PaperBLAST
PaperBLAST Hits for RR42_RS24425 (71 a.a., MDGTTRAQIL...)
Show query sequence
>RR42_RS24425
MDGTTRAQILSSAMRWFARRGFDGASVTQIAADAGVPQPLINYHFGTKLKLWQASVDFLF
DELIKDLAIFS
Running BLASTp...
Found 60 similar proteins in the literature:
PSPA7_2630 TetR family transcriptional regulator from Pseudomonas aeruginosa PA7
41% identity, 31% coverage
- The TetR family of regulators
Cuthbertson, Microbiology and molecular biology reviews : MMBR 2013 - “...while PA7 encodes two TFRs absent from PAO1 (PSPA7_2630 and PSPA7_4004). The PA7-specific TFRs are encoded within genomic islands of this isolate (30). PA2020,...”
NIS_RS00380 TetR/AcrR family transcriptional regulator from Nitratiruptor sp. SB155-2
39% identity, 32% coverage
WP_004080830 TetR/AcrR family transcriptional regulator from Thermotoga sp. EMP
TM0823 transcriptional regulator, TetR family from Thermotoga maritima MSB8
43% identity, 28% coverage
PsrA / VIMSS583573 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Dechloromonas aromatica RCB
39% identity, 28% coverage
Rv1685c hypothetical protein from Mycobacterium tuberculosis H37Rv
42% identity, 29% coverage
- Insight into the on/off switch that regulates expression of the MSMEG-3762/63 efflux pump in Mycobacterium smegmatis
Campolattano, Scientific reports 2023 - “...MSMEG_3762/63/65 operon and of the homologous Rv1687/86/85c operon, encoding the efflux pump and its regulator Rv1685c in M. tuberculosis 20 . We also showed that the MSMEG-3762/63 efflux pump was involved in the extrusion of rifampicin and ciprofloxacin in M. smegmatis by comparative analysis of wild-type...”
- Proteome Profiling of Mycobacterium tuberculosis Cells Exposed to Nitrosative Stress
Birhanu, ACS omega 2022 - “...with unknown function. 16 While Rv1687c was highly abundant at all the time points investigated, Rv1685c, annotated as a transcriptional regulator from the TetR family, was also more abundant in cells treated with NO after 2, 6, and 20 h. The putative drug membrane transporter RV1687c...”
- Functional and Biochemical Characterization of the MazEF6 Toxin-Antitoxin System of Mycobacterium tuberculosis
Chattopadhyay, Journal of bacteriology 2022 (secret) - Efflux Pump Inhibition and Resistance Modulation in Mycobacterium smegmatis by Peucedanum ostruthium and Its Coumarins
Šimunović, Antibiotics (Basel, Switzerland) 2021 - “...mycobacterial biofilms. Furthermore, Cossu et al. [ 34 ] observed that MSMEG_3765 and its ortholog Rv1685c in M. tuberculosis , which code for TetR-like regulator family, were upregulated in acid-nitrosative stress conditions. Especially members of the TetR family of transcriptional regulators (TFTRs) are present in a...”
- Structure-Activity Relationships of Pyrazolo[1,5-a]pyrimidin-7(4H)-ones as Antitubercular Agents
Oh, ACS infectious diseases 2021 - “...mutants selected for resistance to 3 exhibited insertions of a transposon ( IS 6110) in rv1685c , a transcription factor whose biological role and regulatory targets are not known. 6 Furthermore, another analogue 4 ( Figure 1 ) was reported to be an inhibitor of the...”
- TB or not to be: what specificities and impact do antibodies have during tuberculosis?
Hermann, Oxford open immunology 2021 - “...Rv3763 Lipoprotein lpqH/19 kDa Antigen x Rv0324 Sulfurtransferase x Rv0537c Probable integral membrane protein x Rv1685c Transcriptional regulator, TetR family x Rv2072c Precorrin-6Y C(5,15)-methyltransferase x Rv3899c Uncharacterized protein x Rv1100 Conserved protein x Rv1865c Oxidoreductase, short-chain dehydrogenase/reductase family x MT0124 Putative uncharacterized protein x Rv2884 Probable...”
- Characterization of the Mycobacterial MSMEG-3762/63 Efflux Pump in Mycobacterium smegmatis Drug Efflux
De, Frontiers in microbiology 2020 - “...studies demonstrated up-regulation of the TetR-like transcriptional regulator MSMEG_3765 in Mycobacterium smegmatis and its ortholog Rv1685c in Mycobacterium tuberculosis ( Mtb ) in acid-nitrosative stress conditions. MSMEG-3765 regulates the expression of the MSMEG_3762/63/65 operon, and of the orthologous region in Mtb ( Rv1687c/86c/85c ). MSMEG-3762 and...”
- “...smegmatis , both annotated as ABC efflux pump systems. Cossu et al. (2013) showed that Rv1685c and MSMEG_3765 , coding for TetR-like regulators, were upregulated in acid-nitrosative stress conditions, mimicking a macrophage-like intracellular environment. By GFP promoter probe and transcriptional analyses, we strengthened that observation and...”
- A Novel TetR-Like Transcriptional Regulator Is Induced in Acid-Nitrosative Stress and Controls Expression of an Efflux Pump in Mycobacteria
Perrone, Frontiers in microbiology 2017 - “...terms. Mycobacterium tuberculosis has the ability to survive inside macrophages under acid-nitrosative stress. M. tuberculosis Rv1685c and its ortholog in M. smegmatis, MSMEG_3765 , are induced on exposure to acid-nitrosative stress. Both genes are annotated as TetR transcriptional regulators, a family of proteins that regulate a...”
- “...M. tuberculosis and M. smegmatis to acid-nitrosative multi-stress, simulating a macrophage-like environment. In these conditions, Rv1685c in M. tuberculosis and its ortholog MSMEG_3765 in M. smegmatis were found to be up-regulated. Both genes are annotated as transcriptional regulators of the TetR family, sharing a high percentage...”
