PaperBLAST

PaperBLAST Hits for sp|Q9I037|QUEF_PSEAE NADPH-dependent 7-cyano-7-deazaguanine reductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=queF PE=3 SV=1 (276 a.a., MQHPAEHSPL...)

Show query sequence

>sp|Q9I037|QUEF_PSEAE NADPH-dependent 7-cyano-7-deazaguanine reductase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=queF PE=3 SV=1
MQHPAEHSPLGKTSEYVSSYTPSLLFPISRTAKWAELGLSAETLPYRGVDIWNCYELSWL
TPAGKPVVAIGEFSIPADSPNIIESKSFKLYLNSLNQSAFDSREALRAVLQKDLSAAVGA
PVGVRLRSLDEVAEEGIGRLPGRCIDELDIAVDGYEQPRPELLRCDAGRIVEEQLYSHLL
KSNCPVTGQPDWGTLVVDYRGPALDPASLLAYLVSFRQHQDFHEQCVERIFLDLQRLLQP
QALSVYARYVRRGGLDINPYRSLAEVAPDNRRLVRQ

Running BLASTp...

Found 43 similar proteins in the literature:

PA2806 hypothetical protein from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage

• Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics
  Ducret, Frontiers in microbiology 2021
  • “...Supplementary Table 3 ). PA2807 is part of a gene cluster comprised of ptrA ( PA2806 ), PA2807 , and queF ( PA2808 ) next to the CopRS TCS (PA2809-PA2810) ( Quintana et al., 2017 ). PtrA is a small periplasmic protein involved in Cu resistance...”
• Advances in Understanding of the Copper Homeostasis in Pseudomonas aeruginosa
  Hofmann, International journal of molecular sciences 2021
  • “...88 , 122 , 126 ] PA2524 czcS [ 88 , 122 , 126 ] PA2806 Hypothetical protein: potentially a NADPH-dependent reductase [ 107 ] PA2807 Hypothetical protein: azurin/plastocyanin family [ 88 , 107 ] PA2808 ptrA [ 88 , 91 ] PA0958 oprD (downregulation with...”
• Identification and Characterization of Type IV Pili as the Cellular Receptor of Broad Host Range Stenotrophomonas maltophilia Bacteriophages DLP1 and DLP2
  McCutcheon, Viruses 2018
  • “...and regulatory components, pilJ , pilR , pilS , and algR . The additional gene, PA2806 , encodes a conserved hypothetical protein, with homology to QueF, an NADPH-dependent 7-cyano-7-deazaguanine reductase enzyme involved in queuosine biosynthesis, with unknown function related to pilus biogenesis. While the pilus related...”
  • “...mutant, revealed that all lack a twitching zone and therefore functional pili, except for the PA2806 mutant. These findings mirror what others have observed for pilus-specific phages P04, B3, and D3112 [ 45 ], and support the hypothesis that DLP1 uses the type IV pilus for...”
• Copper homeostasis networks in the bacterium Pseudomonas aeruginosa
  Quintana, The Journal of biological chemistry 2017
  • “...cytoplasmic proteins fall into this cluster (i.e. queF (PA2806), PA3520, and PA3574.1, which encode the putative cytoplasmic Cu chaperones CopZ1 and CopZ2, and...”
• A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1
  Lecoutere, MicrobiologyOpen 2012
  • “...70 * PA2800 Conserved hypothetical protein M U 26.1 25 5.41 4.90 0.691 0.226 71 PA2806 Conserved hypothetical protein S C 30.8 30 5.48 5.45 0.569 0.239 72 * PA2851 efp Translation elongation factor P J C 21.0 27 4.82 4.85 0.702 0.283 73 PA2951 etfA...”
  • “...database, 12 of which so far lacked experimental confirmation (PA0446, PA0664, PA0976, PA1597, PA1677, PA1837, PA2806, PA3302, PA3481, PA3801, PA4458, and PA5339). Among those 19 proteins, 12 are conserved in other organisms. Obviously, their substantial expression suggests that they have biological roles in P. aeruginosa ,...”
• Genes involved in copper resistance influence survival of Pseudomonas aeruginosa on copper surfaces
  Elguindi, Journal of applied microbiology 2009
  • “...Cot protein, which is involved in copper tolerance. In addition, the P. aeruginosa homolog, cinA (PA2806), is also transcribed in copper exposed cells and its disruption leads to a slight reduction in copper tolerance, such as 12 mm of inhibition radius in disk assay compared to...”
• The copper-inducible cin operon encodes an unusual methionine-rich azurin-like protein and a pre-Q0 reductase in Pseudomonas putida KT2440
  Quaranta, Journal of bacteriology 2007
  • “...(38). In addition, the P. aeruginosa homolog, cinA (PA2806), is also transcribed in copperexposed cells, and its disruption leads to a slight reduction in...”
  • “...Transcriptional activation by copper was also demonstrated for PA2806, PA2809, and PA2810 (corresponding to the P. putida KT2440 cinQ, cinR, and cinS genes,...”

WP_208691271 NADPH-dependent 7-cyano-7-deazaguanine reductase QueF from Pseudomonas oryzihabitans
68% 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
  • “...Ins 415457 Zinc transporter ZntB WP_197850824 Supplementary Figure S68 1 aa Ins 209245 NADH-dependent 7-cyano-7-deazaguanine WP_208691271 Supplementary Figure S69 1 aa Ins 180220 TerB family tellurite resistance protein WP_017939833 Figure 6A ; Supplementary Figure S70 6 aa Ins 2775 Thermotolerans clade ( Zestomonas gen. nov.) TIGR02099...”

BPP1768 conserved hypothetical protein from Bordetella parapertussis 12822
60% identity, 95% coverage

• Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis
  Gogol, BMC genomics 2007
  • “...7 BPP1024 8 A/T y I M Energy metabolism, carbon 68 BP2084 7 BB3340 7 BPP1768 8 A/T y I H Conserved hypothetical 69 BP1811 6 BB3216 6 BPP1892 8 kdgT A/T y I M Transport/binding proteins 70 BP1781 6 BB2260 7 BPP2012 8 A/T y...”

