outer membrane component of efflux system M Cla_0986 0.81 0.008 CCO1098 0.66 0.036 flgI Flagellar basal body P-ring...”

HP1062 S-adenosylmethionine:tRNA ribosyltransferase-isomerase (queA) from Helicobacter pylori 26695
38% identity, 96% coverage

• Twin-arginine translocation system in Helicobacter pylori: TatC, but not TatB, is essential for viability
  Benoit, mBio 2014
  • “...in each case. Following the same mutant construction strategy, we were able to successfully disrupt hp1062 ( queA ), the gene located downstream of tatC (see Fig.S1 in the supplemental material). In contrast, multiple attempts to disrupt tatA were unsuccessful, and attempts at deleting tatC were...”
  • “...was no transposon insertion in hp1061 ( tatC ), while there was one insertion in hp1062 ( queA ), suggesting that tatC is essential, while queA is not, in agreement with results from the present study. However, these results have to be taken with caution, as...”
• Metabolism and genetics of Helicobacter pylori: the genome era
  Marais, Microbiology and molecular biology reviews : MMBR 1999
  • “...HP no. Gene Protein HP1141 HP1497 HP0361 HP1148 HP1062 fmt pth hisT rnpA queA HP1513 HP1148 HP1415 selA trmD miaA HP0281 tgt Methionyl-tRNA formyltransferase...”

PG0969 S-adenosylmethionine:tRNA ribosyltransferase-isomerase, putative from Porphyromonas gingivalis W83
36% identity, 83% coverage

• Tetratricopeptide repeat protein-associated proteins contribute to the virulence of Porphyromonas gingivalis
  Kondo, Infection and immunity 2010
  • “...genes PG0327 PG0373 PG0546 PG0635 PG0656 PG0722 PG0969 PG1532 PG1866 PG2006 PG2225 Hypothetical protein Hypothetical protein Hypothetical protein Ribosomal...”

PGN_0981 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Porphyromonas gingivalis ATCC 33277
35% identity, 83% coverage

• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
  Hendrickson, BMC microbiology 2009
  • “...(3) PGN_0209 PGN_0360 PGN_0137 PGN_0278 PGN_0266 PGN_0278 PGN_0365 PGN_0517 PGN_0281 PGN_0366 PGN_1157 PGN_0543 PGN_0570 PGN_0569 PGN_0981 PGN_0819 PGN_0962 PGN_1711 PGN_1883 PGN_0987 PGN_1218 PGN_1229 PGN_1381 PGN_1805 PGN_1969 PGN_2045 PGN_2060 Proteins are listed by ORF number in the same manner as in Table 3. Transcription machinery Most of...”

An08g09210 uncharacterized protein from Aspergillus niger
33% identity, 95% coverage

• Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics
  Sun, Genome biology 2007
  • “...Anig10968 K02021 ABC transport system ATP-binding protein An08g04860 0 33 FG02316 0 30 Transport 5.4.99.- An08g09210 Anig02930 K01865 S-adenosylmethionine tRNA ribosyltransferase tRNA modification 4.2.1.94 An08g09920 Anig07347 Scytalone dehydratase FG06477 7E-17 32 Biosynthesis of melanin 4.2.3.19 An11g06270 Anig08665 K04121 Ent-kaurene synthase An18g02710 1.5E-67 31 AN1594 3E-78 31...”

SEN1504 putative isomerase from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
28% identity, 89% coverage

• Rapid identification of novel antigens of Salmonella Enteritidis by microarray-based immunoscreening
  Danckert, Mikrochimica acta 2014
  • “...facilitates initial interaction to the intestinal epithelium [ 28 ]. SEN4030 and the putative isomerase (SEN1504) are conserved in Salmonella [ 27 ]. Membrane-association is another intriguing feature as it enhances the proteins accessibility in a diagnostic assay. This is true for the ais protein (SEN2278),...”
  • “...SEN3053 DNA Primase 1,746 65 Gammaproteobacteria (51) SEN1186 Conserved hypothetical protein 240 9 Enterobacteriaceae (15) SEN1504 Putative isomerase 1,174 41 Salmonella (1) SEN2278 Ais Protein 606 22 Enterobacteriaceae (5) SEN2659 Multidrug resistance protein A 1,173 43 Enterobacteriaceae (18) SEN2832 Membrane-bound lytic murein transglycosylase A precursor 1,098...”

t1467 putative isomerase from Salmonella enterica subsp. enterica serovar Typhi Ty2
28% identity, 88% coverage

• Evaluation of Topical Lysostaphin as a Novel Treatment for Instrumented Rhesus Macaques (Macaca mulatta) Infected with Methicillin-Resistant Staphylococcus aureus
  Cheleuitte-Nieves, Comparative medicine 2020 (secret)

