PaperBLAST
PaperBLAST Hits for sp|Q9HZ17|AZOR3_PSEAE FMN-dependent NADH:quinone oxidoreductase 3 OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=azoR3 PE=1 SV=1 (213 a.a., MSRVLVIESS...)
Show query sequence
>sp|Q9HZ17|AZOR3_PSEAE FMN-dependent NADH:quinone oxidoreductase 3 OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=azoR3 PE=1 SV=1
MSRVLVIESSARQRGSVSRLLTAEFISHWKIAHPADRFQVRDLAREPLPHLDELLLGAWT
TPCDGHSAAERRALERSNRLTEELRMADVLVLAAPMYNFAIPSSLKSWFDHVLRAGLTFR
YAEQGPEGLLQGKRAFVLTARGGIYAGGGLDHQEPYLRQVLGFVGIHDVTFIHAEGMNMG
PEFREKGLARARERMRQALETDTSLCVPLPTLR
Running BLASTp...
Found 128 similar proteins in the literature:
AZOR3_PSEAE / Q9HZ17 FMN-dependent NADH:quinone oxidoreductase 3; Azo-dye reductase 3; FMN-dependent NADH-azo compound oxidoreductase 3; FMN-dependent NADH-azoreductase 3; EC 1.6.5.-; EC 1.7.1.17 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 2 papers)
NP_251913 FMN-dependent NADH-azoreductase from Pseudomonas aeruginosa PAO1
PA3223 acyl carrier protein phosphodiesterase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- function: Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones (PubMed:24915188). Shows a preference for naphthoquinones such as plumbagin (PubMed:24915188).
function: Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines (PubMed:20417637). Preferred substrates are methyl red, amaranth and p-aminoazobenzene sulfonamide (PAABSA) (PubMed:20417637).
catalytic activity: 2 a quinone + NADH + H(+) = 2 a 1,4-benzosemiquinone + NAD(+) (RHEA:65952)
catalytic activity: N,N-dimethyl-1,4-phenylenediamine + anthranilate + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH + 2 H(+) (RHEA:55872)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer. - Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases.
Ryan, Protein & cell 2010 - GeneRIF: detailed enzymic characterization and quinone oxidorductase activity of azoR3 from Pseudomonas aeruginosa
- Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes
Ryan, PloS one 2014 - “...reagents were obtained from Sigma-Aldrich. The pure recombinant proteins paAzoR1 (PA0785), paAzoR2 (PA1962) and paAzoR3 (PA3223) were expressed and purified as described previously [15] , [21] . Rates of quinone reduction were obtained by monitoring the absorbance at 340 nm for oxidation of either NADPH (paAzoR1)...”
- “...83 87 & 80 80 - 82 - pa2580 79 86 76 81 75 - pa3223 i 69 67 - 74 66 - pa4975 - 78 - 82 - - All values are given as percentage identity to the protein from P. aeruginosa PAO1. Homologues are...”
- Pseudomonas aeruginosa NfsB and nitro-CBI-DEI--a promising enzyme/prodrug combination for gene directed enzyme prodrug therapy
Green, Molecular cancer 2013 - “...c Accession no. d NfsB_Pa PA5190 25 (NfsB_Ec) AAG08575.1 AzoR2_Pa PA1962 41 (AzoR_Ec) AAG05350.1 AzoR3_Pa PA3223 45 (AzoR_Ec) AAG06611.1 KefF_Pa PA4975 37 (KefF_Ec) AAG08360.1 MdaB_Pa PA2580 64 (MdaB_Ec) AAG05968.1 WrbA_Pa PA0949 39 (WrbA_Ec) AAG04338.1 YcaK1_Pa PA1225 33 (YcaK_Ec) AAG04614.1 YcaK2_Pa PA0853 27 (YcaK_Ec) AAG04242.1 YdjA_Pa PA3208...”
- Reverting antibiotic tolerance of Pseudomonas aeruginosa PAO1 persister cells by (Z)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one
Pan, PloS one 2012 - “...( Table S2 ). The consistently induced genes encode oxidoreductases (PA4167, PA1334, PA0182, PA2932, PA2535, PA3223, PA1127), transcriptional factors (PA4878, PA1285, PA3133, PA2196), and hypothetical proteins (PA4173, PA0741, PA1210, PA3240, PA2575, PA0565, PA2580, PA2610, PA2839, PA0422, PA1374, PA2691). Since many reductases are involved in metabolism, our...”
AL066_18305 FMN-dependent NADH-azoreductase from Pseudomonas nunensis
69% identity, 92% coverage
- Transcriptomic profiling of microbe-microbe interactions reveals the specific response of the biocontrol strain P. fluorescens In5 to the phytopathogen Rhizoctonia solani
Hennessy, BMC research notes 2017 - “...aphanidermatum AL066_06105 Alpha/beta hydrolase 239.5 1.0 AL066_09895 Hydrolase 194.8 1.0 AL066_14420 Quercetin 2,3-dioxygenase 188.8 1.5 AL066_18305 FMN-dependent NADH-azoreductase 142.0 1.1 AL066_05010 Hypothetical protein 45.9 1.0 AL066_10105 Pirin 43.4 1.1 AL066_04230 Aromatic ring-opening dioxygenase LigB 39.4 1.1 AL066_06100 Mechanosensitive ion channel protein MscS 37.8 1.1 AL066_31290 Hypothetical...”
- “...33 ]. Additional significantly upregulated genes relating to aromatic compound metabolism were two FMN-dependent NADH-azoreductases (AL066_18305, AL066_ 10590), an aromatic ring-opening dioxygenase (AL066_04230) and a glutathionyl-hydroquinone reductase (AL066_05530). Analysis of the quercetinases discussed above found that both proteins belong to the pirin family with one of...”
PP4538 acyl carrier protein phosphodiesterase, putative from Pseudomonas putida KT2440
67% identity, 92% coverage
- Escherichia coli NemA is an efficient chromate reductase that can be biologically immobilized to provide a cell free system for remediation of hexavalent chromium
Robins, PloS one 2013 - “...(PAO1) azoR (PA1962), chrR (PA1204), msuE (PA2357) nfsB (PA5190), ycaK (PA1225); Pseudomonas putida (KT2440) azoR (PP4538), kefF (PP3720), nfsA (PP2490), nfsB (PP2432); Pseudomonas syringae pv. phaseolicola (1448a) azoR, mdaB, wrbA; Salmonella typhi (ATCC l9430) azoR, nfsA, nfsB; Vibrio fischeri (ATCC 7744) nfsB (FRase I); Vibrio harveyi...”
- Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways
del, Journal of bacteriology 2007 - “...PP1897 PP2268 PP2589 PP2805 PP3243 PP3413 PP3717 PP3998 PP4538 PP4983 PP5340 pcaC pcaJ PP3726 (ech) PP5248 PP5255 PP1982 (ibpA) PP3735 PP3961 PP1687 PP2644...”
MYA_0441 FMN-dependent NADH-azoreductase from Burkholderia sp. KJ006
50% identity, 92% coverage
BPSL3056 FMN-dependent NADH-azoreductase from Burkholderia pseudomallei K96243
47% identity, 92% coverage
Bphyt_3502 NAD(P)H dehydrogenase (quinone) from Burkholderia phytofirmans PsJN
48% identity, 93% coverage
- Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species
Nguyen, The plant pathology journal 2017 - “...L28 Bphyt_3149 WP_012434141.1 ABC transporter ATP-binding protein Bphyt_3178 WP_012434224.1 Hypothetical protein Bphyt_3263 WP_012434453.1 FMN-dependent NADH-azoreductase Bphyt_3502 WP_041759656.1 Propionate catabolism operon regulatory protein PrpR - Burkholderia sp. KJ006 WP_011880598.1 MS: DNA-binding response regulator MYA_5939 WP_011881944.1 MS: peroxiredoxin MYA_4577 WP_011882749.1 MS: mannosyltransferase MYA_0030 WP_011883277.1 MS: arginine ABC transporter...”
YPO2323 acyl carrier protein phosphodiesterase from Yersinia pestis CO92
YPTB2242 acyl carrier protein phosphodiesterase from Yersinia pseudotuberculosis IP 32953
48% identity, 93% coverage
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPO1430 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase 0.685 (0.033) YPTB1480 YPO1462 putative acyl carrier protein 1.669 (0.048) YPTB2242 (acpD) YPO2323 acyl carrier protein phosphodiesterase 0.703 (0.013) YPTB2470 (acpP) YPO1600 acyl carrier protein 0.661 (0.002) YPTB2473 (fabH) YPO1597 3-oxoacyl-[acyl-carrier-protein] synthase III 0.757 (0.047) 0.708 (0.017) YPTB2626 (fabB) YPO2757 3-oxoacyl-[acyl-carrier-protein] synthase I...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPTB1450 (fabA) YPO1430 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase 0.685 (0.033) YPTB1480 YPO1462 putative acyl carrier protein 1.669 (0.048) YPTB2242 (acpD) YPO2323 acyl carrier protein phosphodiesterase 0.703 (0.013) YPTB2470 (acpP) YPO1600 acyl carrier protein 0.661 (0.002) YPTB2473 (fabH) YPO1597 3-oxoacyl-[acyl-carrier-protein] synthase III 0.757 (0.047) 0.708 (0.017) YPTB2626 (fabB) YPO2757 3-oxoacyl-[acyl-carrier-protein]...”
bglu_1g04330 (Acyl-carrier-protein) phosphodiesterase from Burkholderia glumae BGR1
48% identity, 85% coverage
- Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species
Nguyen, The plant pathology journal 2017 - “...Locus ID B. glumae BGR1 WP_004186391.1 MS: 50S ribosomal protein L28 bglu_1g28680 WP_012734522.1 FMN-dependent NADH-azoreductase bglu_1g04330 WP_012734950.1 Cytidylate kinase bglu_1g08790 WP_015875283.1 ABC transporter bglu_1g12300 WP_015875291.1 AraC family transcriptional regulator bglu_1g12380 WP_012734097.1 Sigma-54-dependent Fis family transcriptional regulator bglu_1p1190 WP_012733828.1 AraC family transcriptional regulator bglu_2g10410 WP_012733977.1 Protocatechuate 3,4-dioxygenase...”
bgla_1g04700 FMN-dependent NADH-azoreductase from Burkholderia gladioli BSR3
48% identity, 85% coverage
- Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species
Nguyen, The plant pathology journal 2017 - “...ABC transporter ATP-binding protein bglu_2g13960 WP_015877795.1 Hypothetical protein bglu_2g17740 B. gladioli BSR3 WP_013696521.1 FMN-dependent NADH-azoreductase bgla_1g04700 WP_013696998.1 Cytidylate kinase bgla_1g09630 WP_013697336.1 AraC family transcriptional regulator bgla_1g13140 WP_013697551.1 Fis family transcriptional regulator bgla_1g15580 WP_013698566.1 AraC family transcriptional regulator bgla_1g26190 WP_004186391.1 MS: 50S ribosomal protein L28 bgla_1g32050 WP_013690079.1...”
Alvin_2989 NAD(P)H dehydrogenase (quinone) from Allochromatium vinosum DSM 180
49% identity, 90% coverage
- Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source
Alarcon, Applied and environmental microbiology 2024 - “...2.18 1.5E-14 Integral membrane signal transduction histidine kinase 68 Alvin_0900 2.17 2.1E-14 Hypothetical protein 69 Alvin_2989 2.17 2.8E-18 NAD( P )H dehydrogenase (quinone) 70 Alvin_1144 2.15 3.9E-07 CsbD family protein 71 Alvin_1953 2.15 6.9E-25 Flagellar hook-associated two domain protein 72 Alvin_1150 2.12 9.5E-16 Conserved hypothetical protein...”
- “...encoding a Ni/Fe hydrogenase b -type cytochrome subunit, Alvin_24522454, encoding three formate dehydrogenase subunits, and Alvin_2989, encoding NAD( P )H dehydrogenase. The downregulated genes, excluding those tabulated in Tables 1 to 3 (which will be discussed in the following paragraphs), include several genes related to dehydrogenases...”
Q8YV76 azobenzene reductase (EC 1.7.1.6) from Nostoc sp. (see paper)
all2105 acyl carrier protein phosphodiesterase from Nostoc sp. PCC 7120
45% identity, 93% coverage
- Homology modeling, docking studies and functional analysis of various azoreductase accessory interacting proteins of Nostoc sp.PCC7120
Philem, Bioinformation 2012 - “...was retrieved from National Centre for Biotechnology Information protein database at http://www.ncbi.nlm.nih.gov/protein having accession No: Q8YV76 which was isolated from Nostoc sp . PCC7120 [ 17 ]. Confidence interval map of azoreductase accessory proteins were analyzed from STRING database at http://string-db.org/ [ 16 ] and availability...”
- β-N-Methylamino-L-Alanine (BMAA) Causes Severe Stress in Nostoc sp. PCC 7120 Cells under Diazotrophic Conditions: A Proteomic Study
Koksharova, Toxins 2021 - “...protein 1.45 0.0015 *** 62 trxA|thioredoxin alr0052 trxA|thioredoxin 0.23 0.0205 ** 63 FMN-dependent NADH-azoreductase [EC:1.7.1.17] all2105 The biotransformation and/or detoxification of Nitro aromatic compounds can be possible by microbial azoreductase enzyme. Azoreductase enzyme has an ability to reduce the toxic nitro group to the corresponding amino...”
- The Anabaena sp. PCC 7120 Exoproteome: Taking a Peek outside the Box
Oliveira, Life (Basel, Switzerland) 2015 - “...transporter N 2 , NO 3 , NH 4 + Transport and binding proteins - All2105 FMN-dependent NADH-azoreductase NH 4 + Fatty acid, phospholipid and sterol metabolism Anabaena All2108 All2108 protein NO 3 Conserved hypothetical protein - All2315 Ketol-acid reductoisomerase NO 3 , NH 4 +...”
- “...not located contiguously, but still in very close genomic proximity, such as All0875 and Alr0878, All2105 and All2108, All2563 and All2567, Alr1362 and Alr1364, Alr1520 and Alr1524 and Alr4976, Alr4979 and All4985. It is not uncommon to find contiguous or adjacent genes encoding extracellular proteins in...”
4eseA / Q8ZE60 The crystal structure of azoreductase from yersinia pestis co92 in complex with fmn.
47% identity, 93% coverage
- Ligand: flavin mononucleotide (4eseA)
VV1_2341 acyl carrier protein phosphodiesterase from Vibrio vulnificus CMCP6
48% identity, 92% coverage
Q8X9S9 azobenzene reductase (EC 1.7.1.6) from Escherichia coli (see paper)
7n2xA / P41407 The crystal structure of an fmn-dependent nadh:quinone oxidoreductase, azor from escherichia coli
Z2315 acyl carrier protein phosphodiesterase from Escherichia coli O157:H7 EDL933
49% identity, 90% coverage
AzoR / B1412 FMN dependent NADH:quinone oxidoreductase (EC 1.7.1.17) from Escherichia coli K-12 substr. MG1655 (see 12 papers)
azoR / P41407 FMN dependent NADH:quinone oxidoreductase (EC 1.7.1.17) from Escherichia coli (strain K12) (see 11 papers)
AZOR_ECOLI / P41407 FMN-dependent NADH:quinone oxidoreductase; Azo-dye reductase; FMN-dependent NADH-azo compound oxidoreductase; FMN-dependent NADH-azoreductase; EC 1.6.5.-; EC 1.7.1.17 from Escherichia coli (strain K12) (see 5 papers)
P41407 FMN-dependent NADH-azoreductase (EC 1.7.1.17); azobenzene reductase (EC 1.7.1.6) from Escherichia coli (see 3 papers)
NP_415930 FMN dependent NADH:quinone oxidoreductase from Escherichia coli str. K-12 substr. MG1655
b1412 acyl carrier protein phosphodiesterase from Escherichia coli str. K-12 substr. MG1655
49% identity, 90% coverage
- function: Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones. Can reduce several benzo-, naphtho-, and anthraquinone compounds.
function: Also exhibits azoreductase activity (PubMed:11583992, PubMed:18337254). Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines (PubMed:11583992, PubMed:18337254). Can reduce ethyl red, methyl red and p-methyl red, but is not able to convert sulfonated azo dyes (PubMed:11583992, PubMed:18337254, PubMed:23795903). The stoichiometry implies that 2 cycles of the ping-pong mechanism are required for the cleavage of the azo bond (PubMed:11583992). Can also act as a nitroreductase and is able to reduce nitro compounds such as 7-nitrocoumarin-3-carboxylic acid (7NCCA) (PubMed:23795903).
catalytic activity: 2 a quinone + NADH + H(+) = 2 a 1,4-benzosemiquinone + NAD(+) (RHEA:65952)
catalytic activity: N,N-dimethyl-1,4-phenylenediamine + anthranilate + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH + 2 H(+) (RHEA:55872)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer.
disruption phenotype: Deletion mutant displays reduced viability when exposed to electrophilic quinones. - Cell-Free Protein Synthesis for the Screening of Novel Azoreductases and Their Preferred Electron Donor
Rolf, Chembiochem : a European journal of chemical biology 2022 - “...Source organism Clade Reference Ropa AzoR A0A1B1KJ01 Rhodococcus opacus 1CP II/III AzoRo [21] Ecol AzoR P41407 Escherichia coli III AzoR [22] Bsub AzoR O32224 Bacillus subtilis II YvaB [31] Paer AzoR Q9I5F3 Pseudomonas aeruginosa III paAzoR1 [32] Efae AzoR Q831B2 Enterococcus faecalis II AzoA [33] Styp...”