BB3340 7-cyano-7-deazaguanine reductase from Bordetella bronchiseptica RB50
60% identity, 95% coverage

• Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis
  Gogol, BMC genomics 2007
  • “...64 BB1238 7 BPP1024 8 A/T y I M Energy metabolism, carbon 68 BP2084 7 BB3340 7 BPP1768 8 A/T y I H Conserved hypothetical 69 BP1811 6 BB3216 6 BPP1892 8 kdgT A/T y I M Transport/binding proteins 70 BP1781 6 BB2260 7 BPP2012 8...”

BP2084 conserved hypothetical protein from Bordetella pertussis Tohama I
59% identity, 95% coverage

• Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis
  Gogol, BMC genomics 2007
  • “...Conserved hypothetical 64 BB1238 7 BPP1024 8 A/T y I M Energy metabolism, carbon 68 BP2084 7 BB3340 7 BPP1768 8 A/T y I H Conserved hypothetical 69 BP1811 6 BB3216 6 BPP1892 8 kdgT A/T y I M Transport/binding proteins 70 BP1781 6 BB2260 7...”

QUEF_VIBCH / Q9KTK0 NADPH-dependent 7-cyano-7-deazaguanine reductase; 7-cyano-7-carbaguanine reductase; NADPH-dependent nitrile oxidoreductase; PreQ(0) reductase; EC 1.7.1.13 from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (see paper)
Q9KTK0 preQ1 synthase (EC 1.7.1.13) from Vibrio cholerae (see paper)
55% identity, 95% coverage

• function: Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1).
  catalytic activity: 7-aminomethyl-7-carbaguanine + 2 NADP(+) = 7-cyano-7- deazaguanine + 2 NADPH + 3 H(+) (RHEA:13409)
  subunit: Homodimer.

YqcD / b2794 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) from Escherichia coli K-12 substr. MG1655 (see paper)
queF / Q46920 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) from Escherichia coli (strain K12) (see 4 papers)
QUEF_ECOLI / Q46920 NADPH-dependent 7-cyano-7-deazaguanine reductase; 7-cyano-7-carbaguanine reductase; NADPH-dependent nitrile oxidoreductase; PreQ(0) reductase; EC 1.7.1.13 from Escherichia coli (strain K12) (see 3 papers)
Q46920 preQ1 synthase (EC 1.7.1.13) from Escherichia coli (see 2 papers)
WP_000100421 NADPH-dependent 7-cyano-7-deazaguanine reductase QueF from Escherichia coli
NP_417274 7-cyano-7-deazaguanine reductase from Escherichia coli str. K-12 substr. MG1655
NP_417274, b2794 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
53% identity, 95% coverage

• function: Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), a late step in the queuosine pathway. Is highly specific for its natural substrate preQ0, since it cannot use various aliphatic, aromatic, benzylic and heterocyclic nitriles, such as acetonitrile, benzonitrile, benzylcyanide and 2-cyanopyrrole, although it can reduce the substrate analog 5-cyanopyrrolo[2,3-d]pyrimidin-4-one with lesser efficiency.
  catalytic activity: 7-aminomethyl-7-carbaguanine + 2 NADP(+) = 7-cyano-7- deazaguanine + 2 NADPH + 3 H(+) (RHEA:13409)
  subunit: Homodimer.
• Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae
  Marmo, Viruses 2020
  • “...with the two proteins QueF-L of Aeropyrum pernix K1 (BAA80469) and QueF of Escherichia coli (WP_000100421) used as anchors by Hutinet et al. [ 63 ] to search for the respective orthologues in bacteriophages. Interestingly, Gp35 (QueC) lacks the glutamine amido-transferase (GAT) domain found in other...”
• Kinetic Analysis and Probing with Substrate Analogues of the Reaction Pathway of the Nitrile Reductase QueF from Escherichia coli.
  Jung, The Journal of biological chemistry 2016
  • GeneRIF: A model of QueF substrate recognition and a catalytic pathway for the enzyme are proposed based on these data.
• Expression and characterization of the nitrile reductase queF from E. coli.
  Moeller, Enzyme and microbial technology 2013 (PubMed)
  • GeneRIF: The expression of NP-417272 after cloning in E coli BL21 cells was studied, and optimal conditions for its activity toward its natural substrate were determined.
• Four additional natural 7-deazaguanine derivatives in phages and how to make them
  Cui, Nucleic acids research 2023
  • “...to the sequences of three experimentally validated QueF proteins: the bimodular QueF of Escherichia coli (NP_417274), the unimodular QueF of Bacillus subtilis (NP_389258) and the QueF-L of Pyrobaculum calidifontis (WP_011848915). Surprisingly, no phage QueF sequences aligned with QueF-L (Alignment S1). The bimodular sequence aligned with half...”
• 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
  • “...(b2765), CDG synthase (b2777), preQ0 synthethase (b0444), preQ0 reductase (b2794), and Tgt (b0406) lead to disappearance of both Q and oQ from RNA. GCH I is an...”
• Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
  Thiele, Biophysical journal 2010
  • “...genome. The fourth eigen-reaction consists of the synthesis of b2794 (QueF) and b1084 (Rne). QueF is a protein involved in the synthesis of pre_Q0, a precursor...”

c3360 Hypothetical protein yqcD from Escherichia coli CFT073
53% identity, 95% coverage

• Review of past and present research on verocytotoxin producing Escherichia coli (VTEC) in relation to public health protection
  Baylis, 2008

Z4111 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
52% identity, 95% coverage

• Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People's Republic of China
  Wang, Infection and immunity 1992
  • “...Z4022 Z4107 Z4108 Z4023 Z4105, B499 Z4090, Z4114 Z4093 Z4111 Z4095 Z4094 Z4057 Z4060 Z4015 Z4746 Z4753 Z4063, Z4067, Z4074, Z4106 Z4113 Z4064 Z4055 Z4083 B40...”

t2876 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
52% identity, 95% coverage