STM1548 putative S-adenosylmethionine:tRNA-ribosyltransferase-isomerase from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
28% identity, 91% coverage

• Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella
  Yoon, BMC systems biology 2011
  • “...was selected including STM0082 ( srfN /SrfN), STM1244 ( pagD /PagD), STM1246 ( pagC /PagC), STM1548, STM1599 ( pdgL /PdgL), STM1633, STM2585A and STM3595, and their role in virulence was investigated as described below. Analysis of these proteins showed that they are coordinately regulated at the...”
  • “...the four in vitro conditions (Additional file 7 , Figure S3A). All eight proteins (SrfN, STM1548, PdgL, STM1633, STM3595, PagC, PagD, and STM2585A) had increased expression under acidic minimal media (AMMs), which partially mimics the host intracellular environment, compared to log phase growth in LB media....”
• Computational prediction of type III and IV secreted effectors in gram-negative bacteria
  McDermott, Infection and immunity 2011
  • “...STM1599 STM1809 STM1513 STM1633 STM0211 STM1121 STM3392 STM4082 STM3595 STM1548 a SIEVE EffectiveT3 Lower and Schneider 41 CyaA fusion assay 2 3 5 1 14 7 4...”
• Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
  Kingsley, Genome research 2009
  • “...A deletion of 3981 bp has removed some or all of STM1548 through STM1553, which are of unknown function. A 9568 bp deletion in a phage remnant resulted in the...”
• Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium
  Yoon, PLoS pathogens 2009
  • “...analysis. Category No. % Genes co-regulated with SPI-2 Translation, ribosomal structure and biogenesis 4 3.3 STM1548, STM1549, rpsS , STM4508 RNA processing and modification 0 0 Transcription 6 4.9 leuO , STM0859, lrp , STM1547, STM2748, rob Replication, recombination and repair 0 0 Cell cycle control,...”
• The RcsCDB signaling system and swarming motility in Salmonella enterica serovar typhimurium: dual regulation of flagellar and SPI-2 virulence genes
  Wang, Journal of bacteriology 2007
  • “...carA, carB (carA) ilvB, ilvN (ilvB) STM1055 (STM1055) STM1548 STM2137 STM2138 STM2287 STM2585 STM2778 STM2780 STM3133, STM3132 (STM3133) 3.0-3.4 2.7 2.4 2.7 4.1...”

BB0021 S-adenosylmethionine: tRNA ribosyltransferase-isomerase from Borrelia burgdorferi B31
31% identity, 61% coverage

• Cyclic di-GMP modulates gene expression in Lyme disease spirochetes at the tick-mammal interface to promote spirochete survival during the blood meal and tick-to-mammal transmission
  Caimano, Infection and immunity 2015
  • “...bya: Gene RNA-Seq for rrp1 mutant ospC (bbb19) bb0021 malX-1 (bb0116) glpF (bb0240) glpK (bb0241) glpD (bb0243) bb0323 bb0629 bosR (bb0647) bb0680 rpoS (bb0771)...”
• How do lyme borrelia organisms cause disease? The quest for virulence determinants()
  Norris, The open neurology journal 2012
  • “...BB0051 , respectively) serve as negative and positive controls. Mutations in malX , bba06 , bb0021 , and truB yielded consistently low values, indicating loss of infectivity. sodA and erpA mutants yielded intermediate values, whereas rev , gidB , and recG mutants exhibited high levels on...”
• Rrp1, a cyclic-di-GMP-producing response regulator, is an important regulator of Borrelia burgdorferi core cellular functions
  Rogers, Molecular microbiology 2009
  • “...burgdorferi genes activated by Rrp1 BB0014 primosomal protein N ( priA ) R 9.55 0.0117 BB0021 S -adenosylmethionine: tRNA ribosyltransferase-isomerase ARS 8.36 0.00924 Caimano et al . (2007) BB0047 conserved hypothetical protein HX 11.0 0.0275 Ojaimi et al . (2003) ; Hyde et al . (2006)...”
  • “...BBO39 Outer surface protein F ( ospF ) b Genes induced by Rrp1 and RpoS BB0021 S -adenosylmethionine: tRNA ribosyltransferase-isomerase BB0250 dedA protein ( dedA ) BB0567 Chemotaxis histidine kinase ( cheA- 1) c BB0578 Methyl-accepting chemotaxis protein ( mcp-1 ) c BB0588 5-Methylthioadenosine/ S -adenosylhomocysteine...”
• Central role of the Holliday junction helicase RuvAB in vlsE recombination and infectivity of Borrelia burgdorferi
  Lin, PLoS pathogens 2009
  • “...be part of a larger operon containing two additional genes ( Figure S1A ), queA (BB0021, S-adenosylmethionine:tRNA ribosyltransferase-isomerase) and pfpB (BB0020, diphosphate-fructose-6-phosphate 1-phosphotransferase) [34] . To determine whether expression of other genes in the operon might be disturbed by the transposon insertion, we performed RT-PCR on...”
• Analysis of the RpoS regulon in Borrelia burgdorferi in response to mammalian host signals provides insight into RpoS function during the enzootic cycle
  Caimano, Molecular microbiology 2007
  • “...Mut DMC 0.6 0.5 Mut DMC bb0729/gltP WT Mut 37C WT Mut DMC bb0021 0.2 0.15 0.4 0.3 0.2 0 WT 0.25 0.1 0.05 0.1 0.1 Mut 37C 0.4 0.7 0.6 WT 0.8 bb0588/pfs-2 0.7 0...”
  • “...(P 0.05). primarily due to increased RpoS-independent expression. bb0021 was expressed at 2.84-fold higher levels in wildtype compared with rpoS mutant Bb in...”
• MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes
  Cruveiller, Nucleic acids research 2005
  • “...no. O51053), annotated as a putative S -adenosylmethionine:tRNA ribosyl transferase-isomerase ( Figure 2B ). The BB0021 gene, located next to BOBURS0021 and transcribed in the same strand, has been annotated with an identical biological description (Product column, Figure 2B ). An explanation of this observation is...”
  • “...number 3 refers to Identification of probable frameshift, by Zangger N.; Unpublished observations (May-2000). The BB0021 translation product differs from that of the SWISSPROT protein owing to a frameshift in position 205 and the unique AMIGene CDS then corresponds to the missing part of the QUEA...”