- ENZYMAP: exploiting protein annotation for modeling and predicting EC number changes in UniProt/Swiss-Prot
Silveira, PloS one 2014 - “...13 to 14); an EC change that involves both specialization and generalization (for example entry P41407 that changed from 3.1.4.14 to 1.7.-.- from release 7 to 8) may be the result of a correction, where there was a misannotation and now there is enough evidence to...”
- Expansion of substrate specificity and catalytic mechanism of azoreductase by X-ray crystallography and site-directed mutagenesis.
Ito, The Journal of biological chemistry 2008 (PubMed)- GeneRIF: analysis of azoR substrate specificity and catalytic mechanism
- Isolation and properties of acyl carrier protein phosphodiesterase of Escherichia coli.
Fischl, Journal of bacteriology 1990 - GeneRIF: N-terminus verified by Edman degradation on mature peptide
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013
P63462 FMN-dependent NADH:quinone oxidoreductase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
STM1642 acyl carrier protein phosphodiesterase from Salmonella typhimurium LT2
51% identity, 85% coverage
VP1452 acyl carrier protein phosphodiesterase from Vibrio parahaemolyticus RIMD 2210633
46% identity, 92% coverage
1t5bA / P63462 Structural genomics, a protein from salmonella typhimurium similar to e. Coli acyl carrier protein phosphodiesterase
51% identity, 85% coverage
- Ligand: flavin mononucleotide (1t5bA)
E1N14_020345, EEY24_23150, GMX02_01695, TUM4442_38770, WP_025010143 FMN-dependent NADH-azoreductase from Shewanella algae
45% identity, 92% coverage
- Complete genome sequence of Shewanella algae strain 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru
Lizárraga, Biotechnology reports (Amsterdam, Netherlands) 2022 - “...algae, such as strains RQs-106 ( GMX02_01695 ), TUM4442 ( TUM4442_38770 ), CECT 5071 ( E1N14_020345 ), KC-Na-R1 ( EEY24_23150 ), and 150735 ( JKK46_01670 ). It has been previously described for its ability to bio-transform and detoxify azo dyes and aromatic amines by reducing azo...”
- “...RQs-106 ( GMX02_01695 ), TUM4442 ( TUM4442_38770 ), CECT 5071 ( E1N14_020345 ), KC-Na-R1 ( EEY24_23150 ), and 150735 ( JKK46_01670 ). It has been previously described for its ability to bio-transform and detoxify azo dyes and aromatic amines by reducing azo bonds [32] . This...”
- “...AzoR . Azoreductase is widely spread inside the genus algae, such as strains RQs-106 ( GMX02_01695 ), TUM4442 ( TUM4442_38770 ), CECT 5071 ( E1N14_020345 ), KC-Na-R1 ( EEY24_23150 ), and 150735 ( JKK46_01670 ). It has been previously described for its ability to bio-transform and...”
- “...widely spread inside the genus algae, such as strains RQs-106 ( GMX02_01695 ), TUM4442 ( TUM4442_38770 ), CECT 5071 ( E1N14_020345 ), KC-Na-R1 ( EEY24_23150 ), and 150735 ( JKK46_01670 ). It has been previously described for its ability to bio-transform and detoxify azo dyes and...”
- “...of 594bp and codify an azoreductase of 197aa that is mainly related with WP_025888486 and WP_025010143 ( Shewanella sp.). AzoR ( WP_011074045 ) of the reference specie S. oneidensis is the closer gene intraspecie with only 72.02% of identity, suggesting that azoreductase gene of S. algae...”
Q7N511 FMN-dependent NADH:quinone oxidoreductase from Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
43% identity, 92% coverage
HU689_20695, JKK46_01670 FMN-dependent NADH-azoreductase from Shewanella algae
45% identity, 92% coverage
- Complete genome sequence of Shewanella algae strain 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru
Lizárraga, Biotechnology reports (Amsterdam, Netherlands) 2022 - “...to a link between the words. Table 3 Category Gene name Locus tag Description Decolorization HU689_20695 FMN-dependent NADH-azoreductase HU689_04585; HU689_04700; HU689_21345 NADPH-dependent oxidoreductase HU689_05310 Heme-dependent Dyp peroxidase HU689_08360 - HU689_08395 Operon Mtr Metal Resistance cadA HU689_10830 P-type ATPase protein corA a & corC b HU689_12865 a...”
- “...genome contains protein-coding genes previously associated with decolorization, such as an FMN-dependent NADH-azoreductase gene ( HU689_20695 ), NADPH-dependent oxidoreductase genes ( HU689_04585; HU689_04700; HU689_21345 ), and heme-dependent Dyp peroxidase gene ( HU689_05310 ). The operon Mtr ( HU689_08360 - HU689_08395 ), an electron chain transport previously,...”
- “...( TUM4442_38770 ), CECT 5071 ( E1N14_020345 ), KC-Na-R1 ( EEY24_23150 ), and 150735 ( JKK46_01670 ). It has been previously described for its ability to bio-transform and detoxify azo dyes and aromatic amines by reducing azo bonds [32] . This mechanism has been related to...”
WP_025888486 FMN-dependent NADH-azoreductase from Shewanella algae
44% identity, 92% coverage
Q3M1N6 FMN-dependent NADH:quinone oxidoreductase 1 from Trichormus variabilis (strain ATCC 29413 / PCC 7937)
42% identity, 96% coverage
Q8E990 azobenzene reductase (EC 1.7.1.6) from Shewanella oneidensis (see paper)
SO_4396 acyl carrier protein phosphodiesterase from Shewanella oneidensis MR-1
WP_011074045 FMN-dependent NADH-azoreductase from Shewanella oneidensis
43% identity, 92% coverage
SBAL678_RS25030 FMN-dependent NADH-azoreductase from Shewanella baltica OS678
43% identity, 92% coverage
MPHASIOC01_001328 FMN-dependent NADH-azoreductase from Mangrovibacter phragmitis
47% identity, 85% coverage
D0436_01835 FMN-dependent NADH-azoreductase from Shewanella decolorationis
42% identity, 92% coverage
ABZJ_01917 FMN-dependent NADH-azoreductase from Acinetobacter baumannii MDR-ZJ06
39% identity, 92% coverage
- Colistin Resistance in Acinetobacter baumannii MDR-ZJ06 Revealed by a Multiomics Approach
Hua, Frontiers in cellular and infection microbiology 2017 - “...in aminoglycoside resistance (AdeT) 1.17363 8.75427 3.19E-05 0.000202 ABZJ_01874 hypothetical protein 1.17434 5.206346 2.41E-05 0.000159 ABZJ_01917 putative acyl carrier protein phosphodiesterase (ACP phosphodiesterase) 1.18991 7.045816 5.55E-08 6.50E-07 ABZJ_01861 membrane-fusion protein 1.20577 6.002924 1.77E-07 1.87E-06 ABZJ_03742 hypothetical protein 1.20817 3.772045 0.001579 0.005748 ABZJ_01262 hypothetical protein 1.21556 4.167491...”
A6739_RS08375 FMN-dependent NADH-azoreductase from Acinetobacter baumannii
39% identity, 92% coverage
- Transcriptome Analysis of Acinetobacter baumannii in Rapid Response to Subinhibitory Concentration of Minocycline
Gao, International journal of environmental research and public health 2022 - “...chaperonin GroL (A6739_RS03850), class C beta-lactamase ADC-158 (A6739_RS05090), methylmalonate-semialdehyde dehydrogenase (CoA acylating) (A6739_RS05735), FMN-dependent NADH-azoreductase (A6739_RS08375), TIGR01244 family phosphatase (A6739_RS08405), MBL fold metallo-hydrolase (A6739_RS08410), amino acid ABC transporter permease (A6739_RS09455), APC family permease (A6739_RS11485) and copper resistance protein NlpE (A6739_RS12210) were downregulated. 3.6. Validation of sRNA...”
- “...- 1.364873266 up acyl-CoA dehydrogenase oxidoreductase A6739_RS07580 - 1.127894768 up aromatic-ring-hydroxylating dioxygenase subunit beta dioxygenase A6739_RS08375 azr 1.071338077 down FMN-dependent NADH-azoreductase oxidoreductase A6739_RS08405 - 1.139044967 down TIGR01244 family phosphatase hydrolase, oxidoreductase A6739_RS08410 - 1.273424919 down MBL fold metallo-hydrolase beta-lactamase, protein dimerization, zinc ion binding A6739_RS09455 -...”
G5B91_06765 FMN-dependent NADH-azoreductase from Pseudomonas nitroreducens
46% identity, 83% coverage
N5094_18465 FMN-dependent NADH-azoreductase from Shewanella putrefaciens
41% identity, 92% coverage
6dxpA / A6TCS9 The crystal structure of an fmn-dependent nadh-azoreductase from klebsiella pneumoniae
44% identity, 92% coverage
- Ligand: flavin mononucleotide (6dxpA)
SMc01329 PROBABLE ACYL CARRIER PROTEIN PHOSPHODIESTERASE from Sinorhizobium meliloti 1021
42% identity, 92% coverage
- Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium
Barnett, Journal of bacteriology 2012 - “...SMc00049 SMc00814 SMc00949 SMc00969 SMc00970 SMc01180 SMc01329 SMc02382 SMc02433 SMc02575 SMc02576 SMc02577 SMc02769 SMc02857 SMc02863 SMc02900 SMb20117...”
- “...rpoH dependent (SMa0136, SMc00030, SMc00048, SMc00814, SMc00969, SMc01329, SMc02863, and SMc04310 in Table 1). Hence, the final three consensus sequences...”
Q8UG34 FMN-dependent NADH:quinone oxidoreductase from Agrobacterium fabrum (strain C58 / ATCC 33970)
42% identity, 85% coverage
Q39M92 FMN-dependent NADH:quinone oxidoreductase 7 from Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383)
44% identity, 86% coverage
HI1366 acyl carrier protein phosphodiesterase (acpD) from Haemophilus influenzae Rd KW20
39% identity, 92% coverage
DMO12_04230 NAD(P)H-dependent oxidoreductase from Acinetobacter baumannii ACICU
40% identity, 92% coverage
ABUW_2489 NAD(P)H-dependent oxidoreductase from Acinetobacter baumannii
40% identity, 92% coverage
BCAM0341 FMN-dependent NADH-azoreductase from Burkholderia cenocepacia J2315
42% identity, 92% coverage
APC64_12940, AWC45_RS08260, B9Y25_04245, BTH23_04235, CAS91_11825 NAD(P)H-dependent oxidoreductase from Acinetobacter baumannii
39% identity, 92% coverage
- AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates
Chan, The Journal of antimicrobial chemotherapy 2020 - “...genes were as follows: NIPH146, F979_RS13625 to F979_RS13685; HWBA8, B7L46_16170 to B7L46_16265; ABBL20, APC64_12840 to APC64_12940; PR379, B9Y25_04090 to B9Y25_04245; ABUH639, BTH23_04090 to BTH23_04235; ARLG1833, CAS91_11670 to CAS91_11825; ABUH796, EP550_07220 to EP550_07290; ABIsac_ColiR, BN50_RS06860 to BN50_RS06920; and HUMC1, AWC45_RS08085 to AWC45_RS08260. Alignments of the genomic regions...”
- “...CAS91_11670 to CAS91_11825; ABUH796, EP550_07220 to EP550_07290; ABIsac_ColiR, BN50_RS06860 to BN50_RS06920; and HUMC1, AWC45_RS08085 to AWC45_RS08260. Alignments of the genomic regions were performed using Easyfig. 52 The asterisk is representative of isolates ABUH763, ABUH793 and ABUH796. Isolates shown in blue were whole-genome sequenced and finished in...”
- “...NIPH146, F979_RS13625 to F979_RS13685; HWBA8, B7L46_16170 to B7L46_16265; ABBL20, APC64_12840 to APC64_12940; PR379, B9Y25_04090 to B9Y25_04245; ABUH639, BTH23_04090 to BTH23_04235; ARLG1833, CAS91_11670 to CAS91_11825; ABUH796, EP550_07220 to EP550_07290; ABIsac_ColiR, BN50_RS06860 to BN50_RS06920; and HUMC1, AWC45_RS08085 to AWC45_RS08260. Alignments of the genomic regions were performed using Easyfig....”
- “...HWBA8, B7L46_16170 to B7L46_16265; ABBL20, APC64_12840 to APC64_12940; PR379, B9Y25_04090 to B9Y25_04245; ABUH639, BTH23_04090 to BTH23_04235; ARLG1833, CAS91_11670 to CAS91_11825; ABUH796, EP550_07220 to EP550_07290; ABIsac_ColiR, BN50_RS06860 to BN50_RS06920; and HUMC1, AWC45_RS08085 to AWC45_RS08260. Alignments of the genomic regions were performed using Easyfig. 52 The asterisk is...”
- “...ABBL20, APC64_12840 to APC64_12940; PR379, B9Y25_04090 to B9Y25_04245; ABUH639, BTH23_04090 to BTH23_04235; ARLG1833, CAS91_11670 to CAS91_11825; ABUH796, EP550_07220 to EP550_07290; ABIsac_ColiR, BN50_RS06860 to BN50_RS06920; and HUMC1, AWC45_RS08085 to AWC45_RS08260. Alignments of the genomic regions were performed using Easyfig. 52 The asterisk is representative of isolates ABUH763,...”
B7L46_16265 NAD(P)H-dependent oxidoreductase from Acinetobacter baumannii
39% identity, 92% coverage
- AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates
Chan, The Journal of antimicrobial chemotherapy 2020 - “...the hydrolase and reductase genes were as follows: NIPH146, F979_RS13625 to F979_RS13685; HWBA8, B7L46_16170 to B7L46_16265; ABBL20, APC64_12840 to APC64_12940; PR379, B9Y25_04090 to B9Y25_04245; ABUH639, BTH23_04090 to BTH23_04235; ARLG1833, CAS91_11670 to CAS91_11825; ABUH796, EP550_07220 to EP550_07290; ABIsac_ColiR, BN50_RS06860 to BN50_RS06920; and HUMC1, AWC45_RS08085 to AWC45_RS08260. Alignments...”
WP_012445099 FMN-dependent NADH-azoreductase from Xanthomonas oryzae pv. oryzae
42% identity, 85% coverage
DP16_RS07410 FMN-dependent NADH-azoreductase from Stenotrophomonas maltophilia
39% identity, 89% coverage
CPS_RS07440 FMN-dependent NADH-azoreductase from Colwellia psychrerythraea 34H
38% identity, 82% coverage
AZOR2_PSEAE / Q9I2E2 FMN-dependent NADH:quinone oxidoreductase 2; Azo-dye reductase 2; FMN-dependent NADH-azo compound oxidoreductase 2; FMN-dependent NADH-azoreductase 2; EC 1.6.5.-; EC 1.7.1.17 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 2 papers)
PA1962 acyl carrier protein phosphodiesterase from Pseudomonas aeruginosa PAO1
NP_250652 FMN-dependent NADH-azoreductase from Pseudomonas aeruginosa PAO1
41% identity, 85% coverage
- function: Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones (PubMed:24915188). Reduces both benzoquinones and naphthoquinones efficiently (PubMed:24915188).
function: Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines (PubMed:20417637). Preferred substrates are the large bis-azo dye Ponceau BS, amaranth and tropaeolin O (PubMed:20417637).
catalytic activity: 2 a quinone + NADH + H(+) = 2 a 1,4-benzosemiquinone + NAD(+) (RHEA:65952)
catalytic activity: N,N-dimethyl-1,4-phenylenediamine + anthranilate + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH + 2 H(+) (RHEA:55872)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer. - Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes
Ryan, PloS one 2014 - “...Enzymatic Assays All reagents were obtained from Sigma-Aldrich. The pure recombinant proteins paAzoR1 (PA0785), paAzoR2 (PA1962) and paAzoR3 (PA3223) were expressed and purified as described previously [15] , [21] . Rates of quinone reduction were obtained by monitoring the absorbance at 340 nm for oxidation of...”
- “...- pa1224 - 45 76 - 75 - pa1225 68 - - - 72 - pa1962 h 67 71 - 76 67 63 pa2280 83 87 & 80 80 - 82 - pa2580 79 86 76 81 75 - pa3223 i 69 67 - 74 66...”
- Pseudomonas aeruginosa NfsB and nitro-CBI-DEI--a promising enzyme/prodrug combination for gene directed enzyme prodrug therapy
Green, Molecular cancer 2013 - “...Gene locus b % identity c Accession no. d NfsB_Pa PA5190 25 (NfsB_Ec) AAG08575.1 AzoR2_Pa PA1962 41 (AzoR_Ec) AAG05350.1 AzoR3_Pa PA3223 45 (AzoR_Ec) AAG06611.1 KefF_Pa PA4975 37 (KefF_Ec) AAG08360.1 MdaB_Pa PA2580 64 (MdaB_Ec) AAG05968.1 WrbA_Pa PA0949 39 (WrbA_Ec) AAG04338.1 YcaK1_Pa PA1225 33 (YcaK_Ec) AAG04614.1 YcaK2_Pa PA0853...”