• The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021
  European, EFSA journal. European Food Safety Authority 2023
  • “...(1). In 2017, spatypes: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). In 2019, spatypes were not reported; however, 159/160 isolates were confirmed to belong to CC398 using the sau1hsdS1 CC398 PCR reaction (Stegger et al., 2011). The remaining isolate did...”
• The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2019-2020
  European, EFSA journal. European Food Safety Authority 2022
  • “...(1). In 2017, spatypes: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). In 2019, spatypes were not reported; however, 159/160 isolates were confirmed to belong to CC398 using the sau1hsdS1 CC398 PCR reaction (Stegger etal., 2011). The remaining isolate did not...”
• The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019
  European, EFSA journal. European Food Safety Authority 2021
  • “...(1).In 2017, spa types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1).In 2019, spa types were not reported; however, 159/160 isolates were confirmed to belong to CC 398 using the sau1hsdS1 CC 398 PCR reaction (Stegger etal., 2011 ). The remaining...”
• The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018
  European, EFSA journal. European Food Safety Authority 2020
  • “...(1). 13. spa types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). 14. spa types: t011 CC 398 (6 isolates), t034 CC 398 (24), t1250 CC 398 (2), t1793 CC 398 (1), t3171 CC 398 (1). 15. spa types: t011 CC...”
  • “...In 2017, spa types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). 2: In 2011, spa types: t011 (97 isolates), t034 (8), t108 (3), t1197 (7), t1451 (3), t2346 (3), unspecified (68). In 2015, spa types not reported. In 2017, spa...”
• The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2017
  European, EFSA journal. European Food Safety Authority 2019
  • “...The other spa types detected in Switzerland in fattening pigs were t899, t1451, t2330 and t2876 (all associated with CC398). Table 53 Meticillinresistant Staphylococcus aureus in foodproducing animals (excluding clinical investigations), 2017 Country Production type/monitoring description (where specified)) Sample unit Number Units tested Positive for MRSA...”
  • “...(1). g spa types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). h spa types not reported. John Wiley & Sons, Ltd Clinical investigations for MRSA in foodproducing animals Typically, clinical investigations differ from monitoring studies in foodproducing animals; as selective...”

3s19A / Q9KTK0 Crystal structure of the r262l mutant of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae complexed with preq0
54% identity, 95% coverage

• Ligand: 7-deaza-7-aminomethyl-guanine (3s19A)

swp_3543 GTP cyclohydrolase I from Shewanella piezotolerans WP3
52% identity, 93% coverage

• Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
  Ding, Genetics research 2021
  • “...02 Bacterial secretion system swp_0196, swp_0739, swp_0187, swp_0189, swp_0188 13 4 0.67 3.34 E 02 swp_3543, swp_4396, swp_0518, swp_0110 Note: the bold enrichment terms indicate that there was no KEGG enrichment and InterPro enrichment was used alternatively; indicate that the enrichment analysis returned with no results....”

SO_1608 conserved hypothetical protein from Shewanella oneidensis MR-1
51% identity, 90% coverage

• Validating annotations for uncharacterized proteins in Shewanella oneidensis
  Louie, Omics : a journal of integrative biology 2008
  • “...782527, 12799002 10377098 15901686, 16452451 11488932 12055309 SO_1608 SO_1789 SO_1851 SO_1963 SO_2042 SO_2043 SO_2593 SO_2603 SO_2614 SO_2627 SO_3014 SO_3015...”

HD1665 possible GTP cyclohydrolase I from Haemophilus ducreyi 35000HP
48% identity, 96% coverage

• Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants
  Gangaiah, Journal of bacteriology 2013
  • “...and associated proteins Lipooligosaccharide biosynthesis HD0450-4h HD0653 HD1665 Gene(s)b Function and gene identification codea flp operon protein Flp1 DNA...”
  • “...Cpx 2CST system downregulated the expression of waaF and HD1665, while it upregulated the expression of waaA; these genes are involved in the biosynthesis of...”

VP_RS03365 NADPH-dependent 7-cyano-7-deazaguanine reductase QueF from Vibrio parahaemolyticus RIMD 2210633
52% identity, 95% coverage

• Identification of Antibacterial Components in the Methanol-Phase Extract from Edible Herbaceous Plant Rumex madaio Makino and Their Antibacterial Action Modes
  Liu, Molecules (Basel, Switzerland) 2022
  • “...VP_RS16930 3.141 Permease Folate biosynthesis VP_RS17975 0.476 Phenylalanine 4-monooxygenase VP_RS09130 0.494 Aminodeoxychorismate synthase component I VP_RS03365 0.491 NADPH-dependent 7-cyano-7-deazaguanine reductase QueF VP_RS07885 0.497 7-cyano-7-deazaguanine synthase QueC VP_RS09170 0.389 6-carboxytetrahydropterin synthase QueD VP_RS13730 0.433 Aminodeoxychorismate/anthranilate synthase component II VP_RS07890 0.484 7-carboxy-7-deazaguanine synthase QueE VP_RS17980 0.432 4a-hydroxytetrahydrobiopterin dehydratase...”

BMSBPS_0622 NADPH-dependent 7-cyano-7-deazaguanine reductase QueF from Candidatus Pantoea carbekii
48% identity, 95% coverage

• Habitat visualization and genomic analysis of "Candidatus Pantoea carbekii," the primary symbiont of the brown marmorated stink bug
  Kenyon, Genome biology and evolution 2015
  • “...decode all 20 amino acids ( table 1 ), including the translation initiating N -formyl-methionyl-tRNA (BMSBPS_0622), and a isoleucine-charged tRNA (BMSBPS_0773) that, following posttranscriptional lysylation of a position 34 cytidine by TilS, changes the anticodon from CAU to AUA to prevent misreading of AUG as isoleucine...”

wcw_0365 NADPH-dependent 7-cyano-7-deazaguanine reductase QueF from Waddlia chondrophila WSU 86-1044
47% identity, 99% coverage

• Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum
  de, The ISME journal 2016
  • “...++++ wcw_0203 Histone H1-like protein Hc1 hctA wcw_0354 N -acetylmuramoyl- l -alanine amidase amiA +++ wcw_0365 Enzyme related to GTP cyclohydrolase I queF ++++ wcw_0390 Rhs family protein rhs9 ++++ wcw_0423 Signal recognition particle GTPase ftsY +++ wcw_0430 NADH dehydrogenase, FAD-containing subunit ndh ++++ wcw_0544 Integrase...”