SCO1804 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Streptomyces coelicolor A3(2)
32% identity, 91% coverage

• Quantitative Proteome and Phosphoproteome Analyses of Streptomyces coelicolor Reveal Proteins and Phosphoproteins Modulating Differentiation and Secondary Metabolism
  Rioseras, Molecular & cellular proteomics : MCP 2018
  • “...protein n.s. 4.8 n.s. 27.8 Translation/protein folding SCO1491 n.s. Elongation factor - -2.3 - 0.2 SCO1804 5 tRNA ribosyltransferase-isomerase n.s. 2.9 n.s. 7.4 SCO2620 2 Trigger factor chaperone - -1.8 - 0.8 SCO4648 1 Ribosomal protein -1.3 -2.2 0.4 0.2 SCO4725 2 Translation initiation - -1.9...”
• Decoding options and accuracy of translation of developmentally regulated UUA codon in Streptomyces: bioinformatic analysis
  Rokytskyy, SpringerPlus 2016
  • “...synthase, SAM-dependent TadA SCO4038 XNR_2881 tRNA-specific adenosine deaminase FolE SCO3403 XNR_3431 GTP cyclohydrolase I QueA SCO1804 XNR_5018 S-adenosylmethionine:tRNAribosyltransferase-isomerase MnmA SCO5488 XNR_1345 tRNA(Gln,Lys,Glu) U34 2-thiouridylase MiaA SCO5791 XNR_1074 delta(2)-isopentenylpyrophosphatetRNA-adenosine transferase MiaB SCO5787 XNR_1078 tRNA-i(6)A37 methylthiotransferase AroA SCO6819 XNR_1588 5-Enolpyruvylshikimate-3-phosphate synthetase AroB SCO1494 XNR_5357 3-Dehydroquinate synthase AroC SCO1496...”

XNR_5018 S-adenosylmethionine:tRNA ribosyltransferase-isomerase from Streptomyces albidoflavus
30% identity, 81% coverage

• Decoding options and accuracy of translation of developmentally regulated UUA codon in Streptomyces: bioinformatic analysis
  Rokytskyy, SpringerPlus 2016
  • “...SAM-dependent TadA SCO4038 XNR_2881 tRNA-specific adenosine deaminase FolE SCO3403 XNR_3431 GTP cyclohydrolase I QueA SCO1804 XNR_5018 S-adenosylmethionine:tRNAribosyltransferase-isomerase MnmA SCO5488 XNR_1345 tRNA(Gln,Lys,Glu) U34 2-thiouridylase MiaA SCO5791 XNR_1074 delta(2)-isopentenylpyrophosphatetRNA-adenosine transferase MiaB SCO5787 XNR_1078 tRNA-i(6)A37 methylthiotransferase AroA SCO6819 XNR_1588 5-Enolpyruvylshikimate-3-phosphate synthetase AroB SCO1494 XNR_5357 3-Dehydroquinate synthase AroC SCO1496 XNR_5355...”

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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.