- Escherichia coli NemA is an efficient chromate reductase that can be biologically immobilized to provide a cell free system for remediation of hexavalent chromium
Robins, PloS one 2013 - “...Nostoc punctiforme (PCC 73102) nfsA, ycdI; Nostoc sp. (PCC 7120) ycdI; Pseudomonas aeruginosa (PAO1) azoR (PA1962), chrR (PA1204), msuE (PA2357) nfsB (PA5190), ycaK (PA1225); Pseudomonas putida (KT2440) azoR (PP4538), kefF (PP3720), nfsA (PP2490), nfsB (PP2432); Pseudomonas syringae pv. phaseolicola (1448a) azoR, mdaB, wrbA; Salmonella typhi (ATCC...”
- Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases.
Ryan, Protein & cell 2010 - GeneRIF: detailed enzymic characterization of azoR2 from Pseudomonas aeruginosa
- Molecular cloning, characterisation and ligand-bound structure of an azoreductase from Pseudomonas aeruginosa.
Wang, Journal of molecular biology 2007 (PubMed)- GeneRIF: X-RAY CRYSTALLOGRAPHIC STRUCTURE OF AZOREDUCTASE IN COMPLEX WITH THE SUBSTRATE METHYL RED
ACG06_RS16675 FMN-dependent NADH-azoreductase AzoR2 from Pseudomonas aeruginosa
41% identity, 85% coverage
- Whole-transcriptome analysis reveals mechanisms underlying antibacterial activity and biofilm inhibition by a malic acid combination (MAC) in Pseudomonas aeruginosa
Song, PeerJ 2023 - “...FC = 7.35), betaine-aldehyde dehydrogenase ( ACG06_RS30685 , FC = 7.28), FMN-dependent NADH-azoreductase AzoR2 ( ACG06_RS16675 , FC = 7.27), uroporphyrinogen-III C-methyltransferase ( ACG06_RS02660 , FC = 6.38), tryptophan synthase subunit beta ( ACG06_RS00215 , FC = 6.37), MBL fold metallo-hydrolase ( ACG06_RS12740 , FC =...”
A1S_1354 (Acyl-carrier protein) phosphodiesterase from Acinetobacter baumannii ATCC 17978
41% identity, 86% coverage
- Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing
Camarena, PLoS pathogens 2010 - “...Annotation Up-regulated genes A1S_2098 12.6 Ethanol dehydrogenase A1S_2102 13.2 Aldehyde dehydrogenase A1S_0481 4.4 Phosphate acetyltransferase A1S_1354 3.7 Azoreductase (flavodoxin_1 superfamily) A1S_1711 3.3 Homoserine dehydrogenase A1S_0942 3.5 Nicotinamide mononucleotide transporter A1S_2664 2 GroEL A1S_2755 3 Acyltransferase superfamily A1S_3542 3.2 Hypothetical protein 1 A1S_2994 2.4 Hypothetical protein A1S_0913...”
- “...ACP-phosphohydrolase. AcpD was subsequently shown to be an azoreductase [63] . The induction of acpD (A1S_1354) by ethanol supports the idea that this gene is part of a stress response. A reduction of two-fold was detected for a cluster of five genes that could form an...”
Q88IY3 FMN-dependent NADH-azoreductase (EC 1.7.1.17) from Pseudomonas putida (see paper)
PP2866, PP_2866 acyl carrier protein phosphodiesterase, putative from Pseudomonas putida KT2440
WP_010953771 FMN-dependent NADH-azoreductase from Pseudomonas putida KT2440
41% identity, 85% coverage
- Microbial responses to xenobiotic compounds. Identification of genes that allow Pseudomonas putida KT2440 to cope with 2,4,6-trinitrotoluene
Fernández, Microbial biotechnology 2009 - “...PP2489 xen D xenobiotic reductase, putative 2.0 M PP2490 pnrA nitroreductase family protein 2.0 M PP2866 acpD azoreductase 2.1 PP3657 Nitrobenzoate reductase, putative 2.6 2. Resistance efflux pumps PP2065 Multidrug efflux RND transporter 2.0 M PP3427 oprN multidrug efflux RND outer membrane protein OprN 3.8 M...”
- “...may be involved in TNT biotransformation, for example, the azo gene that encodes the azoreductase PP_2866 and a putative nitrobenzoate reductase (PP_3657). Azoreductases are usually involved in the bond cleavage of aromatic azo compounds, but they have been recently linked with TNT metabolism in Rhodobacter sphaeroides...”
- Identification of a repressor and an activator of azoreductase gene expression in Pseudomonas putida and Xanthomonas oryzae.
Whangsuk, Biochemical and biophysical research communications 2018 (PubMed)- GeneRIF: Genes responsible for the production of azoreductase enzymes in 2gram-negative bacteria, the soil bacterium Pseudomonas putida (AzoP) and the plant pathogen Xanthomonas oryzae (AzoX), were identified. [azoreductase]
4c0wA / Q88IY3 The crystal strucuture of native ppazor (see paper)
41% identity, 85% coverage
- Ligand: flavin mononucleotide (4c0wA)
AL066_10590 FMN-dependent NADH-azoreductase from Pseudomonas nunensis
39% identity, 92% coverage
C0STY1 azobenzene reductase (EC 1.7.1.6) from Bacillus sp. B29 (see paper)
BC_2194 FMN-dependent NADH-azoreductase from Bacillus cereus ATCC 14579
BC2194 FMN-dependent NADH-azoreductase from Bacillus cereus ATCC 14579
35% identity, 91% coverage
- Proteomics identifies Bacillus cereus EntD as a pivotal protein for the production of numerous virulence factors
Omer, Frontiers in microbiology 2015 - “...1999 ; Anantharaman et al., 2012 ), (ii) thiol-specific stress-related proteins, such as the azoreductase (BC_2194) (Leelakriangsak et al., 2008 ), the thioredoxin-dependent thiol peroxidase (BC_0517), and the alkyl hydroperoxide reductase (BC_0377), and (iii) other stress-related proteins (Table S4 ). The higher abundance of these proteins...”
- From transcriptional landscapes to the identification of biomarkers for robustness
Abee, Microbial cell factories 2011 - “...a clear overrepresentation of genes predicted to have reductase activity ( BC1835 , BC1844 , BC2194 , BC3024 ,) and arsenate resistance ( BC3152-BC3154 ). In addition several transport systems involved in the transport of metal ions (copper, cadmium, zinc) are activated ( BC3731 , BC3732...”
Q220J4 FMN-dependent NADH:quinone oxidoreductase from Albidiferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118)
38% identity, 84% coverage
3r6wA / Q9I5F3 Paazor1 binding to nitrofurazone (see paper)
38% identity, 92% coverage
- Ligands: flavin mononucleotide; nitrofurazone (3r6wA)
9c0wB / Q738X4 Azrc from bacillus pacificus roc1 bound to malachite green (see paper)
33% identity, 89% coverage
- Ligands: malachite green; flavin mononucleotide (9c0wB)
AZOR1_PSEAE / Q9I5F3 FMN-dependent NAD(P)H:quinone oxidoreductase 1; Azo-dye reductase 1; FMN-dependent NADH-azo compound oxidoreductase 1; FMN-dependent NADH-azoreductase 1; EC 1.6.5.-; EC 1.7.1.17 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 4 papers)
Q9I5F3 azobenzene reductase (EC 1.7.1.6) from Pseudomonas aeruginosa (see paper)
NP_249476 FMN-dependent NADH-azoreductase AzoR from Pseudomonas aeruginosa PAO1
PA0785 probable acyl carrier protein phosphodiesterase from Pseudomonas aeruginosa PAO1
38% identity, 92% coverage
- function: Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones (PubMed:24915188). Shows a preference for benzoquinones (PubMed:24915188).
function: Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines (PubMed:17904577, PubMed:20057057). NADPH is the preferred electron donor for azoreductase activity, but it can also use NADH (PubMed:17904577). Can reduce different classes of azo dyes, including the common azo dyes methyl red and p-aminoazobenzene sulfonamide (PAABSA) (PubMed:17904577, PubMed:20057057). Can activate several azo pro-drugs used in the treatment of inflammatory bowel disease (IBD), including balsalazide, sulfasalazine and olsalazine (PubMed:17904577, PubMed:20057057). Also acts as a nitrodeductase, and can reduce and hence activate the nitroaromatic drug nitrofurazone, a broad spectrum antibiotic (PubMed:22355582).
catalytic activity: 2 a quinone + NADPH + H(+) = 2 a 1,4-benzosemiquinone + NADP(+) (RHEA:14269)
catalytic activity: 2 a quinone + NADH + H(+) = 2 a 1,4-benzosemiquinone + NAD(+) (RHEA:65952)
catalytic activity: N,N-dimethyl-1,4-phenylenediamine + anthranilate + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH + 2 H(+) (RHEA:55872)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer (PubMed:17904577). Homotetramer formed by a dimer of dimers when the ionic strength is high (PubMed:17904577). - Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases.
Ryan, Protein & cell 2010 - GeneRIF: detailed enzymic characterization of azoR1 from Pseudomonas aeruginosa
- Cell-Free Protein Synthesis for the Screening of Novel Azoreductases and Their Preferred Electron Donor
Rolf, Chembiochem : a European journal of chemical biology 2022 - “...Escherichia coli III AzoR [22] Bsub AzoR O32224 Bacillus subtilis II YvaB [31] Paer AzoR Q9I5F3 Pseudomonas aeruginosa III paAzoR1 [32] Efae AzoR Q831B2 Enterococcus faecalis II AzoA [33] Styp AzoR P63462 Salmonella typhimurium III This study Rfer AzoR Q220J4 Rhodoferax ferrireducens III This study Plau...”
- Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes
Ryan, PloS one 2014 - “...and oxidation. Enzymatic Assays All reagents were obtained from Sigma-Aldrich. The pure recombinant proteins paAzoR1 (PA0785), paAzoR2 (PA1962) and paAzoR3 (PA3223) were expressed and purified as described previously [15] , [21] . Rates of quinone reduction were obtained by monitoring the absorbance at 340 nm for...”
- “...b P. stutzeri c P. denitrificans d P. aureofaciens e P. syringae pv. tomato f pa0785 g 78 - - 68 77 - pa0949 84 83 86 92 81 81 pa1204 - - - - - - pa1224 - 45 76 - 75 - pa1225 68...”
- Fitness of isogenic colony morphology variants of Pseudomonas aeruginosa in murine airway infection
Rakhimova, PloS one 2008 - “...wild type morphotype PA0482 - glcB Malate synthase G PA0728 - - Probable bacteriophage integrase PA0785 * - azoR Azobenzene reductase PA0920 - - Hypothetical membrane protein PA1589 - sucD Succinyl-CoA synthetase alpha chain PA1633 - kdpA Potassium-transporting ATPase PA1823 - - Hypothetical protein, predicted NADH...”
- “...PA4640 mqoB, malate:quinone oxidoreductase Category 3: non-competitive (no survival in vitro and in vivo ) PA0785 azoR , azobenzene reductase PA3194 edd , phosphogluconate dehydratase phiCTX Pseudomonas phage phiCTX, hypothetical protein Ten of the 15 mutants belonged to the group with robust morphotypes which included all...”
- Molecular cloning, characterisation and ligand-bound structure of an azoreductase from Pseudomonas aeruginosa
Wang, Journal of molecular biology 2007 (PubMed)- “...Coughtrie, Michael Sim, Edith Westwood, Isaac AbstractThe gene PA0785 from Pseudomonas aeruginosa strain PAO1, which is annotated as a probable acyl carrier...”
- “...transcription-polymerase chain reaction (RT-PCR) Cloning of PA0785 from P. aeruginosa PAO1 Heterologous overexpression and purification of recombinant PA0785...”
- A chromosomally located transposon in Pseudomonas aeruginosa
Sinclair, Journal of bacteriology 1982 - “...20 3 PA025 PA0222 PA0286 PA0422 PA0442 PA0674 PA0785 PA01719 PAO2001 PA02003 study study study study study Bacteriophages E79tvl F116L 22 Virulent, transducing...”
- “...by reintroducing pMG5 into one of the cured transductants (PA0785) and testing for transfer of Tn2521 to pMG5. Transposition of Cbr Smr Spr Sur from the...”
AZOR1_BACSU / O35022 FMN-dependent NADH:quinone oxidoreductase 1; Azo-dye reductase 1; FMN-dependent NADH-azo compound oxidoreductase 1; FMN-dependent NADH-azoreductase 1; EC 1.6.5.-; EC 1.7.1.17 from Bacillus subtilis (strain 168) (see paper)
BSU19230 azoreductase from Bacillus subtilis subsp. subtilis str. 168
33% identity, 91% coverage
- function: Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones (Probable). Contributes to resistance to 2-methylhydroquinone (2-MHQ) and catechol (PubMed:18208493).
function: Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines.
catalytic activity: 2 a quinone + NADH + H(+) = 2 a 1,4-benzosemiquinone + NAD(+) (RHEA:65952)
catalytic activity: N,N-dimethyl-1,4-phenylenediamine + anthranilate + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH + 2 H(+) (RHEA:55872)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer. - Secondary structural entropy in RNA switch (Riboswitch) identification
Manzourolajdad, BMC bioinformatics 2015 - “...746478 746634 forward BSU06780 yeeC -400 0.5095 3219 yeeG BSU06820 0.878 25 2096100 2096256 reverse BSU19230 yocJ -171 0.4268 393 yocI BSU19220 0.877 26 300673 300829 forward BSU02770 yccK -1196 0.3822 79 ycdB BSU02790 0.875 27 3373963 3374119 reverse BSU32890 yusQ -2575 0.4076 393 fadM BSU32850...”
- “...-57.14 - 0.4800 122.8730011 - 0.4100 1499 yqhR BSU24480 0.8008475304 200 nt 2096086 2096285 reverse BSU19230 yocJ -165 -39.50 - 0.2800 123.2190018 - 0.4150 399 yocI BSU19220 0.8003621101 200 nt 4107928 4108127 reverse BSU40010 yxaD -1158 -51.01 - 0.4150 123.1330032 - 0.3800 99 yxaF BSU39990 0.8002312183...”
- Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis
Maaβ, Molecular & cellular proteomics : MCP 2014 - “...MhqD BshA MsrB BshB1 BshC KatA HxlA BSU19230 BSU33540 BSU21690 BSU12870 BSU08720 BSU07830 BSU38370 BSU32990 BSU33680 BSU19550 BSU23820 BSU19560 BSU22460...”
- Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment
Reddy, PloS one 2015 - “...P37809 ATP synthase beta chain AtpD 51.42 29 1.96 NS NS 1350 1192 0.045 U-11 O35022 FMN-dependent NADH-azoreductase 1 AzoR1 22.98 17 1.78 1.85 NI 436 391 0.036 U-12 P28599 10 kDa chaperonin GroS 10.17 5 1.51 1.81 1.65 157 122 0.038 120 min curcumin treatment...”
A8FA13 FMN-dependent NADH:quinone oxidoreductase from Bacillus pumilus (strain SAFR-032)
35% identity, 92% coverage
- Microwave supported hydrolysis prepares Bacillus spores for proteomic analysis
Chen, International journal of mass spectrometry 2019 - “...FPGDDVPVVKGSALKALEG A7Z0N5 Elongation factor Tu 2015.3 2015.6 FPGDDVPVVKGSALKALEGD A7Z0N5 Elongation factor Tu 1365.6 1365.1 AKVLYITAHPHD A8FA13 FMN-dependent NADH-azoreductase 2698.2 2698.7 LmLKERRFVPFLSGEKEMAHFD P40806 Polyketide synthase PksJ 2212.5 2211.1 PSRVLAVVLDAGTNQESLLND 034389 Probable NAD-dependent malic enzyme 3 8890.3 8890.2 ANSNNKTNAQQVRKQNQQSASGQGQFGTEFASETNVQQVRKQNQQSAAGQGQFGTEFASETDAQQVRQQNQSAEQNKQQNS P84585 Small, acid-soluble spore protein gamma-type 6694.0 6693.2 ANSNNKTNAQQVRKQNQQSASGQGQFGTEFASETNVQQVRKQNQQSAAGQGQFGTEFASETD...”
lmo0786 similar to acyl-carrier protein phosphodiesterase and to NAD(P)H dehydrogenase from Listeria monocytogenes EGD-e
33% identity, 93% coverage
LMOf2365_0802 acyl-carrier protein phosphodiesterase, putative from Listeria monocytogenes str. 4b F2365
33% identity, 93% coverage
- Transcriptomic Analysis of Listeria monocytogenes in Response to Bile Under Aerobic and Anaerobic Conditions
Chakravarty, Frontiers in microbiology 2021 - “...galU LMOf2365_1099 UTP-glucose-1-phosphate uridylyltransferase 7.7 LMOf2365_0582 CBS domain protein 8.5 LMOf2365_2144 Nitroreductase family protein 9.3 LMOf2365_0802 Putative acyl-carrier protein phosphodiesterase 9.4 ald LMOf2365_1601 Alanine dehydrogenase 11.9 manA LMOf2365_2143 Mannose-6-phosphate isomerase, class I 13.6 LMOf2365_1608 Putative inorganic polyphosphate/ATP-NAD kinase 13.6 LMOf2365_2308 Aminopeptidase C 13.9 pfl-2 LMOf2365_1946 Formate...”