A1S_2313 7-cyano-7-deazaguanine reductase from Acinetobacter baumannii ATCC 17978
49% identity, 92% coverage

• Comparative analysis of Acinetobacters: three genomes for three lifestyles
  Vallenet, PloS one 2008
  • “...gamma subunit ABAYE2778,ABSDF2377,ACIAD1089 No No A1S_2447 pstC EsvD high-affinity phosphate transport protein ABAYE1033,ABSDF1101,ACIAD1213 No No A1S_2313 queF EsvE1 7-cyano-7-deazaguanine reductase ABAYE1164,ABSDF1213,ACIAD2261 No No A1S_2314 - EsvE2 conserved hypothetical protein ABAYE1163,ABSDF1212,ACIAD2262 No No A1S_2315 rodA EsvE3 rod shape-determining protein ABAYE1162,ABSDF1211,ACIAD2263 No Yes A1S_3218 czcB EsvF1 RND divalent...”

P44165 Uncharacterized protein HI_1340 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI1340 conserved hypothetical protein from Haemophilus influenzae Rd KW20
39% identity, 59% coverage

• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...phosphatase SixA 210. HP HI1339 950818 P71378 Late embryogenesis abundant protein 211. HP HI1340 950814 P44165 Outer membrane efflux porinTdeA 212. HP HI1343 949643 P71379 cysteine desulfurase, catalytic subunit CsdA 213. HP HI1349 950182 P45173 DNA-binding ferritin-like protein 214. HP HI1351 950443 P44167 tRNAmo(5)U34 methyltransferase, SAM-dependent...”
  • “...26. P44132 Yes Metabolism molecule 27. P44138 Yes Cellular process 28. P44140 Yes Yes 29. P44165 Yes Yes 30. P45182 Yes Yes 31. P44169 Yes Yes 32. P44183 Yes Yes 33. P56507 Yes Yes 34. P45217 Yes Yes 35. P44242 Yes Cellular process 36. P44246 Yes...”
• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...P44164 phosphohistidine phosphatase SixA 210. HP HI1339 950818 P71378 Late embryogenesis abundant protein 211. HP HI1340 950814 P44165 Outer membrane efflux porinTdeA 212. HP HI1343 949643 P71379 cysteine desulfurase, catalytic subunit CsdA 213. HP HI1349 950182 P45173 DNA-binding ferritin-like protein 214. HP HI1351 950443 P44167 tRNAmo(5)U34...”
• Identification of new genetic regions more prevalent in nontypeable Haemophilus influenzae otitis media strains than in throat strains
  Xie, Journal of clinical microbiology 2006
  • “...1.00 0.69 0.64 0.42 0.06 0 0 0 HI1339, HI1340, HI1462, HI1462.1 HI0416, HI0417 HI1154 HI1730, HI1731 Phage gene in H. influenzae R2866 Hinf801001934 in H....”

jhp1308 putative from Helicobacter pylori J99
43% identity, 31% coverage

• Identification of target genes regulated by the two-component system HP166-HP165 of Helicobacter pylori
  Dietz, Journal of bacteriology 2002
  • “...HP1408 to HP1412 and JHP1300 to JHP1307 (i.e., HP1413 and JHP1308) are orthologs. ORF JHP925 is an ortholog of HP1408 and HP427 and is preceded by a promoter...”

HP1413 conserved hypothetical protein from Helicobacter pylori 26695
37% identity, 41% coverage

• Structure based annotation of Helicobacter pylori strain 26695 proteome
  Singh, PloS one 2014
  • “...HP0031 (USP like protein, universal stress protein), HP0728 (isoleucyl-tRNA lysidine synthetase), HP1211 (alginate lyase) and HP1413 ( NADPH-dependent 7-cyano-7-deazaguanine reductase ). Using the protein sequence based annotation, the function of some proteins could be predicted. Some of these examples include; HP0129 (zinc ion binding protein), HP0130...”
• Two-component systems of Helicobacter pylori contribute to virulence in a mouse infection model
  Panthel, Infection and immunity 2003
  • “...the regions between the 23S ribosomal DNA and ORFs HP1413 and HP422, encoding target genes under the control of the PHP1408 promoter, were replaced by kanamycin...”
• Identification of target genes regulated by the two-component system HP166-HP165 of Helicobacter pylori
  Dietz, Journal of bacteriology 2002
  • “...by cloning a 506-bp PstI-SacI fragment derived from ORF HP1413 (PCR amplified with primer pair 1413-5-1413-3 from chromosomal DNA of H. pylori G27) and a 543-bp...”
  • “...located between the 23S rDNA loci and ORFs HP1413 and HP422 replaced by kanamycin and chloramphenicol resistance cassettes, respectively P76 with the regions...”

NGO1684 hypothetical protein from Neisseria gonorrhoeae FA 1090
NGFG_02134 preQ(1) synthase from Neisseria gonorrhoeae MS11
37% identity, 35% coverage

• A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur
  Yu, PloS one 2014
  • “...+ NR TAATATCAATATATTGATT NGO1284 hypothetical protein + NR ACAAAGAAGTATACTTCTT NGO1419 hypothetical protein + NR TAATATAAGCGGCGGTATT NGO1684 hypothetical protein NE CCATACAACTATATTTTTT NGO1738 NADH dehydrogenase I subunit M + Activated TAACAGCACGCTCATTGTC NGO1745 NADH dehydrogenase I subunit G NE TCAAATAAGAATCGTTATC NGO1751 3 NADH dehydrogenase I subunit A + 4...”
• Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins
  Phillips, PloS one 2012
  • “...carriers NGO0704 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein Riboflavin, FMN, and FAD 1.100 (1) NGO1684 7-cyano-7-deazaguanine reductase Folic acid 1.210 (1) Energy metabolism NGO2149 F0F1 ATP synthase subunit gamma; F-type H+-transporting ATPase subunit gamma ATP-proton motive force interconversion 2.138 (1) NGO2148 F0F1 ATP synthase subunit...”
• RpoH mediates the expression of some, but not all, genes induced in Neisseria gonorrhoeae adherent to epithelial cells
  Du, Infection and immunity 2006
  • “...is necessary for this step of infection. Two genes, NGO1684 and NGO0340, while greatly induced by host cell contact, were found to be RpoH independent,...”
  • “...to host cell contact. Furthermore, NGO0340, but not NGO1684, was shown to be important for both adherence and invasion of epithelial cells, suggesting a...”
• Transcriptional landscape and essential genes of Neisseria gonorrhoeae
  Remmele, Nucleic acids research 2014
  • “...67 ) (NGFG_01512) and a riboswitch involved in the biosynthesis of queuosine ( 68 ) (NGFG_02134) have been identified. Another queuosine riboswitches (NGFG_00267) and a riboswitch for S- adenosylmethionine ( 69 )(NGFG_00245) were also predicted but did not reach significance. Gonococcal promoters frequently contain DUS Next...”