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MSMEG_3765 transcriptional regulator from Mycobacterium smegmatis str. MC2 155
44% identity, 28% coverage
- Efflux Pump Inhibition and Resistance Modulation in Mycobacterium smegmatis by Peucedanum ostruthium and Its Coumarins
Šimunović, Antibiotics (Basel, Switzerland) 2021 - “...in the formation of mycobacterial biofilms. Furthermore, Cossu et al. [ 34 ] observed that MSMEG_3765 and its ortholog Rv1685c in M. tuberculosis , which code for TetR-like regulator family, were upregulated in acid-nitrosative stress conditions. Especially members of the TetR family of transcriptional regulators (TFTRs)...”
- Characterization of the Mycobacterial MSMEG-3762/63 Efflux Pump in Mycobacterium smegmatis Drug Efflux
De, Frontiers in microbiology 2020 - “...as a mechanism of drug resistance. Previous studies demonstrated up-regulation of the TetR-like transcriptional regulator MSMEG_3765 in Mycobacterium smegmatis and its ortholog Rv1685c in Mycobacterium tuberculosis ( Mtb ) in acid-nitrosative stress conditions. MSMEG-3765 regulates the expression of the MSMEG_3762/63/65 operon, and of the orthologous region...”
- “...both annotated as ABC efflux pump systems. Cossu et al. (2013) showed that Rv1685c and MSMEG_3765 , coding for TetR-like regulators, were upregulated in acid-nitrosative stress conditions, mimicking a macrophage-like intracellular environment. By GFP promoter probe and transcriptional analyses, we strengthened that observation and defined the...”
- A Novel TetR-Like Transcriptional Regulator Is Induced in Acid-Nitrosative Stress and Controls Expression of an Efflux Pump in Mycobacteria
Perrone, Frontiers in microbiology 2017 - “...survive inside macrophages under acid-nitrosative stress. M. tuberculosis Rv1685c and its ortholog in M. smegmatis, MSMEG_3765 , are induced on exposure to acid-nitrosative stress. Both genes are annotated as TetR transcriptional regulators, a family of proteins that regulate a wide range of cellular activities, including multidrug...”
- “...cluster, and the orthologous region in M. tuberculosis ( Rv1687c/86c/85c ), was up-regulated in a MSMEG_3765 null mutant, suggesting that MSMEG_3765 acts as a repressor, typical of this family of regulators. We further defined the MSMEG_3765 regulon using genome-wide transcriptional profiling and used reporter assays to...”
SACE_0820 TetR-family transcriptional regulator from Saccharopolyspora erythraea NRRL 2338
42% identity, 26% coverage
- Inactivation of SACE_3446, a TetR family transcriptional regulator, stimulates erythromycin production in Saccharopolyspora erythraea
Wu, Synthetic and systems biotechnology 2016 - “...(DE3) Novagen S. erythraea A226 CGMCC 8279, an erythromycin low producer China Pharmaceutical Culture Collection SACE_0820 A226 derivative with SACE_0820 deleted This study SACE_1874 A226 derivative with SACE_1874 deleted This study SACE_2947 A226 derivative with SACE_2947 deleted This study SACE_6589 A226 derivative with SACE_6589 deleted This...”
- “...TetR family regulatory genes in S. erythraea A226 Six putative TetR family regulatory genes ( SACE_0820 , SACE_1874 , SACE_2947 , SACE_3446 , SACE_6589 , and SACE_7325 ) were individually inactivated in the parental strain A226 as follows: a region spanning ~1.5kb of DNA on either...”
cg1098 TetR family regulatory protein from Corynebacterium glutamicum ATCC 13032
48% identity, 24% coverage
RutR / VIMSS7086436 RutR regulator of Pyrimidine utilization, effector Uracil (activator/repressor) from Burkholderia phymatum STM815
41% identity, 25% coverage
BB1797 Putative TetR-family regulatory protein from Bordetella bronchiseptica RB50
41% identity, 29% coverage
P354_12810 TetR/AcrR family transcriptional regulator from Streptomyces noursei PD-1
42% identity, 25% coverage
SCO3346 transcriptional regulator from Streptomyces coelicolor A3(2)
40% identity, 28% coverage
DVU0057 / VIMSS8505916 DVU0057 from Desulfovibrio salexigens DSM 2638
37% identity, 31% coverage
SCO3129 TetR-family transcriptional regulator from Streptomyces coelicolor A3(2)
42% identity, 26% coverage
- Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein-Protein Interactions
Escorcia-Rodríguez, Microorganisms 2021 - “...already part of the strong network ( Figure S5 ). Cg1098 is an ortholog of SCO3129, a TetR family regulator involved in S. coelicolor osmotic stress [ 48 ]. In S. coelicolor , it regulates the transcription of two ( SCO3128 and SCO3130 ) genes and...”
- “...10.1128/JB.01896-07 18245289 48. He X. Li H. Pan Y. Wang L. Tan H. Liu G. SCO3129, a TetR family regulator, is responsible for osmotic stress in Streptomyces coelicolor Synth. Syst. Biotechnol. 2018 3 261 267 10.1016/j.synbio.2018.10.012 30417142 49. Cuthbertson L. Nodwell J.R. The TetR Family of...”
- SCO3129, a TetR family regulator, is responsible for osmotic stress in Streptomyces coelicolor
He, Synthetic and systems biotechnology 2018 - “...Biotechnol Synth Syst Biotechnol Synthetic and Systems Biotechnology 2405-805X KeAi Publishing 6223229 S2405-805X(18)30052-8 10.1016/j.synbio.2018.10.012 Article SCO3129, a TetR family regulator, is responsible for osmotic stress in Streptomyces coelicolor He Xihong a b 1 Li Hong a d 1 Pan Yuanyuan a Wang Linqi c Tan Huarong...”
- “...nature. In the genome of Streptomyces coelicolor M145, SCO3128 (encodes a putative fatty acid desaturase), SCO3129 (encodes a putative TetR family regulator) and SCO3130 (encodes a putative l -carnitine dehydratase) constitute a transcriptional unit, and its transcript was found to be in response to osmotic stress....”
- Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor
Iqbal, Nucleic acids research 2012 - “...GlnR (SCO4159), ( e ) motif 34: MarR, MerR regulatory proteins (SCO5405, SCO2105) and TetR (SCO3129) family transcriptional regulators and a conserved hypothetical protein(SCO4639) as well as an anti Sigma factor (SCO7324), ( f ) motif 36: Matches to this motif include important transcriptional and response...”
PsrA / VIMSS2702720 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Idiomarina baltica OS145
45% identity, 24% coverage
MCOL_RS22650 TetR/AcrR family transcriptional regulator from Mycobacterium colombiense CECT 3035
42% identity, 29% coverage
lmo1962 similar to transcription regulators (TetR family) from Listeria monocytogenes EGD-e
41% identity, 27% coverage
Psyr_1780 regulatory protein, TetR from Pseudomonas syringae pv. syringae B728a
48% identity, 25% coverage
NP_215535 transcriptional regulator from Mycobacterium tuberculosis H37Rv
Rv1019 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) from Mycobacterium tuberculosis H37Rv
43% identity, 29% coverage
- Mycobacterium tuberculosis TetR family transcriptional regulator Rv1019 is a negative regulator of the mfd-mazG operon encoding DNA repair proteins.
Pushparajan, FEBS letters 2020 (PubMed)- GeneRIF: Mycobacterium tuberculosis TetR family transcriptional regulator Rv1019 is a negative regulator of the mfd-mazG operon encoding DNA repair proteins.
- Mycobacterium tuberculosis transcriptional regulator Rv1019 is upregulated in hypoxia, and negatively regulates Rv3230c-Rv3229c operon encoding enzymes in the oleic acid biosynthetic pathway
Pushparajan, The FEBS journal 2023 (PubMed)- “...in their adapting to the challenging environment inside the host cells. Previously, we demonstrated that Rv1019, a putative transcriptional regulator of M. tuberculosis H37Rv, is an autorepressor. We showed that Rv1019 is cotranscribed with Rv1020 (mfd) and Rv1021 (mazG) which encode DNA repair proteins and negatively...”
- “...Rv3230c and Rv3229c (desA3) also which form a two-gene operon in M. tuberculosis. Overexpression of Rv1019 in M. tuberculosis significantly downregulated the expression of these genes. Employing Wayne's hypoxia-induced dormancy model of M. tuberculosis, we show that Rv1019 is upregulated three-fold under hypoxia. Finally, by reporter...”
- Mycobacterium tuberculosis transcriptional regulator Rv1019 is upregulated in hypoxia and negatively regulates Rv3230c-Rv3229c operon encoding enzymes in the oleic acid biosynthetic pathway
Pushparajan, 2022 - The evolving biology of <i>Mycobacterium tuberculosis</i> drug resistance
Jones, Frontiers in cellular and infection microbiology 2022 - “...of spontaneous resistant mutants to RIF, EMB and ciprofloxacin ( Ragheb etal., 2019 ). Recently, Rv1019, a transcriptional regulator of the TetR family, was found to negatively regulate mfd expression. Overexpression of Rv1019 leads to the downregulation of mfd and decreased Mtb survival under oxidative stress...”
- “...hypoxia and reactivation ( Schubert etal., 2015 ), it would be interesting to know if Rv1019 is the key regulator of Mfd-mediated changes in Mtb leading to drug resistance. In an in vitro persistence model, Mtb was found to develop resistance to RIF or MOX at...”
- Shotgun proteomic profiling of dormant, 'non-culturable' Mycobacterium tuberculosis
Nikitushkin, PloS one 2022 - “...a down-shift of a number of other transcriptional regulatory proteins, e.g., Rv0275c , Rv1556 , Rv1019 , Rv0818 , Rv3058c , Rv3249c , etc. Analogously, in the absence of translational processes, the abundancy of translation initiation factors ( Rv3462c , Rv2839c ) as well as 30s...”
- Applications of Transcriptomics and Proteomics for Understanding Dormancy and Resuscitation in Mycobacterium tuberculosis
Kundu, Frontiers in microbiology 2021 - “...Rv0818, Rv0981, SigK, CspA, Rv2258c, PrrA, WhiA, and DosR were up-regulated during NRP1. MprA, SigK, Rv1019, HrcA, Crp, DosS, and DosR were up-regulated during NRP2 Gopinath et al., 2015 Nutrient starvation Model of Betts et al. (2002) Transcriptional repressors CmtR, Rv0144, Rv0158, Rv0328, Rv1219c, Rv1556, Rv3295,...”
- “...2014 ). Proteomic analyses confirmed the upregulation of the stringent response regulator RelA (Rv2583c), and Rv1019 (a tetR family transcriptional regulator), during hypoxia ( Gopinath et al., 2015 ). Peterson et al. (2020) reported a transcriptional program that coordinates sequential state transitions to drive M. tuberculosis...”
- Mycobacterium tuberculosis TetR family transcriptional regulator Rv1019 is a negative regulator of the mfd-mazG operon encoding DNA repair proteins
Pushparajan, FEBS letters 2020 (PubMed)- “...Rv1019, a member of an uncharacterized tetracycline resistance regulator family of transcriptional regulators of Mycobacterium tuberculosis H37Rv, was found to be differentially expressed during dormancy and reactivation in vitro. In this...”
- “...dimers in vitro which is essential for the DNA binding activity. We also show that Rv1019 and downstream genes Rv1020 (mfd) and Rv1021 (mazG) are cotranscribed. Constitutive expression of Rv1019 in M. smegmatis downregulated MSMEG_5423 (mfd) and MSMEG_5422 (mazG), suggesting that Rv1019 negatively regulates these downstream...”
- Putative TetR family transcriptional regulator Rv1019 ofMycobacterium tuberculosisis an auto-repressor and a negative regulator ofmfd-mazGoperon
Pushparajan, 2020 - Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions
Balhana, BMC genomics 2015 - “...3.00E16 Rv0452 4.90E13 Rv0472c 5.60E16 Rv0653c 1.10E18 Rv0681 6.00E17 Rv0691c 4.60E02 Rv0767c 1.20E14 Rv0825c 4.20E14 Rv1019 1.90E17 Rv1776c 4.00E16 Rv2250c 2.40E11 Rv3058c 2.00E12 Rv3167c 4.20E16 Rv3173c 3.00E18 Rv3295 2.30E16 The motif logo is given along with a significance estimate The experimentally verified motifs show an e-value...”