- “...conditions at pH 5.5. Gene ID Gene name Transcript levels Metabolism LMOf2365_2610 Putative lipoprotein 29.9 LMOf2365_0802 FMN-dependent NADH-azoreductase 21.6 LMOf2365_1226 Putative peptidase 18.2 LMOf2365_0565 6-phospho-beta-glucosidase 18.2 pflA LMOf2365_1426 Pyruvate formate lyase activating enzyme 11.1 LMOf2365_1975 Riboflavin transporter 10.2 pyrH LMOf2365_1330 Uridylate kinase 8.7 LMOf2365_1597 Bifunctional oligoribonuclease...”
DVU2548 acyl carrier protein phosphodiesterase from Desulfovibrio vulgaris Hildenborough
36% identity, 94% coverage
- Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris
Wu, The ISME journal 2020 - “...stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate...”
- “...[14, 50] and exists in the same operon with DVU2548 (acpD, five mutations in three EN populations) [51]; (b) nitrogen regulatory protein C family genes (NRC:...”
- Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough
Chhabra, Journal of bacteriology 2006 - “...11, 2017 by University of California, Berkeley DVU2548 DVU2652 DVU2653 DVU2659 DVU2917 DVU2949 DVU2951 DVU2956 DVU2957 DVU2988 DVU3020 DVU3120 DVU3142 DVU3143...”
- “...DVU0811 DVU0847 DVU0910 DVU1468 DVU1636 DVU1772 DVU2247 DVU2548 DVU2643 DVU2744 DVU0095 DVU0177 DVU0712 DVU0745 DVU0966 DVU1932 DVU2667 DVU3245 DVU0322 DVU0386...”
LMHCC_1847 fmn-dependent NADH-azoreductase 2 (fmn-dependent nadh-azocompound oxidoreductase 2) (azo-dye reductase 2) from Listeria monocytogenes HCC23
33% identity, 93% coverage
6qu0A / A0A0B0IKH9 Structure of azoreductase from bacillus sp. A01 (see paper)
34% identity, 91% coverage
- Ligand: flavin mononucleotide (6qu0A)
BMD_3385 Flavodoxin-like fold family protein from Bacillus megaterium DSM319
32% identity, 92% coverage
AZOR_ENTFA / Q831B2 FMN-dependent NADH:quinone oxidoreductase; Azo-dye reductase; FMN-dependent NADH-azo compound oxidoreductase; FMN-dependent NADH-azoreductase; EC 1.6.5.-; EC 1.7.1.17 from Enterococcus faecalis (strain ATCC 700802 / V583) (see paper)
Q831B2 FMN-dependent NADH-azoreductase (EC 1.7.1.17); azobenzene reductase (EC 1.7.1.6) from Enterococcus faecalis (see 7 papers)
EF2601 acyl carrier protein, putative from Enterococcus faecalis V583
31% identity, 91% coverage
- function: Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones.
function: Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity. The enzyme can also reduce a wide range of sulfonated azo dyes. The substrate preference order is methyl Red > Orange II > Ponceau BS > Ponceau S > Orange G > Amaranth.
catalytic activity: 2 a quinone + NADH + H(+) = 2 a 1,4-benzosemiquinone + NAD(+) (RHEA:65952)
catalytic activity: N,N-dimethyl-1,4-phenylenediamine + anthranilate + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH + 2 H(+) (RHEA:55872)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer. - Cell-Free Protein Synthesis for the Screening of Novel Azoreductases and Their Preferred Electron Donor
Rolf, Chembiochem : a European journal of chemical biology 2022 - “...Bacillus subtilis II YvaB [31] Paer AzoR Q9I5F3 Pseudomonas aeruginosa III paAzoR1 [32] Efae AzoR Q831B2 Enterococcus faecalis II AzoA [33] Styp AzoR P63462 Salmonella typhimurium III This study Rfer AzoR Q220J4 Rhodoferax ferrireducens III This study Plau AzoR Q7N511 Photorhabdus laumondii subsp . laumondii III...”
- Functional studies of E. faecalis RNase J2 and its role in virulence and fitness
Gao, PloS one 2017 - “...3.33 0.025 ef2598 PTS system component 3.57 0.048 ef2599 transcription antiterminator, BglG family 2.56 0.044 ef2601 conserved hypothetical protein 2.44 0.013 a EF numbers and the encoded protein are from the V583 genome sequenced by TIGR (NCBI ID, NC_004668 ). b The change represents mRNA expression...”
AZOR2_BACSU / O32224 FMN-dependent NADH:quinone oxidoreductase 2; Azo-dye reductase 2; FMN-dependent NADH-azo compound oxidoreductase 2; FMN-dependent NADH-azoreductase 2; EC 1.6.5.-; EC 1.7.1.17 from Bacillus subtilis (strain 168) (see 3 papers)
BSU33540, NP_391234 azoreductase from Bacillus subtilis subsp. subtilis str. 168
32% identity, 91% coverage
- function: Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones (Probable). Contributes to resistance to 2-methylhydroquinone (2-MHQ) and catechol (PubMed:17725564, PubMed:18208493). Exhibits NADH-dependent 2,6- dichloroindophenol (DCIP) oxidoreductase activity (PubMed:17284825).
function: Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines (PubMed:17284825). Can reduce methyl red (PubMed:17284825).
catalytic activity: 2 a quinone + NADH + H(+) = 2 a 1,4-benzosemiquinone + NAD(+) (RHEA:65952)
catalytic activity: N,N-dimethyl-1,4-phenylenediamine + anthranilate + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH + 2 H(+) (RHEA:55872)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer.
disruption phenotype: Deletion mutant is sensitive to 2-MHQ and catechol. - Cell-Free Protein Synthesis for the Screening of Novel Azoreductases and Their Preferred Electron Donor
Rolf, Chembiochem : a European journal of chemical biology 2022 - “...opacus 1CP II/III AzoRo [21] Ecol AzoR P41407 Escherichia coli III AzoR [22] Bsub AzoR O32224 Bacillus subtilis II YvaB [31] Paer AzoR Q9I5F3 Pseudomonas aeruginosa III paAzoR1 [32] Efae AzoR Q831B2 Enterococcus faecalis II AzoA [33] Styp AzoR P63462 Salmonella typhimurium III This study Rfer...”
- Construction of Cellulose Binding Domain Fusion FMN-Dependent NADH-Azoreductase and Glucose 1-Dehydrogenase for the Development of Flow Injection Analysis with Fusion Enzymes Immobilized on Cellulose
Yano, Journal of applied glycoscience 2019 - “...biosensor production without complicated processing. In this study, we selected FMN-dependent NADH-azoreductase (AZR, accession No. NP_391234) and glucose 1-dehydrogenase (GDH, NP_388275) of Bacillus subtilis 168, 13) 14) as a model oxidoreductase for the biosensor and a recipient of CBD fusion. AZR is an FMN-linked enzyme and...”
- Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis
Maaβ, Molecular & cellular proteomics : MCP 2014 - “...BshA MsrB BshB1 BshC KatA HxlA BSU19230 BSU33540 BSU21690 BSU12870 BSU08720 BSU07830 BSU38370 BSU32990 BSU33680 BSU19550 BSU23820 BSU19560 BSU22460 BSU21680...”
- Identification and molecular characterization of a novel flavin-free NADPH preferred azoreductase encoded by azoB in Pigmentiphaga kullae K24
Chen, BMC biochemistry 2010 - “...)_ Staphylococcus aureus subsp. aureus MRSA252; AcpD ( YP_149218 )_ Geobacillus kaustophilus HTA426; YvaB ( NP_391234 )_ Bacillus subtilis subsp. subtilis strain 168; YvaB ( YP_001422634 )_ Bacillus amyloliquefaciens FZB42; AzoR ( AAG04174 )_ Pseudomonas aeruginosa PAO1; AZOR ( Q8X9S9 )_ Escherichia coli O157:H7; AzoR (1V4B_A)_...”
A4W2Z7 FMN-dependent NADH:quinone oxidoreductase from Streptococcus suis (strain 98HAH33)
SSU1383 acyl carrier protein phosphodiesterase from Streptococcus suis P1/7
31% identity, 94% coverage
NOV99_03505 FMN-dependent NADH-azoreductase from Streptococcus suis
31% identity, 94% coverage
YP_001422634 YvaB from Bacillus amyloliquefaciens FZB42
31% identity, 91% coverage
6jxnB / G9QLG5 Crystal structure of indigo reductase from bacillus smithii type strain dsm 4216 (see paper)
33% identity, 91% coverage
- Ligands: flavin mononucleotide; 2-[n-cyclohexylamino]ethane sulfonic acid (6jxnB)
2hpvA / Q831B2 Crystal structure of fmn-dependent azoreductase from enterococcus faecalis
32% identity, 93% coverage
- Ligand: flavin mononucleotide (2hpvA)
SH0386, YP_252301 hypothetical protein from Staphylococcus haemolyticus JCSC1435
31% identity, 91% coverage
A2RIA7 FMN dependent NADH:quinone oxidoreductase from Lactococcus lactis subsp. cremoris (strain MG1363)
34% identity, 94% coverage
TERTU_2193 FMN-dependent NADH-azoreductase 2 from Teredinibacter turnerae T7901
28% identity, 91% coverage
UH47_06375 FMN-dependent NADH-azoreductase from Staphylococcus pseudintermedius
33% identity, 87% coverage
HXW73_07605 FMN-dependent NADH-azoreductase from Halomonas sp. SH5A2
32% identity, 85% coverage
LMRG_00294 flavodoxin-like fold domain protein from Listeria monocytogenes 10403S
32% identity, 85% coverage
GK3428 acyl carrier protein phosphodiesterase (ACP phosphodiesterase) from Geobacillus kaustophilus HTA426
33% identity, 94% coverage
LMOf2365_0640 acyl carrier protein phosphodiesterase from Listeria monocytogenes str. 4b F2365
32% identity, 85% coverage
Plano_0380 FMN-dependent NADH-azoreductase from Planococcus sp. PAMC 21323
30% identity, 93% coverage
- Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants
Jung, Standards in genomic sciences 2018 - “...Plano_2901 Plano_0315 Pentachlolophenol-4-monooxygenase Plano_2834 Nitroalkane degradation Nitropropane dioxygenase Plano_2019 Plano_2569 Nitroreductase Plano_0226 Plano_0336 Plano_2301 Azoreductase Plano_0380 Metal ion detoxification Arsenate reductase Plano_0840 Plano_1482 Plano_0928 Mecuric ion reductase Plano_1475 Tellurite resistance TelA Plano_1607 TehB Plano_1454 Nitroalkane is a type of organic compound containing a nitro group, which...”
- “...and 2569). It also has three nitroreductases (Plano_226, 336, and 2301) and one azoreductase (AzoR, Plano_0380), which are generally observed in bacteria isolated from soil contaminated with industrial pollutants like trinitrotoluene (dynamite) [ 34 ]. For the detoxification of heavy metal ions, Planococcus sp. PAMC21323 has...”
lmo0611 similar to acyl-carrier protein phosphodiesterase and NAD(P)H dehydrogenase from Listeria monocytogenes EGD-e
32% identity, 85% coverage
Q9X4K2 FMN-dependent NADH-azoreductase (EC 1.7.1.17); azobenzene reductase (EC 1.7.1.6) from Geobacillus stearothermophilus (see paper)
33% identity, 94% coverage
4m0cA / Q81UB2 The crystal structure of a fmn-dependent nadh-azoreductase from bacillus anthracis str. Ames ancestor in complex with fmn.
29% identity, 83% coverage
- Ligands: flavin mononucleotide; zinc ion (4m0cA)
GBAA0966 conserved hypothetical protein from Bacillus anthracis str. 'Ames Ancestor'
29% identity, 80% coverage
- Transcriptional profiling of Bacillus anthracis Sterne (34F2) during iron starvation
Carlson, PloS one 2009 - “...GBAA1093 13.7 18.8 S-layer protein, putative GBAA4595 12.8 15.5 iron compound ABC transporter, ATP-binding protein GBAA0966 12.4 14.1 hypothetical protein GBAA0966 GBAA4594 12.3 13.8 ankyrin repeat-containing protein GBAA2255 12.1 13.2 substrate-binding family protein, putative GBAA0552 12.0 13.0 internalin, putative GBAA3595 12.0 12.9 BNR repeat-containing protein GBAA3596...”
Q0WXX2 FMN-dependent NADH-azoreductase (EC 1.7.1.17) from Bacillus sp. B29 (see paper)
30% identity, 91% coverage
lp_0955 NAD(P)H-dependent oxidoreductase from Lactiplantibacillus plantarum WCFS1
lp_0955 acyl carrier protein phosphodiesterase from Lactobacillus plantarum WCFS1
32% identity, 90% coverage
Gbem_2529 NAD(P)H dehydrogenase (quinone) from Geobacter bemidjiensis Bem
30% identity, 90% coverage
C0STY0 azobenzene reductase (EC 1.7.1.6) from Bacillus sp. B29 (see paper)
Q81EX6 FMN-dependent NADH:quinone oxidoreductase 1 from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
BC1835 FMN-dependent NADH-azoreductase from Bacillus cereus ATCC 14579
30% identity, 92% coverage
3w77A / Q0WXX2 Crystal structure of azoreductase azra (see paper)
30% identity, 91% coverage
- Ligand: flavin mononucleotide (3w77A)
BMD_3384 Flavodoxin-like fold family protein from Bacillus megaterium DSM319
30% identity, 90% coverage
BC5410, NP_835071 FMN-dependent NADH-azoreductase from Bacillus cereus ATCC 14579
30% identity, 91% coverage
- SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus
Yeak, BMC microbiology 2023 - “...YdjE Fructokinase 3.5 G 23 BC3576 BC3576 Spore germination protein SC 3.4 3.2 S 24 BC5410 YocJ FMN-dependent NADH-azoreductase 3.3 5.2 I 25 BC0999 b BC0999 General stress protein (hyperosmotic & cold) 3.1 S 26 BC3292 BC3292 hypothetical protein 3.0 S 27 BC1662 FliM Flagellar motor...”
- “...chemotaxis protein 1.7 1.1 NT 44 BC4403 YrvE Single-stranded-DNA-specific exonuclease recJ 1.5 1.3 LS 45 BC5410 YocJ FMN-dependent NADH-azoreductase 1.5 1.1 I 46 BC5120 hypothetical Cytosolic Protein 1.5 1.3 S 47 BC1850 Transcriptional regulator 1.5 1.0 K 48 BC1660 YjbJ Soluble lytic murein transglycosylase 1.4 1.8...”
- Methionine Residues in Exoproteins and Their Recycling by Methionine Sulfoxide Reductase AB Serve as an Antioxidant Strategy in Bacillus cereus
Madeira, Frontiers in microbiology 2017 - “...copper homeostasis protein cutC 3.00 NP_834331 BC4625 UspA Universal stress protein 3.19 Stress response NP_835071 BC5410 AcpD Azoreductase 4.87 5.83 NP_830954 BC1168 ClpB ATP-dependent chaperone 2.99 Chaperones NP_830829 BC1043 PrsA1 Peptidylprolyl isomerase 1.08 NP_833827 BC4109 RibD Diaminohydroxyphosphoribosylaminopyrimidine deaminase 2.78 2.92 4.42 Riboflavin biosynthesis NP_833829 BC4111 RibA...”
- “...CutC copper homeostasis protein cutC 3.00 NP_834331 BC4625 UspA Universal stress protein 3.19 Stress response NP_835071 BC5410 AcpD Azoreductase 4.87 5.83 NP_830954 BC1168 ClpB ATP-dependent chaperone 2.99 Chaperones NP_830829 BC1043 PrsA1 Peptidylprolyl isomerase 1.08 NP_833827 BC4109 RibD Diaminohydroxyphosphoribosylaminopyrimidine deaminase 2.78 2.92 4.42 Riboflavin biosynthesis NP_833829 BC4111...”
HU689_21345 FMN-dependent NADH-azoreductase from Shewanella algae
27% identity, 90% coverage
- Complete genome sequence of Shewanella algae strain 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru
Lizárraga, Biotechnology reports (Amsterdam, Netherlands) 2022 - “...words. Table 3 Category Gene name Locus tag Description Decolorization HU689_20695 FMN-dependent NADH-azoreductase HU689_04585; HU689_04700; HU689_21345 NADPH-dependent oxidoreductase HU689_05310 Heme-dependent Dyp peroxidase HU689_08360 - HU689_08395 Operon Mtr Metal Resistance cadA HU689_10830 P-type ATPase protein corA a & corC b HU689_12865 a &(HU689_16615; HU689_20255; HU689_07770) b Magnesium...”