SERP0394 hypothetical protein from Staphylococcus epidermidis RP62A
SE0510 conserved hypothetical protein from Staphylococcus epidermidis ATCC 12228
36% identity, 47% coverage

• Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis
  Gonçalves, Frontiers in microbiology 2022
  • “...Response regulator SERP0365 saeR Staphylococcal Accessory Regulator family SERP1849/76/79 SarR/Z/V t-RNA modification NADPH-dependent 7-cyano-7-deazaguanine reductase SERP0394 queF Queuine trna-ribosyltransferase SERP1203 tgt Epoxyqueuosine reductase QueH SERP2147 queH tRNA (guanine-N(1)-)-methyltransferase SERP0806 trmD S. epidermidis metabolic and biological activities induced at skin pH Promotion of bacterial growth We found...”
• Transporters and Efflux Pumps Are the Main Mechanisms Involved in Staphylococcus epidermidis Adaptation and Tolerance to Didecyldimethylammonium Chloride
  Ribič, Microorganisms 2020
  • “...Lipoprotein signal peptidase Metabolism and SE0274 8.0 Imidazole glycerol phosphate synthase subunit HisH biosynthesis of SE0510 8.0 7Cyano7deazaguanine reductase secondary metabolites SE0873 7.0 Bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase Ribosome SE1017 rpmG2 5.3 50S ribosomal protein L33 2 SE0913 rpsP 5.6 30S ribosomal protein S16...”

NMB0317 hypothetical protein from Neisseria meningitidis MC58
37% identity, 35% coverage

• Characterization of a transcriptional TPP riboswitch in the human pathogen Neisseria meningitidis
  Righetti, RNA biology 2020
  • “...The programme identified four putative elements (Table S1). A preQ1 RS candidate was located upstream NMB0317 ( queF ), coding for a 7-cyano-7-deazaguanine reductase; an S-adenosylmethionine (SAM) RS mapped upstream NMB1799 ( metK ), coding for an S-adenosylmethionine synthetase; two TPP RSs were identified upstream NMB2040...”
• The Hfq regulon of Neisseria meningitidis
  Huis, FEBS open bio 2017
  • “...Sodium/alanine symporter Membrane components 13.1 4.0 NMB0227 Mn 2+ iron transporter Membrane components 3.3 2.4 NMB0317 queF 7cyano7deazaguanine reductase tRNA modification 4.5 4.5 NMB0325 rplU 50S ribosomal protein L21 Ribosomal proteins 22.9 5.2 NMB0430 prpB 2methylisocitrate lyase Propionate metabolism 9.1 20.4 28.2 NMB0431 prpC Methylcitrate synthase...”
  • “...zinccontaining alcohol dehydrogenase AdhP) is known to be downregulated under conditions of zinc limitation, while NMB0317 (NADPHdependent 7cyano7deazaguanine reductase QueF, involved in queuosine biosynthesis) is downregulated when zinc is abundant. Both genes are upregulated in the hfq deletion mutant strain. Therefore, the interplay of Hfq, Zur,...”
• The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element
  Pawlik, Journal of bacteriology 2012
  • “...470 MP18 MP183 MP19 MP184 475 469 qRT-PCR nmb0317 nmb0525 nmb0546 nmb0577 nmb0586 nmb0587 nmb0588 nmb0817 nmb0819 nmb0820 nmb0942 nmb0964 nmb0990 nmb1475...”
  • “...genes were organized in four transcriptional units: nmb0317 and nmb0316 encode a 7-cyano-7-deazaguanine reductase and an integral membrane protein,...”
• Fur-mediated global regulatory circuits in pathogenic Neisseria species
  Yu, Journal of bacteriology 2012
  • “...FT 53 NGO0322 Hypothetical protein FT 53 NGO0114 NMB1898 NMB0317 NMB0294 FT FT NGO0108 Biosynthesis fetA 44 44 44 44 Adaption/stress response dnaK, heat shock...”

QUEF_GEOKA / Q5L1B7 NADPH-dependent 7-cyano-7-deazaguanine reductase; 7-cyano-7-carbaguanine reductase; NADPH-dependent nitrile oxidoreductase; Nitrile reductase; NRed; PreQ(0) reductase; EC 1.7.1.13 from Geobacillus kaustophilus (strain HTA426)
43% identity, 28% coverage

• function: Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), a late step in the queuosine pathway. Is highly specific for its natural substrate preQ0, since it cannot use various aliphatic, aromatic and heterocyclic nitriles, although it can reduce the substrate analog 5- cyanopyrrolo[2,3-d]pyrimidin-4-one with lesser efficiency.
  catalytic activity: 7-aminomethyl-7-carbaguanine + 2 NADP(+) = 7-cyano-7- deazaguanine + 2 NADPH + 3 H(+) (RHEA:13409)

DNO_0818 7-cyano-7-deazaguanine reductase from Dichelobacter nodosus VCS1703A
39% identity, 37% coverage

• Genomic evidence for a globally distributed, bimodal population in the ovine footrot pathogen Dichelobacter nodosus
  Kennan, mBio 2014
  • “...192 4 1 ABC iron transporter permease DNO_0817 13 816 2 0 2,3,4,5-Tetrahydropyridine-2-carboxylate N -succinyltransferase DNO_0818 17 474 2 0 GTP cyclohydrolase I DNO_0819 48 1,236 1 0 Two-component phosphate sensor PhoR DNO_0820 19 675 7 1 Conserved hypothetical membrane protein DNO_0823 31 1,197 2 1...”