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PsrA / VIMSS839393 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Colwellia psychrerythraea 34H
40% identity, 28% coverage
PsrA / VIMSS572739 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Rhodopseudomonas palustris CGA009
42% identity, 29% coverage
MSMEG_5424 transcriptional regulator, TetR family protein from Mycobacterium smegmatis str. MC2 155
A0R3C6 Transcriptional regulator, TetR family protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
35% identity, 30% coverage
- Associating H2O2-and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage
Ganief, Emerging microbes & infections 2018 - “...a change in abundance of several virulence factors, such as RegX3, MtrA, DevR, MSMEG_3240, and MSMEG_5424, which are all members of two-component systems (see Fig. 4a ). In addition to the increase of DevR abundance, other proteins controlled by the DosR regulon also increased in abundance,...”
- “...DosR regulon A0QXB5 MSMEG_3240 DNA-binding response regulator, LuxR family protein N/A 0.49 DosR regulon A0R3C6 MSMEG_5424 Transcriptional regulator, TetR family protein N/A 0.31 DosR regulon A0R478 MSMEG_5733 Putative universal stress protein UspA (universal stress protein family protein) N/A 0.58 DosR regulon A0QZ91 MSMEG_3940 Universal stress protein...”
- Characterisation of the Mycobacterium smegmatis transcriptional regulator MSMEG_5424
Sikder, 2013 - Associating H2O2-and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage.
Ganief, Emerging microbes & infections 2018 - “...0.79 DosR regulon A0QXB5 MSMEG_3240 DNA-binding response regulator, LuxR family protein N/A 0.49 DosR regulon A0R3C6 MSMEG_5424 Transcriptional regulator, TetR family protein N/A 0.31 DosR regulon A0R478 MSMEG_5733 Putative universal stress protein UspA (universal stress protein family protein) N/A 0.58 DosR regulon A0QZ91 MSMEG_3940 Universal stress...”
VCA0767 transcriptional regulator, TetR family from Vibrio cholerae O1 biovar eltor str. N16961
38% identity, 25% coverage
- A TetR family regulator of an RND efflux system that directs artemisinin resistance in <i>Vibrio cholerae</i>
Chung, mSystems 2024 - “...action, we have isolated V. cholerae mutants with enhanced ARS resistance and identified a gene (VCA0767) whose loss-of-function resulted in the ARS resistance phenotypes. This gene ( atrR ) encodes a TetR family transcriptional regulator, and its deletion mutant displayed the reduction in ARS-induced ROS formation...”
- “...of ARS in V. cholerae . All three atr mutants carry mutations in a gene (VCA0767), which encodes a TetR family transcriptional regulator with previously undefined roles in V. cholerae . Here, we named this gene as atrR ( a r t emisinin r esistance r...”
- Identification of Small Molecule Inhibitors of the Pathogen Box against Vibrio cholerae
Kim, Microbiology spectrum 2021 - “...were selected from cells grown at 25 nM MMV675968. Both mutants showed a mutation in vca0767 , a gene responsible for another HTH transcriptional regulator with an unknown target. To confirm that the mutation in these identified genes leads to resistance against these two compounds, we...”
- “...gene with an arabinose-inducible plasmid containing each of our genes of interest ( vc1408 and vca0767 ). When vc1408 was induced in the VC1408::Tn mutant, the cells lost resistance to MMV687807 compared with the cells expressing an empty plasmid ( Fig.3A ). Although the strains induced...”
Q8VV87 LexA repressor-like protein from Terrabacter sp.
38% identity, 20% coverage
- The TetR family of transcriptional repressors
Ramos, Microbiology and molecular biology reviews : MMBR 2005 - “...KstR Rhodococcus erythropolis strain SQ1 55 56 Q8VV87 LexA-like AcnR Terrabacter sp. strain DBF63 Corynebacterium glutamicum 57 Q9FA56 PaaR Azoarcus evanssi...”
PsrA / VIMSS862841 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Idiomarina loihiensis L2TR
46% identity, 24% coverage
DVU0436 / VIMSS209372 DVU0436 from Desulfovibrio vulgaris Hildenborough
DVU0436 transcriptional regulator, TetR family from Desulfovibrio vulgaris Hildenborough
35% identity, 28% coverage
- Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
Trotter, Frontiers in microbiology 2023 - “...media and added molybdate also had tungstate added (at 0.5 or 2.0mM). First, mutations in DVU0436, encoding a TetR-type transcriptional regulator, displayed a fitness advantage for the mutants in the presence of molybdate ( Figure 7A ). In contrast, strains lacking DVU0437 or DVU0438, which are...”
- “...fitness defects in the presence of molybdate ( Figure 7A ). These data suggest that DVU0436 represses transcription of the RND-type efflux pump encoded by DVU0437:DVU0438. Indeed, the RegPrecise database predicts that DVU0436 regulates the operon DVU0436:DVU0438 via a site just upstream of DVU0436 ( Novichkov...”
- Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions
Turkarslan, The ISME journal 2021 - “...significant parallel evolution across lines. With the exception of five high G-score genes (DVU0597, DVU1862, DVU0436, DVU0013, and DVU2394), which were mutated during long term salt adaptation of Dv [ 19 ], mutations in other high G-score genes appeared to be putatively specific to syntrophic interactions....”
Rv0144 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR-FAMILY) from Mycobacterium tuberculosis H37Rv
38% identity, 21% coverage
- Immunogenicity of Mycobacterial Extracellular Vesicles Isolated From Host-Related Conditions Informs About Tuberculosis Disease Status
Schirmer, Frontiers in microbiology 2022 - “...0 Regulatory proteins 19 Rv1479 MoxR1 0.16 2 Rv1479 MoxR1 0.26 Rv3295 probably TetR-family 0.11 Rv0144 possibly TetR-family 0.22 Rv0144 possibly TetR-family 0.11 Rv1267c EmbR 0.1 Rv3692 MoxR2 0.08 Conserved hypotheticals 132 Rv3127 Conserved protein 0.62 31 Rv2744c Conserved 35 kDa alanine rich protein 1.58 Rv3131...”
- Practical approach to detection and surveillance of emerging highly resistant Mycobacterium tuberculosis Beijing 1071-32-cluster
Mokrousov, Scientific reports 2021 - “...phylogenetic analysis of the available WGS data, we identified three synonymous SNPs in the genes Rv0144 , Rv0373c , and Rv0334 that were specific for the Beijing 1071-32-cluster and developed a real-time PCR assay for their detection. Analysis of the 2375 genetically diverse M. tuberculosis isolates...”
- “...the Beijing 1071-32-cluster. Gene, codon Position in gene Position in genome Primer, probe, and sequence Rv0144 74GCC/GCT 222 C>T 170505 C>T 170505F 5-CCAACGGTAGGTACCAAGC 170505R 5-GCTTCCGAGTCTCATCTGCT 170505C wt 5-[HEX]GTTCAATGTCGCTCACGGC[C-LNA]G[BHQ1] 170505T mut 5-[FAM]GTTCAATGTCGCTCACGGC[T-LNA]G[BHQ1] Rv0373c 98CCG/CCA 294 G>A 451510 C>T 451510F 5-CGCATCGATGTGACTGCC 451510R 5-CACGGCTTGTACGTCGTTG 451510G wt 5-[HEX]GCCTGGCTTGGATGCC[G-LNA]ACA[BHQ1] 451510A mut...”
- Applications of Transcriptomics and Proteomics for Understanding Dormancy and Resuscitation in Mycobacterium tuberculosis
Kundu, Frontiers in microbiology 2021 - “...Gopinath et al., 2015 Nutrient starvation Model of Betts et al. (2002) Transcriptional repressors CmtR, Rv0144, Rv0158, Rv0328, Rv1219c, Rv1556, Rv3295, Rv3557c; the serine threonine kinase PknH; 11 members of the TA family (MazF6, ParE2, RelE2,VapB32, VapC13, VapC19, VapC22, VapC39, VapC4, VapC41, VapC5); AtpA, C, D,...”
- An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome
Gomez-Gonzalez, Scientific reports 2019 - “...whiB 1.2.2** 0.021 0 Rv0023 G217D 4.9** 0 0.001 Rv0042c L186R* MarR 4.9** 0 0 Rv0144 P36L* tetR 4.9** 0 0 Rv0195 C41STOP LuxR 1.2.2** 0.021 0 Rv0275c S24L tetR 1 0.973 0 iniR E23K 1.2.2** 0.019 0 Rv0377 P302R* LysR 1 0.973 0 Rv0386 L475R*...”
- Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid
Saw, PeerJ 2016 - “...Four of the enriched proteins were found in three different CSF strains each. These were Rv0144 (probable transcriptional regulatory protein with Leu to Asp substitution), Rv3730c (hypothetical protein with Thr to Asp substitution), Rv0802c (possible succinyltransferase with Ser to Pro substitution) and Rv2034 (transcriptional regulatory protein...”
- The preprotein translocase YidC controls respiratory metabolism in Mycobacterium tuberculosis
Thakur, Scientific reports 2016 - “...RNA polymerase subunits (RpoC and RpoZ), transcription regulators (SigA, Rho, Crp, DosR, EspR, GreA, MtrA, Rv0144 and Rv3295) and stress response regulators (AhpC, GroEL1, GroEL2, GroES, Rv2581c and VapB47) are downregulated in yidC ( ) relative to control ( Fig. 3d ). Several other proteins including...”
- CsoR Is Essential for Maintaining Copper Homeostasis in Mycobacterium tuberculosis
Marcus, PloS one 2016 - “...4.11 3.51E-19 Rv0970 conserved membrane protein 1.96 8.89E-05 Transcriptional Regulators Rv0081 transcriptional regulator 6.99 2.46E-28 Rv0144 transcriptional regulator, tetR -family -2.28 2.67E-06 Rv0386 transcriptional regulator, luxR / uhpA -family 2.42 4.60E-07 Rv0452 transcriptional regulator 2.31 1.30E-05 Rv0981 mprA mycobacterial persistence regulator -2.16 4.05E-06 Rv1129c transcriptional regulator...”
- Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions
Balhana, BMC genomics 2015 - “...6.00E80 Rv0273c 1.20E43 Rv0275c 9.00E27 Rv0775 3.00E34 Rv3055 1.80E31 Rv3208 1.00E25 Rv3405c 3.20E28 Rv3830 6.20E20 Rv0144 3.00E16 Rv0452 4.90E13 Rv0472c 5.60E16 Rv0653c 1.10E18 Rv0681 6.00E17 Rv0691c 4.60E02 Rv0767c 1.20E14 Rv0825c 4.20E14 Rv1019 1.90E17 Rv1776c 4.00E16 Rv2250c 2.40E11 Rv3058c 2.00E12 Rv3167c 4.20E16 Rv3173c 3.00E18 Rv3295 2.30E16 The...”
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MAP3562 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
42% identity, 25% coverage
MAV_5151 transcriptional regulator, TetR family protein from Mycobacterium avium 104
42% identity, 25% coverage
- Metabolic pathways that permit Mycobacterium avium subsp. hominissuis to transition to different environments encountered within the host during infection
Abukhalid, Frontiers in cellular and infection microbiology 2023 - “...condition in biofilm. In addition, the participation of regulatory genes/proteins such as the TetR family MAV_5151 appear to be necessary for M. avium survival under biofilm and anaerobic conditions. Conclusion Collectively, our data reveal important core metabolic pathways that M. avium utilize under different stress conditions...”
- “...a broad-spectrum drug target ( Colclough etal., 2019 ). In our data, a TetR-family regulator, MAV_5151 was found to regulate several virulence traits by responding to fluctuating environmental nutrients and oxygen levels in the surroundings. MAV_5151 repress the expression of several proteins known to be associated...”
RutR / VIMSS908916 RutR regulator of Pyrimidine utilization, effector Uracil (repressor) from Silicibacter pomeroyi DSS-3
42% identity, 28% coverage
PsrA / VIMSS3565141 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Aeromonas salmonicida subsp. salmonicida A449
40% identity, 29% coverage
CCNA_00337 transcriptional regulator, TetR family from Caulobacter crescentus NA1000
47% identity, 19% coverage
- Correction of the Caulobacter crescentus NA1000 genome annotation
Ely, PloS one 2014 - “...the original CCNA_00338 reading frame. Note that the original start site was upstream of the CCNA_00337 stop codon. 10.1371/journal.pone.0091668.t004 Table 4 Genes with modified start sites. Gene Gene Position * Modified Gene Position Gene Function CCNA_00156 164586..164951 164685..164951 ArsR family transcriptional regulator CCNA_00176 191399.191956 191468..191956 Type...”
PsrA / VIMSS736161 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Burkholderia mallei ATCC 23344
38% identity, 20% coverage
DVU0057 / VIMSS8501435 DVU0057 from Desulfovibrio vulgaris str. Miyazaki F
39% identity, 21% coverage
BAB1_0578 Bacterial regulatory protein TetR, HTH motif from Brucella melitensis biovar Abortus 2308
36% identity, 35% coverage
- Molecular control of gene expression by Brucella BaaR, an IclR-type transcriptional repressor
Herrou, The Journal of biological chemistry 2018 - “...made (bab1_0303, UreG1 urease accessory protein; bab1_0578, BetI TetR transcriptional regulator; bab1_0914, DUF1127; bab2_0548, ABC transmembrane transporter)....”
- “...genes bab1_0303 (UreG1 urease accessory protein), bab1_0578 (BetI TetR transcriptional regulator), bab1_0914 (DUF1127), and bab2_0548 (ABC transmembrane...”
- Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308
Caswell, Molecular microbiology 2012 - “...abcR2 double mutant compared to the parental strain 2308, while other mRNA transcripts (BAB1_0310 and BAB1_0578) did not appear to be significantly stabilized in the abcR1 abcR2 mutant ( Fig. 5A ). In order to determine the half-lives of the transcripts in the different strains, the...”
VPA0806 transcriptional regulator, TetR family from Vibrio parahaemolyticus RIMD 2210633
WP_005478460 efflux transporter transcriptional repressor VdeR from Vibrio parahaemolyticus RIMD 2210633
39% identity, 26% coverage
BCAL1542 TetR family regulatory protein from Burkholderia cenocepacia J2315
38% identity, 23% coverage
SCO2223 tetR-family transcriptional regulator from Streptomyces coelicolor A3(2)
36% identity, 25% coverage
Q8YFY3 HTH-type transcriptional regulator BetI from Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)
BMEI1379 REGULATORY PROTEIN BETI from Brucella melitensis 16M
37% identity, 34% coverage
- Molecular Mechanism and Genetic Determinants of Buprofezin Degradation
Chen, Applied and environmental microbiology 2017 (secret) - Differential expression of iron acquisition genes by Brucella melitensis and Brucella canis during macrophage infection
Eskra, PloS one 2012 - “...BMEI1767 BCAN_A0185 hypothetical protein BMEI1767 - NC 56.28 BMEI1768 BCAN_A0184 uroporphyrin-III c-methyltransferase - NC 29.25 BMEI1379 BCAN_A0566 transcriptional regulator betI NC 6.92 BMEI1380 BCAN_A0565 choline dehydrogenase betA 2.07 2.86 BMEII0906 BCAN_B0343 stress-response and acid-resistance protein hdeA 3.72 2.59 BMEI0070 BCAN_A2047 aquaporin Z aqpZ 3.17 2.11 BMEI0239...”
- Brucella melitensis global gene expression study provides novel information on growth phase-specific gene regulation with potential insights for understanding Brucella:host initial interactions
Rossetti, BMC microbiology 2009 - “...encoding transcriptional regulators belonging to the AraC (BMEI1384, BMEII0143, BMEII0721), AsnC (BMEI1098, BMEI1845, BMEII0346), BetI (BMEI1379), DeoR (BMEII0426, BMEII0436, BMEII1093), GntR (BMEII0383, BMEII0807, BMEII1007), IclR (BMEI1717), LysR (BMEII0902, BMEII1077, BMEII1135), LuxR (BMEI1758), MarR (BMEII0520), MerR (BMEII0372, BMEII0467), and RpiR (BMEII0573) families were differentially expressed in late-log...”
BCAN_A0566 HTH-type transcriptional regulator betI from Brucella canis ATCC 23365
37% identity, 34% coverage
RutR / VIMSS1776949 RutR regulator of Pyrimidine utilization, effector Uracil (activator/repressor) from Ralstonia metallidurans CH34
46% identity, 23% coverage
CG479_RS07860 TetR/AcrR family transcriptional regulator from Bacillus cytotoxicus
40% identity, 32% coverage
NGR_RS06710 CerR family C-terminal domain-containing protein from Sinorhizobium fredii NGR234
44% identity, 24% coverage
SACE_5754 transcriptional regulator, TetR family from Saccharopolyspora erythraea NRRL 2338
43% identity, 26% coverage
- Uncovering and Engineering a Mini-Regulatory Network of the TetR-Family Regulator SACE_0303 for Yield Improvement of Erythromycin in Saccharopolyspora erythraea
Liu, Frontiers in bioengineering and biotechnology 2021 - “...Wu et al., 2016 ), and only five of them (SACE_3986, SACE_7301, SACE_3446, PccD, and SACE_5754) have been successively reported to control the biosynthesis of erythromycin so far ( Wu et al., 2014a , b , 2016 , 2019 ; Xu et al., 2018 ). These...”
- “...of the ery cluster ( Wu et al., 2014a , 2016 ), and SACE_3986 and SACE_5754 indirectly controlled the transcription of the ery cluster ( Wu et al., 2014b , 2019 ). However, the regulatory network regarding erythromycin biosynthesis has been seldom reported; in particular, hierarchical...”
- Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea
Wu, Journal of biological engineering 2019 - “...1754-1611 BioMed Central London 6346578 135 10.1186/s13036-018-0135-2 Research Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea Wu Hang 1 Chu Zuling 1 Zhang Wanxiang 1 Zhang Chi 1 Ni Jingshu 1 Fang Heshi 1 Chen Yuhong 1 Wang...”
- “...elements in S. erythraea . Results Here, we identified a TetR family transcriptional regulator (TFR), SACE_5754, negatively controlling erythromycin production. SACE_5754 indirectly repressed the transcription of ery cluster and cannot regulate itself and its adjacent gene SACE_5753 . RNA-seq coupled with EMSAs and qRT-PCR was performed...”
AcrR / VIMSS551346 AcrR regulator of Multidrug resistance, effector Rhodamine 6G; Ethidium bromide; Proflavin (repressor) from Photorhabdus luminescens TTO1
38% identity, 29% coverage
PsrA / VIMSS7086604 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Burkholderia phymatum STM815
38% identity, 23% coverage
JIP62_11565 TetR/AcrR family transcriptional regulator from Brevundimonas vitisensis
40% identity, 22% coverage
- Pyomelanin-Producing Brevundimonas vitisensis sp. nov., Isolated From Grape (Vitis vinifera L.)
Jiang, Frontiers in microbiology 2021 - “...araT (JIP62_09170), aromatic amino acid aminotransferase (EC 2.6.1.57); hppD (JIP62_07560), hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27); hmgR (JIP62_11565; JIP62_04630; and JIP62_01885), TetR family member transcriptional regulator; hmgA (JIP62_08245), homogentisate dioxygenase; hmgC / maiA (JIP62_08415), maleylacetoacetate isomerase; and fahA / hmgB (JIP62_RS07590; JIP62_RS08410; and JIP62_RS01250), fumarylacetoacetate hydrolase. Pigment Characterization...”
PsrA / VIMSS6896230 PsrA regulator of Fatty acid degradation, effector Oleate (repressor) from Alteromonas macleodii 'Deep ecotype'
37% identity, 32% coverage
K2Z90_RS14485 TetR/AcrR family transcriptional regulator from Rhodococcus opacus PD630
39% identity, 26% coverage
- Increased triacylglycerol production in Rhodococcus opacus by overexpressing transcriptional regulators
Anthony, Biotechnology for biofuels and bioproducts 2024 - “...under both stress conditions (Fig. 1 a). And 11/33 (41%) TRs, including K2Z90_RS32760 (WG013) and K2Z90_RS14485 (WG020) decreased expression in phenol and increased in nitrogen starvation. The observed changes in the expression of 33 TR under diverse lipid production conditions highlight the potential for controlling TAG...”
- “...WG013 (6) overexpress TR K2Z90_RS09960, K2Z90_RS10170 and K2Z90_RS32760, respectively, and finally strain WG020 (7) expresses K2Z90_RS14485. These 7 strains were tested in fermentation using either glucose or phenol as a sole carbon source with or without nitrogen limitation (Fig. 1 b). In comparison to wild-type (WT)...”
FASR_MYCS2 / A0QTR3 HTH-type transcriptional activator FasR; Fatty acid synthesis regulator from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see paper)
MSMEG_1935 TetR-family protein transcriptional regulator from Mycobacterium smegmatis str. MC2 155
37% identity, 27% coverage
- function: Transcriptional activator that plays a central role in sensing mycobacterial long-chain fatty acids and regulating lipid biosynthesis (PubMed:23721164). Activates the expression of the genes encoding the fatty acid synthase (fas) and the 4-phosphopantetheinyl transferase (acpS), whose products are involved in the fatty acid and mycolic acid biosynthesis (PubMed:23721164). Specifically binds to three conserved operator sequences present in the fas-acpS promoter region (By similarity). Essential for M.smegmatis viability (PubMed:23721164).
subunit: Homodimer.
disruption phenotype: Essential, cannot be deleted. - A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations.
Giddey, Scientific reports 2017 - “...protein MSMEG_3063 0.71 8.75E-03 53.4 A0R1D5 HpcH/HpaI aldolase/citrate lyase family protein MSMEG_4713 0.84 3.63E-02 29 A0QTR3 TetR-family protein transcriptional regulator MSMEG_1935 0.94 3.26E-02 49.8 A0R316 Uncharacterized protein MSMEG_5308 1.52 9.14E-03 34.2 A0R722 Glucanase MSMEG_6752 1.69 3.82E-03 32.3 Time Point 2 A0QVH8 Zinc metalloprotease Rip1 rip1 1.15...”
- A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations
Giddey, Scientific reports 2017 - “...A0R1D5 HpcH/HpaI aldolase/citrate lyase family protein MSMEG_4713 0.84 3.63E-02 29 A0QTR3 TetR-family protein transcriptional regulator MSMEG_1935 0.94 3.26E-02 49.8 A0R316 Uncharacterized protein MSMEG_5308 1.52 9.14E-03 34.2 A0R722 Glucanase MSMEG_6752 1.69 3.82E-03 32.3 Time Point 2 A0QVH8 Zinc metalloprotease Rip1 rip1 1.15 7.04E-03 11.1 A0R2B2 Major facilitator...”
- Transcriptional regulation of fatty acid biosynthesis in mycobacteria
Mondino, Molecular microbiology 2013 - “...Hup (MSMEG_2389) and Lsr2 (MSMEG_1060 and MSMEG_6092). The fourth one was the product of the MSMEG_1935 gene, a putative TetR transcriptional regulator. Consistent with most TetR family of regulators whose molecular masses range from 21 to 25 kDa, MSMEG_1935 has a calculated molecular mass of 24,410...”
- “...protein in M. tuberculosis identified Rv3208. This M. tuberculosis protein has 84 % identity with MSMEG_1935 and they are both located in the same loci of the corresponding bacterial chromosome. Therefore, we identify orthologous proteins from M. tuberculosis and M. smegmatis whose most probable role is...”
SM_b21208 putative transcriptional regulator, TetR family protein from Sinorhizobium meliloti 1021
42% identity, 23% coverage
- Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis
Taboada-Castro, Frontiers in bioinformatics 2024 - “...the plasmid located gstR -like TF SM_b20004, MucR family TF SMa0748, and tetR family TF SM_b21208 were identified altogether with 10TFs; SMc00241, SMc03820, SMa0748, SM_b21021, SMc02504, SMc02523, SM_b21115, SMc00679, SMc03046, and SMc02984 were found. For level_6, three sigma factors, the first sigma-32 rpoH1, rpoE5, SM_b21484, and...”
- “...the plasmid-borne lysR SM_b20582, the chvI chromosomal encoded SMc02560, and the TetR family TF plasmid-encoded SM_b21208 in addition to six TFs, SM_b20162, SM_b21222, SMc02470, SMc04163, SMc02323, and SMc02560, were detected, and in level_4, the first sigma fecl chromosomal-encoded SMc04203, the cbbR TFR, betI SMc00095, irr chromosomal-encoded...”
MAB_3527 Putative transcriptional regulator, TetR family from Mycobacterium abscessus ATCC 19977
35% identity, 27% coverage
PA14_35210 putative transcriptional regulator, TetR family from Pseudomonas aeruginosa UCBPP-PA14
39% identity, 30% coverage
- History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment
Yen, PLoS biology 2017 - “...regulation iscR , mucB , mvfR , np20 , pauR , rnk , PA14_09960, PA14_12140, PA14_35210, PA14_37170/ ada , PA14_38500, PA14_39360 2-component sensor envZ , cpxR , pmrB , PA14_22730, PA14_27940 Beta-lactamases ampR , dacB Stringent response spoT Quorum sensing ptsP Large deletions [ aldG ][...”
YE105_C1162 multidrug efflux transporter transcriptional repressor AcrR from Yersinia enterocolitica subsp. palearctica 105.5R(r)
44% identity, 25% coverage
- Expression of the AcrAB Components of the AcrAB-TolC Multidrug Efflux Pump of Yersinia enterocolitica Is Subject to Dual Regulation by OmpR
Raczkowska, PloS one 2015 - “...which displays significant similarity to DsrE, an essential factor in oxidative sulfur metabolism. Notably, gene YE105_C1162, encoding transcriptional repressor AcrR was identified immediately upstream of dsrE . In strain AR704 (negative effect) the lacZ reporter gene was transcribed from the promoter of gene YE105_C2117, encoding a...”
- “...effect of OmpR) occurred in gene YE105_C1163 (encoding a DsrE homolog) located upstream of gene YE105_C1162, encoding transcriptional repressor AcrR. To determine whether these two genes are organized in an operon, RT-PCR analysis was performed ( Fig 3 ). Our data showed that the putative acrR...”
RutR / VIMSS3134196 RutR regulator of Pyrimidine utilization, effector Uracil (repressor) from Alteromonadales bacterium TW-7
41% identity, 23% coverage
SMc01819 PUTATIVE TRANSCRIPTION REGULATOR PROTEIN from Sinorhizobium meliloti 1021
37% identity, 30% coverage
- A signaling complex of adenylate cyclase CyaC of Sinorhizobium meliloti with cAMP and the transcriptional regulators Clr and CycR
Klein, BMC microbiology 2023 - “...clustered [ 14 ]. Interestingly, cyaC ( smc01818 ) is preceded by a gene ( smc01819 ) that encodes a putative transcriptional regulator (TR01819) of the TetR family with an N -terminal Helix-Turn-Helix DNA binding motif. TetR regulators often bind small-molecular ligands as signals for modulating...”
- “...(Smc02175), and the TetR-like transcriptional regulator CycR (Smc protein 01819) that is encoded by gene smc01819 preceding cyaC ( smc01818 gene). First, the interaction of CyaC with Clr and CycR and was tested in vivo (Fig. 1 AB) using the bacterial adenylate cyclase based two-hybrid system...”
- Absence of functional TolC protein causes increased stress response gene expression in Sinorhizobium meliloti
Santos, BMC microbiology 2010 - “...assimilation regulatory protein -8.0 SMc01043 ntrC nitrogen assimilation regulatory protein -6.9 SMc01504 Receiver domain -7.2 SMc01819 Transcription regulator TetR family -10.0 SMc03806 glnK probable nitrogen regulatory protein PII 2 -9.1 Metabolism SMa0387 hisC3 histidinol-phosphate aminotransferase -11.4 SMa0398 hisD2 histidinol dehydrogenase -10.6 SMa1683 Arylsulfatase -5.0 SMb20984 nirB...”
WP_021595170 TetR/AcrR family transcriptional regulator from Actinomadura madurae LIID-AJ290
43% identity, 24% coverage
RutR / VIMSS6896853 RutR regulator of Pyrimidine utilization, effector Uracil (repressor) from Alteromonas macleodii 'Deep ecotype'
40% identity, 24% coverage
AFA_03875 TetR/AcrR family transcriptional regulator from Alcaligenes faecalis
36% identity, 34% coverage
MCOL_RS23260 TetR/AcrR family transcriptional regulator from Mycobacterium colombiense CECT 3035
44% identity, 29% coverage
- In silico analysis of promoter regions to identify regulatory elements in TetR family transcriptional regulatory genes of Mycobacterium colombiense CECT 3035
Hamde, Journal, genetic engineering & biotechnology 2022 - “...2 0.97, 0.99 1780, 952 MCOL_RS07580 31526928 1 0.93 52 MCOL_RS05990 31526617 1 0.9 7888 MCOL_RS23260 31530032 1 0.82 6063 MCOL_RS22650 31529910 1 0.85 677 MCOL_RS17010 31528795 1 0.82 10425 MCOL_RS03070 31526050 1 0.95 1426 MCOL_RS04305 31526295 1 0.9 2778 MCOL_RS22305 31529842 2 0.82, 0.91 4568,...”
- “...158, 200, 459, 554, 586, 616) 59, 42, 95 MCOL_RS05990 Multiple (185, 274, 539) 89 MCOL_RS23260 Multiple (4, 118, 214, 225, 263, 276, 280, 320, 369, 519, 541) 114, 96, 40, 49, 150 MCOL_RS22650 Multiple (16, 23, 39, 43, 261, 361, 442, 592, 603) 218, 55,...”
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