- “...such as an FMN-dependent NADH-azoreductase gene ( HU689_20695 ), NADPH-dependent oxidoreductase genes ( HU689_04585; HU689_04700; HU689_21345 ), and heme-dependent Dyp peroxidase gene ( HU689_05310 ). The operon Mtr ( HU689_08360 - HU689_08395 ), an electron chain transport previously, encodes two OmcA genes ( HU689_08375, HU689_08380 )...”
YP_039668 putative phosphodiesterase from Staphylococcus aureus subsp. aureus MRSA252
SAR0203 FMN-dependent NADH-azoreductase from Staphylococcus aureus subsp. aureus MRSA252
31% identity, 87% coverage
GBAA1908 conserved hypothetical protein from Bacillus anthracis str. 'Ames Ancestor'
29% identity, 92% coverage
SACOL0190 NAD(P)H dehydrogenase (quinone), putative from Staphylococcus aureus subsp. aureus COL
SA0204 acyl carrier protein phosphodiesterase from Staphylococcus aureus subsp. aureus N315
SAOUHSC_00173 acyl carrier phosphodiesterase from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0206 flavodoxin family protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
30% identity, 87% coverage
- Effect of Rocket (Eruca sativa) Extract on MRSA Growth and Proteome: Metabolic Adjustments in Plant-Based Media
Doulgeraki, Frontiers in microbiology 2017 - “...Nitroreductase 5 P99077 Peptide deformylase 21683 5.87 SACOL1100; SACOL1227 6 Q7A782 FMN-dependent NADPH-azoreductase 19732 5.76 SACOL0190 10 P99068 Nucleotide diphosphate kinase 14586 5.04 SACOL1509 Purine and pyrimidine synthesis; Synthesis of secondary metabolites In all cases, COL and N315 homolog genes had 99100% identity. As mentioned above,...”
- VraT/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus
Boyle-Vavra, Antimicrobial agents and chemotherapy 2013 - “...amino acid transport protein AcpD, FMN-dependent NADH azoreductase SAUSA300_0206 SA0204 3.7 2.9 4.4 2.3 3.9 3.4 2.6 3.7 2.6 2.4 2 1.8 2.6 2.1 2.8 synthesis of...”
- 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 - “...dehydrogenase sa_c7032s9332_a_at * 5.4 2.5 stable glpT SA0407 glycerol-3-phosphate transporter sa_c9250s8097_a_at 2.2 2.5 stable pflB SA0204 formate acetyltransferase sa_c8390s7366_a_at 3.0 15 30 pgk SA0839 phosphoglycerate kinase sa_c853s654_a_at 10.4 2.5 15 pyc SA1123 pyruvate carboxylase sa_c8397s7370_a_at * 2.7 15 stable tpiA SA0840 triosephosphate isomerase sa_c3742s3217_a_at * 6.7...”
- Serial daptomycin selection generates daptomycin-nonsusceptible Staphylococcus aureus strains with a heterogeneous vancomycin-intermediate phenotype
Camargo, Antimicrobial agents and chemotherapy 2008 - “...Dehydrogenases and oxidoreductases SA0171 SA0204 SA2311 polysaccharide polysaccharide polysaccharide polysaccharide polysaccharide polysaccharide polysaccharide...”
- “...2). Among these, the open reading frames (ORFs) SA0204, which encodes an NAD(P)H dehydrogenase homologue, and SA2311, which encodes a hypothetical protein...”
- Global transcriptome analysis of Staphylococcus aureus response to hydrogen peroxide
Chang, Journal of bacteriology 2006 - “...Primer sequence (sense, antisense) Microarray Real-time PCR SA0204 ( pflB) 25.1 107.3 50.5 SA0205 ( pflA) 33.2 81.8 38.1 5-TGACAAACATATTAGATTGACAGGAAAGC-3...”
- Overexpression of genes of the cell wall stimulon in clinical isolates of Staphylococcus aureus exhibiting vancomycin-intermediate- S. aureus-type resistance to vancomycin
McAleese, Journal of bacteriology 2006 - “...SA0325 SA1992 SA1993 SA1994 SA1995 SA1996 SA1997 SA2241 SA2294 SA0204 SA0241 Gene 1126 MCALEESE ET AL. J. BACTERIOL. TABLE 1--Continued N315 ORF no. a SA1418...”
- “...SA0166 csbD yvqF tcaA dmp1 spsA spsB SA0825 SA0826 SA0204 SA0022 SA0918 purC SA0921 SA1549 purL htrA SA1659 SA0108 SA0573 SA1195 prsA sarS sarA msrR SA1583...”
- Physiological characterization of a heme-deficient mutant of Staphylococcus aureus by a proteomic approach
Kohler, Journal of bacteriology 2003 - “...pflB (SA0204) ..................................................................................CATGCAACAGCTTGGCAAGG...”
- Staphylococcus aureus Tolerance and Genomic Response to Photodynamic Inactivation
Snell, mSphere 2021 - “...regulated collectively among the three groups included SAOUHSC_00320, which encodes a NADH-dependent flavin mononucleotide reductase; SAOUHSC_00173, which encodes a flavin mononucleotide (FMN)-dependent NADH-azoreductase; SAOUHSC_00833, which encodes a nitroreductase family protein; SAOUHSC_02825, which encodes a glyoxalase family protein; SAOUHSC_00318, which encodes a glyoxalase/bleomycin resistance protein; and SAOUHSC_00093,...”
- Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) Genetic Factors Involved in Human Endothelial Cells Damage, an Important Phenotype Correlated with Persistent Endovascular Infection
Xiao, Antibiotics (Basel, Switzerland) 2022 - “...hypothetical conserved hypothetical protein 61.86 6.12 SAUSA300_2221 moaD molybdopterin converting factor, subunit 1 61.64 3.61 SAUSA300_0206 azoR flavodoxin family protein 60.82 6.24 SAUSA300_0335 mepA MATE efflux family protein 60.15 8.13 a ND: not determined. antibiotics-11-00316-t003_Table 3 Table 3 Verification of EC damage of JE WT strain...”
- “...3.05 66.92 0.84 SAUSA300_1485 hypothetical 61.86 6.12 61.75 a SAUSA300_2221 moaD 61.64 3.61 59.90 1.08 SAUSA300_0206 hypothetical 60.82 6.24 69.33 0.48 SAUSA300_0335 hypothetical 60.15 8.31 63.35 2.06 SAUSA300_1040 EC damage 30% in 384-well plates hypothetical 26.74 8.21 30.92 a SAUSA300_1875 hypothetical 24.52 10.68 30.51 a SAUSA300_0871...”
- Bayesian Modeling and Intrabacterial Drug Metabolism Applied to Drug-Resistant <i>Staphylococcus aureus</i>
Patel, ACS infectious diseases 2021 - “.... Whole-genome sequencing found the four strains had single nucleotide polymorphisms (SNP) in the gene SAUSA300_0206 ( azoR ). The mutations in azoR resulted in the following protein changes: Trp 100 stop ( azoR1 ), Trp 60 stop ( azoR2 ), Thr 121 Ile ( azoR3...”
- Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
Kulkarni, American journal of respiratory cell and molecular biology 2016 - “...SAUSA300_0076 SAUSA300_2617 SAUSA300_2492 SAUSA300_2638 SAUSA300_0206 SAUSA300_0784 SAUSA300_2326 SAUSA300_0075 SAUSA300_0952 SAUSA300_0747 SAUSA300_0121...”
- VraT/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus
Boyle-Vavra, Antimicrobial agents and chemotherapy 2013 - “...Branched-chain amino acid transport protein AcpD, FMN-dependent NADH azoreductase SAUSA300_0206 SA0204 3.7 2.9 4.4 2.3 3.9 3.4 2.6 3.7 2.6 2.4 2 1.8 2.6 2.1 2.8...”
7awvA / A0A1B1KJ01 Azoreductase (azoro) from rhodococcus opacus 1cp (see paper)
36% identity, 82% coverage
- Ligand: flavin mononucleotide (7awvA)
BCAS0186 putative acyl carrier protein phosphodiesterase from Burkholderia cenocepacia J2315
33% identity, 82% coverage
- Global changes in gene expression by the opportunistic pathogen Burkholderia cenocepacia in response to internalization by murine macrophages
Tolman, BMC genomics 2012 - “...included BCAM0314 (hypothetical protein), BCAM2141 (ABC transporter ATP-binding protein), BCAM0276 (putative universal stress protein), and BCAS0186 (putative acyl carrier protein phosphodiesterase), all of which show high expression in intracellular bacteria. BCAM1928 (putative transcription elongation factor) was chosen as an example of a gene with decreased expression...”
- “...30 ]. The ten deleted genes were: BCAL0124 (subunit of the flagellar regulon master regulator), BCAS0186 (putative acyl carrier protein phosphodiesterase), BCAM0434-5, (cation efflux system), BCAM2837 (response regulator component of a two-component regulatory system), BCAL1726 (putative oxidoreductase), BCAM0276 (putative universal stress protein), BCAM0411 (MgtC family protein),...”
TS60_0029 FMN-dependent NADH-azoreductase from Mycoplasma mycoides subsp. mycoides
29% identity, 85% coverage
MSC_0029 Acyl carrier protein phosphodiesterase from Mycoplasma mycoides subsp. mycoides SC str. PG1
29% identity, 85% coverage
lp_0075 acyl carrier protein phosphodiesterase (putative) from Lactobacillus plantarum WCFS1
25% identity, 93% coverage
- Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1
Serrano, Microbial cell factories 2007 - “..., Em R pUC18EM derivative carrying 1.0 kb DNA fragments of both L. plantarum WCFS1 lp_0075 and lp_0077 genes. This work pNZ7131 Amp R , Em R , pNZ7130 derivative with extra cloning sites Nsa1 and NsiI. This work ppNZ7132 Cm R , Em R ,...”
- “...L. plantarum WCFS1 as template. The primers used to amplify the 5'- and 3'-regions of lp_0075 and lp_0077 respectively were lp_0075-FORW and lp_0075-REV; lp_0077-FORW and lp_0077-REV, shown in Table 6 . The PCR amplicons obtained were digested with EcorI-BamhI, and BamhI-XbaI (sites introduced in the primers...”
MG_333 azoreductase from Mycoplasma genitalium G37
28% identity, 78% coverage
- Transcriptional response of Mycoplasma genitalium to osmotic stress
Zhang, Microbiology (Reading, England) 2011 - “...DegV family protein 2.08 0.00169 0.00136 MG_332 Expressed protein of unknown function 2.47 0.00003 0.00136 MG_333 Acyl carrier protein phosphodiesterase, putative 4.21 0.00001 0.00136 MG_348 Lipoprotein, putative 2.80 0.00002 0.00136 MG_353 DNA-binding protein HU, putative 3.47 0.00001 0.00136 MG_354 Conserved hypothetical protein 2.16 0.00006 0.00136 MG_357...”
MPN479 ACYL CARRIER PROTEIN PHOSPHODIESTERASE from Mycoplasma pneumoniae M129
28% identity, 84% coverage
- Comparative genome analysis of Mycoplasma pneumoniae
Xiao, BMC genomics 2015 - “...pheS, polA, ppnK, pstB, rimK, rnc, udk, upp, yaaC, yacA, ygiH, yjeQ, yjfU, yjfW, MPN047, MPN479 mpn03011 Ribosome 25 50S and 30S ribosomal proteins, 5S rRNA mpn0200 Transporters 9 amiD, permease, glnQ, dnaK, pstA, pstB, oppB, yjfU mpn03029 Mitochondrial biogenesis 9 grs1, gatB, dnaJ, dnaK, groEL,...”
- Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
Dandekar, Nucleic acids research 2000 - “...P01_orf292 MPN170 662.0 PID:g1674366 VXpSPT7_orf184 MPN479 361.0 PID:g1674040 P01_orf197 MPN210 622.0 PID:g1674324 G07_orf808 MPN482 358.0-359.0 hypothetical...”
CPR_0519 putative acyl carrier protein phosphodiesterase 1 from Clostridium perfringens SM101
22% identity, 92% coverage
SMM_0597 FMN-dependent NADH-azoreductase from Spiroplasma mirum ATCC 29335
30% identity, 77% coverage
- The genome and antigen proteome analysis of Spiroplasma mirum
Liu, Frontiers in microbiology 2022 - “...phage. The phage with a length of 16,008 bp includes 21 genes (From SMM_0576 to SMM_0597). Particularly, SMM_578, SMM_579, SMM_580, SMM_581, and SMM_583 were identified as putative adhesin p58, P12, P54, P123, and P18 of S. citri , respectively. Thus, the phage may be acquired from...”
MHO_0860 Acyl carrier protein phosphodiesterase from Mycoplasma hominis
27% identity, 67% coverage
PP3720 NAD(P)H quinone oxidoreductase, putative from Pseudomonas putida KT2440
32% identity, 54% coverage
- Escherichia coli NemA is an efficient chromate reductase that can be biologically immobilized to provide a cell free system for remediation of hexavalent chromium
Robins, PloS one 2013 - “...(PA1962), chrR (PA1204), msuE (PA2357) nfsB (PA5190), ycaK (PA1225); Pseudomonas putida (KT2440) azoR (PP4538), kefF (PP3720), nfsA (PP2490), nfsB (PP2432); Pseudomonas syringae pv. phaseolicola (1448a) azoR, mdaB, wrbA; Salmonella typhi (ATCC l9430) azoR, nfsA, nfsB; Vibrio fischeri (ATCC 7744) nfsB (FRase I); Vibrio harveyi (ATCC 33843)...”
PA4975 NAD(P)H quinone oxidoreductase from Pseudomonas aeruginosa PAO1
33% identity, 54% coverage
- Investigating azoreductases and NAD(P)H dependent quinone oxidoreductases in Pseudomonas aeruginosa
Holland, 2017 - Azoreductases in drug metabolism
Ryan, British journal of pharmacology 2017 - “...from P. aeruginosa. paWrbA, PA1224, PA1225, and PA4975 are NAD(P)H quinone oxidoreductases from P. aeruginosa. bsAzoR, efAzoR and rsAzoR are azoreductases...”
- Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes
Ryan, PloS one 2014 - “...fungal enzymes and those in yellow are archeal. PA0949, PA1204, PA1224, PA1225, PA2280, PA2580, and PA4975 are proteins from P. aeruginosa . ecAzoR, bsAzoR, efAzoR and rsAzoR are azoreductases from E. coli , Bacillus subtilis , Enterococcus faecalus and Rhodobacter sphaeroides . hNQO1 hNQO2, rNQO1 and...”
- “...pa2580 79 86 76 81 75 - pa3223 i 69 67 - 74 66 - pa4975 - 78 - 82 - - All values are given as percentage identity to the protein from P. aeruginosa PAO1. Homologues are defined as having >45% sequence identity based upon...”
- Pseudomonas aeruginosa NfsB and nitro-CBI-DEI--a promising enzyme/prodrug combination for gene directed enzyme prodrug therapy
Green, Molecular cancer 2013 - “...PA5190 25 (NfsB_Ec) AAG08575.1 AzoR2_Pa PA1962 41 (AzoR_Ec) AAG05350.1 AzoR3_Pa PA3223 45 (AzoR_Ec) AAG06611.1 KefF_Pa PA4975 37 (KefF_Ec) AAG08360.1 MdaB_Pa PA2580 64 (MdaB_Ec) AAG05968.1 WrbA_Pa PA0949 39 (WrbA_Ec) AAG04338.1 YcaK1_Pa PA1225 33 (YcaK_Ec) AAG04614.1 YcaK2_Pa PA0853 27 (YcaK_Ec) AAG04242.1 YdjA_Pa PA3208 42 (YdjA_Ec) AAG06596.1 YieF_Pa PA1204...”
- Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1
Oberhardt, Journal of bacteriology 2008 - “...catalyzed by the electron transport enzyme NADPH-quinone oxidoreductase (PA4975; EC 1.6.5.5) was found upon analysis of free ATP production to be necessarily...”
- Functional genomics enables identification of genes of the arginine transaminase pathway in Pseudomonas aeruginosa
Yang, Journal of bacteriology 2007 - “...on LB plates supplemented with tetracycline and streptomycin. PA4975, PA4976 (aruH), and PA5304 (dadA) knockout mutants were also constructed by a strategy...”
- “...3 ends of the PCR products: for PA4975 and PA4976 (aruH), 5-GTCTAAGCTTGACTGGCCTGGCGCGCGTCG-3 and 5-CGCA AGCTTCGGGCAGTCCGGCGTGACCCT-3; for PA5304 (dadA), 5-ACGG...”
- Direct continuous method for monitoring biofilm infection in a mouse model
Kadurugamuwa, Infection and immunity 2003 - “...coli. Upstream of PA4974 was thiC and downstream was PA4975; both of these ORF were in the opposite direction to the PA4974. Comparisons of transformants and...”