SAUSA300_0713 GTP cyclohydrolase I from Staphylococcus aureus subsp. aureus USA300_FPR3757
40% identity, 31% coverage

• Identification of novel genetic factors that regulate c-di-AMP production in <i>Staphylococcus aureus</i> using a riboswitch-based biosensor
  Kviatkovski, mSphere 2024
  • “...1S3D6 Between SAUSA300_0714 and SAUSA300_0715 SAUSA300_0715: nrdI (ribonucleotide reductase stimulatory protein) 793599 Between operon SAUSA300_0714, SAUSA300_0713 and operon SAUSA300_0715 ( nrdI ), SAUSA300_0716 ( nrdE ), SAUSA300_0717 ( nrdF ) 1S3C9 SAUSA300_0014 gdpP (phosphodiesterase) 18536 1S3H10 SAUSA300_0014 gdpP (phosphodiesterase) 18362 2S1G4 Between SAUSA300_0672 and SAUSA300_0673 SAUSA300_0672:...”
  • “...2S2F4 Between SAUSA300_0714 and SAUSA300_0715 SAUSA300_0715: nrdI (ribonucleotide reductase stimulatory protein) 793572 Between operon SAUSA300_0714, SAUSA300_0713 and operon SAUSA300_0715 ( nrdI ), SAUSA300_0716 ( nrdE ), SAUSA300_0717 ( nrdF ) 2S3D4 SAUSA300_2553 sycG (syroheme synthase) 2761481 SAUSA300_2554 ( cysJ ), SAUSA300_2553 ( cysG ) 2S3G11 SAUSA300_2160...”

BMMGA3_03100 preQ(1) synthase from Bacillus methanolicus MGA3
41% identity, 31% coverage

• Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape
  Irla, BMC genomics 2015
  • “...catabolism BMMGA3 _ 10440 - BMMGA3 _ 10445 (PreQ 1 )- queF 7-amminomethyl-7-deazaguanine Queuosine biosynthesis BMMGA3_03100 (PreQ 1 )- queC - queD - queE Queuosine biosynthesis BMMGA3_09070-BMMGA3_09080 (c-di-GMP)- BMMGA3 _ 15625 Cyclic di-GMP Unknown function BMMGA3 _ 15625 (c-di-GMP)- BMMGA3 _ 04760 - BMMGA3 _ 04765...”

STER_RS04310 preQ(1) synthase from Streptococcus thermophilus LMD-9
41% identity, 31% coverage

• Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome
  Henry, Frontiers in microbiology 2019
  • “...release factor A YP_820239.1 WP_002948472.1 STER_0793 STER_RS03890 QueF NADPH-dependent 7-cyano-7-deazaquanine reductase YP_820305.1 WP_002946191.1 STER_ 0872 STER_RS04310 RpmC 50S Ribosomal protein L29 YP_821209.1 WP_002952156.1 STER_1899 STER_RS09305 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...”

QUEF_BACSU / O31678 NADPH-dependent 7-cyano-7-deazaguanine reductase; 7-cyano-7-carbaguanine reductase; NADPH-dependent nitrile oxidoreductase; PreQ(0) reductase; EC 1.7.1.13 from Bacillus subtilis (strain 168) (see 3 papers)
O31678 preQ1 synthase (EC 1.7.1.13) from Bacillus subtilis (see 2 papers)
NP_389258 NADPH-dependent 7-cyano-7-deazaguanine reductase from Bacillus subtilis subsp. subtilis str. 168
BSU13750 7-cyano-7-deazaguanine reductase from Bacillus subtilis subsp. subtilis str. 168
40% identity, 31% coverage

• function: Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), a late step in the queuosine pathway.
  catalytic activity: 7-aminomethyl-7-carbaguanine + 2 NADP(+) = 7-cyano-7- deazaguanine + 2 NADPH + 3 H(+) (RHEA:13409)
  cofactor: Note=Does not require a metal cofactor
  subunit: Forms an asymmetric tunnel-fold homodecamer of two head-to- head facing pentamers, harboring 10 active sites at the intersubunit interfaces.
• S-bacillithiolation protects conserved and essential proteins against hypochlorite stress in firmicutes bacteria
  Chi, Antioxidants & redox signaling 2013
  • “...1. (Continued) 1284 YumC ThrS QueF O05268 P18255 O31678 A7ZAR2 PpaC B. amyloliquefaciens A7Z3U1 MetE YphP*,# AroA P39912 P54170 SerA* P35136 GuaB PpaC* P37487...”
• Four additional natural 7-deazaguanine derivatives in phages and how to make them
  Cui, Nucleic acids research 2023
  • “...QueF proteins: the bimodular QueF of Escherichia coli (NP_417274), the unimodular QueF of Bacillus subtilis (NP_389258) and the QueF-L of Pyrobaculum calidifontis (WP_011848915). Surprisingly, no phage QueF sequences aligned with QueF-L (Alignment S1). The bimodular sequence aligned with half of the phage QueF sequences ( Supplementary...”
• Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme
  Swairjo, Acta crystallographica. Section F, Structural biology and crystallization communications 2005
  • “...QueF sequence was obtained from GenBank (accession No. NP_389258, GeneID 939296). The sequence similarity and identity between the two proteins is 26 and 14%,...”
  • “...QueF N-terminal His6-tagged B. subtilis QueF (GenBank NP_389258) was overexpressed, purified and processed for His6-tag removal as described in Van Lanen...”
• A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century
  Bremer, Microbial biotechnology 2023
  • “...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 NADPHdependent 7cyano7deazaguanine reductase (moonlighting hydratase) 1.7.1.13 BSU08910 queG ygaP, yhbA epoxyqueuosine reductase 1.17.99.6 BSU15750 rlmN yloN 23S rRNA m2A2503 methyltransferase and tRNA A37 C2 methyltransferase 2.1.1.192 BSU00180 tadA...”

4f8bB / O31678 Crystal structure of the covalent thioimide intermediate of unimodular nitrile reductase quef (see paper)
40% identity, 31% coverage

• Ligands: 2-amino-5-[(z)-iminomethyl]-3,7-dihydro-4h-pyrrolo[2,3-d]pyrimidin-4-one; magnesium ion (4f8bB)

Bd0087 GTP cyclohydrolase I from Bdellovibrio bacteriovorus HD100
36% identity, 38% coverage

• A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus
  Crossman, The ISME journal 2013
  • “...The remaining five orthologues with a predicted encoded function include BMS_2143 , the homolog of Bd0087 . This resembles a guanosine triphosphate cyclohydrolase that encodes the de novo synthesis pathway for tetrahydrofolate, a coenzyme involved in transfer of one-carbon groups. A second orthologue, BMS_0990 (a Bd1990...”

PG1347 conserved hypothetical protein from Porphyromonas gingivalis W83
42% identity, 29% coverage

• PG1058 Is a Novel Multidomain Protein Component of the Bacterial Type IX Secretion System
  Heath, PloS one 2016
  • “...In P . gingivalis W83, queC and queF homologues are likely to be pg1310 and pg1347 respectively. Although the pg1056 - pg1058 gene arrangement is conserved within some species of the Bacteroidetes, it is not ubiquitous. The association of pg1056 and pg1057 with pg1058 is likely...”
• VimA mediates multiple functions that control virulence in Porphyromonas gingivalis
  Aruni, Molecular oral microbiology 2013
  • “...Tatar et al ., 2007 ). It is noteworthy that some of the proteins (PG1346, PG1347 and PG1348) that are predicted to play a role in lipid biosynthesis interacted with the purified VimA ( Aruni et al ., 2012 ). Together, the alterations in this pathway(s)...”
• VimA-dependent modulation of acetyl coenzyme A levels and lipid A biosynthesis can alter virulence in Porphyromonas gingivalis
  Aruni, Infection and immunity 2012
  • “...peptide peptidase SppA (PG0639) Conserved hypothetical protein, PG1347 Alanyl-tRNA synthetase, PG1246 Isoleucyl-tRNA synthetase, PG1596 2 21 20 19 18 17 16...”
  • “...It is noteworthy that some of the proteins (PG1346, PG1347, and PG1348) that are predicted to play a role in lipid biosynthesis interacted with the purified...”

WP_071153391 preQ(1) synthase from Planococcus faecalis
40% identity, 31% 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
  • “...clade Hypothetical protein WP_065528121 Supplementary Figure 75 3 aa ins 5696 NADPH-dependent 7-cyano-7-deazaguanine reductase QueF WP_071153391 Supplementary Figure 76 1 aa del 1465 ACT domain-containing protein WP_112232475 Supplementary Figure 77 1 aa del 1164 Methylmalonyl-CoA mutase WP_065525509 Supplementary Figure 78 2 aa del 10091053 ABC transporter...”

SPD_1568 GTP cyclohydrolase, putative from Streptococcus pneumoniae D39
38% identity, 33% coverage

• Deletion of the Zinc Transporter Lipoprotein AdcAII Causes Hyperencapsulation of Streptococcus pneumoniae Associated with Distinct Alleles of the Type I Restriction-Modification System
  Durmort, mBio 2020
  • “...3.73 3.58 1.42 SPD_1503 Hypothetical protein 3.25 4.03 1.09 SPD_1513 Hypothetical protein 1.77 2.68 1.40 SPD_1568 GTP cyclohydrolase 1.80 1.55 1.53 SPD_1584 ABC transporter permease 2.30 2.16 2.08 SPD_1650 fatC Iron uptake ABC transporter permease 2.84 2.23 1.30 SPD_1793 Universal stress protein family 1.54 1.74 2.00...”

SPCG_RS09080 preQ(1) synthase from Streptococcus pneumoniae CGSP14
35% identity, 38% coverage

• The transcriptomic response of Streptococcus pneumoniae following exposure to cigarette smoke extract
  Manna, Scientific reports 2018
  • “...protein NrdG 1.92 0.022 SPCG_RS09500 Nicotinamide mononucleotide transporter PnuC 1.89 0.006 SPCG_RS01150 Phosphoribulokinase 1.73 0.038 SPCG_RS09080 NADPH-dependent 7-cyano-7-deazaguanine reductase QueF 1.49 0.011 Glycine betaine transport SPCG_RS09515 Hypothetical protein 2.75 0.008 SPCG_RS09520 MarR family transcriptional regulator 2.70 0.008 SPCG_RS09510 Glycine/betaine ABC transporter ATP-binding protein ProV 2.57 0.011...”

SP_1777 7-cyano-7-deazaguanine reductase from Streptococcus pneumoniae TIGR4
38% identity, 33% coverage

• The biofilm inhibitor Carolacton inhibits planktonic growth of virulent pneumococci via a conserved target
  Donner, Scientific reports 2016
  • “...competence protein comFC 2.21 2.18E-05 sp_2208 helicase comFA 2.22 3.04E-09 sp_1793 hypothetical protein 2.17 9.19E-32 sp_1777 hypothetical protein 2.22 2.46E-25 sp_2013 hypothetical protein 2.13 4.64E-31 Nicotinate and nicotinamide metabolism sp_2015 IS630-Spn1, transposase Orf1 2.74 2.48E-40 sp_2016 nicotinate-nucleotide pyrophosphorylase 2.60 1.07E-46 sp_0539 bacteriocin blpM 2.59 1.38E-04 Starch...”

Q9A515 NADPH-dependent 7-cyano-7-deazaguanine reductase from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)
40% identity, 29% coverage

• In Silico Subtractive Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pneumoniae Strain D39.
  Shami, Life (Basel, Switzerland) 2023
  • “...Protein Name Gene Name Uniprot ID Drug Bank ID Location 1 DNA-binding response regulator SPD_1085 Q9A515 DB01972 Cytoplasm 2 UDP-N-acetylmuramateL-alanine ligase murC SPD_1349 P45066 DB01673 Cytoplasm 3 RNA polymerase sigma factor SigA rpoD SigA SPD_0958 Q18BX5 DB08874 Cytoplasm life-13-01128-t003_Table 3 Table 3 Information about the quality...”
• A c-di-GMP-Modulating Protein Regulates Swimming Motility of Burkholderia cenocepacia in Response to Arginine and Glutamate
  Kumar, Frontiers in cellular and infection microbiology 2018
  • “...B4ED05 ; WspR, UniProt Id Q9HXT9 ; RpfR, UniProt Id B4EKM4 ; PleD, UniProt Id Q9A515 ; AdrA, UniProt Id Q9L401 ; RocR, UniProt Id Q9HX69 ; YhjH, UniProt Id P37646 ; VieA, UniProt Id O68318 . (B) Relative intracellular c-di-GMP levels in the WT:BCAL1069 mutant....”

Atu2273 7-cyano-7-deazaguanine reductase from Agrobacterium tumefaciens str. C58 (Cereon)
35% identity, 42% coverage

• Discrete Responses to Limitation for Iron and Manganese in Agrobacterium tumefaciens: Influence on Attachment and Biofilm Formation
  Heindl, Journal of bacteriology 2015
  • “...translation factors, and queF, a 7-cyano-7-deazaguanine reductase (Atu2273) likely involved in biosynthesis of the modified ribonucleotide queuosine. Atu2273 is...”

SMc02723 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
Q92N45 NADPH-dependent 7-cyano-7-deazaguanine reductase from Rhizobium meliloti (strain 1021)
41% identity, 29% coverage

• Queuosine biosynthesis is required for sinorhizobium meliloti-induced cytoskeletal modifications on HeLa Cells and symbiosis with Medicago truncatula
  Marchetti, PloS one 2013
  • “...Looking for additional genes belonging 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...”
• Comparative Proteomic Analysis Revealing ActJ-Regulated Proteins in Sinorhizobium meliloti.
  Albicoro, Journal of proteome research 2023

BAB1_1206 GTP cyclohydrolase I from Brucella melitensis biovar Abortus 2308
39% identity, 35% coverage

• Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid
  Barton, mBio 2023
  • “...ND yebE BAB1_0893 Uncharacterized membrane protein ND rssA BAB1_1099 Patatin family protein 115 queFC c BAB1_1206 Queuosine biosynthesis + ND acm BAB1_1465 Muramidase 66,348 mutT BAB1_1511 DNA mismatch repair ND yraI BAB1_1529 SH3 domain protein 34 BAB1_1689 DUF6536 family protein 417 aqpZ b BAB1_2001 Aquaporin Z...”
• Transposon Sequencing of Brucella abortus Uncovers Essential Genes for Growth In Vitro and Inside Macrophages
  Sternon, Infection and immunity 2018
  • “...BAB1_1695 BAB1_1757 BAB1_0861 BAB1_0024 BAB1_0168 BAB1_0172 BAB2_0643 BAB1_0003 BAB1_1206 Gene name 2 h p.i. 5 h p.i. 24 h p.i. Predicted function virB1 virB2...”
• Diverse genetic regulon of the virulence-associated transcriptional regulator MucR in Brucella abortus 2308
  Caswell, Infection and immunity 2013
  • “...BAB1_0512 BAB1_0655 BAB1_0738 BAB1_1035 BAB1_1099 BAB1_1206 BAB1_1511 BAB1_1535 BAB1_2001 BAB1_2010 BAB1_2041 BAB2_0196 BAB2_0257 BAB2_0348 BAB2_0607 BAB2_0846...”

ZMO0326 7-cyano-7-deazaguanine reductase from Zymomonas mobilis subsp. mobilis ZM4
41% identity, 29% coverage

• Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era
  Yang, Biotechnology for biofuels 2019
  • “...Nucleotidyl transferase 12.58 7.18 2.82 0.050.0012 0.050.0023 ZMO1392 Hypothetical protein 12.46 7.43 2.45 0.040.0012 0.040.0012 ZMO0326 7-cyano-7-deazaguanine reductase 12.65 7.41 2.7 0.030.0018 0.040.0012 ZMO0570 prmA Ribosomal L11 methyltransferase 12.38 7.32 2.45 0.030.0030 0.040.0013 Candidate promoters with weak strength ZMO1231 recJ Single-stranded-DNA-specific exonuclease RecJ 11.03 5.7 0.07...”
• Discovery of ethanol-responsive small RNAs in Zymomonas mobilis
  Cho, Applied and environmental microbiology 2014
  • “...Nitrogen fixation protein (ZMO1829) 7-Cyano-7-deazaguanine reductase (ZMO0326) Ppx/GppA phosphatase (ZMO0403) Zms18 Cation efflux protein (ZMO0204) explain why...”

Q8F4F6 NADPH-dependent 7-cyano-7-deazaguanine reductase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
Q72RB6 NADPH-dependent 7-cyano-7-deazaguanine reductase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)
35% identity, 26% coverage

• In silico identification of common putative drug targets in Leptospira interrogans
  Amineni, Journal of chemical biology 2010
  • “...Uniprot ID Gene product name (Lai) queF Q8F5S2 Q8F4F6 bioB slyD Q8F498 Q8F453 hprK xerD lexA Q8F3J9 Q7ZAM7 Q8F663 Perosamine synthetase NADPH-dependent...”
• In silico identification of common putative drug targets in Leptospira interrogans
  Amineni, Journal of chemical biology 2010
  • “...Gene product name (Copenhageni) 60 61 Q72QC5 Q72RB6 62 63 Q72RG8 Q72RL4 Perosamine synthetase NADPH-dependent 7-cyano-7deazaguanine reductase Biotin synthase...”

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How It Works

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

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

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

PaperBLAST also incorporates manually-curated protein functions:

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

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

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

Changes to PaperBLAST since the paper was written:

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

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

Secrets

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

Omissions from the PaperBLAST Database

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

References

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

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

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

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

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

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

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

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

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

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

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

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