PFL_2716 NAD(P)H dehydrogenase, quinone family from Pseudomonas fluorescens Pf-5
34% identity, 55% coverage
NQO2_HUMAN / P16083 Ribosyldihydronicotinamide dehydrogenase [quinone]; NRH dehydrogenase [quinone] 2; NRH:quinone oxidoreductase 2; Quinone reductase 2; QR2; EC 1.10.5.1 from Homo sapiens (Human) (see 7 papers)
P16083 ribosyldihydronicotinamide dehydrogenase (quinone) (EC 1.10.5.1) from Homo sapiens (see 8 papers)
NP_001277150 ribosyldihydronicotinamide dehydrogenase [quinone] isoform 1 from Homo sapiens
30% identity, 58% coverage
- function: The enzyme apparently serves as a quinone reductase in connection with conjugation reactions of hydroquinones involved in detoxification pathways as well as in biosynthetic processes such as the vitamin K-dependent gamma-carboxylation of glutamate residues in prothrombin synthesis.
catalytic activity: 1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone + H(+) = beta-nicotinamide D-riboside + a quinol (RHEA:12364)
cofactor: Zn(2+) Note=Binds 1 zinc ion per subunit
cofactor: FAD
subunit: Homodimer. - A proteogenomic view of Parkinson's disease causality and heterogeneity.
Kaiser, NPJ Parkinson's disease 2023 - “...0.05 0.79 MANEA 8014_359 Q5SRI9 79694 17 IVW 0.05 3.2110 4 0.10 0.94 NQO2 9754_33 P16083 4835 11 IVW 0.05 3.2110 4 0.05 0.98 OID01173 r 2 =0.276 p =0.018 ARSA a 3583_54 P15289 410 5 IVW 0.13 6.8210 4 0.58 0.62 OID01479 r 2 =0.383...”
- Uncovering the mechanism of Radix Paeoniae Alba in the treatment of restless legs syndrome based on network pharmacology and molecular docking
Liu, Medicine 2022 - “...kDa protein P11142 11 IGF1R Insulin-like growth factor 1 recepto P08069 15 NQO2 Ribosyldihydronicotinamide dehydrogenase P16083 0 NR3C2 Mineralocorticoid receptor P08235 5 PPARG Peroxisome proliferator-activated receptor gamma P37231 17 REN Renin P00797 9 RTN4R Reticulon-4 receptor Q9BZR6 0 3.4. Active components-overlapping targets network and key active...”
- Insight into the Molecular Signature of Skeletal Muscle Characterizing Lifelong Football Players
Orrù, International journal of environmental research and public health 2022 - “...RAB14 1.61 P62277 40S ribosomal protein S13 RPS13 1.61 Q15084 Protein disulfide-isomerase A6 PDIA6 1.61 P16083 Ribosyldihydronicotinamide dehydrogenase (quinone) NQO2 1.61 P47985 Cytochrome b-c1 complex subunit Rieske, mitochondrial UQCRFS1 1.53 P02545 Prelamin-A/C LMNA 1.53 P24844 Myosin regulatory light polypeptide 9 MYL9 1.51 P09382 Galectin-1 LGALS1 1.51...”
- The exploration of the potential mechanism of oxymatrine-mediated antipruritic effect based on network pharmacology and weighted gene co-expression network analysis
Luo, Frontiers in pharmacology 2022 - “...0.9207 AK1C2_HUMAN AKR1C2 7 1rs0_v 3 2.685 0.8951 CFAB_HUMAN CFB 8 3gam_v 3 2.662 0.8874 P16083 NQO2 9 1pmv_v 3 2.62 0.8734 MK10_HUMAN MAPK10 10 1uki_v 3 2.582 0.8607 MK08_HUMAN MAPK8 11 1l6l_v 3 2.4 0.7999 APOA2_HUMAN APOA2 12 1if4_v 3 2.277 0.7591 CAH2_HUMAN CA2 13...”
- Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids.
Rodrigues, International journal of molecular sciences 2022 - “...2-alpha P14550 AKR1A1 Aldo-keto reductase family 1 member A1 P15559 NQO1 NAD(P)H dehydrogenase [quinone] 1 P16083 NQO2 Ribosyldihydronicotinamide dehydrogenase [quinone] P16152 CBR1 Carbonyl reductase [NADPH] 1 P16435 POR NADPH--cytochrome P450 reductase P29474 NOS3 Nitric oxide synthase, endothelial P29475 NOS1 Nitric oxide synthase, brain Q14978 NOLC1 Nucleolar...”
- Targeted Proteins Reveal Cathepsin D as a Novel Biomarker in Differentiating Hepatocellular Carcinoma from Cirrhosis and Other Liver Cancers.
Chuaypen, Asian Pacific journal of cancer prevention : APJCP 2022 - “...50.83671.6628 7.68131.2693 0.1511 0.0034 P50897 Palmitoyl-protein thioesterase 1 71.99 15.03 34.2 4.82100.0751 2.29100.0970 0.4752 0.0045 P16083 Ribosyldihydronicotinamide dehydrogenase 74.47 25.11 25.9 12.80001.7481 0.62400.6240 0.0488 0.0092 Q16762 Thiosulfate sulfurtransferase 99.98 26.26 33.4 44.36336.0569 7.86570.3117 0.1773 0.0289 Proteins that were absent in tumor tissues Q68CK6 Acyl-coenzyme A synthetase...”
- Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment
Stevenson, NPJ breast cancer 2021 - “...N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 6 62.68 146.63 1.23 0.04 Q15848 Adiponectin 2 62.36 147.03 1.24 0.04 P16083 Ribosyldihydronicotinamide dehydrogenase [quinone] 6 61.62 147.98 1.26 0.04 P29401 Transketolase 28 61.58 148.03 1.27 0.03 Q14126 Desmoglein-2 6 61.34 148.35 1.27 0.0006 O75368 SH3 domain-binding glutamic acid-rich-like protein 9 60.98...”
- Filtration of Active Components with Antioxidant Activity Based on the Differing Antioxidant Abilities of Schisandrae Sphenantherae Fructus and Schisandrae Chinensis Fructus through UPLC/MS Coupling with Network Pharmacology.
Xin, Evidence-based complementary and alternative medicine : eCAM 2021 - “...PTGS1 Cyclooxygenase-1 11 Q01959 SLC6A3 Dopamine transporter (by homology) 12 P09917 ALOX5 Arachidonate 5-lipoxygenase 13 P16083 NQO2 Quinone reductase 2 14 P14416 DRD2 Dopamine D2 receptor (by homology) 15 P00813 ADA Adenosine deaminase 16 P23443 RPS6KB1 Ribosomal protein S6 kinase 1 17 P09237 MMP7 Matrix metalloproteinase...”
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- Polymorphisms and Pharmacogenomics of NQO2: The Past and the Future.
Janda, Genes 2024 - GeneRIF: Polymorphisms and Pharmacogenomics of NQO2: The Past and the Future.
- An Axis between the Long Non-Coding RNA HOXA11-AS and NQOs Enhances Metastatic Ability in Oral Squamous Cell Carcinoma.
Nakashima, International journal of molecular sciences 2022 - GeneRIF: An Axis between the Long Non-Coding RNA HOXA11-AS and NQOs Enhances Metastatic Ability in Oral Squamous Cell Carcinoma.
- Cancer-associated variants of human NQO1: impacts on inhibitor binding and cooperativity.
Megarity, Bioscience reports 2019 - GeneRIF: Cancer-associated variants of human NQO1: impacts on inhibitor binding and cooperativity.
- Oxidative stress and neurodegeneration: The possible contribution of quinone reductase 2.
Cassagnes, Free radical biology & medicine 2018 (PubMed)- GeneRIF: these data suggest that the overexpression of QR2 in brain cells in the presence of catechol quinones might lead to reactive oxygen species-induced cell death via the rapid conversion of superoxide radicals into hydrogen peroxide and then into highly reactive hydroxyl radicals
- The ontogeny and population variability of human hepatic dihydronicotinamide riboside:quinone oxidoreductase (NQO2).
Riches, Journal of biochemical and molecular toxicology 2017 (PubMed)- GeneRIF: The ontogeny and population variability of human hepatic dihydronicotinamide riboside:quinone oxidoreductase (NQO2).
- Expression of Quinone Reductase-2 in the Cortex Is a Muscarinic Acetylcholine Receptor-Dependent Memory Consolidation Constraint.
Rappaport, The Journal of neuroscience : the official journal of the Society for Neuroscience 2015 - GeneRIF: In patients with Alzheimer's disease, QR2 is overexpressed in the insular cotex.
- The two common polymorphic forms of human NRH-quinone oxidoreductase 2 (NQO2) have different biochemical properties.
Megarity, FEBS letters 2014 - GeneRIF: NQO2-L47 is less stable towards proteolytic digestion and thermal denaturation than NQO2-F47.
- Chloroquine binding reveals flavin redox switch function of quinone reductase 2.
Leung, The Journal of biological chemistry 2013 - GeneRIF: This first structure of a reduced quinone reductase shows that reduction of the FAD cofactor and binding of a specific inhibitor lead to global changes in NQO2 structure and is consistent with a functional role for NQO2 as a flavin redox switch.
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4fglD / P16083 Reduced quinone reductase 2 in complex with chloroquine
30% identity, 58% coverage
- Ligands: n4-(7-chloro-quinolin-4-yl)-n1,n1-diethyl-pentane-1,4-diamine; zinc ion; flavin-adenine dinucleotide (4fglD)
Q5RBB9 Ribosyldihydronicotinamide dehydrogenase [quinone] from Pongo abelii
29% identity, 59% coverage
Q6AY80 Ribosyldihydronicotinamide dehydrogenase [quinone] from Rattus norvegicus
XP_006253929 ribosyldihydronicotinamide dehydrogenase [quinone] isoform X1 from Rattus norvegicus
27% identity, 63% coverage
XP_005022918 ribosyldihydronicotinamide dehydrogenase [quinone] isoform X4 from Anas platyrhynchos
33% identity, 39% coverage
NQO1_RAT / P05982 NAD(P)H dehydrogenase [quinone] 1; Azoreductase; DT-diaphorase; DTD; Menadione reductase; NAD(P)H:quinone oxidoreductase 1; Phylloquinone reductase; Quinone reductase 1; QR1; EC 1.6.5.2 from Rattus norvegicus (Rat) (see 4 papers)
P05982 NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) from Rattus norvegicus (see 2 papers)
NP_058696 NAD(P)H dehydrogenase [quinone] 1 from Rattus norvegicus
35% identity, 23% coverage
- function: Flavin-containing quinone reductase that catalyzes two- electron reduction of quinones to hydroquinones using either NADH or NADPH as electron donors. In a ping-pong kinetic mechanism, the electrons are sequentially transferred from NAD(P)H to flavin cofactor and then from reduced flavin to the quinone, bypassing the formation of semiquinone and reactive oxygen species (PubMed:1703398, PubMed:7862630, PubMed:8999809). Regulates cellular redox state primarily through quinone detoxification. Reduces components of plasma membrane redox system such as coenzyme Q and vitamin quinones, producing antioxidant hydroquinone forms. In the process may function as superoxide scavenger to prevent hydroquinone oxidation and facilitate excretion (By similarity). Alternatively, can activate quinones and their derivatives by generating redox reactive hydroquinones with DNA cross-linking antitumor potential (By similarity). Acts as a gatekeeper of the core 20S proteasome known to degrade proteins with unstructured regions. Upon oxidative stress, interacts with tumor suppressors TP53 and TP73 in a NADH-dependent way and inhibits their ubiquitin-independent degradation by the 20S proteasome (By similarity).
catalytic activity: a quinone + NADH + H(+) = a quinol + NAD(+) (RHEA:46160)
catalytic activity: a quinone + NADPH + H(+) = a quinol + NADP(+) (RHEA:46164)
catalytic activity: ubiquinone-10 + NADH + H(+) = ubiquinol-10 + NAD(+) (RHEA:61984)
catalytic activity: menadione + NADH + H(+) = menadiol + NAD(+) (RHEA:69695)
cofactor: FAD
subunit: Homodimer (PubMed:7568029). Interacts with PDLIM4 isoform 2; this interaction stabilizes PDLIM4 isoform 2 in response to oxidative stress and protects it from ubiquitin-independent degradation by the core 20S proteasome (By similarity). Interacts with TP73 (via SAM domain); this interaction is NADH-dependent, stabilizes TP73 in response to oxidative stress and protects it from ubiquitin-independent degradation by the 20S proteasome (By similarity). Interacts with TP53; this interaction is NADH-dependent, stabilizes TP53 in response to oxidative stress and protects it from ubiquitin-independent degradation by the 20S proteasome (By similarity). - PPAR beta/gamma mediates the antihypertensive activity of a synbiotic preparation of Bifidobacterium lactis and Lactobacillus acidophilus in spontaneous hypertensive rats
Huang, Heliyon 2024 - “...0.2475 65 P62994 Growth factor receptor-bound protein 2 GRB2 5 2.8840 0.0407 1.0666 0.8967 66 P05982 NAD(P)H dehydrogenase [quinone] 1 NQO1 7 6.3680 0.0105 0.6855 0.4866 67 P02651 Apolipoprotein A-IV APOA4 4 2.2699 0.0157 0.3802 0.0317 68 P01836 Ig kappa chain C region, A allele KACA...”
- Characterizations of annexin A1-interacting proteins in apical membrane and cytosolic compartments of renal tubular epithelial cells.
Peerapen, Computational and structural biotechnology journal 2023 - “...-lactate dehydrogenase A chain P06151 LDHA 218 12.0 4/28 36.82 7.62 NAD(P)H dehydrogenase [quinone] 1 P05982 NQO1 132 3.6 1/5 30.98 8.42 Parathymosin Q9D0J8 PTMS 43 10.9 1/7 11.42 4.17 *Peroxiredoxin-1 Q6B4U9 PRDX1 76 18.6 4/7 22.34 8.27 Platelet factor 4 P02777 PF4 498 9.1 1/50...”
- “...-lactate dehydrogenase A chain P06151 LDHA 218 12.0 4/28 36.82 7.62 NAD(P)H dehydrogenase [quinone] 1 P05982 NQO1 132 3.6 1/5 30.98 8.42 Parathymosin Q9D0J8 PTMS 43 10.9 1/7 11.42 4.17 # Peptidyl-prolyl cis-trans isomerase FKBP1A P18203 FKBP1A 112 12.0 1/5 11.96 7.88 # Peroxiredoxin-2 (Fragment) P52552...”
- Identification of differentially expressed proteins involved in fetal scarless wound healing using a rat model of cleft lip.
Yan, Molecular medicine reports 2021 - “...Annexin a3 0.010 5.005 P22985 Xdh Xanthine dehydrogenase/oxidase 0.003 4.802 Q91zn1 Coro1a Coronin-1a 0.001 4.694 P05982 Nqo1 Nad(p)h quinone dehydrogenase 1 0.001 4.334 P23640 Rab27a Ras-related protein rab-27a 0.019 3.830 Q6ifu9 Krt16 Keratin, type i cytoskeletal 16 0.001 3.797 Q62894 Ecm1 Extracellular matrix protein 1 0.039...”
- Analysis of the Effect of Intestinal Ischemia and Reperfusion on the Rat Neutrophils Proteome
Tahir, Frontiers in molecular biosciences 2018 - “...mitochondrial EC 1.3.99.- Q8JZN5 Acad9 4 0.094393882 0.091932542 0.186326425 NAD(P)H dehydrogenase [quinone] 1 EC 1.6.5.2 P05982 Nqo1 4 0.094854334 0.270101397 0.175247063 Thioredoxin reductase 1, cytoplasmic EC 1.8.1.9 O89049 Txnrd1 4 0.001836217 0.119040483 0.117204265 L-lactate dehydrogenase C chain EC 1.1.1.27 P19629 Ldhc 5 0.156311009 0.132653839 0.288964848 TRANSFERASES...”
- ATP Modifies the Proteome of Extracellular Vesicles Released by Microglia and Influences Their Action on Astrocytes
Drago, Frontiers in pharmacology 2017 - “...(Vim) P04785 Protein disulfide-isomerase (P4hb) P05370 Glucose-6-phosphate 1-dehydrogenase (G6pdx) P10960 Prosaposin (Sulfated glycoprotein 1) (Psap) P05982 NAD(P)H dehydrogenase 1 (Nqo1) P11598 Protein disulfide-isomerase A3 (Pdia3) P0CG51 Polyubiquitin-B (Ubb) P12346 Serotransferrin (Tf) P13471 40S ribosomal protein S14 (Rps14) P17132/Q9JJ54 Heterogeneous nuclear ribonucleoprotein D0 (Hnrnpd) P18588 Interferon-induced GTP-binding...”
- Proteomic Expression Changes in Large Cerebral Arteries After Experimental Subarachnoid Hemorrhage in Rat Are Regulated by the MEK-ERK1/2 Pathway.
Müller, Journal of molecular neuroscience : MN 2017 - “...protein 109 2.02 O55096 Dipeptidyl peptidase 3 2.01 P39069 Adenylate kinase isoenzyme 1 (Fragments) 1.98 P05982 NAD(P)H dehydrogenase [quinone] 1 1.34 Q9QXQ0 Alpha-actinin-4 1.27 Q62507 Cochlin 1.26 P19132 Ferritin heavy chain 1.20 P38983 40S ribosomal protein SA 1.17 P52944 PDZ and LIM domain protein 1 1.17...”
- Influence of age on rat bone-marrow mesenchymal stem cells potential
Fafián-Labora, Scientific reports 2015 - “...heavy polypeptide 9, non-muscle 98 0,9405 0,0071 1,1877 0 1,0117 0,6464 0,957 0,2338 1,3299 0 P05982 NAD(P)H dehydrogenase [quinone] 1 8 1,3454 0,0036 0,7746 0,0108 1,2457 0,0611 0,817 0,2198 1,7303 0,0017 G3V8R1 Nucleobindin 2, isoform CRA_b 3 0,7234 0,0259 2,0743 0,0023 0,5945 0,0061 0,8133 0,1039 1,5101...”
- Proteomic Identification of Nrf2-Mediated Phase II Enzymes Critical for Protection of Tao Hong Si Wu Decoction against Oxygen Glucose Deprivation Injury in PC12 Cells.
Qi, Evidence-based complementary and alternative medicine : eCAM 2014 - “...70 442 1.8 74099/5.97 Pre-mtHSP70 P48721 1 102 483 1.2 30868/9.34 NAD(P)H dehydrogenase [quinone] 1 P05982 2 83 511 1.3 33006/6.09 Heme oxygenase 1 P06762 2 75 561 1.3 32622/6.42 Stanniocalcin-2 Q9R0K8 563 1.3 40927/4.81 Protooncogene c-Fos P12841 3 116 734 1.3 41643/5.31 Actin, gamma-enteric smooth...”
- NQO1 regulates expression and alternative splicing of apoptotic genes associated with Alzheimer's disease in PC12 cells.
Du, Brain and behavior 2023 - GeneRIF: NQO1 regulates expression and alternative splicing of apoptotic genes associated with Alzheimer's disease in PC12 cells.
- MiR-766-3p and miR-671-5p attenuate aristolochic acid-induced hepatotoxicity by directly targeting the key bioactivating enzyme NQO1.
Liu, Ecotoxicology and environmental safety 2023 (PubMed)- GeneRIF: MiR-766-3p and miR-671-5p attenuate aristolochic acid-induced hepatotoxicity by directly targeting the key bioactivating enzyme NQO1.
- A single evolutionarily divergent mutation determines the different FAD-binding affinities of human and rat NQO1 due to site-specific phosphorylation.
Pacheco-Garcia, FEBS letters 2022 (PubMed)- GeneRIF: A single evolutionarily divergent mutation determines the different FAD-binding affinities of human and rat NQO1 due to site-specific phosphorylation.
- Oltipraz Prevents High Glucose-Induced Oxidative Stress and Apoptosis in RSC96 Cells through the Nrf2/NQO1 Signalling Pathway.
Jiang, BioMed research international 2020 - GeneRIF: Oltipraz Prevents High Glucose-Induced Oxidative Stress and Apoptosis in RSC96 Cells through the Nrf2/NQO1 Signalling Pathway.
- Increased NADPH-diaphorase reactivity in the hypothalamic paraventricular nucleus and tanycytes following systemic administration of leptin in rats.
Hristov, Acta histochemica 2019 (PubMed)- GeneRIF: Increased NADPH-diaphorase reactivity in the hypothalamic paraventricular nucleus and tanycytes following systemic administration of leptin in rats.
- Coenzyme Q10 Regulation of Apoptosis and Oxidative Stress in H2O2 Induced BMSC Death by Modulating the Nrf-2/NQO-1 Signaling Pathway and Its Application in a Model of Spinal Cord Injury.
Li, Oxidative medicine and cellular longevity 2019 - GeneRIF: Coenzyme Q10 Regulation of Apoptosis and Oxidative Stress in H2O2 Induced BMSC Death by Modulating the Nrf-2/NQO-1 Signaling Pathway and Its Application in a Model of Spinal Cord Injury.
- Overexpression of CYB5R3 and NQO1, two NAD+ -producing enzymes, mimics aspects of caloric restriction.
Diaz-Ruiz, Aging cell 2018 - GeneRIF: results highlight the importance of CYB5R3 and NQO1, two NAD(+) producers, for the promotion of health and extended lifespan
- DNA methylation of a non-CpG island promoter represses NQO1 expression in rat arsenic-transformed lung epithelial cells.
Huang, Acta biochimica et biophysica Sinica 2018 (PubMed)- GeneRIF: Data indicate that non-CpGI promoters exert important functions in the epigenetic regulation of NAD(P)H:quinone oxidoreductase 1 (NQO1).
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OP10G_3171 NAD(P)H-dependent oxidoreductase from Fimbriimonas ginsengisoli Gsoil 348
29% identity, 55% coverage
- The first complete genome sequence of the class Fimbriimonadia in the phylum Armatimonadetes
Hu, PloS one 2014 - “...one is ubiE which encoded ubiquinone/menaquinone biosynthesis methyltransferase (OP10G_1873), and another is NAD(P)H dehydrogenase (quinone) (OP10G_3171), which could transform Menaquinone/Phylloquinone to Menaquinol/Phylloquinol. This is in coincidence with the fact that the major respiratory quinones are menaquinones MK-11 and MK-10. Energy metabolism Two pathways, Emden-Meyerhof-Parnas (EMP) pathway...”
Q9JI75 ribosyldihydronicotinamide dehydrogenase (quinone) (EC 1.10.5.1) from Mus musculus (see 2 papers)
28% identity, 62% coverage
PA1224 probable NAD(P)H dehydrogenase from Pseudomonas aeruginosa PAO1
35% identity, 27% coverage
- The AhR ligand phthiocol and vitamin K analogs as Pseudomonas aeruginosa quorum sensing inhibitors
Jia, Frontiers in microbiology 2022 - “...protein PhzD2 0.68 purE N5-carboxyaminoimidazole ribonucleotide mutase 0.64 pqsB 2-heptyl-4(1H)-quinolone synthase subunit PqsB 0.59 Up-regulated: PA1224 Probable NAD(P)H dehydrogenase 1.56 fabZ 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ 1.39 ribH 6,7-dimethyl-8-ribityllumazine synthase 1.33 PA5076 Probable binding protein component of ABC transporter 1.32 PA4880 Probable bacterioferritin 1.29 PA4739 BON domain-containing protein...”
- Bacterial persisters in long-term infection: Emergence and fitness in a complex host environment
Bartell, PLoS pathogens 2020 - “...PA0977 hypothetical protein 3 3 2.395 3 PA3183 zwf glucose-6-phosphate 1-dehydrogenase 4 4 2.391 4 PA1224 probable NAD(P)H dehydrogenase 3 3 2.186 3 PA1600 probable cytochrome c 3 3 2.179 3 PA2685 vgrG4 VgrG4 3 3 2.099 3 PA3640 dnaE DNA polymerase III, alpha chain 3...”
- Investigating azoreductases and NAD(P)H dependent quinone oxidoreductases in Pseudomonas aeruginosa
Holland, 2017 - Azoreductases in drug metabolism
Ryan, British journal of pharmacology 2017 - “...and paMdaB are azoreductases from P. aeruginosa. paWrbA, PA1224, PA1225, and PA4975 are NAD(P)H quinone oxidoreductases from P. aeruginosa. bsAzoR, efAzoR and...”
- Evolved resistance to colistin and its loss due to genetic reversion in Pseudomonas aeruginosa
Lee, Scientific reports 2016 - “...Pseudomonas Genome Database ( www.pseudomonas.com ). Out of these 13 genes, six genes (PA0334, PA1028, PA1224, PA2760, PA4089 and PA4092) were related to transport and metabolism. PA0334 encodes a major facilitator superfamily (MFS) transporter, and PA1028 encodes a oxidoreductase and is involved in the oxidation-reduction process...”
- “...in the removal or addition of one or more electrons to or from a substance. PA1224, PA2760, PA4089, and PA4092 encodes a NAD(P)H dehydrogenase, a porin, a short-chain dehydrogenase involves in fatty acid biosynthesis, and a 4-hydroxyphenylacetate 3-monooxygenase, respectively. Another two genes (PA1180 and PA4108) were...”
- Pseudomonas aeruginosa LysR PA4203 regulator NmoR acts as a repressor of the PA4202 nmoA gene, encoding a nitronate monooxygenase
Vercammen, Journal of bacteriology 2015 - “...Genes upregulated in the PA4203 mutant PA0672 PA1223 PA1224 PA1225 PA3032 PA4202 PA4204 Operon Presence of signal peptide Fold change NmoR Regulates NmoA...”
- Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes
Ryan, PloS one 2014 - “...enzymes, those in pink are fungal enzymes and those in yellow are archeal. PA0949, PA1204, PA1224, PA1225, PA2280, PA2580, and PA4975 are proteins from P. aeruginosa . ecAzoR, bsAzoR, efAzoR and rsAzoR are azoreductases from E. coli , Bacillus subtilis , Enterococcus faecalus and Rhodobacter sphaeroides...”
- “...- pa0949 84 83 86 92 81 81 pa1204 - - - - - - pa1224 - 45 76 - 75 - pa1225 68 - - - 72 - pa1962 h 67 71 - 76 67 63 pa2280 83 87 & 80 80 - 82 -...”
mdaB / Q92LV5 roxarsone nitroreductase from Rhizobium meliloti (strain 1021) (see 3 papers)
37% identity, 23% coverage
CAC0018 Putative NADPH-quinone reductase, YabF family from Clostridium acetobutylicum ATCC 824
24% identity, 59% coverage
Q8CHK7 NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) from Cavia porcellus (see paper)
28% identity, 32% coverage
Q99KL8 NAD(P)H dehydrogenase [quinone] 1 from Mus musculus
34% identity, 23% coverage
1dxqA / Q64669 Crystal structure of mouse nad[p]h-quinone oxidoreductase (see paper)
34% identity, 23% coverage
- Ligand: flavin-adenine dinucleotide (1dxqA)
NQO1_MOUSE / Q64669 NAD(P)H dehydrogenase [quinone] 1; Azoreductase; DT-diaphorase; DTD; Menadione reductase; NAD(P)H:quinone oxidoreductase 1; Phylloquinone reductase; Quinone reductase 1; QR1; EC 1.6.5.2 from Mus musculus (Mouse) (see 2 papers)
Q64669 NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) from Mus musculus (see 9 papers)
NP_032732 NAD(P)H dehydrogenase [quinone] 1 from Mus musculus
Q542Y0 NAD(P)H dehydrogenase [quinone] 1 from Mus musculus
34% identity, 23% coverage
- function: Flavin-containing quinone reductase that catalyzes two- electron reduction of quinones to hydroquinones using either NADH or NADPH as electron donors. In a ping-pong kinetic mechanism, the electrons are sequentially transferred from NAD(P)H to flavin cofactor and then from reduced flavin to the quinone, bypassing the formation of semiquinone and reactive oxygen species (By similarity) (PubMed:8999809). Regulates cellular redox state primarily through quinone detoxification. Reduces components of plasma membrane redox system such as coenzyme Q and vitamin quinones, producing antioxidant hydroquinone forms. In the process may function as superoxide scavenger to prevent hydroquinone oxidation and facilitate excretion (By similarity). Alternatively, can activate quinones and their derivatives by generating redox reactive hydroquinones with DNA cross-linking antitumor potential (By similarity). Acts as a gatekeeper of the core 20S proteasome known to degrade proteins with unstructured regions. Upon oxidative stress, interacts with tumor suppressors TP53 and TP73 in a NADH-dependent way and inhibits their ubiquitin-independent degradation by the 20S proteasome (By similarity).
catalytic activity: a quinone + NADH + H(+) = a quinol + NAD(+) (RHEA:46160)
catalytic activity: a quinone + NADPH + H(+) = a quinol + NADP(+) (RHEA:46164)
catalytic activity: ubiquinone-10 + NADH + H(+) = ubiquinol-10 + NAD(+) (RHEA:61984)
catalytic activity: menadione + NADH + H(+) = menadiol + NAD(+) (RHEA:69695)
cofactor: FAD
subunit: Homodimer (PubMed:10706635). Interacts with PDLIM4 isoform 2; this interaction stabilizes PDLIM4 isoform 2 in response to oxidative stress and protects it from ubiquitin-independent degradation by the core 20S proteasome (By similarity). Interacts with TP73 (via SAM domain); this interaction is NADH-dependent, stabilizes TP73 in response to oxidative stress and protects it from ubiquitin-independent degradation by the 20S proteasome (By similarity). Interacts with TP53; this interaction is NADH-dependent, stabilizes TP53 in response to oxidative stress and protects it from ubiquitin-independent degradation by the 20S proteasome (By similarity). - Tanshinone functions as a coenzyme that confers gain of function of NQO1 to suppress ferroptosis.
Wang, Life science alliance 2023 - GeneRIF: Tanshinone functions as a coenzyme that confers gain of function of NQO1 to suppress ferroptosis.
- Forced Hepatic Expression of NRF2 or NQO1 Impedes Hepatocyte Lipid Accumulation in a Lipodystrophy Mouse Model.
Wakabayashi, International journal of molecular sciences 2023 - GeneRIF: Forced Hepatic Expression of NRF2 or NQO1 Impedes Hepatocyte Lipid Accumulation in a Lipodystrophy Mouse Model.
- NAD(P)H: quinone oxidoreductase 1 attenuates oxidative stress and apoptosis by regulating Sirt1 in diabetic nephropathy.
Qiu, Journal of translational medicine 2022 - GeneRIF: NAD(P)H: quinone oxidoreductase 1 attenuates oxidative stress and apoptosis by regulating Sirt1 in diabetic nephropathy.
- Antioxidative enzyme NAD(P)H quinone oxidoreductase 1 (NQO1) modulates the differentiation of Th17 cells by regulating ROS levels.
Nishida-Tamehiro, PloS one 2022 - GeneRIF: Antioxidative enzyme NAD(P)H quinone oxidoreductase 1 (NQO1) modulates the differentiation of Th17 cells by regulating ROS levels.
- Exosomes derived from human umbilical cord mesenchymal stem cells ameliorate experimental non-alcoholic steatohepatitis via Nrf2/NQO-1 pathway.
Kang, Free radical biology & medicine 2022 (PubMed)- GeneRIF: Exosomes derived from human umbilical cord mesenchymal stem cells ameliorate experimental non-alcoholic steatohepatitis via Nrf2/NQO-1 pathway.
- β-Caryophyllene exerts protective antioxidant effects through the activation of NQO1 in the MPTP model of Parkinson's disease.
Flores-Soto, Neuroscience letters 2021 (PubMed)- GeneRIF: beta-Caryophyllene exerts protective antioxidant effects through the activation of NQO1 in the MPTP model of Parkinson's disease.
- A redox-mediated conformational change in NQO1 controls binding to microtubules and α-tubulin acetylation.
Siegel, Redox biology 2021 - GeneRIF: A redox-mediated conformational change in NQO1 controls binding to microtubules and alpha-tubulin acetylation.
- Docosahexanoic acid signals through the Nrf2-Nqo1 pathway to maintain redox balance and promote neurite outgrowth.
Drolet, Molecular biology of the cell 2021 - GeneRIF: Docosahexanoic acid signals through the Nrf2-Nqo1 pathway to maintain redox balance and promote neurite outgrowth.
- More
- Redox Proteomic Profile of Tirapazamine-Resistant Murine Hepatoma Cells
Nemeikaitė-Čėnienė, International journal of molecular sciences 2023 - “...acyl-coenzyme A oxidase 1 1.60 21 Cbr1 B2RXY7 Carbonyl reductase 1 1.59 1.32 22 Nqo1 Q542Y0 NAD(P)H dehydrogenase (quinone) 1.55 <0.10 23 Pnpo Q91XF0 Pyridoxine-5-phosphate oxidase 1.53 Downregulated 24 Nsdhl Q3US15 NAD(P) dependent steroid dehydrogenase-like protein 0.66 25 Ldha P06151 L-lactate dehydrogenase A 0.66 1.27 26...”
- “...Ubiquitin carboxyl-terminal hydrolase 25 1.88 7 Oxr1 E9Q0A7 Oxidation resistance protein 1 1.77 8 Nqo1 Q542Y0 NAD(P)H dehydrogenase [quinone] 1.55 <0.1 ijms-24-06863-t003_Table 3 Table 3 Differently expressed enzymes of xenobiotics metabolism and catabolism, and glutathione metabolism in TPZ-resistant MH22a cells. No. Gene Uniprot Accession Code Protein...”
- Proteomics Analysis of the Protective Effect of Polydeoxyribonucleotide Extracted from Sea Cucumber (Apostichopus japonicus) Sperm in a Hydrogen Peroxide-Induced RAW264.7 Cell Injury Model.
Shu, Marine drugs 2024 - “...2 /Control a PDRN/H 2 O 2 b P01942 Hemoglobin subunit alpha Hba 1.718 0.607 Q64669 NAD(P)H dehydrogenase [quinone] 1 Nqo1 1.641 0.515 Q9D0U6 Repressor of RNA polymerase III transcription MAF1 homolog Maf1 2.329 0.035 P51667 Myosin regulatory light chain 2, ventricular/cardiac muscle isoform Myl2 5.929...”
- Zhilong Huoxue Tongyu capsule attenuates intracerebral hemorrhage induced redox imbalance by modulation of Nrf2 signaling pathway.
Mazhar, Frontiers in pharmacology 2023 - “...Cruz Biotechnology, Inc., CA, United States. HO1(F-4) Monoclonal 1:1000 P14901 sc-390991 NQO1 (A180) Monoclonal 1:1000 Q64669 sc-32793 GAPDH Monoclonal 1:10 000 P04406 AB0037 Abways Technology, Inc., Shanghai, China. Fluoro-jade C staining Frozen brain tissues were cryo-sectioned and fixed in 4% paraformaldehyde for 30min, with subsequent 5min...”
- Proteomic Analysis of Mouse Kidney Tissue Associates Peroxisomal Dysfunction with Early Diabetic Kidney Disease
Tserga, Biomedicines 2022 - “...0.0321 2.16 0.00377 4.55 NO YES Q8CFA2 Aminomethyltransferase, mitochondrial 0.04 2.17 0.00295 2.95 YES YES Q64669 NAD(P)H dehydrogenase [quinone] 1 0.043 6.96 0.01 1.60 NO YES biomedicines-10-00216-t004_Table 4 Table 4 Consistently downregulated glomerular proteins in early and late DKD. Eighteen consistently downregulated glomerular proteins in early...”
- The Gut Microbial Metabolite Pyrogallol Is a More Potent Inducer of Nrf2-Associated Gene Expression Than Its Parent Compound Green Tea (-)-Epigallocatechin Gallate.
Liu, Nutrients 2022 - “...non-significant) in the other groups. The FCs of NAD(P)H dehydrogenase (quinone) 1 (Nqo1, protein ID: Q64669) in PG and t-BHQ treatments were 3.1 ( p < 0.05) and 4.3 ( p < 0.05), respectively, while they ranged from 0.9 to 1.1 (all non-significant) in EGCG, EGC,...”
- Intra- and Inter-individual Differences in the Human Intestinal Microbial Conversion of (-)-Epicatechin and Bioactivity of Its Major Colonic Metabolite 5-(3',4'-Dihydroxy-Phenyl)-γ-Valerolactone in Regulating Nrf2-Mediated Gene Expression.
Liu, Frontiers in nutrition 2022 - “...at 30 M. (A) Hepa1c1c7 cell samples Protein IDs Protein names Gene names EC 3,4-diHPV Q64669 NAD(P)H dehydrogenase [quinone] 1 Nqo1 1.15 (0.901) 3.60 (0.138) Q9JI75 Ribosyldihydronicotinamide dehydrogenase [quinone] Nqo2 1.08 (0.294) 1.31 (0.041) Q8CHT0 Aldehyde dehydrogenase family 4 memberA1 Aldh4a1 1.21 (0.317) 1.46 (0.045) D3Z0B9...”
- Protein Expression Analysis of an In Vitro Murine Model of Prostate Cancer Progression: Towards Identification of High-Potential Therapeutic Targets
Bahmad, Journal of personalized medicine 2020 - “...Growth factor receptor-bound protein 10 Grb10 70,585 Infinity 0.0005 P24270 Catalase Cat 59,795 Infinity 0.0370 Q64669 NAD(P)H dehydrogenase (quinone) 1 Nqo1 30,960 Infinity 0.0007 O88587 Catechol O-methyltransferase Comt 29,486 Infinity 0.0139 P62281 40S ribosomal protein S11 Rps11 18,431 Infinity 0.0244 P21981 Protein-glutamine gamma-glutamyltransferase 2 Tgm2 77,061...”
- Functional, proteomic and bioinformatic analyses of Nrf2- and Keap1- null skeletal muscle
Gao, The Journal of physiology 2020 - “...muscle. Keap1 KO-upregulated 108 Proteins Gene ID Protein ID Protein Name P val. Fold Nqo1 Q64669 NAD(P)H dehydrogenase [quinone] 1 0.0001 17.47 Gsta4 P24472 Glutathione S-transferase A4 0.0004 5.24 Gsta2 P10648 Glutathione S-transferase A2 0.0006 10.24 Gbe1 Q9D6Y9 1,4-alpha-glucan-branching enzyme 0.0009 5.03 Srxn1 Q9D975 Sulfiredoxin-1 0.0013...”
- Label-Free Neuroproteomics of the Hippocampal-Accumbal Circuit Reveals Deficits in Neurotransmitter and Neuropeptide Signaling in Mice Lacking Ethanol-Sensitive Adenosine Transporter.
Oliveros, Journal of proteome research 2017 - “...cycle 1.46 3.8 10 4 Q05920 PC pyruvate carboxylase mitochondrial dysfunction 1.48 1.2 10 5 Q64669 NQO1 NAD(P)H dehydrogenase, quinone 1 mitochondrial dysfunction 1.53 4.0 10 4 Q9QXV0 PCSK1N proSAAS neuropeptide signaling 2.14 1.0 10 3 P05064 ALDOA aldolase A, fructose-bisphosphate glycolysis 1.49 2.0 10 3...”
- More
C0J56_15400 NAD(P)H-dependent oxidoreductase from Pseudomonas fluorescens
34% identity, 45% coverage
- Characterization of the SPI-1 Type III Secretion System in Pseudomonas fluorescens 2P24
Wang, Frontiers in microbiology 2021 - “...(Sec/SPI) Transcriptome analysis C0J56_14275 Fap system putative outer membrane protein Signal peptide (Sec/SPI) Transcriptome analysis C0J56_15400 NAD(P)H dehydrogenase None Transcriptome analysis C0J56_13875 Protein iolH None Transcriptome analysis C0J56_22285 DNA-binding response regulator None Promoter analysis C0J56_19280 SDR family oxidoreductase None Promoter analysis C0J56_14205 LEA type 2 family...”
TRAD_PENCR / A0A481WNM5 Ribosyldihydronicotinamide dehydrogenase-like protein traD; Terrestric acid biosynthesis cluster protein D; EC 1.10.-.- from Penicillium crustosum (Blue mold fungus) (see 2 papers)
24% identity, 53% coverage
- function: Ribosyldihydronicotinamide dehydrogenase-like protein; part of the tra gene cluster that produces terrestric acid (PubMed:30811183). The clavatol biosynthesis cluster cla and the terrestric acid cluster tra are both involved in the production of peniphenones and penilactones (PubMed:30811183). The non-reducing PKS claF is responsible for the formation of clavatol from successive condensations of 3 malonyl-CoA units, presumably with a simple acetyl- CoA starter unit, and 2 methylation steps (PubMed:30811183). The esterase claE probably collaborates with claF by catalyzing the hydrolysis of ACP-bound acyl intermediates to free the ACP from stalled intermediates (By similarity). The clavatol oxidase claD then converts clavatol to hydroxyclavatol (PubMed:30811183). Spontaneous dehydration of hydroxyclavatol leads to the accumulation of the highly active ortho-quinone methide (PubMed:30811183, PubMed:31860310). On the other hand, the PKS-NRPS hybrid traA is involved in the formation of crustosic acid, with the help of traB and traD (PubMed:30811183). The polyketide synthase module (PKS) of traA is responsible for the synthesis of the polyketide backbone via the condensation of an acetyl- CoA starter unit with 3 malonyl-CoA units (PubMed:30811183). The downstream nonribosomal peptide synthetase (NRPS) module then amidates the carboxyl end of the polyketide with L-malic acid (PubMed:30811183). Because traA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase traG (By similarity). Crustosic acid undergoes decarboxylation and isomerization to the terrestric acid, catalyzed by the 2-oxoglutarate-dependent dioxygenase traH (PubMed:30811183). Both acids are further converted to the 2 gamma-butyrolactones (R)-5-methyltetronic acid and (S)-5- carboxylmethyltetronic acid, with involvement of the cytochrome P450 monooxygenase claJ (PubMed:30811183). Spontaneous addition of the methide to these gamma-butyrolactones leads to peniphenone D and penilactone D, which undergo again stereospecific attacking by methide to give penilactones A and B (PubMed:30811183, PubMed:31860310).
cofactor: FAD
subunit: Homodimer.
disruption phenotype: Completely abolishes the production of peniphenone D, penilactone D, penilactone A and penilactone B, as well as of crustosic acid and terrestric acid.
4gi5B / A6THR9 Crystal structure of a putative quinone reductase from klebsiella pneumoniae (target psi-013613)
29% identity, 39% coverage
- Ligand: flavin-adenine dinucleotide (4gi5B)
FMNRE_PSEAE / Q9I4D4 NAD(P)H-dependent FMN reductase PA1204; EC 1.-.-.- from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
PA1204 hypothetical protein from Pseudomonas aeruginosa PAO1
33% identity, 42% coverage
- function: Has NAD(P)H-dependent FMN reductase activity.
cofactor: FMN
subunit: Homodimer. - The structural and functional basis of catalysis mediated by NAD(P)H:acceptor Oxidoreductase (FerB) of Paracoccus denitrificans
Sedláček, PloS one 2014 - “...GH-ChrR_ G. hanseii (D5QFC5, gi: 388603906), ChrR_ E. coli (P0AGE6, gi: 84028020), T1501_ P. aeruginosa (Q9I4D4, gi: 81541544), FerB_ P. denitrificans (A1B9E3, gi: 69933457), ArsH_ S. flexneri (Q7UC03, gi: 75386123), ArsH_ S. meliloti (Q92R45, gi: 81634873), WrbA_ E. coli (P0A8G6, gi: 67475535), WrbA_ P. aeruginosa (Q9I509,...”
- Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal
Agarwal, Acta crystallographica. Section D, Biological crystallography 2006 - “...FMN reductase flavoprotein from Pseudomonas aeruginosa PA01-derived protein Q9I4D4 using the anomalous signal from an unusually small number of S atoms is...”
- “...(Benson et al., 1980). The Pseudomonas aeruginosa PA01-derived Q9I4D4 open reading frame codes for a 20 kDa protein with unknown function and is annotated...”
- Steric hindrance controls pyridine nucleotide specificity of a flavin-dependent NADH:quinone oxidoreductase
Ball, Protein science : a publication of the Protein Society 2019 (secret) - Increased ParB level affects expression of stress response, adaptation and virulence operons and potentiates repression of promoters adjacent to the high affinity binding sites parS3 and parS4 in Pseudomonas aeruginosa
Kawalek, PloS one 2017 - “...1 hypothetical protein PA1202 6,9 5,8 2 probable hydrolase PA1203 3,3 3,2 2 hypothetical protein PA1204 2,3 2,2 2 NAD(P)H quinone oxidoreductase PA1205 2,5 2,3 2 conserved hypothetical protein PA2698 2,1 2,1 2 probable hydrolase PA1337 ansB -2,0 6 glutaminase-asparaginase PA1338 ggt -2,5 6 gamma-glutamyltranspeptidase precursor...”
- “...encoding a bistable response regulator BexR [ 67 ]. Six genes, PA1202 , PA1203 , PA1204 , PA1205 , PA2433 and PA2698 , previously identified as upregulated in response to BexR overproduction [ 67 ], are also upregulated in ParB- overproducing strains. Similarly, five genes downregulated...”
- Azoreductases : genes and proteins in Pseudomonas aeruginosa
Crescente, 2015 - Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes
Ryan, PloS one 2014 - “...plant enzymes, those in pink are fungal enzymes and those in yellow are archeal. PA0949, PA1204, PA1224, PA1225, PA2280, PA2580, and PA4975 are proteins from P. aeruginosa . ecAzoR, bsAzoR, efAzoR and rsAzoR are azoreductases from E. coli , Bacillus subtilis , Enterococcus faecalus and Rhodobacter...”
- “...[15] This paper ND paAzoR3 ND [15] This paper ND PA0949 1ZWL ND [75] ND PA1204 1X77 ND ND ND ecAzoR 2Z98 [8] [8] [83] ecMdaB 2B3D ND [66] ND ecWrbA 2R96 ND [74] ND ecYieF 3SVL ND [84] ND ArsH 2Q62 [58] ND ND rsAzoR...”
- Pseudomonas aeruginosa NfsB and nitro-CBI-DEI--a promising enzyme/prodrug combination for gene directed enzyme prodrug therapy
Green, Molecular cancer 2013 - “...PA1225 33 (YcaK_Ec) AAG04614.1 YcaK2_Pa PA0853 27 (YcaK_Ec) AAG04242.1 YdjA_Pa PA3208 42 (YdjA_Ec) AAG06596.1 YieF_Pa PA1204 45 (YieF_Ec) AAG04593.1 NfsA_Ec - 100 (NfsA_Ec) BAA35562.1 NfsB_Ec - 100 (NfsB_Ec) AAC73679.1 a Protein nomenclature as assigned in this study, based on existing nomenclature of closest E. coli orthologue,...”
- Escherichia coli NemA is an efficient chromate reductase that can be biologically immobilized to provide a cell free system for remediation of hexavalent chromium
Robins, PloS one 2013 - “...(PCC 73102) nfsA, ycdI; Nostoc sp. (PCC 7120) ycdI; Pseudomonas aeruginosa (PAO1) azoR (PA1962), chrR (PA1204), msuE (PA2357) nfsB (PA5190), ycaK (PA1225); Pseudomonas putida (KT2440) azoR (PP4538), kefF (PP3720), nfsA (PP2490), nfsB (PP2432); Pseudomonas syringae pv. phaseolicola (1448a) azoR, mdaB, wrbA; Salmonella typhi (ATCC l9430) azoR,...”
- Genotypic and phenotypic variation in Pseudomonas aeruginosa reveals signatures of secondary infection and mutator activity in certain cystic fibrosis patients with chronic lung infections
Warren, Infection and immunity 2011 - “...1,262 812 323 943 2,679 1,388 PA1133 PA1152 PA1204 PA1239-PA1241 350 344 557 2,463 PA1368-PA1372 PA1385 PA1394 PA1509-PA1510 7,761 1,124 254 2,848 PA1887-PA1888...”
- Epigenetic control of virulence gene expression in Pseudomonas aeruginosa by a LysR-type transcription regulator
Turner, PLoS genetics 2009 - “...BexR-regulated operon. This putative operon includes PA1203, which is predicted to encode a redox protein, PA1204, which is predicted to encode a NADPH-dependent FMN reductase, and PA1205, which is predicted to encode a homolog of pirin, a widely conserved protein with oxygenase activity [18] . PA2698,...”
ZMO1949 Ribosyldihydronicotinamide dehydrogenase (quinone) from Zymomonas mobilis subsp. mobilis ZM4
33% identity, 35% coverage
- Functional analysis of the methylerythritol phosphate pathway terminal enzymes IspG and IspH from Zymomonas mobilis
Misra, Microbiology spectrum 2024 - “...ZMO0220, ZMO2028, ZMO0860, and ZMO0456) and one predicted flavodoxin (ZMO1851) and a second possible flavodoxin (ZMO1949) that are possible candidates for these electron transfer reactions. A recent study suggests that organisms with multiple protein electron donors are more likely to have evolved specialists by optimizing binding...”
- Design and construction of microbial cell factories based on systems biology
Yan, Synthetic and systems biotechnology 2023 - “...ZMO1885 [ 55 ] p-benzoq-uinone Z. mobilis transcriptomics Zinc-binding alcohol dehydrogenase ZMO1696 , NAD(P)H dehydrogenase ZMO1949 , short-chain dehydrogenase/reductase ZMO1576 , aldo-keto reductase ZMO1984 , fatty acid hydroxylase ZMO1399 [ 56 ] formate, acetate S. cerevisiae transcriptomics transcriptional/translational machinery-related genes: RTC3 and ANB1 [ 57 ]...”
- Mechanism of Tolerance to the Lignin-Derived Inhibitor p-Benzoquinone and Metabolic Modification of Biorefinery Fermentation Strains
Yan, Applied and environmental microbiology 2019 - “...30 five key genes in Z. mobilis (ZMO1696, ZMO1949, ZMO1576, ZMO1984 and ZMO1399) 31 accelerated its cell growth and cellulosic ethanol production in...”
- “...an aldo/keto reductase); three 171 dehydrogenase genes (ZMO1949, encoding an NAD(P)H dehydrogenase, ZMO1696, 172 encoding a zinc-binding alcohol dehydrogenase,...”
- The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4
Seo, Nature biotechnology 2005 - “...PhzC/PhzF homolog ZMO1946 oxidoreductase (short-chain alcohol dehydrogenases) ZMO1947 translational inhibitor protein ZMO1948 conserved hypothetical protein ZMO1949 NAD(P)H quinone oxidoreductase, putative ZMO1950 aspartate/tyrosine/aromatic aminotransferase ZMO1951 demethylmenaquinone methyltransferase ZMO1952 3-methyl-2-oxobutanoate hydroxymethyltransferase; PanB, probable ZMO1953 hypothetical protein ZMO1954 type IV secretory pathway, VirB10, conjugal transfer TrbL transmembrane protein Most...”
- “...ORFs, four ORFs that encode transport proteins or permeases, and two genes for NAD(P)H:quinone oxidoreductase (ZMO1949) and oxidoreductase (short-chain alcohol dehydrogenases; ZMO1946) were found to be very highly expressed. It is quite likely that these genes contribute to the higher rates of glucose uptake and ethanol...”
1x77A / Q9I4D4 Crystal structure of a NAD(p)h-dependent fmn reductase complexed with fmn (see paper)
32% identity, 43% coverage
- Ligand: flavin mononucleotide (1x77A)
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory