PaperBLAST
PaperBLAST Hits for 74 a.a. (NINKQSPIPI...)
Show query sequence
>74 a.a. (NINKQSPIPI...)
NINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNE
GLLYRLKGRGTFVS
Running BLASTp...
Found 250 similar proteins in the literature:
4wwcA / O34817 Crystal structure of full length yvoa in complex with palindromic operator DNA (see paper)
100% identity, 35% coverage
4u0vA / O34817 Crystal structure of yvoa from bacillus subtilis in complex with glucosamine-6-phosphate (see paper)
100% identity, 30% coverage
- Ligand: 2-amino-2-deoxy-6-o-phosphono-alpha-d-glucopyranose (4u0vA)
NAGR_BACSU / O34817 HTH-type transcriptional repressor NagR; N-acetylglucosamine utilization regulator from Bacillus subtilis (strain 168) (see 7 papers)
NagR / VIMSS40042 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Bacillus subtilis subsp. subtilis str. 168
NP_391383 transcriptional regulator (GntR family) from Bacillus subtilis subsp. subtilis str. 168
BSU35030 transcriptional regulator (GntR family) from Bacillus subtilis subsp. subtilis str. 168
100% identity, 30% coverage
- function: Main transcriptional repressor of genes involved in N- acetylglucosamine (GlcNAc) transport and utilization (PubMed:20047956, PubMed:21602348, PubMed:23667565, PubMed:24673833). Represses the expression of the nagAB and nagP operons by binding directly within their upstream regions (PubMed:21602348, PubMed:24673833). Binds to the DNA consensus sequence 5'-ATTGGTATAGACAACT-3' (PubMed:21602348). Also acts as a weak repressor of mapB expression (PubMed:16207374).
subunit: Homodimer (PubMed:19342794, PubMed:20047956, PubMed:25564531). Forms dimers via the C-terminal effector-binding domain (PubMed:20047956). At high concentrations, probably forms polymers along the DNA (PubMed:24673833).
disruption phenotype: Deletion of the gene results in the modulation of the expression of many important genes, probably indirectly due to an excess of the crucial molecules acetate, ammonia, and fructose-6- phosphate, resulting from complete hydrolysis of GlcNAc (PubMed:21602348). Disruption of the gene induces a slight but consistent increase in MapB activity (PubMed:16207374). Deletion of the gene improves the growth rate on N-acetylglucosamine (PubMed:23667565). - Regulon of the N-acetylglucosamine utilization regulator NagR in Bacillus subtilis
Bertram, Journal of bacteriology 2011 - “...(v) YmfC (NP_389563), (vi) YydK (NP_391893), (vii) YvoA (NP_391383), and (viii) DasR, the GlcNAc utilization regulator from S. coelicolor (NP_629378) (51). The...”
- Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of YvoA from Bacillus subtilis.
Resch, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - GeneRIF: YvoA (BSU35030) from Bacillus subtilis was purified by immobilized metal-affinity chromatography and size-exclusion chromatography and subsequently crystallized.
- The Functional Network of PrkC and Its Interaction Proteins in <i>Bacillus subtilis</i> Spores
Mu, Microorganisms 2025 (no snippet) - Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein
Chauhan, Microbiology spectrum 2023 - “...Rv0792c, and Rv3060c), Burkholderia sp. (EEA00313), Pseudomonas putida (P22773), Escherichia coli (P0A8V8, P13669), Bacillus subtilis (O34817), Streptomyces coelicolor (Q9K492), Salmonella enterica (AAB39463), Corynebacterium glutamicum (BAC00309), Thermotoga maritima (NP_228249), Streptococcus pyogenes (AMY97465), Vibrio cholerae (SYZ81202), Pseudomonas syringae (WP_044310692), Brucella sp. (WP_006173453), and Klebsiella pneumoniae (EPP09325). (B) Sedimentation...”
- Crystal Structures of the Global Regulator DasR from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors
Fillenberg, PloS one 2016 - “...pET15b vectors (Novagen, EMD Biosciences, Darmstadt, Germany) that contain either the dasR (residues 1254; UniProtKB O34817, [ 19 ]) or the dasR-ebd gene (residues 88254). Both constructs display an additional N-terminal hexahistidine tag and a thrombin cleavage site. The cells were grown at 310 K in...”
- “...with CLUSTAL OMEGA [ 59 ] using the canonical protein sequences of entries Q9K492 and O34817 from the UniProt database [ 19 ]. Secondary structure elements refer to the topology of DasR and are marked with (h) or (s) for -helices and -strands, respectively. For a...”
- Insight into the induction mechanism of the GntR/HutC bacterial transcription regulator YvoA
Resch, Nucleic acids research 2010 - “...of YvoA. MATERIALS AND METHODS Protein cloning, mutagenesis, expression and purification YvoA (BSU35030, UniProtKB/TrEMBL entry O34817) from B. subtilis and mutants thereof were expressed and purified as described ( 21 ). Amino acid exchanges were introduced by site-directed mutagenesis using the QuikChange site-directed mutagenesis kit (Stratagene,...”
- DevA, a GntR-like transcriptional regulator required for development in Streptomyces coelicolor
Hoskisson, Journal of bacteriology 2006 - “...Bacillus subtilis 248 252 243 P22773 Q9ACN8 O34817 HutC SAV4023 SAV4021 SCO4188 DevA Unknown Unknown Unknown Developmental regulator Streptomyces Streptomyces...”
- Insight into the induction mechanism of the GntR/HutC bacterial transcription regulator YvoA
Resch, Nucleic acids research 2010 - “...the allosteric induction of YvoA. MATERIALS AND METHODS Protein cloning, mutagenesis, expression and purification YvoA (BSU35030, UniProtKB/TrEMBL entry O34817) from B. subtilis and mutants thereof were expressed and purified as described ( 21 ). Amino acid exchanges were introduced by site-directed mutagenesis using the QuikChange site-directed...”
- Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of YvoA from Bacillus subtilis
Resch, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - “...The putative transcriptional regulator protein YvoA (BSU35030) from Bacillus subtilis was cloned and heterologously expressed in Escherichia coli....”
- “...2. Experimental methods 2.1. Cloning Genomic yvoA DNA (BSU35030) from B. subtilis 168 was used as a template for the polymerase chain reaction (PCR)....”
NagR / VIMSS3428080 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Bacillus pumilus SAFR-032
79% identity, 30% coverage
NagR / VIMSS822969 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Bacillus clausii KSM-K16
66% identity, 30% coverage
NagR / VIMSS277398 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Oceanobacillus iheyensis HTE831
63% identity, 29% coverage
NagR / VIMSS63000 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Bacillus halodurans C-125
64% identity, 30% coverage
NagR / VIMSS854146 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Geobacillus kaustophilus HTA426
62% identity, 30% coverage
BC_4053, BTF1_18580 GntR family transcriptional regulator from Bacillus cereus ATCC 14579
56% identity, 30% coverage
- NagRBt Is a Pleiotropic and Dual Transcriptional Regulator in Bacillus thuringiensis
Cao, Frontiers in microbiology 2018 - “.../ / / 0.116 NT BTF1_17540 acpP Acyl carrier protein / / / 0.206 NT BTF1_18580 nagR GntR family transcriptional regulator NagR / / / 0.0312 NT BTF1_19025 Hypothetical protein 107 aatcatctagacaact 10.1 0.0187 0.570 0.030 BTF1_23020 pgi Glucose-6-phosphate isomerase 168 agatgtatatacatca 7.08 0.188 0.6781 0.038...”
- Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
Laouami, PloS one 2014 - “...0,034 Transcriptional Regulation NP_833888.1 ArgR2 BC_4174 Arginine biosynthesis repressor 1,511 0,030 1,269 0,079 NP_833771.1 - BC_4053 Transcriptional regulator, GntR family 0,895 0,019 0,227 0,399 NP_833799.1 - BC_4081 MarR family transcriptional regulator 0,029 0,464 1,903 0,001 NP_834861.1 - BC_5197 MarR family transcriptional regulator 0,345 0,029 0,604 0,123...”
NagR / VIMSS361309 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Bacillus cereus ATCC 14579
56% identity, 30% coverage
NagR / VIMSS730314 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Bacillus licheniformis DSM 13
55% identity, 30% coverage
Clo1313_1482 GntR family transcriptional regulator from Acetivibrio thermocellus DSM 1313
51% identity, 30% coverage
GSU0267 transcriptional regulator, GntR family from Geobacter sulfurreducens PCA
49% identity, 29% coverage
bgla_2g16570 GntR family transcriptional regulator from Burkholderia gladioli BSR3
49% identity, 29% coverage
ManR / VIMSS351631 ManR regulator of Mannose utilization; Mannosides utilization, effector Mannose (repressor) from Bacteroides thetaiotaomicron VPI-5482
BT2103 transcriptional regulator from Bacteroides thetaiotaomicron VPI-5482
56% identity, 30% coverage
AraR / VIMSS6925973 AraR regulator of Arabinose utilization, effector Arabinose (repressor) from Paenibacillus sp. JDR-2
49% identity, 19% coverage
AOT13_11450 GntR family transcriptional regulator from Parageobacillus thermoglucosidasius
49% identity, 20% coverage
- Development of a xylose-inducible and glucose-insensitive expression system for Parageobacillus thermoglucosidasius
Wang, Applied microbiology and biotechnology 2024 - “...protein, and permease, respectively), were found to be directly upstream of the ara operon ( AOT13_11450 to AOT13_11485 ) (Liang et al. 2022a ), which showed moderate sequence identities to XylF, XylG, and XylH of G. kaustophilus HTA426 (35.8%, 54.6%, and 43.1%, respectively, Fig. S3 and...”
NagQ / VIMSS7040739 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Caulobacter sp. K31
53% identity, 28% coverage
LMOSA_18480 GntR family transcriptional regulator from Listeria monocytogenes str. Scott A
lmo0958 similar to transcription regulator (GntR family) from Listeria monocytogenes EGD-e
LMRG_02057 hypothetical protein from Listeria monocytogenes 10403S
47% identity, 30% coverage
- The Natural Antimicrobial trans-Cinnamaldehyde Interferes with UDP-N-Acetylglucosamine Biosynthesis and Cell Wall Homeostasis in Listeria monocytogenes
Sun, Foods (Basel, Switzerland) 2021 - “...glmS gene (locus tag: LMOSA_16310) from Scott A pIMK2-nagR pIMK2 with nagR gene (locus tag: LMOSA_18480) from Scott A pIMK2-nagR M pIMK2 with mutated nagR M gene from M 2.2 suppression mutant strain pKSV7-oriT Temperature-sensitive shuttle vector for making gene deletion in L. monocytogenes , 6742...”
- Integrative analysis of transcriptomic and immunoproteomic data reveals stress response mechanisms in Listeria monocytogenes
D'Onofrio, Heliyon 2024 - “...integrity, and sensitivity to antibiotics. Lmo0956 is part of operon 150, along with lmo0957 and lmo0958 , which are involved in amino-sugar metabolism. Mutational analysis of lmo0956 revealed its significance in bacterial physiology and virulence, suggesting it as a potential target for anti-listerial drug therapy [...”
- N-acetylglucosamine-6-phosphate deacetylase (NagA) of Listeria monocytogenes EGD, an essential enzyme for the metabolism and recycling of amino sugars
Popowska, Archives of microbiology 2012 - “...colistin. The gene products of operon 150, consisting of three genes: lmo0956 , lmo0957, and lmo0958 , are necessary for the cytosolic steps of the amino-sugar-recycling pathway. The cytoplasmic de- N -acetylase Lmo0956 of L. monocytogenes is required for cell wall peptidoglycan and teichoic acid biosynthesis...”
- “...was cDNA formed with the use of RTB1 primer, for the genes downstream lmo0957 and lmo0958 cDNA formed with the use of RTA1 primer. For mutant MP2, the template used to demonstrate the presence of the transcript for the gene upstream lmo2107 was cDNA formed using...”
- Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
Oliver, Applied and environmental microbiology 2010 - “...genes encoding 4 GntR family transcriptional regulators (lmo0958, lmo1725, lmo2003, lmo2004) and 2 MerR family transcriptional regulators (lmo1788, lmo2593)....”
- “...Berkeley lmo0130 lmo0188 lmo0217 lmo0239 lmo0315 lmo0640 lmo0958 lmo0959 lmo1076 lmo1237 lmo1255 lmo1293 lmo1348 lmo1357 lmo1389 lmo1390 lmo1391 lmo1538 lmo1539...”
- Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σB
Liu, Frontiers in microbiology 2017 - “...18 LMRG_02028 A , B srtA , DE fragments identified in 5'UTR 19 LMRG_02055, LMRG_02056 LMRG_02057 B , A frag 38333 nagA and nagB operon. Two NagR attenuatormotives were identified suggesting co-regulation with NagR 20 LMRG_02215, LMRG_02216 LMRG_02217 A , B LMRG_02217 21 LMRG_02219 LMRG_02218 B...”
AraR / P96711 Transcription factor AraR (repressor) from Bacillus subtilis 168 (see paper)
P96711 Arabinose metabolism transcriptional repressor from Bacillus subtilis (strain 168)
NP_391277 transcriptional repressor of the ara regulon (LacI family) from Bacillus subtilis subsp. subtilis str. 168
45% identity, 19% coverage
- A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications
Broto, Nature communications 2022 - “...substituted by the different RS sequences tested. Genes coding for the AraR repressor (Uniprot no. P96711) and the AraE l -arabinose permease (Uniprot no. A0A6M3ZGR6) were isolated from B. subtilis str. 168 genomic DNA (ATCC 23857D-5). Mycoplasma codon-optimised genes purchased from GenScript were used for the...”
- Expanding the Cyanobacterial Nitrogen Regulatory Network: The GntR-Like Regulator PlmA Interacts with the PII-PipX Complex
Labella, Frontiers in microbiology 2016 - “...GntR subfamily: DevA (accession ), MocR (accession P49309 ), PlmA (accession ABB56122 ), AraR (accession P96711 ), FadR (accession P0A8V6 ), HutC (accession P22773 ), and YtrA (accession O34712 ). The neighbor-joining phylogenetic tree for PlmA orthologs (234 sequences from bidirectional blast search) was constructed using...”
- GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
Vindal, BMC genomics 2007 - “...126 Q99SV4 Bacillus subtilis YhcF 121 P54590 Bacillus subtilis YtrA 130 O34712 AraR Bacillus subtilis P96711 362 P96711 Bacillus halodurans Q9KBQ0 375 Q9KBQ0 Bacillus stearothermophilus Q9S470 364 Q9S470 PlmA Synechocystis sp. strain PCC 6803 sll1961 388 P73804 Anabaena sp. strain PCC 7120 Q8YXY0 328 Q8YXY0 Synechococcus...”
- Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon
Franco, Nucleic acids research 2007 - “...( 24 ). The microorganisms of source and accession numbers are: AraR from B. subtilis (P96711); GntR from B. subtilis (P10585); FadR from E. coli (P09371). ( B ) Structure of the modelled N-terminal domain of AraR (depicted in green ribbons; only one monomer is represented...”
- DevA, a GntR-like transcriptional regulator required for development in Streptomyces coelicolor
Hoskisson, Journal of bacteriology 2006 - “...repressor of the L-arabinose operon Bacillus subtilis 362 P96711 AraR carrying devB and part of devA was amplified from cosmid D66 by using oligonucleotides...”
- Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding
Franco, Journal of bacteriology 2006 - “...accession numbers are as follows: B. su, B. subtilis (P96711); B. li, B. licheniformis (Q62R80 and Q62UH0); B. hd, B. halodurans (Q9KBQ0); B. st, Geobacillus...”
- PlmA, a new member of the GntR family, has plasmid maintenance functions in Anabaena sp. strain PCC 7120
Lee, Journal of bacteriology 2003 - “...440 328 P09371 P22773 P49309 O34712 P96711 Q8YXY0 P73804 BAC09669 ZP_00112619 ZP_00105573 ZP_00074937 ZP_00114559 ZP_00107916 Downloaded from http://jb.asm.org/...”
- Towards novel amino acid-base contacts in gene regulatory proteins: AraR--a case study.
Correia, PloS one 2014 - GeneRIF: These new findings not only contribute to a more detailed comprehension of AraR-operator interactions
- Identification and functional analysis of the gene cluster for L-arabinose utilization in Corynebacterium glutamicum
Kawaguchi, Applied and environmental microbiology 2009 - “...subtilis AraR and CcpA (accession numbers NP_414879, NP_391277, and NP_390852, respectively) (data not shown). The putative AraE protein exhibited high levels...”
- Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding.
Franco, Journal of bacteriology 2006 - GeneRIF: In vivo analysis identified particular amino acids required for dimer assembly, formation of the nucleoprotein complex, and composition of the sugar-binding cleft.
AraR / VIMSS39936 AraR regulator of Arabinose utilization, effector Arabinose (repressor) from Bacillus subtilis subsp. subtilis str. 168
45% identity, 17% coverage
5d4sB / P96711 Crystal structure of arar(dbd) in complex with operator orx1 (see paper)
45% identity, 81% coverage
AraR / VIMSS853771 AraR regulator of Arabinose utilization, effector Arabinose (repressor) from Geobacillus kaustophilus HTA426
GK1907 arabinose metabolism transcriptional repressor from Geobacillus kaustophilus HTA426
46% identity, 20% coverage
Q9S470 Arabinose metabolism transcriptional repressor from Geobacillus stearothermophilus
46% identity, 20% coverage
GYMC52_1867 GntR family transcriptional regulator from Geobacillus sp. Y412MC52
46% identity, 20% coverage
GmuR / VIMSS853719 GmuR regulator of Glucomannan utilization (repressor) from Geobacillus kaustophilus HTA426
52% identity, 28% coverage
NagQ / VIMSS10185949 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Azospirillum sp. B510
50% identity, 27% coverage
AgaR2 / VIMSS3649412 AgaR2 regulator of N-acetylgalactosamine utilization, effector N-acetylgalactosamine from Lactobacillus helveticus DPC 4571
52% identity, 28% coverage
PA14_34880 putative transcriptional regulator, GntR family from Pseudomonas aeruginosa UCBPP-PA14
46% identity, 28% coverage
Q9I1H6 Probable transcriptional regulator from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA2299 probable transcriptional regulator from Pseudomonas aeruginosa PAO1
IS492_19235 GntR family transcriptional regulator from Pseudomonas aeruginosa
46% identity, 28% coverage
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...1899 Q9I2B1 2981 Q9HWK3 4063 Q9I1H4 5145 Q9I7A3 818 Q9I0J6 1900 Q9I2B3 2982 Q9HWK4 4064 Q9I1H6 5146 Q9I7A6 819 Q9I0J7 1901 Q9I2B7 2983 Q9HWK5 4065 Q9I1H7 5147 Q9I7A7 820 Q9I0J8 1902 Q9I2C1 2984 Q9HWK7 4066 Q9I1H8 5148 Q9I7B0 821 Q9I0J9 1903 Q9I2C2 2985 Q9HWK8 4067 Q9I1H9...”
- The Fem cell-surface signaling system is regulated by ExsA in Pseudomonas aeruginosa and affects pathogenicity
Li, iScience 2025 - “...) while the levels of two other transcriptional regulators, VqsM and a hypothetical GntR regulator PA2299, were increased. Altogether, it is evident that the FemI not only regulates femA and mycobactin-mediated iron uptake but can also affect multiple genes and activities in P.aeruginosa . The fem...”
- The secondary metabolite hydrogen cyanide protects Pseudomonas aeruginosa against sodium hypochlorite-induced oxidative stress
da, Frontiers in microbiology 2023 - “...0.323 6.828 2.660 PA0435 PA0435 PW1795 9.452 0.502 7.005 4.078 PA14_05650 8.162 0.38 7.520 1.772 PA2299 PA2299 PW4885 9.393 0.366 8.354 1.937 PA14_15830 8.208 0.190 7.609 1.386 PA2328 PA2328 PW4927 9.510 0.164 8.565 1.505 PA14_41480 8.365 0.455 7.592 1.655 PA2329 PA14_02330 8.137 0.621 7.728 1.317 PA2330...”
- Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
Valzano, Microbiology spectrum 2022 - “...Flagellar biosynthesis protein FlhF (motility) 7.6E03 0.6 IS492_19230 PA2298 PA14_34900 Probable oxidoreductase 4.9E05 0.7 IS492_19235 PA2299 PA14_34880 Probable transcriptional regulator 3.2E04 0.7 IS492_26340 PA3391 PA14_20230 nosR Regulatory protein NosR (denitrification) 3.2E04 0.6 IS492_26345 PA3392 PA14_20200 nosZ Nitrous oxide reductase (denitrification) 4.1E05 0.8 IS492_26895 PA3519 PA14_18810 Iron-containing...”
- Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells
Coleman, Antimicrobial agents and chemotherapy 2020 (secret) - Transcriptomic analysis of the sulfate starvation response of Pseudomonas aeruginosa
Tralau, Journal of bacteriology 2007 - “...were not repressed by cyclamate-sul- fate (PA2298 and PA2299), suggesting that these may be specifically cyclamate induced. Although cells grown with cyclamate...”
- “...PA2092 PA2292 PA2293 PA2294 PA2295 PA2296 PA2297 PA2298 PA2299 PA2307 PA2308 PA2309 PA2310 PA2324 PA2325 PA2326 PA2346 PA2347 PA2348 PA2349 PA2350 PA2351 PA2354...”
- An improved method for rapid generation of unmarked Pseudomonas aeruginosa deletion mutants
Choi, BMC microbiology 2005 - “...deleted 25 of the 27 genes (we could not delete the presumably essential PA1285 and PA2299 ) in less than 4 weeks in strain PAO1 with a chromosomally integrated fabA'-lacZ transcriptional fusion and analyzed -galactosidase expression in the resulting mutant strains (Fig. 6 ). In exponential...”
- Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
Valzano, Microbiology spectrum 2022 - “...flhF Flagellar biosynthesis protein FlhF (motility) 7.6E03 0.6 IS492_19230 PA2298 PA14_34900 Probable oxidoreductase 4.9E05 0.7 IS492_19235 PA2299 PA14_34880 Probable transcriptional regulator 3.2E04 0.7 IS492_26340 PA3391 PA14_20230 nosR Regulatory protein NosR (denitrification) 3.2E04 0.6 IS492_26345 PA3392 PA14_20200 nosZ Nitrous oxide reductase (denitrification) 4.1E05 0.8 IS492_26895 PA3519 PA14_18810...”
lp_0563 GntR family transcriptional regulator from Lactiplantibacillus plantarum WCFS1
53% identity, 28% coverage
CC0445 transcriptional regulator, GntR family from Caulobacter crescentus CB15
52% identity, 27% coverage
ABAYE1931 GntR family transcriptional regulator from Acinetobacter baumannii AYE
52% identity, 27% coverage
- Evolution of a pathogen: a comparative genomics analysis identifies a genetic pathway to pathogenesis in Acinetobacter
Sahl, PloS one 2013 - “...ABAYE2456 beta-lactamase b,n gain 26 HMPREF0021_00524 hypothethical b,n gain 27 ABAYE0983 hypothethical b,n gain 28 ABAYE1931 GntR family transcriptional regulator b,n gain 29 HMPREF0012_03541 hypothethical b loss 30 HMPREF0012_00124 glyoxylase b loss 31 HMPREF0012_00560 hypothethical b loss 32 HMPREF0012_00562 RNA polymerase sigma factor b loss 33...”
- “...Genes unique to this clade include a class A beta-lactamase (TEM-1), a GntR-family transcriptional regulator (ABAYE1931), and conserved hypothetical proteins ( Table 1 ); the acquired transcriptional regulator shares homology (56% ID over 100% of the peptide length) with a transcriptional regulator (bgla_2g16570) in the plant...”
A9801_RS13465 GntR family transcriptional regulator from Acinetobacter baumannii
52% identity, 27% coverage
- Characterization and Transcriptome Studies of Autoinducer Synthase Gene from Multidrug Resistant Acinetobacter baumannii Strain 863
Ng, Genes 2019 - “...hydratase 9.00212 A9801_RS14855 MFS transporter 8.94764 Up-regulated genes A9801_RS10685 UmuC 3.880526 A9801_RS13285 hypothetical protein 2.842797 A9801_RS13465 GntR family transcriptional regulator 2.737668 A9801_RS06690 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase 2.725173 A9801_RS13170 alpha/beta hydrolase 2.641788 A9801_RS01690 terminase 2.622548 A9801_RS10575 ammonium transporter 2.621587 A9801_RS16845 allantoin permease 2.61855 A9801_RS05955 MFS transporter 2.613142 A9801_RS12660 non-ribosomal...”
SCO6256 transcriptional regulator from Streptomyces coelicolor A3(2)
45% identity, 30% coverage
SPD_1275 transcriptional regulator, GntR family protein from Streptococcus pneumoniae D39
52% identity, 29% coverage
BMEI0881 TRANSCRIPTIONAL REGULATOR, GNTR FAMILY from Brucella melitensis 16M
42% identity, 29% coverage
PP0204 transcriptional regulator, GntR family from Pseudomonas putida KT2440
45% identity, 28% coverage
BAB1_1124 Bacterial regulatory protein, GntR family from Brucella melitensis biovar Abortus 2308
42% identity, 29% coverage
- Immunization of mice with recombinant protein CobB or AsnC confers protection against Brucella abortus infection
Fu, PloS one 2012 - “...the purified fusion proteins: BAB1_0063, BAB1_0116, BAB1_0381, BAB1_0512, BAB1_0553, BAB1_0560, BAB1_0597, BAB1_0722, BAB1_0812, BAB1_0917, BAB1_1108, BAB1_1124. Proteins that induce IFN- secretions in splenocytes of S19 immunized mice To assess the T-cell immunity inducing activity of the 35 proteins, sensitized splenocytes were firstly prepared. BALB/c mice were...”
HutC / VIMSS3381234 HutC regulator of Histidine utilization, effector cis-Urocanic acid (repressor) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
A6T6K9 Histidine utilization repressor from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
44% identity, 29% coverage
NagR / VIMSS927077 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Streptococcus thermophilus CNRZ1066
46% identity, 29% coverage
SP_1446 GntR family transcriptional regulator from Streptococcus pneumoniae TIGR4
52% identity, 29% coverage
AgaR2 / VIMSS530369 AgaR2 regulator of N-acetylgalactosamine utilization, effector N-acetylgalactosamine from Lactobacillus johnsonii NCC 533
47% identity, 28% coverage
A0AKK7 Transcriptional regulator, GntR family/aminotransferase family protein from Listeria welshimeri serovar 6b (strain ATCC 35897 / DSM 20650 / CCUG 15529 / CIP 8149 / NCTC 11857 / SLCC 5334 / V8)
45% identity, 15% coverage
WP_232000148 histidine utilization repressor from Pseudomonas fluorescens
46% identity, 30% coverage
SMc02340 PUTATIVE TRANSCRIPTION REGULATOR PROTEIN from Sinorhizobium meliloti 1021
41% identity, 30% coverage
JUK32_RS24680 GntR family transcriptional regulator from Halomicronema sp. CCY15110
45% identity, 26% coverage
YPO1973 putative GntR-family transcriptional regulatory protein from Yersinia pestis CO92
46% identity, 27% coverage
- Molecular Darwinian evolution of virulence in Yersinia pestis
Zhou, Infection and immunity 2009 - Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...for trehalosemaltose transp... 1.403 (0.025) YPTB1721 YPO1849 conserved hypothetical (pseudogene. F/S) 1.366 (0.025) YPTB1967 (hutC) YPO1973 putative GntR-family transcriptional regulatory protein 0.739 (0.018) YPTB2048 (hexR) YPO2065 hex regulon repressoR 1.51 (0.013) YPTB2072 (fadR) YPO2144 fatty acid metabolism regulatory protein 1.494 (0.01) YPTB2177 (araC) YPO2258 arabinose operon...”
- Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus
Zhou, Journal of bacteriology 2004 - “...YPCD1.26c, YPCD1.31c, YPCD1.39c, YPMT1.23c, YPMT1.25c, YPMT1.43c, YPO1956, YPO1973, YPO2729, YPO2731, and YPO3049 according to the CO92 genome annotation [Table...”
- “...YPCD1.26c YPCD1.31c YPCD1.39c YPMT1.23c YPMT1.25c YPMT1.43c YPO1956 YPO1973 Annotated function 5150 NOTES J. BACTERIOL. TABLE 4. Oligonucleotide primers used in...”
YPTB1967 putative GntR-family transcriptional regulatory protein from Yersinia pseudotuberculosis IP 32953
46% identity, 27% coverage
SGO_1121 transcription regulator, GntR family from Streptococcus gordonii str. Challis substr. CH1
51% identity, 29% coverage
FXO12_16525 histidine utilization repressor from Pseudomonas sp. J380
44% identity, 30% coverage
EF1328 transcriptional regulator, GntR family from Enterococcus faecalis V583
OG1RF_11099 GntR family transcriptional regulator from Enterococcus faecalis OG1RF
49% identity, 29% coverage
- Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria
Chatterjee, PLoS genetics 2021 - “...and non-host environments. It is possible that in E . faecalis V583, the OG1RF_11099 homolog (EF1328) has been retained to regulate other genes within the regulon that are less dispensable than T7SS. Additionally, our data indicate that OG1RF_11099 transcription is not dependent on IreK or and...”
- A pathogenicity locus of Streptococcus gallolyticus subspecies gallolyticus
Taylor, Scientific reports 2023 - “...family transcriptional regulator 31 . A recent publication indicated that a GntR family transcriptional regulator (OG1RF_11099) of Enterococcus faecalis controls the expression of T7SS genes 32 . Using Global Align (NCBI), we found that SparF is highly homologous to OG1RF_11099, showing an overall 74% similarity at...”
- Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria
Chatterjee, PLoS genetics 2021 - “...Phage induction of T7SS gene expression and bystander inhibition requires IreK, a serine/threonine kinase, and OG1RF_11099, a predicted GntR-family transcription factor. Additionally, sub-lethal doses of membrane targeting and DNA damaging antibiotics activated T7SS expression independent of phage infection, triggering T7SS antibacterial activity against bystander bacteria. Our...”
- “...induction in E . faecalis occurs in response to select cell envelope stressors. IreK and OG1RF_11099 facilitate T7SS expression in phage infected E. faecalis OG1RF via a non-canonical signaling pathway Having established that both phage and daptomycin mediated membrane damage independently stimulates heightened E . faecalis...”
- Phage infection and sub-lethal antibiotic exposure mediateEnterococcus faecalistype VII secretion system dependent inhibition of bystander bacteria
Chatterjee, 2020
PFLU0359 histidine utilization repressor GntR-family from Pseudomonas fluorescens SBW25
46% identity, 28% coverage
EAMY_1256 Histidine utilization repressor from Erwinia amylovora CFBP1430
44% identity, 25% coverage
HutC / VIMSS10477260 HutC regulator of Histidine utilization, effector cis-Urocanic acid (repressor) from Erwinia amylovora ATCC 49946
44% identity, 27% coverage
SCO6974 GntR-family regulatory protein from Streptomyces coelicolor A3(2)
SLIV_04375 GntR family transcriptional regulator from Streptomyces lividans TK24
44% identity, 28% coverage
- Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
Rebets, Frontiers in microbiology 2018 - “...the function of SLIV_18945 is not known, the ortholog of SLIV_04375 in S. coelicolor ( SCO6974 ) is involved in regulation of myo-inositol catabolism ( Yu et al., 2015 ). To delete the selected genes the recombinant BAC clones were generated with the -Red recombination approach...”
- “...0.4 34 0.4 34 3.7 18945 SCO3864 GntR3 33 0.4 34 0.4 34 3.3 04375 SCO6974 GntR4 30 2.3 34 0.4 31 2.3 Effect of Sigma Factor Gene Deletions on the Secretome Streptomyces lividans is an established host for secreted protein production and many of the...”
- GntR family regulator SCO6256 is involved in antibiotic production and conditionally regulates the transcription of myo-inositol catabolic genes in Streptomyces coelicolor A3(2)
Yu, Microbiology (Reading, England) 2016 (PubMed)- “...GntR family and shows 74 % identity with SCO6974, which is the repressor of myo-inositol catabolism in Streptomyces coelicolor A3(2). Disruption of SCO6256...”
- “...same sites in the myo-inositol catabolic gene cluster as SCO6974. The expression of SCO6256 was repressed by SCO6974 in minimal medium with myo-inositol as the...”
- Regulation of myo-inositol catabolism by a GntR-type repressor SCO6974 in Streptomyces coelicolor
Yu, Applied microbiology and biotechnology 2015 (PubMed)- “...Regulation of myo-inositol catabolism by a GntR-type repressor SCO6974 in Streptomyces coelicolor Lingjun Yu & Shuxian Li & Wenyan Gao & Yuanyuan Pan &...”
- “...myo-inositol in minimal medium. A putative regulatory gene SCO6974, encoding a GntR family protein, is situated in the cluster. Disruption of SCO6974...”
- Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
Rebets, Frontiers in microbiology 2018 - “...located in close proximity to the actinorhodin biosynthesis gene cluster. Two other genes, SLIV_18945 and SLIV_04375 , are transcribed at moderate and low levels, respectively. While the function of SLIV_18945 is not known, the ortholog of SLIV_04375 in S. coelicolor ( SCO6974 ) is involved in...”
LSA1587 Putative transcriptional regulator, GntR family from Lactobacillus sakei subsp. sakei 23K
50% identity, 28% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...transcriptional regulator, TetR family 0.6 LSA1554 lsa1554 Putative transcriptional regulator, LacI family -0.7 -0.9 -0.5 LSA1587 lsa1587 Putative transcriptional regulator, GntR family 0.6 LSA1611 lsa1611 Putative DNA-binding protein, PemK family -0.5 -0.7 LSA1653 lsa1653 Putative transcriptional regulator, MarR family -0.6 LSA1692 lsa1692 Putative transcriptional regulator, GntR...”
lmo2100 similar to transcriptional regulator (GntR family) and to aminotransferase (MocR-like) from Listeria monocytogenes EGD-e
Q8Y5G3 Lmo2100 protein from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
LMRG_01251 hypothetical protein from Listeria monocytogenes 10403S
46% identity, 14% coverage
- Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Lagoon and Soil Matrices Associated with a Piggery Environment: Comparison of Expression Profiles
Vivant, Frontiers in microbiology 2017 - “...repressor Up Wurtzel et al., 2012 Lmo2099 PTS systems activators Up Wurtzel et al., 2012 Lmo2100 Vitamin B6 activator Up Belitsky, 2014 Lmo2107 Heat shock Down van der Veen et al., 2007 Lmo2138 PTS systems activators Up Wurtzel et al., 2012 Lmo2200 Hydroxyperoxide resistance regulator Down...”
- A prl mutation in SecY suppresses secretion and virulence defects of Listeria monocytogenes secA2 mutants
Durack, Journal of bacteriology 2015 - “...dehydrogenase/cyclohydrolase DNA mismatch repair protein MutS lmo1901 lmo2100 panC 2323057 2447109 G CAAAAAAA A CAAAAAAAA lmo2278 lmo2421 lysA 2468643 CTTTTTTTT...”
- Role of PdxR in the activation of vitamin B6 biosynthesis in Listeria monocytogenes
Belitsky, Molecular microbiology 2014 - “...which PdxR proteins regulate expression of their target genes, I studied a putative PdxR-like protein, Lmo2100, of Listeria monocytogenes, a Gram-positive, facultative intracellular bacterium and an important food-borne bacterial pathogen that can cause severe disease in mammals and birds ( Vazquez-Boland et al. , 2001 )....”
- “...( Belitsky and Sonenshein, 2002 ; Rigali et al., 2002 ) is encoded by the lmo2100 gene that is adjacent to and transcribed divergently from the L. monocytogenes pdxS gene (the two genes are separated by 125 bp) ( Glaser et al., 2001 ). A deletion-insertion...”
- Data from computational analysis of the peptide linkers in the MocR bacterial transcriptional regulators
Angelaccio, Data in brief 2016 - “...Anaerocellum thermophilum DSM6725 Firmicutes A4XIB4 Caldicellulosiruptor saccharolyticus DSM 8903 Firmicutes Q929S0 Listeria innocua Clip11262 Firmicutes Q8Y5G3 Listeria monocytogenes EGD e Firmicutes A0AKK7 Listeria welshimeri serovar 6b str. SLCC5334 Firmicutes C7MF20 Brachybacterium faecium DSM 4810 Actinobacteria Q6AFC0 Leifsonia xyli subsp.xyli str . CTCB07 Actinobacteria B3GXB5 Actinobacillus pleuropneumoniae...”
- Identification of Listeria monocytogenes determinants required for biofilm formation
Alonso, PloS one 2014 - “...Signal peptidase I lmrg_00721 1000.34 2 1 phoR lmrg_01748 990.02 1 1 GntR family regulator lmrg_01251 900.21 1 1 Putative rRNA methylase lmrg_01305 870.33 1 1 DNA polymerase lmrg_01402 1000.36 2 1 Putative Rrf2 family regulator lmrg_01481 700.28 1 1 ATP synthase beta subunit F1 lmrg_01719...”
- “...; D-alanylation genes lmrg_02073 ( dltA ) and lmrg_02072 ( dltB ) [15] ; and lmrg_01251 GntR family response regulator [23] . Excluding transposon insertions into two genetic loci which resulted in severe general growth defects ( lmrg_00956 ( plsX ) and lmrg_01912 catalase), novel recovered...”
GW13_PRO2606 GntR family transcriptional regulator from Salmonella enterica subsp. enterica serovar Cerro
43% identity, 30% coverage
- Regulation of DNA phosphorothioate modification in Salmonella enterica by DndB
He, Scientific reports 2015 - “...of the differentially expressed members of the proteome. Four transcriptional regulatorsMalT (GW13_PRO2528), NanR (GW13_PRO2351), TorR (GW13_PRO2606), and a GntR family regulator (GW13_PRO2829) as well as a transcription associated protein (GW13_PRO2516) and an RNA polymerase associated protein (RapA; GW13_PRO3646), were significantly up-regulated. More than half of the...”
Q929S0 Lin2204 protein from Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
44% identity, 16% coverage
MngR / b0730 DNA-binding transcriptional repressor MngR from Escherichia coli K-12 substr. MG1655 (see 4 papers)
MNGR_ECOLI / P13669 Mannosyl-D-glycerate transport/metabolism system repressor MngR; Fatty acyl-responsive regulator; Protein P30 from Escherichia coli (strain K12) (see 2 papers)
MngR / P13669 Transcription factor MngR (repressor) from Escherichia coli K12 MG1655 (see paper)
b0730 DNA-binding transcriptional dual regulator, fatty-acyl-binding from Escherichia coli str. K-12 substr. MG1655
46% identity, 27% coverage
- function: Represses mngA and mngB. Regulates its own expression.
disruption phenotype: In cells lacking this gene the expression of mngA and mngB increases by 9-fold and 23-fold, respectively. - Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein
Chauhan, Microbiology spectrum 2023 - “...Rv0494, Rv0586, Rv1152, Rv0792c, and Rv3060c), Burkholderia sp. (EEA00313), Pseudomonas putida (P22773), Escherichia coli (P0A8V8, P13669), Bacillus subtilis (O34817), Streptomyces coelicolor (Q9K492), Salmonella enterica (AAB39463), Corynebacterium glutamicum (BAC00309), Thermotoga maritima (NP_228249), Streptococcus pyogenes (AMY97465), Vibrio cholerae (SYZ81202), Pseudomonas syringae (WP_044310692), Brucella sp. (WP_006173453), and Klebsiella pneumoniae...”
- Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
Mariño-Ramírez, Journal of bacteriology 2004 - “...b3075 b0543 b0596 b2927 b2439 b2457 b2459 b3963 b0180 b0730 b1385 b0587 b1940 b1946 b2303 b0080 b0825 b2800 b1493 b2151 b3126 b3125 b2808 b1761 b2977 b3945...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...ytfA gadB b2880 b2879 b3108 b2635 b1445 b2274 b2450 b0730 b1310 b2552 b2125 b0695 b2473 b0037 b3563 b4183 b4184 b2460 b2279 b3120 b3596 b2666 b0359 b1416 b1004...”
NagR / VIMSS3591890 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Streptococcus suis 05ZYH33
SSU0817 GntR family regulatory protein from Streptococcus suis P1/7
48% identity, 28% coverage
NagQ / VIMSS515716 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Chromobacterium violaceum ATCC 12472
42% identity, 27% coverage
SMa2215 putative GntR-family transcriptional regulator from Sinorhizobium meliloti 1021
46% identity, 25% coverage
- Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis
Taboada-Castro, Frontiers in bioinformatics 2024 - “...Table 5 c), and the five most regulated genes were SM_b20129, SM_b21080, SMc04134, SMc02172, and SMa2215 genes, with gradually diminishing times in the range of 23 to 19 ( Supplementary Table 5 d). Meanwhile, in the bacteroid S. meliloti 1021 network, based on the node root...”
- “...15 times ( Supplementary Table 6 c). Moreover, the five most regulated genes were SMc02172, SMa2215, SMa0830, the nitrogenase nifE gene for the synthesis of the molybdenum cofactor of the nitrogenase enzymatic complex, SMa1505, and SMc04348, which are regulated in the range of 16 to 12...”
STM3785 putative regulatory protein, gntR family from Salmonella typhimurium LT2
41% identity, 30% coverage
- CTAG-containing cleavage site profiling to delineate Salmonella into natural clusters
Tang, PloS one 2014 - “...3855779 3795761 XbaI 20 STM3714STM3715 3910705 3910806 3910806 3924498 3933683 3932120 3932121 3872105 XbaI 21 STM3785 3984439 3985182 3984523 3998215 4007398 4005836 4005837 3945822 XbaI 22 STM3846STM3847 4053276 4054076 4053903 4067596 4076779 4075214 4075215 4015203 XbaI 23 STM3890 4101759 4101831 4101769 4115462 4124645 4123076 4123077 4063068...”
NSP_RS03415 phosphonate metabolism transcriptional regulator PhnF from Nodularia spumigena CCY9414
49% identity, 27% coverage
S0580 transcriptional regulator of succinyl CoA synthetase operon from Shigella flexneri 2a str. 2457T
46% identity, 21% coverage
SLUG_00760 GntR family transcriptional regulator from Staphylococcus lugdunensis N920143
44% identity, 30% coverage
Z4874 putative regulator from Escherichia coli O157:H7 EDL933
40% identity, 29% coverage
STM3602 putative regulatory protein, gntR family from Salmonella typhimurium LT2
A0A0F6B872 Putative regulatory protein from Salmonella typhimurium (strain 14028s / SGSC 2262)
STM14_4332 GntR family transcriptional regulator from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
43% identity, 30% coverage
- Application of Genomic Selection in Beef Cattle Disease Prevention
Kasimanickam, Animals : an open access journal from MDPI 2025 - “...influence the persistence of E. coli O157 in cattle at high concentrations [ 130 ]. STM3602 and STM3846 genes represent an exciting new class of virulence determinants directly linking these genes to colonization of Salmonella in the small intestines of cattle [ 131 ]. CRISPR-mediated homology-directed...”
- A Salmonella Regulator Modulates Intestinal Colonization and Use of Phosphonoacetic Acid
Elfenbein, Frontiers in cellular and infection microbiology 2017 - “...cycle. The role of phosphonates during enteric salmonellosis is unexplored. We have previously shown that STM3602 , encoding a putative regulator of phosphonate metabolism, is needed for colonization in calves. Here, we report that the necessity of STM3602 in colonization of the murine intestine results from...”
- “...full activation of the type-3 secretion system-1 and for optimal invasion of epithelial cells. The STM3602 mutant grows poorly in phosphonoacetic acid (PA) as the sole phosphorus source, but can use 2-aminoethylphosphonate. PhnA, an enzyme required for PA breakdown, is not controlled by STM3602 suggesting an...”
- Novel determinants of intestinal colonization of Salmonella enterica serotype typhimurium identified in bovine enteric infection
Elfenbein, Infection and immunity 2013 - “...ligated ileal loops. Two of these mutants, STM3602 and STM3846, recapitulated the phenotype observed in the mutant pool. Complementation experiments...”
- “...colonization defects of the corresponding mutant strains. STM3602 encodes a putative transcriptional regulator that may be involved in phosphonate utilization,...”
- Analysis of Tagged Proteins Using Tandem Affinity-Buffer Exchange Chromatography Online with Native Mass Spectrometry
Busch, Biochemistry 2021 - “...Salmonella YidA (UniProt ID: A0A0F6B8Z9), Salmonella FrlB (UniProt ID: A0A0F6BB82), and Salmonella FraR (UniProt ID: A0A0F6B872). References [1] Tabor S , and Richardson CC ( 1985 ) A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes , Proc. Natl. Acad. Sci. U.S.A...”
- Use of Attenuated but Metabolically Competent Salmonella as a Probiotic To Prevent or Treat Salmonella Infection
Sabag-Daigle, Infection and immunity 2016 - “...Red mutagenic forward primer for STM14_4332 with P1 priming site ACGCCCCTGGTTAATACTCTATTAACCTCATTCTTCGGGCGTGTAGGCTGGAGCTGCTTC Lambda Red mutagenic forward...”
- Fructose-asparagine is a primary nutrient during growth of Salmonella in the inflamed intestine
Ali, PLoS pathogens 2014 - “...gor and treF genes at 77.7 centisomes of the Salmonella 14028 genome (ORFs STM14_4328 to STM14_4332). We have named these genes fraBDAE and fraR for reasons to be described below. A fraB1 ::kan mutation was constructed and tested for fitness in germ-free and Enterobacter colonized mice...”
ABUW_0075 histidine utilization repressor from Acinetobacter baumannii
41% identity, 30% coverage
NP_391136 FrlR transcriptional regulator (GntR family) from Bacillus subtilis subsp. subtilis str. 168
42% identity, 30% coverage
CD630_10090, CDIF630erm_01145 GntR family transcriptional regulator from Clostridioides difficile
42% identity, 30% coverage
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...0.30 CD630_35150 CDIF630erm_03829 glmU Bifunctional N -acetylglucosamine-1- phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 1.51 -0.27 2.04 0.40 + CD630_10090 CDIF630erm_01145 GntR family transcriptional regulator -3.62 -2.36 CD630_10100 CDIF630erm_01146 nagA N -acetylglucosamine-6-phosphate deacetylase -2.69 -2.60 -2.02 -0.22 CD630_10110 CDIF630erm_01147 nagB Glucosamine-6-phosphate deaminase -2.74 1.69 -1.74 0.19 Energy metabolism CD630_32370 CDIF630erm_03533...”
- “...CD630_35150 CDIF630erm_03829 glmU Bifunctional N -acetylglucosamine-1- phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 1.51 -0.27 2.04 0.40 + CD630_10090 CDIF630erm_01145 GntR family transcriptional regulator -3.62 -2.36 CD630_10100 CDIF630erm_01146 nagA N -acetylglucosamine-6-phosphate deacetylase -2.69 -2.60 -2.02 -0.22 CD630_10110 CDIF630erm_01147 nagB Glucosamine-6-phosphate deaminase -2.74 1.69 -1.74 0.19 Energy metabolism CD630_32370 CDIF630erm_03533 prdF...”
FrlR / VIMSS39795 FrlR regulator of Fructoselysine utilization, effector Fructoselysine 6-phosphate (repressor) from Bacillus subtilis subsp. subtilis str. 168
42% identity, 27% coverage
PAM18_5219 histidine utilization repressor from Pseudomonas aeruginosa M18
Q9HU78 Histidine utilization repressor from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA5105 histidine utilization repressor HutC from Pseudomonas aeruginosa PAO1
41% identity, 28% coverage
- Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18
Wu, BMC genomics 2011 - “...PAM18_0945, PAM18_0966, PAM18_1156, PAM18_1507, PAM18_2031, PAM18_2078, PAM18_2114, PAM18_2280, PAM18_2571, PAM18_2608, PAM18_3035, PAM18_3129, PAM18_3270, PAM18_3440, PAM18_4328, PAM18_5219, PAM18_5273 2.0-3.9 Cells were grown to OD 600 = 5.0-6.0 (late exponential phase) in LB medium at 28C and 37C, respectively. The effects on gene expression were monitored by microarray...”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...4533 Q9I3E7 206 P49988 1288 Q9HU76 2370 Q9HT93 3452 Q9HYS5 4534 Q9I3E8 207 P50597 1289 Q9HU78 2371 Q9HT94 3453 Q9HYS6 4535 Q9I3E9 208 P53593 1290 Q9HU86 2372 Q9HT96 3454 Q9HYS7 4536 Q9I3F0 209 P53652 1291 Q9HU88 2373 Q9HT98 3455 Q9HYS8 4537 Q9I3F2 210 P57112 1292 Q9HU99...”
- Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
Amemiya, Transcription 2021 (secret) - Pseudomonas aeruginosa mutants defective in glucose uptake have pleiotropic phenotype and altered virulence in non-mammal infection models
Raneri, Scientific reports 2018 - “...adenylyltransferase PA4920 nadE 1.5 0.5 0.8 NAD synthetase PA5100 hutU 0.8 0.0 0.0 urocanate hydratase PA5105 hutC 0.8 0.2 0.1 Transcriptional regulator HutC Genes for glucose IM transporters deleted in this work PA2262 kguT 1.3 0.3 0.4 2-ketogluconate transporter PA2322 gntP 35.5 0.0 0.6 gluconate permease...”
- 1,2,4-Triazolidine-3-thiones Have Specific Activity against Acinetobacter baumannii among Common Nosocomial Pathogens
Corey, ACS infectious diseases 2017 - “...Murray/BAMC Pseudomonas aeruginosa PA4761 MRSN Pseudomonas aeruginosa PA4910 MRSN Pseudomonas aeruginosa PA4962 MRSN Pseudomonas aeruginosa PA5105 MRSN Pseudomonas aeruginosa PA5151 MRSN Pseudomonas aeruginosa PA105738 Clinton Murray/BAMC Pseudomonas aeruginosa PA105777 Clinton Murray/BAMC Pseudomonas aeruginosa PA105819 Clinton Murray/BAMC Pseudomonas aeruginosa PA105857 Clinton Murray/BAMC Pseudomonas aeruginosa PA105880 Clinton Murray/BAMC...”
- The regulatory repertoire of Pseudomonas aeruginosa AmpC ß-lactamase regulator AmpR includes virulence genes
Balasubramanian, PloS one 2012 - “...9.10E-03 2.8 PA4853 fis DNA-binding protein Fis 6.65E-03 3.3 PA5059 probable transcriptional regulator 6.33E-03 4.0 PA5105 hutC histidine utilization repressor HutC 8.27E-03 3.1 PA5380 gbdR GbdR 5.75E-03 2.6 PA5483 algB two-component response regulator AlgB 7.83E-03 2.4 Sigma factors Locus Tag Gene Name Product Name Corrected p...”
- Swarming of Pseudomonas aeruginosa is controlled by a broad spectrum of transcriptional regulators, including MetR
Yeung, Journal of bacteriology 2009 - “...(mvaT) PA4398b PA4725 (cbrA)b PA4778b PA4853 (fis)b PA5105 (hutC)b PA5124 (ntrB)b PA5125 (ntrC)b PA5261 (algR) PA5536b Change (fold) compared to wild-type...”
- Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25
Zhang, Genetics 2007 - “...available PP5036 (82) PA5106 (76) (38) (97) (86) (80) PA5105 (84) PA5104 (54) HutU (91) PA5099 (79) PA5096 (77) PA5095 (90) PA5094 (87) PA5093 (76) HutH (81)...”
NagQ / VIMSS871718 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Pseudomonas fluorescens Pf-5
40% identity, 30% coverage
c4276 Putative regulator from Escherichia coli CFT073
40% identity, 29% coverage
XCC3414 transcriptional regulator gntR family from Xanthomonas campestris pv. campestris str. ATCC 33913
40% identity, 29% coverage
alr2226 transcriptional regulator from Nostoc sp. PCC 7120
48% identity, 27% coverage
PP5035 histidine utilization repressor from Pseudomonas putida KT2440
43% identity, 28% coverage
LBPC_0276 GntR family transcriptional regulator from Lacticaseibacillus paracasei subsp. paracasei
48% identity, 28% coverage
- Genomic adaptation of the Lactobacillus casei group
Toh, PloS one 2013 - “...LBCZ_0065 LBCZ_0076 12.6 transposase, conserved hypothetical protein LRHM_0086 LRHM_0096 10.5 carbohydrate utilization gene cluster (region-1) LBPC_0276 LBPC_0297 23.8 carbohydrate utilization gene cluster LBCZ_0159 LBCZ_0174 15.7 myo-inositol catabolism protein LRHM_0149 LRHM_0156 6.1 carbohydrate transporter, two-componentsystem LBPC_0331 LBPC_0359 30.6 PTS transporter, amino acid ABC transporter LBCZ_0223 LBCZ_0252 33.8...”
NagR / VIMSS78245 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Lactococcus lactis subsp. lactis Il1403
L0151 GntR family transcriptional regulator from Lactococcus lactis subsp. lactis Il1403
46% identity, 29% coverage
- Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Dijkstra, PloS one 2016 - “...0.8 L102317 hslA HU like DNA-binding protein negative 11.1 L0285 dnaD hypothetical protein positive 2.7 L0151 rgrB GntR family transcription regulator negative 4.1 L188392 ybiH hypothetical protein positive 0.2 L192589 pydA dihydroorotate dehydrogenase 1A negative 4.8 L19745 bar acyltransferase negative 2.4 L117821 yxdC cation-transporting ATPase negative...”
NagQ / VIMSS256610 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Xanthomonas axonopodis
40% identity, 29% coverage
AgaR2 / VIMSS1795424 AgaR2 regulator of N-acetylgalactosamine utilization, effector N-acetylgalactosamine from Pediococcus pentosaceus ATCC 25745
48% identity, 27% coverage
BAB2_0725 Bacterial regulatory protein, GntR family:Bacterial regulatory protein, DeoR family from Brucella melitensis biovar Abortus 2308
48% identity, 25% coverage
NagQ / VIMSS181612 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Brucella melitensis 16M
48% identity, 25% coverage
HutC / VIMSS3620076 HutC regulator of Histidine utilization, effector cis-Urocanic acid (repressor) from Serratia proteamaculans 568
42% identity, 27% coverage
EQB38_RS16630 GntR family transcriptional regulator from Enterococcus faecium
40% identity, 31% coverage
- Colonization of vancomycin-resistant Enterococcus faecium in human-derived colonic epithelium: unraveling the transcriptional dynamics of host-enterococcal interactions
Stege, FEMS microbes 2024 - “...and EQB38_RS16240, putatively encode an ABC transporter system. A final cluster of seven upregulated genes (EQB38_RS16630, EQB38_RS16695, EQB38_RS16700, EQB38_RS16705, EQB38_RS16710, EQB38_RS16715, EQB38_RS16720) were predicted to encode a PTS system and regulatory genes). In addition, 13 genes, not contained in larger gene clusters, were significantly upregulated (...”
- “...proteins and 2974 (EQB38_RS16695), tentatively encoding a sigma 54-interacting transcriptional regulator and possibly locus 2964 (EQB38_RS16630) encoding a putative GntR family transcriptional regulator (Yamamoto et al. 2001 , Deutscher et al. 2006 ). KEGG pathways analysis also revealed changes in expression of several E. faecium genes...”
SEN2647 putative transcriptional regulator from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
49% identity, 15% coverage
ECA1849 GntR-family transcriptional regulator from Erwinia carotovora subsp. atroseptica SCRI1043
47% identity, 26% coverage
ECA1849 GntR family transcriptional regulator from Pectobacterium atrosepticum SCRI1043
47% identity, 27% coverage
GmuR / VIMSS66498 GmuR regulator of Glucomannan utilization (repressor) from Bacillus halodurans C-125
46% identity, 24% coverage
OG1RF_11857 PLP-dependent aminotransferase family protein from Enterococcus faecalis OG1RF
42% identity, 15% coverage
MUL_0525 transcriptional regulatory protein from Mycobacterium ulcerans Agy99
47% identity, 27% coverage
AgaR2 / VIMSS7617614 AgaR2 regulator of N-acetylgalactosamine utilization, effector N-acetylgalactosamine from Lactobacillus rhamnosus GG
LRHM_0319 GntR family transcriptional regulator from Lacticaseibacillus rhamnosus GG
48% identity, 28% coverage
- Genomic adaptation of the Lactobacillus casei group
Toh, PloS one 2013 - “...myo-inositol catabolism protein LBPC_0579 LBPC_0584 6.7 PTS transporter, 6-phospho-beta-galactosidase LBCZ_0338 LBCZ_0388 41.1 prophage region I LRHM_0319 LRHM_0350 34.6 carbohydrate utilization gene cluster (region-2) LBPC_0636 LBPC_0648 12.1 prophage region I LBCZ_0605 LBCZ_0617 11.9 hypothetical protein LRHM_0376 LRHM_0466 97.8 carbohydrate utilization gene cluster (region-3), amino acid ABC transporter,...”
EF2426 transcriptional regulator, GntR family from Enterococcus faecalis V583
42% identity, 15% coverage
YPTB2183 putative transcriptional regulator from Yersinia pseudotuberculosis IP 32953
42% identity, 27% coverage
P22773 Histidine utilization repressor from Pseudomonas putida
41% identity, 28% coverage
- Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein
Chauhan, Microbiology spectrum 2023 - “...M. tuberculosis (Rv0043c, Rv0165c, Rv0494, Rv0586, Rv1152, Rv0792c, and Rv3060c), Burkholderia sp. (EEA00313), Pseudomonas putida (P22773), Escherichia coli (P0A8V8, P13669), Bacillus subtilis (O34817), Streptomyces coelicolor (Q9K492), Salmonella enterica (AAB39463), Corynebacterium glutamicum (BAC00309), Thermotoga maritima (NP_228249), Streptococcus pyogenes (AMY97465), Vibrio cholerae (SYZ81202), Pseudomonas syringae (WP_044310692), Brucella sp....”
- Expanding the Cyanobacterial Nitrogen Regulatory Network: The GntR-Like Regulator PlmA Interacts with the PII-PipX Complex.
Labella, Frontiers in microbiology 2016 - “...), PlmA (accession ABB56122 ), AraR (accession P96711 ), FadR (accession P0A8V6 ), HutC (accession P22773 ), and YtrA (accession O34712 ). The neighbor-joining phylogenetic tree for PlmA orthologs (234 sequences from bidirectional blast search) was constructed using the web tool ClustalW (Sievers et al., 2011...”
- GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
Vindal, BMC genomics 2007 - “...leguminosarum MatR 222 Q9JP74 MocR Rhizobium meliloti MocR 493 P49309 HutC Pseudomonas putida HutC 248 P22773 YtrA Bacillus halodurans BH0651 123 Q9KF35 Bacillus halodurans BH2647 123 Q9K9J9 Staphylococcus aureus SAV1934 126 Q99SV4 Bacillus subtilis YhcF 121 P54590 Bacillus subtilis YtrA 130 O34712 AraR Bacillus subtilis P96711...”
- DevA, a GntR-like transcriptional regulator required for development in Streptomyces coelicolor
Hoskisson, Journal of bacteriology 2006 - “...Streptomyces lividans Bacillus subtilis 248 252 243 P22773 Q9ACN8 O34817 HutC SAV4023 SAV4021 SCO4188 DevA Unknown Unknown Unknown Developmental regulator...”
- Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding
Franco, Journal of bacteriology 2006 - “...P. pu, histidine utilization repressor of Pseudomonas putida (P22773); GntR, B. su gluconate utilization repressor of B. subtilis (P10585); FadR E. co,...”
- PlmA, a new member of the GntR family, has plasmid maintenance functions in Anabaena sp. strain PCC 7120
Lee, Journal of bacteriology 2003 - “...367 329 323 327 440 328 P09371 P22773 P49309 O34712 P96711 Q8YXY0 P73804 BAC09669 ZP_00112619 ZP_00105573 ZP_00074937 ZP_00114559 ZP_00107916 Downloaded from...”
- ATP-binding cassette transport system involved in regulation of morphological differentiation in response to glucose in Streptomyces griseus
Seo, Journal of bacteriology 2002 - “...database accession number AAG31030), HutC from P. putida (P22773), and FarR from E. coli (S04645) are shown. Asterisks indicate similar amino acids that are...”
YPK_1988 GntR family transcriptional regulator from Yersinia pseudotuberculosis YPIII
42% identity, 30% coverage
- Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud, mSystems 2020 - “...32,70,54,38,28 YPK_1853 NA 44, 44, 22, 135 IrGS17 2211354 7.4 3.4 4.5 TTGGTACATTTATTGCGC 10.4 24,54,38 YPK_1988 NA 49, 123 IrGS18 2408285 4.5 NA 3.6 CTGGCACGTCTGATGCAA + 9.98 32,54 YPK_2169 YPK_2170, YPK_2171 19 IrGS19 2536664 7.6 4.1 5.5 TTGGCATGGTAATTGAAT 10.7 24,54,28,32 YPK_2282 YPK_2281 44, 7, 8 IrGS20...”
GMUR_BACSU / O05509 HTH-type transcriptional regulator GmuR; Glucomannan utilization operon repressor; Glucomannan utilization protein R from Bacillus subtilis (strain 168) (see paper)
GmuR / VIMSS37118 GmuR regulator of Glucomannan utilization (repressor) from Bacillus subtilis subsp. subtilis str. 168
46% identity, 27% coverage
- function: Transcriptional repressor of the gmuBACDREFG operon which is involved in the uptake and degradation of glucomannan.
HutC / VIMSS550691 HutC regulator of Histidine utilization, effector cis-Urocanic acid (repressor) from Photorhabdus luminescens TTO1
43% identity, 28% coverage
EF1809 transcriptional regulator, GntR family from Enterococcus faecalis V583
47% identity, 27% coverage
- Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections
Zhang, MicrobiologyOpen 2015 - “...AgaR1specific DNA probes used here included SSU05_0448/9 site1 probe (38bp), EF814 site1 probe (38bp), and EF1809 site1 probe (38bp). In addition to SSU05_0447 probe (36bp) as the negative control, the other four tested AgaR2recognizable sites corresponded to SSU05_0195 probe (36bp), SSU05_1259 probe (36bp), 5 SSU05_0448/9 site2...”
- “...AgaR2 protein to evaluate the function of the two AgaRbinding sites in front of the EF1809 locus of E. faecalis V583, a close relative of S. suis . As a result, AgaR2 physically interacted with the EF1809 site 2, TTGTGGTTATAACCAGTT (Fig. 5 H), but not the...”
- Role of a GntR-family response regulator LbrA in Listeria monocytogenes biofilm formation
Wassinger, PloS one 2013 - “...as a positive involvement of a GntR family regulator gene in biofilm formation in Enterococcus EF1809 ( e nterococcal b iofilm r egulator ebrA ) was recently reported [26] . The lbrA gene is well-conserved in L. monocytogenes genomes. In F2365, it is followed by coding...”
- Use of recombinase-based in vivo expression technology to characterize Enterococcus faecalis gene expression during infection identifies in vivo-expressed antisense RNAs and implicates the protease Eep in pathogenesis
Frank, Infection and immunity 2012 - “...deletion of locus EF0038 Markerless in-frame deletion of locus EF1809 21 This study 4; K. S. Ballering and G. M. Dunny, unpublished data 29 This study OG1RF...”
- “...2--proB (EF0038), encoding glutamate 5-kinase; ebrA (EF1809), encoding a transcriptional regulator; and eep (EF2380), encoding a membrane metalloprotease--in...”
- Functional genomics of Enterococcus faecalis: multiple novel genetic determinants for biofilm formation in the core genome
Ballering, Journal of bacteriology 2009 - “...candidate genes. Of particular interest was genetic locus EF1809, predicted to encode a regulatory protein of the GntR family. We isolated 14 independent...”
- “...promoter region for this gene in the RIVET screen; EF1809 also showed the largest increase in expression during biofilm growth of any of the genes tested. Since...”
Dred_2751 UbiC transcription regulator-associated domain protein from Desulfotomaculum reducens MI-1
40% identity, 31% coverage
lmo1974 similar to transcription regulators, (GntR family) from Listeria monocytogenes EGD-e
42% identity, 30% coverage
- ClpP2 proteasomes and SpxA1 determine Listeria monocytogenes tartrolon B hyper-resistance
Engelgeh, PLoS genetics 2025 - “...cobalt-zinc-cadmium resistance protein 2.57 7.8x10 -3 no lmo1495 conserved hypothetical protein 2.35 3.5x10 -2 no lmo1974 putative transcriptional regulator, GntR family 2.05 1.5x10 -2 no lmo2229 pbpA2 penicillin binding protein A2 2.61 2.3x10 -2 no 1 fold change = n = 1 3 n u m...”
- The Combined Effect of Cold and Copper Stresses on the Proliferation and Transcriptional Response of Listeria monocytogenes
Quesille-Villalobos, Frontiers in microbiology 2019 - “...level among L. monocytogenes strains. Moreover, signals for other four genes were not detected (lmo0236, lmo1974, lmo1997 and lmo2175) in these two strains. Genomic information recently obtained demonstrated that those genes are not present in APA13-2 or Al152-2A strains (data not shown). FIGURE 3 Fold changes...”
- Pyruvate carboxylase plays a crucial role in carbon metabolism of extra- and intracellularly replicating Listeria monocytogenes
Schär, Journal of bacteriology 2010 - “...(panB) lmo1903 lmo1954 (drm) lmo1955b lmo1970 lmo1972 lmo1974 lmo1999b lmo2007 lmo2084d Similar to transcriptional regulatory proteins, AraC family Similar to...”
- Development of a mariner-based transposon and identification of Listeria monocytogenes determinants, including the peptidyl-prolyl isomerase PrsA2, that contribute to its hemolytic phenotype
Zemansky, Journal of bacteriology 2009 - “...lmo1814 lmo1821 lmo1829 lmo1878 lmo1922 lmo1952, lmo1954 lmo1974 lmo2055 lmo2072, lmo2103, lmo2110 lmo2203 lmo2217 lmo2219 lmo2230 lmo2361 lmo2376 lmo2460...”
- Genomic and proteomic analysis of the Alkali-Tolerance Response (AlTR) in Listeria monocytogenes 10403S
Giotis, BMC microbiology 2008 - “...NA 4.22 0.002 Similar to alkali phosphatase lmo0820 NA 4.7 0.000 Some similarity to acatyltransferases lmo1974 NA 5.12 0.001 Similar to transcription regulators, (GntR family) LMOh7858_0838 NA 3.24 0.104 PTS PTS system, mannose/fructose/sorbose family, IIA component subfamily lmo2632 rplC -3.44 0.003 Ribosomal proteins : synthesis and...”
- Identification of Listeria monocytogenes genes contributing to intracellular replication by expression profiling and mutant screening
Joseph, Journal of bacteriology 2006 - “...a species-specific region spanning from lmo1968 to lmo1974 (lmo1968-1974) were performed in parental strains Sv1/2a, EGD, and EGD-e, respectively, as described...”
- “...second, 861-bp fragment, which is localized upstream of lmo1974, was amplified with oligonucleotides CAH3 and CAH4 from chromosomal DNA derived from strain...”
- Intracellular gene expression profile of Listeria monocytogenes
Chatterjee, Infection and immunity 2006 - “...lmo1786 lmo1876 lmo1877 lmo1968 lmo1969 lmo1970 lmo1971 lmo1973 lmo1974 lmo2085 lmo2157 lmo2226 lmo2257 lmo2270 lmo2672 lmo2773 lmo2826 7.20 2.32 2.35 4.55 4.33...”
- “...2.59 2.10 lmo1876 lmo1877 lmo1968 lmo1969 lmo1970 lmo1971 lmo1973 lmo1974 lmo2269 lmo2270 2.32 2.35 4.55 4.33 3.55 3.12 6.16 10.53 7.48 5.15 IC gene (8 h) FC...”
- New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays
Doumith, Infection and immunity 2004 - “...0 0 0 0 0 0 0 0 0 0 0 Lmo1973 27 12 0 0 0 0 Lmo1974 bvrC bvrB 27 27 27 12 12 12 0 0 0 0 0 0 0 0 0 0 2 2 Lmo0151 Lmo0466 Lmo0467 Lmo0469 Lmo0470 3 2 2 2 2 12 12...”
- More
PA14_15830 putative transcriptional regulator, GntR family from Pseudomonas aeruginosa UCBPP-PA14
39% identity, 29% coverage
LGG_02757, LGG_RS13185, LRHM_2651 GntR family transcriptional regulator from Lacticaseibacillus rhamnosus GG
LGG_02757 GntR family regulatory protein from Lactobacillus rhamnosus GG
41% identity, 30% coverage
- Characterization of Highly Mucus-Adherent Non-GMO Derivatives of Lacticaseibacillus rhamnosus GG
Rasinkangas, Frontiers in bioengineering and biotechnology 2020 - “...genes potentially affecting pilin production, like the gluconate operon repressor family regulator farR ( LGG_RS13185, LGG_02757 ), transporters, surface and membrane proteins. Especially the large amount metal and cation transporters affected by SNPs stand out: LGG_RS11535 ( LGG_02411, mntH ), LGG_RS11610 ( LGG_02426, psaA ), LGG_RS12705...”
- “...be the farR transcriptional regulator belonging to the gluconate operon repressor (GntR) family ( LGG_RS13185, LGG_02757 ). A member of this family, YtrA, has been shown to regulate expression of type III protein secretion system and control several biological processes, such as adhesion and extracellular enzyme...”
- “...in genes potentially affecting pilin production, like the gluconate operon repressor family regulator farR ( LGG_RS13185, LGG_02757 ), transporters, surface and membrane proteins. Especially the large amount metal and cation transporters affected by SNPs stand out: LGG_RS11535 ( LGG_02411, mntH ), LGG_RS11610 ( LGG_02426, psaA ),...”
- “...could be the farR transcriptional regulator belonging to the gluconate operon repressor (GntR) family ( LGG_RS13185, LGG_02757 ). A member of this family, YtrA, has been shown to regulate expression of type III protein secretion system and control several biological processes, such as adhesion and extracellular...”
- Genomic adaptation of the Lactobacillus casei group
Toh, PloS one 2013 - “...transposase LRHM_2545 LRHM_2597 57.7 carbohydrate utilization gene cluster (region-5) LBCZ_2698 LBCZ_2704 7.6 PTS transporter LRHM_2635 LRHM_2651 15.4 carbohydrate utilization gene cluster (region-6) LRHM_2779 LRHM_2793 12.5 prophage region III Similarly, compared with L. paracasei ATCC 334, 15 and 24 GIs were found in L. paracasei JCM 8130...”
Q9HXN8 Probable transcriptional regulator from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA3757 probable transcriptional regulator from Pseudomonas aeruginosa PAO1
39% identity, 29% coverage
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...4307 Q9I2G6 1062 G3XCZ2 2144 Q9I6H4 3226 Q9HXN6 4308 Q9I2G7 1063 G3XCZ5 2145 Q9I6H5 3227 Q9HXN8 4309 Q9I2G8 1064 G3XCZ6 2146 Q9I6I6 3228 Q9HXP1 4310 Q9I2G9 1065 G3XD00 2147 Q9I6I7 3229 Q9HXP2 4311 Q9I2H0 1066 G3XD05 2148 Q9I6I8 3230 Q9HXP4 4312 Q9I2H1 1067 G3XD11 2149 Q9I6J4...”
- Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations
Ruparel, Drug target insights 2023 - “...50 PA5431 GntR family transcriptional regulator 2.67 1.41E-08 51 PA0941 Hypothetical protein 2.66 0.01 52 PA3757 GntR family transcriptional regulator 2.64 0.01 53 PA2679 Hypothetical protein 2.61 0 54 PA1343 Bacteriophage protein 2.59 1.03E-08 55 mraY Phospho-N-acetylmuramoyl-pentapeptide-transferase 2.59 1.92E-10 56 PA0622 Bacteriophage protein 2.59 3.12E-11 57...”
- Pseudomonas aeruginosa Initiates a Rapid and Specific Transcriptional Response during Surface Attachment
Jones, Journal of bacteriology 2022 - “...PA2788 Chemotaxis transducer 2.549 PA3120 leuD Isopropylmalate dehydratase 2.180 PA3477 rhlR Transcriptional regulator 2.411 2.224 PA3757 nagR Transcriptional regulator 3.294 PA3895 Transcriptional regulator 2.065 PA3916 moaE Molybdopterin-converting factor 0.217 PA4296 pprB Two-component response regulator 2.538 2.442 4.038 PA4309 pctA Chemotactic transducer 2.273 2.273 PA4499 psdR Transcriptional...”
- The Small RNAs PA2952.1 and PrrH as Regulators of Virulence, Motility, and Iron Metabolism in Pseudomonas aeruginosa
Coleman, Applied and environmental microbiology 2021 (secret) - Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells
Coleman, Antimicrobial agents and chemotherapy 2020 (secret) - Transcriptome profiling reveals links between ParS/ParR, MexEF-OprN, and quorum sensing in the regulation of adaptation and virulence in Pseudomonas aeruginosa
Wang, BMC genomics 2013 - “...Rhamnosyltransferase chain B PA3479 rhlA 4.37 3.31 Rhamnosyltransferase chain A PA3724 lasB 4.29 3.32 Elastase PA3757 nagR 1.75 3.48 Transcriptional regulator PA3974 ladS 1.52 1.40 Sensor protein PA4133 4.07 4.47 Cytochrome C oxidase subunit PA4209 phzM 4.22 1.94 Phenazine-specific methyltransferase PA4211 phzB1 5.72 8.13 Phenazine biosynthesis...”
- Pseudomonas aeruginosa enhances production of an antimicrobial in response to N-acetylglucosamine and peptidoglycan
Korgaonkar, Journal of bacteriology 2011 - “...Category or classa Fold upregulationb GlcNAc catabolism PA3757 PA3758 PA3759 PA3760 PA3761 nagR nagA glmS nagF nagE Probable transcriptional regulator...”
- “...4). The first gene in the nag operon, PA14_15830 (PA3757 in strain PAO1), encodes a protein with 77% identity (E value, 1078 using BLASTp) to the Collimonas...”
- A eukaryotic-type signalling system of Pseudomonas aeruginosa contributes to oxidative stress resistance, intracellular survival and virulence
Goldová, BMC genomics 2011 - “...molecules) 8.3 5.2 9.3 5.3 PA3309 3.88 0.010 CHP 7.7 7.3 5.7 7.2 Other genes PA3757 -5.59 0.005 Pr. transcriptional regulator (Transcriptional regulators) 3.4 3.4 5.9 2.8 PA2414 2.70 0.039 L-sorbosone dehydrogenase (Carbon compound catabolism) 6.2 5.2 4.8 4.5 PA2416 ( treA ) 3.31 0.025 periplasmic...”
- “...osmotically inducible enzyme necessary for the catabolism of trehalose [ 74 ]. In addition, gene PA3757 coding for probable trehalose operon repressor was significantly downregulated in the mutant strain (5.59-fold) which could result in observed increased expression of other trehalose metabolism-related genes. Therefore, it is possible...”
- Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
Palmer, Journal of bacteriology 2005 - “...PA3284 PA3407 PA3444 PA3526 PA3598 PA3600 PA3601 PA3662 PA3749 PA3757 PA3758 PA3759 PA3789 PA3790 PA3922 PA3936 PA3938 PA4063 PA4064 Genea 5272 PALMER ET AL. J....”
LMRG_01121 hypothetical protein from Listeria monocytogenes 10403S
42% identity, 30% coverage
TDE2650 transcriptional regulator, putative from Treponema denticola ATCC 35405
37% identity, 60% coverage
- Localization and pathogenic role of the cysteine protease dentipain in Treponema denticola
Miyai-Murai, Molecular oral microbiology 2023 - “...isolated from the cells in the mid-log phase. The expression of TDE0191, TDE1948, TDE2204, and TDE2650 was evaluated using qRT-PCR. Expression levels of each gene were normalized using 16S rRNA level as the internal control; they are expressed as fold modulation relative to that of the...”
- “...TDE0043 The tetratricopeptide repeat (TPR) domain protein 27.49 TDE0190 drug/metabolite transporter (DMT) family transporter 7.00 TDE2650 transcriptional regulator 5.68 TDE0189 4-toluene sulfonate uptake permease (TSUP) family transporter 4.81 TDE0684 pseudo 3.61 TDE1484 hypothetical protein 3.54 TDE2204 Na + /H + antiporter 3.27 TDE0500 hypothetical protein 3.27...”
- Transcriptional profiles of Treponema denticola in response to environmental conditions
McHardy, PloS one 2010 - “...factor 2.1 TDE2324 DNA-binding response regulator 1.8 TDE2420 DNA-directed RNA polymerase, beta subunit, putative 2.0 TDE2650 transcriptional regulator, putative 2.5 Transcriptional profile in response to osmotic downshift Saliva, crevicular fluid, and tissue, represent a range of osmotic conditions experienced by oral bacteria. Since oral spirochetes predominantly...”
GSU1626 transcriptional regulator, GntR family from Geobacter sulfurreducens PCA
45% identity, 30% coverage
NagR / VIMSS5936138 NagR regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine-6-phosphate (repressor) from Streptococcus uberis 0140J
45% identity, 29% coverage
LP_RS11220, lp_2651 GntR family transcriptional regulator from Lactiplantibacillus plantarum WCFS1
41% identity, 27% coverage
lp_2651 transcription regulator from Lactobacillus plantarum WCFS1
41% identity, 28% coverage
GBAA2609 transcriptional regulator, GntR family from Bacillus anthracis str. 'Ames Ancestor'
44% identity, 14% coverage
TDE_2650 GntR family transcriptional regulator from Treponema denticola ATCC 35405
37% identity, 49% coverage
- Localization and pathogenic role of the cysteine protease dentipain in Treponema denticola
Miyai-Murai, Molecular oral microbiology 2023 - “...encodes transcriptional regulator, and 1 encodes hypothetical protein. In the mutant strain, seven predicted transporters (TDE_2650, TDE_0190, TDE_0189, TDE_1947-1948, TDE_0012, TDE_2431, and TDE_0333), a GntR family transcriptional regulator, an Na + /H + antiporter, and a GNAT family N -acetyltransferase were upregulated ( Table 2 )....”
SpyM3_0843 putative transcription regulator (GntR family) from Streptococcus pyogenes MGAS315
46% identity, 29% coverage
- The phage protein paratox is a multifunctional metabolic regulator of Streptococcus
Muna, Nucleic acids research 2025 - “...pathway (Figure 1 ). These include proteins such as SpyM3_0977, NrdR ( 36 ) and SpyM3_0843 that are possible transcriptional regulators, and proteins like SpyM3_1248 and RecU involved in DNA recombination ( 37 ). Additionally, the detected proteins span both GAS proteins and phage proteins. For...”
- “...DBD. This includes SpyM3_0964/1346 (which has the same HTH subclass as ComR, cro/C1-type), SpyM3_0169, SpyM3_0977, SpyM3_0843 and SpyM3_1036 (Figure 1 and Supplementary Figure S1 ). Of note, SpyM3_0964 and SpyM3_1346 have the same amino acid sequence but are encoded as distinct genes making them impossible to...”
SPy1602 putative transcription regulator from Streptococcus pyogenes M1 GAS
45% identity, 19% coverage
- Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models
Buckley, Scientific reports 2021 - “...2 spy1934 3 spy0715 ( gntR -like) 4 3 rivR 5 M28_spy1337 6 spy1325 7 spy1602 ( gntR -like) 8 spy1817 9 crgR 10 4 copY 3 The optimal feature set is the set of features (from 53 response regulator alleles) selected in attaining the highest...”
- “..., lrp , spy1934 , spy0715 ( gntR -like), rivR , M28_spy1337 , spy1325 , spy1602 ( gntR -like), spy1817 , and crgR . The optimal feature set for the RF algorithms were of different composition (that is, size and constituents). It should be noted that...”
- In silico characterisation of stand-alone response regulators of Streptococcus pyogenes
Buckley, PloS one 2020 - “...RopB in NZ131 background [ 70 ] spy1258 spy1258 944/944 (100) TetR-like [ 72 ] spy1602 spy1602 942/944 (99.8) GntR-like spy2177 spy2177 944/944 (99.8) TetR-like under regulatory influence of RopB in NZ131 background. [ 70 ] srv spy1857 940/944 (99.6) Mga regulon genes (via Mga ),...”
- “...the ten most variable RRs alleles were lrp , mtsR , rivR , atoR , spy1602 , spy0715 , regR , ccpA , rgg3 , and copY ( Table 2 ). Multiple RRs including atoR , mga-1 , comR , copY , lrp , ralp3 ,...”
- Functional analysis of a group A streptococcal glycoside hydrolase Spy1600 from family 84 reveals it is a beta-N-acetylglucosaminidase and not a hyaluronidase
Sheldon, The Biochemical journal 2006 - “...transcriptional repressor of the arabinose operon, ORF spy1602, (b) other glycosidases, including a putative -glucosidase, ORF spy1599, and a putative...”
CH1034_280070 PLP-dependent aminotransferase family protein from Klebsiella pneumoniae
46% identity, 15% coverage
SPy1202 putative transcription regulator, GntR family from Streptococcus pyogenes M1 GAS
M28_Spy0889 transcriptional regulator, GntR family from Streptococcus pyogenes MGAS6180
46% identity, 28% coverage
NagQ / VIMSS128519 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Agrobacterium tumefaciens C58
43% identity, 26% coverage
XCC0672 transcriptional regulator from Xanthomonas campestris pv. campestris str. ATCC 33913
45% identity, 31% coverage
ABBFA_001779 UTRA domain protein from Acinetobacter baumannii AB307-0294
62% identity, 20% coverage
SPD_1524 transcriptional regulator, GntR family protein from Streptococcus pneumoniae D39
SP_1714 GntR family transcriptional regulator from Streptococcus pneumoniae TIGR4
spr1558 Conserved hypothetical protein from Streptococcus pneumoniae R6
SPV_1524 GntR family transcriptional regulator from Streptococcus pneumoniae
44% identity, 55% coverage
- Comparative analysis of the Streptococcus pneumoniae competence development in vitro versus in vivo during pneumonia-derived sepsis
Chong, Frontiers in microbiology 2025 - “...gntR and htrA in the infected lungs were not appreciably changed. The GntR-like transcriptional regulator (SPD_1524) has been shown to sense environmental and nutritional changes by regulating sugar transport and metabolism ( Li et al., 2018 ) and glutamine/glutamate metabolism ( Hendriksen et al., 2008 ),...”
- Klebsiella pneumoniae peptide hijacks a Streptococcus pneumoniae permease to subvert pneumococcal growth and colonization
Lux, Communications biology 2024 - “...gene was SPD_0161, a Mn 2+ /Fe 2+ transporter and the most upregulated gene was SPD_1524 (transcriptional regulator, gntR ). We confirmed significant downregulation of aliA, ilvB , livJ and significant upregulation of gntR by real-time RT-PCR (Supplementary Fig. 6c ). We found codY , a...”
- Proteomic Adaptation of Streptococcus pneumoniae to the Antimicrobial Peptide Human Beta Defensin 3 (hBD3) in Comparison to Other Cell Surface Stresses
Mücke, Microorganisms 2020 - “...t -tests parameters) were enriched after hBD3 stress in combination with their genetic regulator GntR (SPD_1524) (fc of 6.4). On the other hand, SPD_0115 (fc of 0.6), SPD_0161 (fc of 0.4), SPD_1263 (fc of 0.3), SPD_1264 (fc of 0.4), SPD_1267 (only identified under control conditions), and...”
- Proteomic Adaptation of Streptococcus pneumoniae to the Human Antimicrobial Peptide LL-37
Mücke, Microorganisms 2020 - “...1h of stress and 0.3-fold after 2h of stress for SPD_1527). Likewise, the transcriptional regulator SPD_1524 (GntR) was found in considerably higher abundance after LL-37 stress. Additionally, the sensor histidine kinase CiaH and the response regulator CiaR increased after stress at both timepoints. Other proteins involved...”
- “...adaptation in response to LL-37 seems to be mainly mediated by the transcriptional regulator GntR (SPD_1524) and the two-component systems, TCS05 CiaHR, TCS12 ComDE and TCS13 BlpHR (BlpS). In detail, GntR shows a substantial fold change at both timepoints, and corresponding RNA was also found to...”
- Proteomic Investigation Uncovers Potential Targets and Target Sites of Pneumococcal Serine-Threonine Kinase StkP and Phosphatase PhpP
Hirschfeld, Frontiers in microbiology 2019 - “...ATP synthase subunit alpha Oxidative phosphorylation SPD_1064 LVFAVDVG T 115 NQLAWK Hemolysin-like protein, putative Pathogenesis SPD_1524 LQIVSHTLEPNQQLP T 36 VR Transcriptional regulator, GntR family protein Transcription factor SPD_0592 ELPTV M DLLPSDIQ S 92 DK Pseudouridine synthase tRNA and rRNA base modification ** SPD_1233 FEPSFALGLALKP S 371...”
- A Novel Iron Transporter SPD_1590 in Streptococcus pneumoniae Contributing to Bacterial Virulence Properties
Miao, Frontiers in microbiology 2018 - “...Transcriptional regulator, GntR family protein SPD_0064 1.37 0.001 SPD_0158 DNA-binding response regulator SPD_0158 1.27 0.012 SPD_1524 Transcriptional regulator, GntR family protein SPD_1524 0.69 0.003 SPD_1605 Sugar-binding transcriptional regulator, LacI family protein SPD_1605 0.76 0.006 SPD_1904 Arginine repressor argR 0.75 0.023 SPD_0467 BlpS protein blpS 0.66 0.011...”
- Arachidonic Acid Stress Impacts Pneumococcal Fatty Acid Homeostasis
Eijkelkamp, Frontiers in microbiology 2018 - “...down-regulation upon exposure to AA may restrict the ability of the pneumococcus to cause disease. SPD_1524 encodes a YtrA-like regulator of the GntR family of transcriptional regulators, which are commonly co-transcribed with ABC transporters (Suvorova et al., 2015 ), as seen with this particular cluster. Although...”
- “...of ABC transporters (Suvorova et al., 2015 ). A putative YtrA-binding site identified upstream of SPD_1524 indicates its auto-regulation (data not shown). Further genomic analyses revealed highly homologous YtrA-binding motifs upstream of SPD_0686-8, but this cluster, encoding various efflux systems, was only marginally down-regulated (<2-fold). Collectively,...”
- Pneumococcal galactose catabolism is controlled by multiple regulators acting on pyruvate formate lyase
Al-Bayati, Scientific reports 2017 - “...were, as annotated in the D39 genome ( http://www.ncbi.nlm.nih.gov ), MarR (SPD_0379), GlnR (SPD_0447), GntR (SPD_1524), SPD_1594, PlcR (SPD_1745), CcpA (SPD_1797), and NmlR (SPD_1637). These regulators are known to be involved in diverse metabolic functions in bacteria, from the control of sugar metabolism (CcpA), fatty acid...”
- “...iron compound-binding protein 2 SPD_0918 Iron-compound ABC transporter, ATP-binding protein 2 SPD_1375 Hypothetical protein 2.3 SPD_1524 Transcriptional regulator, GntR family 4.1 SPD_1525 ABC transporter, ATP-binding protein 2.2 SPD_1588 Hypothetical protein 2.1 SPD_1589 Hypothetical protein 3 SPD_1590 General stress protein 24, putative 2.6 SPD_1591 Hypothetical protein 2.2...”
- More
- Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae
Hendriksen, Infection and immunity 2008 - “...SP_2166 SP_0100 SP_0418 SP_0502 SP_0910 SP_1241 SP_1242 SP_1572 SP_1714 spr1560 SP_1715 SP_1824 SP_2239 adh2 fucA acp glnA glnP glnQ dpr htrA Annotation...”
- Altered lipid composition in Streptococcus pneumoniae cpoA mutants
Meiers, BMC microbiology 2014 - “...spr1549), and the 5-7-fold upregulation of two ABC transporters ( vex , spr0524 - spr0526; spr1558 - spr1560) and spr0307 clpL (approximately 4-fold; Additional file 2 : Table S3). No effect on PBP genes or genes involved in lipid biosynthesis was apparent. Discussion Glycolipids in cpoA...”
- Refining the Pneumococcal Competence Regulon by RNA Sequencing
Slager, Journal of bacteriology 2019 - “..., hypergeometric test). First, transcription of all six genes predicted to be regulated by GntR (SPV_1524), on the basis of homology to Streptococcus pyogenes Spy_1285 ( 67 ), was found to be upregulated 10 and 20 min after addition of CSP. These six genes are distributed...”
SEQ_1694 GntR family regulatory protein from Streptococcus equi subsp. equi 4047
43% identity, 18% coverage
YdfD/YisV / VIMSS6924547 YdfD/YisV regulator of Metabolite transport (activator/repressor) from Paenibacillus sp. JDR-2
39% identity, 15% coverage
SPy1285 / VIMSS10162275 SPy1285 regulator of Transport (repressor) from Streptococcus mitis B6
44% identity, 55% coverage
cg0196 GntR family regulatory protein from Corynebacterium glutamicum ATCC 13032
NCgl0154 GntR family transcriptional regulator IolR from Corynebacterium glutamicum ATCC 13032
38% identity, 29% coverage
- Azido Inositol Probes Enable Metabolic Labeling of Inositol-Containing Glycans and Reveal an Inositol Importer in Mycobacteria
Hodges, ACS chemical biology 2023 - “..., a close relative of Mycobacterium that possesses PIM, LM, and LAM 41 (IolR, Cgl1057 (cg0196), 55% shared nucleotide identity to MSMEG_4659 ). 42 Our examination of genes immediately downstream of MSMEG_4659 ( Figure 4B ) revealed a cluster of 6 genes ( MSMEG_4661 MSMEG_4666 )...”
- Fermentative N-Methylanthranilate Production by Engineered Corynebacterium glutamicum
Walter, Microorganisms 2020 - “...pK19- iolR :: P tuf -aroE pK19 mobsacB with a construct for replacement of iolR (cg0196) by aroE (cg1835) with an artificial RBS under control of C. glutamicum promoter P tuf This work pK19- sugR :: sugR pK19 mobsacB with a construct for reintegration of sugR...”
- Miniaturized and automated adaptive laboratory evolution: Evolving Corynebacterium glutamicum towards an improved d-xylose utilization
Radek, Bioresource technology 2017 (PubMed)- “...revealed potential key mutations, e.g. in the gene cg0196 (encoding for the transcriptional regulator IolR of the myo-inositol metabolism). These findings open...”
- “...0.02 Multiple breakpoints (45%) nt 168,365 > 168,464; In cg0196, iolR , repressor of myo -inositol utilization genes SNV A to G (16%) nt 526,417 Exchange I15V...”
- Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria
Ibarra-Arellano, Database : the journal of biological databases and curation 2016 - “..., cgtR3 ( phoR ), cg0156 ( cysR ), sigM , cg1324 ( rosR ), cg0196 ( pckR ) and sigB . These global regulators comprise four out of the seven sigma factors encoded in the genome of C. glutamicum ( 31 ). All of these...”
- “...hrrA ), ripA , cg0156 ( cysR ), sigM , cg1324 ( rosR ), and cg0196 ( pckR ). Nevertheless, cgtR11 ( hrrA ) ( 33 ) has also been individually reported as global regulator. In our set of global regulators we only missed arnR (...”
- Complex regulation of the phosphoenolpyruvate carboxykinase gene pck and characterization of its GntR-type regulator IolR as a repressor of myo-inositol utilization genes in Corynebacterium glutamicum
Klaffl, Journal of bacteriology 2013 - “...and GntR2 (44), and another GntR-type regulator, Cg0196. The relevance of these regulators for pck expression under glycolytic and gluconeogenic conditions...”
- “...was investigated. Additionally, we analyzed the regulon of Cg0196 by transcriptome analysis of a cg0196 mutant and by DNA binding studies with purified Cg0196....”
- GntR-type transcriptional regulator PckR negatively regulates the expression of phosphoenolpyruvate carboxykinase in Corynebacterium glutamicum
Hyeon, Journal of bacteriology 2012 - “...approach. An isolated protein was identified to be PckR (Cg0196), a GntR family transcriptional regulator which consists of 253 amino acids with a mass of 27...”
- “...RBC Wild-type strain Wild-type strain with deletion in cg0196 ATCC This study Ampr; TA cloning vector (PT7, PSP6) Ampr; vectors for overexpression of genes...”
- The role of the transcriptional repressor CssR in Corynebacterium glutamicum in response to phenolic compounds
Zhang, Heliyon 2024 - “...NCgl0108 Mannitol 2-dehydrogenase 1.26 0.04 NCgl0116 Hypothetical protein 1.36 2.58E-03 NCgl0122 Hypothetical protein 2.04 0.02 NCgl0154 GntR family transcriptional regulator 1.16 4.69E-04 NCgl0173 ArsR family transcriptional regulator 1.48 0.01 NCgl0201 Hypothetical protein 4.83 4.27E-06 NCgl0204 Hypothetical protein 2.54 5.0E-04 NCgl0227 Hypothetical membrane protein 1.24 3.29E-04 NCgl0231...”
NP_349157 Transcriptional regulator, FadR family from Clostridium acetobutylicum ATCC 824
44% identity, 29% coverage
SO0072 / VIMSS6939482 SO0072 regulator of Hypothetical ABC transporter (repressor) from Shewanella amazonensis SB2B
42% identity, 60% coverage
Mvan_4015 UbiC transcription regulator-associated domain protein from Mycobacterium vanbaalenii PYR-1
39% identity, 30% coverage
NagQ / VIMSS1840510 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Paracoccus denitrificans PD1222
45% identity, 26% coverage
EF3034 transcriptional regulator, GntR family from Enterococcus faecalis V583
39% identity, 30% coverage
BBMN68_905 PLP-dependent aminotransferase family protein from Bifidobacterium longum subsp. longum BBMN68
39% identity, 13% coverage
- Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock
Zuo, Scientific reports 2018 - “...lysR NS 1.38 BBMN68_843 Putative transcriptional regulator 2.44 2.51 BBMN68_1661 Putative transcriptional regulator 1.29 NS BBMN68_905 Hypothetical protein Hypothetical protein 4.79 4.64 BBMN68_1400 Hypothetical protein 4.63 4.00 BBMN68_582 Hypothetical protein 2.87 3.49 BBMN68_105 Hypothetical protein 1.92 3.02 BBMN68_248 Hypothetical protein 1.70 2.71 BBMN68_519 Hypothetical protein 1.58...”
NagQ / VIMSS908978 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Silicibacter pomeroyi DSS-3
39% identity, 26% coverage
SO0072 / VIMSS6908413 SO0072 regulator of Hypothetical ABC transporter (repressor) from Shewanella denitrificans OS217
42% identity, 57% coverage
SACE_0500 putative GntR-family transcriptional regulator from Saccharopolyspora erythraea NRRL 2338
42% identity, 26% coverage
YdfD/YisV / VIMSS63013 YdfD/YisV regulator of Metabolite transport (activator/repressor) from Bacillus halodurans C-125
BH0432 transcriptional regulator (GntR family) from Bacillus halodurans C-125
41% identity, 15% coverage
SO0072 / VIMSS7103238 SO0072 regulator of Hypothetical ABC transporter (repressor) from Shewanella woodyi ATCC 51908
42% identity, 59% coverage
lp_3633 GntR family transcriptional regulator from Lactiplantibacillus plantarum WCFS1
43% identity, 18% coverage
MSMEG_0124 transcriptional regulator, GntR family protein from Mycobacterium smegmatis str. MC2 155
44% identity, 27% coverage
- GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
Vindal, BMC genomics 2007 - “...List of Classified M. smegmatis GntR regulators Gene Subfamily Amino acid Gene Subfamily Amino acid MSMEG_0124 FadR 227 MSMEG_2546 FadR 239 MSMEG_0130 FadR 230 MSMEG_2599 FadR 224 MSMEG_0166 FadR 242 MSMEG_2605 FadR 255 MSMEG_0179 FadR 223 MSMEG_2682 FadR 262 MSMEG_0268 HutC 292 MSMEG_2794 FadR 225 MSMEG_0286...”
- “...]. Table 3 List of predicted potential operator sites Subfamily Regulator Potential Operator sequence FadR MSMEG_0124 --CCACT GT TCA AC G A GCG--- MSMEG_0179 -AAGA T C GT CCG AC A A TT---- MSMEG_0454 --CAA T C GT CAT AC G A TTG--- MSMEG_0596 --GTG T...”
BMEII0383 TRANSCRIPTIONAL REGULATOR, GNTR FAMILY from Brucella melitensis 16M
BAB_RS27910 GntR family transcriptional regulator from Brucella abortus 2308
42% identity, 26% coverage
- 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 - “...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 phase B. melitensis cultures compared to...”
- Characterization of Brucella abortus mutant strain Δ22915, a potential vaccine candidate
Bao, Veterinary research 2017 - “...protein Amino acid transport and metabolism 1.370.35 BAB_RS 28215 Transposase Replication, recombination and repair 1.250.23 BAB_RS27910 Transcriptional regulator Transcription 0.810.19 BAB_RS22920 Auxin efflux carrier Function unknown 0.760.11 Genes with over twofold changes levels and high probability were further validated with qRT-PCR. a Based on B. abortus...”
PhnF / VIMSS7531259 PhnF regulator of Phosphonate utilization from Desulfomicrobium baculatum DSM 4028
40% identity, 30% coverage
PdhR / VIMSS2703284 PdhR regulator of Pyruvate metabolism, effector Pyruvate (repressor) from Idiomarina baltica OS145
43% identity, 26% coverage
Y11_21251 GntR family transcriptional regulator from Yersinia enterocolitica subsp. palearctica Y11
44% identity, 27% coverage
- RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica
Leskinen, Viruses 2016 - “...of down-regulated genes, the most prominently affected include the transcriptional regulator of the GntR family (Y11_21251; 3.81), nitrite reductase large subunit (Y11_32431; 3.24), ADP-glucose synthase (Y11_14901; 2.80), as well as several membrane proteins. This type of bacterial response is not distinct from other lytic host-phage systems,...”
- “...PhoB (SphR) 3.73 Y11_22431 Transcriptional regulator, ArsR family 2.67 Y11_10431 Transcriptional regulatory protein YciT 2.44 Y11_21251 Transcriptional regulator, GntR family 3.66 Other Y11_34281 RNA polymerase sigma factor 2.30 Y11_28241 Regulator of ribonuclease activity A 2.26 Y11_21021 Phosphate regulon sensor protein PhoR (SphS) (EC 2.7.13.3) 1.69...”
BP0888 GntR-family transcriptional regulator from Bordetella pertussis Tohama I
42% identity, 25% coverage
PdhR / VIMSS2830154 PdhR regulator of Pyruvate metabolism, effector Pyruvate (repressor) from Oceanospirillum sp. MED92
48% identity, 24% coverage
Z4736 putative transcriptional regulator from Escherichia coli O157:H7 EDL933
39% identity, 24% coverage
- Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People's Republic of China
Wang, Infection and immunity 1992 - “...Z4073, Z4075, Z4079, Z4081, Z4097, Z4104, Z4109, Z4115, Z4736, Z4737, Z4738, Z4739, Z4740, Z4744, Z4745, Z4747, Z4748, Z4749, Z4750 Z4752, Z4061 Z4755 Z4049,...”
AHA_0117 transcriptional regulator, GntR family from Aeromonas hydrophila subsp. hydrophila ATCC 7966
40% identity, 28% coverage
- Proteomics Analysis Reveals Bacterial Antibiotics Resistance Mechanism Mediated by ahslyA Against Enoxacin in Aeromonas hydrophila
Li, Frontiers in microbiology 2021 - “...at least 11 TRs ( gltR , yidZ , ycaN , citA , AHA_3297 , AHA_0117 , AHA_3721 , AHA_1240 , AHA_4233 , AHA_1862 , and AHA_3966 ), which indicating that these TRs may construct a complicated gene regulatory network to maintain the intracellular homeostasis during...”
NagQ / VIMSS86363 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Mesorhizobium loti MAFF303099
41% identity, 27% coverage
BCAM2774 GntR family regulatory protein from Burkholderia cenocepacia J2315
42% identity, 26% coverage
- Comparative Genomics of Burkholderia singularis sp. nov., a Low G+C Content, Free-Living Bacterium That Defies Taxonomic Dissection of the Genus Burkholderia
Vandamme, Frontiers in microbiology 2017 - “...in Burkholderia species ( Cooper et al., 2010 ) and none of the genes (i.e., BCAM2774, BCAM0964, BCAM0057, BCAM0941, BCAM2347, and BCAM2389) containing the indels appeared essential for growth on either rich or minimal media ( Wong et al., 2016 ). Together, these data demonstrate that...”
SAV_3023 GntR-family transcriptional regulator from Streptomyces avermitilis MA-4680
44% identity, 28% coverage
SMc00674 PUTATIVE HISTIDINE UTILIZATION REPRESSOR TRANSCRIPTION REGULATOR PROTEIN from Sinorhizobium meliloti 1021
37% identity, 28% coverage
EF1709 sugar-binding transcriptional regulator, GntR family from Enterococcus faecalis V583
38% identity, 19% coverage
LBA0882 transcriptional regulator from Lactobacillus acidophilus NCFM
38% identity, 27% coverage
AgaR2 / VIMSS3591460 AgaR2 regulator of N-acetylgalactosamine utilization, effector N-acetylgalactosamine (repressor) from Streptococcus suis 05ZYH33
SSU05_0447 Transcriptional regulator from Streptococcus suis 05ZYH33
42% identity, 26% coverage
- Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections
Zhang, MicrobiologyOpen 2015 - “...G (Feng etal. 2012 ). Plasmids and DNA manipulations The S. suis agaR 2 ( SSU05_0447 ) gene was amplified using polymerase chain reaction (PCR) with primers SSU05_0447 F plus SSU05_0447 R (Table S2) and ligated into the BamHI and XhoI sites of pET28a(+) expression vector...”
- “...in vitro proteins of AgaR2 and AgaR1, respectively. For functional complementation, the two genes ( SSU05_0447 and SSU05_0448 ) were separately inserted into the lowcopy shuttle vector pVA838 (Romero etal. 1987 ), giving the plasmids pVA838447 and pVA838448, respectively (Table S2). All the recombinant plasmids involved...”
SO0072 transcriptional regulator, GntR family from Shewanella oneidensis MR-1
42% identity, 60% coverage
GAMR_BACSU / O31459 HTH-type transcriptional repressor GamR from Bacillus subtilis (strain 168) (see 2 papers)
GamR / VIMSS36771 GamR regulator of Glucosamine utilization, effector Glucosamine-6-phosphate (repressor) from Bacillus subtilis subsp. subtilis str. 168
BSU02370 putative transcriptional regulator (GntR family) from Bacillus subtilis subsp. subtilis str. 168
51% identity, 23% coverage
- function: Transcriptional repressor of genes involved in glucosamine transport and utilization (PubMed:23667565, PubMed:24673833). Represses the expression of the gamAP operon by binding to the gamA-gamR intergenic region (PubMed:24673833).
disruption phenotype: Deletion of the gene improves the growth rate on N-acetylglucosamine. - Secondary structural entropy in RNA switch (Riboswitch) identification
Manzourolajdad, BMC bioinformatics 2015 - “...0.3694 236 treP BSU07800 0.817 75 255279 255435 forward BSU02330 ybfQ -1718 0.2994 2434 ybgA BSU02370 0.816 76 1541729 1541885 forward BSU14680 ykzC -2958 0.3376 79 ylaA BSU14710 0.816 77 909862 910018 forward BSU08330 yfiN -658 0.3503 79 estB BSU08350 0.816 78 4109617 4109773 reverse BSU40030...”
VPA0240 putative repressor protein PhnR from Vibrio parahaemolyticus RIMD 2210633
45% identity, 27% coverage
LBCZ_2704 GntR family transcriptional regulator from Lacticaseibacillus casei DSM 20011 = JCM 1134 = ATCC 393
41% identity, 30% coverage
- Genomic adaptation of the Lactobacillus casei group
Toh, PloS one 2013 - “...ABC transporter LBCZ_2678 LBCZ_2694 15.0 transposase LRHM_2545 LRHM_2597 57.7 carbohydrate utilization gene cluster (region-5) LBCZ_2698 LBCZ_2704 7.6 PTS transporter LRHM_2635 LRHM_2651 15.4 carbohydrate utilization gene cluster (region-6) LRHM_2779 LRHM_2793 12.5 prophage region III Similarly, compared with L. paracasei ATCC 334, 15 and 24 GIs were found...”
HutC / VIMSS3783927 HutC regulator of Histidine utilization, effector cis-Urocanic acid (repressor) from Shewanella halifaxensis HAW-EB4
42% identity, 28% coverage
PXO_RS20790 UTRA domain-containing protein from Xanthomonas oryzae pv. oryzae PXO99A
48% identity, 26% coverage
- Transcriptional regulator Sar regulates the multiple secretion systems in Xanthomonas oryzae
Shao, Molecular plant pathology 2023 - “...such as pathogenicity in the host plant. Our previous study identified a new master regulator PXO_RS20790 that is involved in pathogenicity for Xoo against the host rice. However, the molecular functions of PXO_RS20790 are still unclear. Here, we demonstrate that transcriptional regulator Sar (PXO_RS20790) regulates multiple...”
- “...pathogenicityrelated regulators were participating in raxSTAB and/or raxX expression, such as HrpG, HrpX, VemR, and PXO_RS20790 (Zheng et al., 2021 ). However, the regulation of raxX and raxSTAB cluster expressions remains elusive. The T6SS is a bacterial contactdependent contractile nanomachine used to inject proteinaceous protein effectors...”
- Xanthomonas oryzae Pv. oryzicola Response Regulator VemR Is Co-opted by the Sensor Kinase CheA for Phosphorylation of Multiple Pathogenicity-Related Targets
Cai, Frontiers in microbiology 2022 - “...( Teper et al., 2021 ). Regulome analyses revealed that the orphan RR VemR (and PXO_RS20790) are the master positive regulators of HrpX and execute extensive cross-talk within other pathogenicity-associated signaling networks in X. oryzae pv. oryzae ( Zheng et al., 2021 ). Here, we report...”
- Elucidation of the Pathogenicity-Associated Regulatory Network in Xanthomonas oryzae pv. oryzae
Zheng, mSystems 2021 - “...talk with others and all these regulators function as a regulatory network, with VemR and PXO_RS20790 being the master pathogenicity-associated regulators and HrpX being the final executant. Moreover, regulome analysis showed that numerous genes other than genes in pathogenicity islands are finely regulated within the regulatory...”
- “...(PXO_RS02870), Zur (PXO_RS06520), and HpaR1 (PXO_RS13460) which regulate the pathogenicity of Xanthomonas and transcription factor PXO_RS20790 of unknown function showed important roles in the pathogenicity of Xoo ( Fig.1A ). Given that PXO_RS20790 was previously uncharacterized, the complementation of PXO_RS20790 deleted mutant RS20790 was conducted. As...”
F9ULB4 Transcription regulator, GntR family from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
HGB56_08965 GntR family transcriptional regulator from Lactiplantibacillus plantarum
41% identity, 18% coverage
- Phenotypic and proteomic differences in biofilm formation of two Lactiplantibacillus plantarum strains in static and dynamic flow environments
Huijboom, Biofilm 2024 - “...to magnesium (binding) (F9URJ9 and F9USN4), along with two transcription regulators of the TntR family (F9ULB4 and F9URB9). Of the lower expressed proteins in the static biofilm, nine out of 15 were related to the cell wall/surface (F9ULM2, F9UNC2, F9URS2, F9URU9, F9USE1, F9UTQ7, F9UU93, F9UUA0), including...”
- “...Gene code Annotation Gene Fold change 1 F9URY4 lp _2888 Cystathionine beta-lyase cblA2 8.4 2 F9ULB4 lp _3558 Transcription regulator, GntR family araR 1.6 3 F9URB9 lp _2615 Transcription regulator, GntR family - 1.5 4 F9ULK7 lp _3660 Ribokinase rsbK1 3.1 5 F9URE1 lp _2648 PTS...”
- The Carbohydrate Metabolism of Lactiplantibacillus plantarum
Cui, International journal of molecular sciences 2021 - “...( araB , HGB56_08955), arabinose transporter ( araP , HGB56_08960), transcription regulator ( araR , HGB56_08965, GntR family), and hypothetical protein (HGB56_08935). The strains WCFS1, LP-F1, JDM1, 5-2, SN35N, K25, ST-III, CAUH2, J26, and LZ95 possess the gene cluster ( Supplementary Table S3-6 ). Some strains...”
lmo2144 similar to transcription regulator GntR family from Listeria monocytogenes EGD-e
42% identity, 27% coverage
RPA1394 transcriptional regulator, GntR family with aminotransferase domain from Rhodopseudomonas palustris CGA009
40% identity, 15% coverage
LLKF_1613 GntR family transcriptional regulator from Lactococcus lactis subsp. lactis KF147
39% identity, 19% coverage
CDR20291_2781 GntR family transcriptional regulator from Clostridioides difficile R20291
CDR20291_2781 GntR-family transcriptional regulator from Clostridium difficile R20291
42% identity, 28% coverage
SMc02876 PUTATIVE TRANSCRIPTION REGULATOR PROTEIN from Sinorhizobium meliloti 1021
43% identity, 26% coverage
SO0072 / VIMSS5211367 SO0072 regulator of Hypothetical ABC transporter (repressor) from Shewanella loihica PV-4
41% identity, 59% coverage
A3852_29435 GntR family transcriptional regulator from Rhodococcus qingshengii
42% identity, 29% coverage
- Enhancement of Microbial Biodesulfurization via Genetic Engineering and Adaptive Evolution
Wang, PloS one 2017 - “...+ non-synonymous false positive non-ribosomal peptide synthetase A3852_20720 synonymous + non-synonymous false positive hypothetical protein A3852_29435 non-synonymous true SNP GntR family transcriptional regulator A3852_29860 not-applicable false positive 23S ribosomal RNA The complete genomes of P0 and P100 from the first selection experiment were compared and the...”
- “...the other hand, the single mutation observed in the transcriptional regulator of the GntR family (A3852_29435) appears genuine, and the non-synonymous change from a hydrophilic residue (Ser-215) to a hydrophobic one (Gly) in P100 could have implications on its overall fitness, and thus potentially affect the...”
SO0072 / VIMSS6935672 SO0072 regulator of Hypothetical ABC transporter (repressor) from Shewanella baltica OS155
42% identity, 60% coverage
NagQ / VIMSS1098848 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Hahella chejuensis KCTC 2396
41% identity, 23% coverage
AraR / VIMSS5504069 AraR regulator of Arabinose utilization, effector Arabinose (repressor) from Lactobacillus fermentum IFO 3956
44% identity, 17% coverage
NagQ / VIMSS1918928 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Burkholderia cepacia AMMD
39% identity, 27% coverage
GmuR / VIMSS3427031 GmuR regulator of Glucomannan utilization (repressor) from Bacillus pumilus SAFR-032
43% identity, 26% coverage
DASR_STRCO / Q9K492 HTH-type transcriptional repressor DasR from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (see 4 papers)
SCO5231 gntR-family transcriptional regulator from Streptomyces coelicolor A3(2)
42% identity, 28% coverage
- function: Global regulator that is part of the nutrient-sensing system. In the absence of glucosamine 6-P (GlcN6P), represses the phosphotransferase system (PTS) specific for the uptake of N- acetylglucosamine (PTSNag), and genes involved in the metabolism of chitin, as well as several genes involved in development, thereby linking carbon availability to morphogenesis (PubMed:15247334, PubMed:16925557). Also regulates the expression of the ABC transporters DasABC and NgcEFG, which are involved in N,N'-diacetylchitobiose ((GlcNAc)2) uptake (PubMed:17351098, PubMed:30089751). Binds to the DNA consensus sequence 5'-ACTGGTCTAGACCACT-3' (PubMed:15247334, PubMed:16925557).
disruption phenotype: Deletion of the gene results in a bald phenotype, mutant fails to produce aerial hyphae and spores on glucose-containing media. The mutant is arrested at an early stage of the developmental program. - Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein
Chauhan, Microbiology spectrum 2023 - “...Burkholderia sp. (EEA00313), Pseudomonas putida (P22773), Escherichia coli (P0A8V8, P13669), Bacillus subtilis (O34817), Streptomyces coelicolor (Q9K492), Salmonella enterica (AAB39463), Corynebacterium glutamicum (BAC00309), Thermotoga maritima (NP_228249), Streptococcus pyogenes (AMY97465), Vibrio cholerae (SYZ81202), Pseudomonas syringae (WP_044310692), Brucella sp. (WP_006173453), and Klebsiella pneumoniae (EPP09325). (B) Sedimentation velocity analytical ultracentrifugation...”
- Crystal Structures of the Global Regulator DasR from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors
Fillenberg, PloS one 2016 - “...was performed with CLUSTAL OMEGA [ 59 ] using the canonical protein sequences of entries Q9K492 and O34817 from the UniProt database [ 19 ]. Secondary structure elements refer to the topology of DasR and are marked with (h) or (s) for -helices and -strands, respectively....”
- A rational multi-target combination strategy for synergistic improvement of non-ribosomal peptide production
Yan, Nature communications 2025 - “...we identified 10 targets for inhibiting thaxtomin A. They are sco5803 (named as thaR1 ), sco5231 ( thaR2 ), sco3226 ( thaR3 ), sco4230 ( thaR4 ), sco3818 ( thaR5 ), sco5862 ( thaR6 ), sco1596 ( thaR7 ), sco2794 ( thaR8 ), sco1745 ( thaR9...”
- Impact of the Deletion of Genes of the Nitrogen Metabolism on Triacylglycerol, Cardiolipin and Actinorhodin Biosynthesis in Streptomyces Coelicolor
Sonia, 2024 - Allosteric regulation by c-di-AMP modulates a complete N-acetylglucosamine signaling cascade in Saccharopolyspora erythraea
You, Nature communications 2024 - “...insights, the S. erythraea DasR sequence was aligned with homologs in other c-di-AMP-producing species, including SCO5231 from S. coelicolor , MSMEG_0286 from Mycobacterium smegmatis , and RV0792c from Mycobacterium tuberculosis , etc. (Fig. 5a ). Phylogenetic survey revealed that DasR homologs are broadly distributed among c-di-AMP...”
- DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor
Šmídová, Nucleic acids research 2019 - “...which is recognized by RNase III endoribonuclease. Other examples of HrdB-controlled pleiotropic regulators are dasR (SCO5231, a transcriptional repressor of antibiotic biosynthesis, nitrate metabolism, sugar transporters, etc. ( 55 , 56 )) and a putative methyltransferase SCO2525 with a morphogenetic role ( 57 ). Other HrdB-regulated...”
- Quantitative Proteome and Phosphoproteome Analyses of Streptomyces coelicolor Reveal Proteins and Phosphoproteins Modulating Differentiation and Secondary Metabolism
Rioseras, Molecular & cellular proteomics : MCP 2018 - “...EQGDNTGSPVR n.s. 3.1 n.s. 8.5 DevA (SCO4190) ALQEDGLLTNV pS K n.s. 2.1 n.s. 4.2 DasR (SCO5231) STDVSSAENEGGA pT VR n.s. 2.1 n.s. 4.3 SCO5357 VNASAEQAAPADDAP pS ER n.s. 1.6 n.s. 3 SCO5544 GHDEPD pS SRTDR n.s. 3.2 n.s. 9.2 SCO5544 GHDEPDS pS RTDRTPR n.s. 1.9 n.s....”
- Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution
Lacombe-Harvey, Applied microbiology and biotechnology 2018 - “...regulatory proteins. Such specific binding has been demonstrated for the protein DasR encoded by the SCO5231 gene in Str. coelicolor (Colson et al. 2007 ), first discovered in Str. griseus (Seo et al. 2002 ). Binding of DasR to promoter segments of several chitinase genes (...”
- The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)
Jeong, Nature communications 2016 - “...Blue dots indicate other known regulators of secondary metabolism: SCO2792 (AdpA), SCO5803 (LexA), SCO3226 (AbsA2), SCO5231, SCO3063, SCO4907 (AfsQ1), SCO5260 (AtrA), SCO6008, SCO4159 (GlnR), SCO0310, SCO3932, SCO5405, SCO6265 (ScbR) and SCO4230 (PhoP). Grey dots and dark grey dots indicate, respectively, all genes and secondary metabolic genes....”
- Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins
Driessen, Biochemistry 2014 - “...and Bam HI site of pET3-his. 34 pBTH154 was constructed by inserting the dasR gene (SCO5231) of Streptomyces coelicolor A3(2) 35 into the Xba I and Xma I site of pUT18C (Euromedex). All PCR products were purified using a GenElute PCR Clean-up kit (Sigma-Aldrich). DNA substrates...”
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YhfR / b3375 putative DNA-binding transcriptional regulator FrlR from Escherichia coli K-12 substr. MG1655 (see 6 papers)
frlR / GB|AAC76400.2 HTH-type transcriptional regulator frlR from Escherichia coli K12 (see 3 papers)
P45544 Probable fructoselysine utilization operon transcriptional repressor from Escherichia coli (strain K12)
39% identity, 26% coverage
- Toward Single Bacterium Proteomics
Végvári, Journal of the American Society for Mass Spectrometry 2023 - “...1488.95 744.97 +2 82.06 1 181.64 31.25% 945 Probable fructelysine utilization operon transcriptional repressor frlR P45544 [179197] [R].VVSDKKTIDIFAATRPQAK.[W] 2318.33 773.44 +3 86.67 5 218.51 6.25% DNA polymerase III subunit delta holA P28630 [293299] [R].LSQTQLR.[Q] 1075.63 538.32 +2 46.97 1 186.37 6.25% glutamine-binding periplasmic protein gln H...”
YtrA / VIMSS104067 YtrA regulator of Hypothetical ABC transporter (repressor) from Staphylococcus aureus, N315
SACOL1997 transcriptional regulator, GntR family from Staphylococcus aureus subsp. aureus COL
SA1748 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV1934 transcription regulator GntR family from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_02155 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1914 GntR family regulatory protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
MW1875 ORFID:MW1875~hypothetical protein, similar to transcription regulator, GntR family from Staphylococcus aureus subsp. aureus MW2
MW_RS10215 PSM export ABC transporter transcriptional regulator PmtR from Staphylococcus aureus subsp. aureus MW2
40% identity, 54% coverage
- Inhibition of Staphylococcus aureus biofilm formation by gurmarin, a plant-derived cyclic peptide
Chang, Frontiers in cellular and infection microbiology 2022 - “...SACOL0962 -2.45 Glycerophosphoryl diester phosphodiesterase GlpQ, putative glpQ 0.04 SACOL1410 -2.39 FemA protein femA 0.01 SACOL1997 -2.35 Transcriptional regulator, GntR family 0.04 SACOL0485 -2.28 Staphylococcus tandem lipoprotein 0.02 SACOL0652 -2.25 Conserved hypothetical protein 0.03 SAV0564 -2.25 Similar to poly (glycerol-phosphate) alpha-glucosyltransferase 0.03 SACOL2548 -2.24 Conserved hypothetical...”
- A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus
Chen, Molecular microbiology 2009 - “...ABC transporter SACOL0910 -3.0 Hypothetical protein SACOL1164 -3.1 Fibrinogen-binding related protein SACOL1996 -2.4 ABC transporter SACOL1997 -2.7 GntR family protein SACOL2295 -3.1 Staphyloxanthine biosynthesis protein SACOL2709 -2.5 Conserved hypothetical protein SACOL2710 -2.6 Conserved hypothetical protein Genes upregulated in the sarZ mutant SACOL1783 acs 2.2 - Acetyl-CoA...”
- Different bacterial gene expression patterns and attenuated host immune responses are associated with the evolution of low-level vancomycin resistance during persistent methicillin-resistant Staphylococcus aureus bacteraemia
Howden, BMC microbiology 2008 - “...family regulators SACOL2193 and SACOL2517 in 4 and 3 pairs respectively, the GntR family regulator (SACOL1997) in 2 pairs, and up-regulation of a putative regulatory gene (SACOL2585) in 2 pairs, but down-regulation in another pair. Previous studies have demonstrated significant transcriptional changes in S. aureus isolates...”
- Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence
Ravcheev, Journal of bacteriology 2011 - “...NreC SA0476 SA1678 SA0454 SA0261 SA1851 SA0661 SA1847 SA0434 SA1748 SA1383 Genomeb PdxR* PerR PurR RbsR Rex SaeR ScrR TreR YtrA Zur NrdR MarR DtxR BglG RpiR...”
- 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 - “...5.5 2.5 2.5 accC SA1571 acetyl-CoA carboxylase biotin carboxylase subunit sa_c3110s2665_a_at 4.1 2.5 2.5 accD SA1748 acetyl-CoA carboxylase sa_c1264s1041_at 3.0 15 30 acpP SA1247 acyl carrier protein sa_c9605s8367_a_at * 12.1 2.5 2.5 cdsA SA1280 phosphatidate cytidylyltransferase sa_c1624s9141_a_at 2.7 2.5 5 cls1 SA1351 cardiolipin synthetase sa_c4357s3707_at 2.7...”
- Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
Donat, Journal of bacteriology 2009 - “...of California, Berkeley SA1287 SA1305 SA1360 SA1586 SA1659 SA1748 SA1836 SA2089 SA2103 SA2108 SA2296 Gene 4064 J. BACTERIOL. DONAT ET AL. TABLE 3--Continued...”
- Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome
Ben, Journal of bacteriology 2008 - “...SA0627 Cytoplasm SA1159 Not clear SA1591 Cytoplasm SA1748 Cytoplasm SA1930 Cytoplasm SA2340 Cytoplasm SA2364 Cytoplasm SAR0836 SA1114 Cytoplasm Cytoplasm...”
- Global regulatory impact of ClpP protease of Staphylococcus aureus on regulons involved in virulence, oxidative stress response, autolysis, and DNA repair
Michel, Journal of bacteriology 2006 - “...regulators, encoded by SA0322 (MarA family) and SA1748 (GntR family). In addition, transcription of 10 transcriptional regulators was increased, including those...”
- “...SA0573 SA1041 Down-regulated SA0250 SA0322 SA0454 SA0641 SA1248 SA1509 SA1748 yycF (vicR) ctsR sarA pyrR codY glpP lexA hrcA sarT lytS purR rat arlR SA1801...”
- GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
Vindal, BMC genomics 2007 - “...248 P22773 YtrA Bacillus halodurans BH0651 123 Q9KF35 Bacillus halodurans BH2647 123 Q9K9J9 Staphylococcus aureus SAV1934 126 Q99SV4 Bacillus subtilis YhcF 121 P54590 Bacillus subtilis YtrA 130 O34712 AraR Bacillus subtilis P96711 362 P96711 Bacillus halodurans Q9KBQ0 375 Q9KBQ0 Bacillus stearothermophilus Q9S470 364 Q9S470 PlmA Synechocystis...”
- Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA
Yokoyama, Genome biology 2018 - “...pmt genes have not been annotated on the NCTC8325 genome, they are present (locus tags SAOUHSC_02155, SAOUHSC_02154, SAOUHSC_02153, SAOUHSC_02152, SAOUHSC_02151). This locus encodes a regulatory protein, two membrane bound ABC transporter proteins and two ATP binding proteins that fuel the export system, where the four structural...”
- Genomic Signatures of Experimental Adaptation to Antimicrobial Peptides in Staphylococcus aureus
Johnston, G3 (Bethesda, Md.) 2016 (no snippet) - Global analysis of transcriptional regulators in Staphylococcus aureus
Ibarra, BMC genomics 2013 - “...] SAUSA300_1469 ArgR 28% identity with S.aureus ArgR. In operon with a DNA repair protein SAUSA300_1914 GltR B. subtilis YtrA (39.45%), possible repressor of an operon for a putative ATP-binding cassette transport system involved in acetoin utilization. YtrA is an additional regulator of cell envelope stress...”
- Staphylococcus aureus Virulence Affected by an Alternative Nisin A Resistance Mechanism
Kawada-Matsuo, Applied and environmental microbiology 2020 (secret) - An alternative nisin A resistance mechanism affects virulence inStaphylococcus aureus
Kawada-Matsuo, 2019 - Mechanism of Gene Regulation by a Staphylococcus aureus Toxin
Joo, mBio 2016 - “...strains a New NCBI ID Old ID Gene Function P value Fold change b MW_RS10215 MW1875 pmtR GntR type transcriptional regulator 0.01817 50.9 MW_RS10210 MW1874 pmtA ABC transporter ATPase domain 0.01905 7.3 MW_RS10205 MW1873 pmtB ABC transporter membrane domain 0.01921 14.6 MW_RS10200 MW1872 pmtC ABC transporter...”
- Genetic changes that correlate with reduced susceptibility to daptomycin in Staphylococcus aureus
Friedman, Antimicrobial agents and chemotherapy 2006 - “...30S ribosomal protein S21 41 nt upstream of MW1875, hypothetical protein, putative transcription regulator, GntR family 77 nt upstream of MW2528 (acetate-CoA...”
- Mechanism of Gene Regulation by a Staphylococcus aureus Toxin
Joo, mBio 2016 - “...mutant strains a New NCBI ID Old ID Gene Function P value Fold change b MW_RS10215 MW1875 pmtR GntR type transcriptional regulator 0.01817 50.9 MW_RS10210 MW1874 pmtA ABC transporter ATPase domain 0.01905 7.3 MW_RS10205 MW1873 pmtB ABC transporter membrane domain 0.01921 14.6 MW_RS10200 MW1872 pmtC ABC...”
MSMEG_4659 GntR-family protein transcriptional regulator from Mycobacterium smegmatis str. MC2 155
36% identity, 29% coverage
- Azido Inositol Probes Enable Metabolic Labeling of Inositol-Containing Glycans and Reveal an Inositol Importer in Mycobacteria
Hodges, ACS chemical biology 2023 - “...4 selected suppressor mutant clones from the 5-InoAz-treated culture. WGS revealed independent non-synonymous mutations in MSMEG_4659 , which were confirmed by Sanger sequencing in 6 other strains ( Table S2 ). All strains harbored frameshift mutations (nucleotide C724insC, C480del, C252insC, C348insA, A270insA) or introduced STOP codons...”
- “...indicated in Figure S5 . Further characterization efforts were focused on the common mutated gene, MSMEG_4659 . MSMEG_4659 is predicted to encode a GntR-like bacterial transcription factor (PFAM: PF00392). These transcription factors generally possess an N-terminal DNA-binding domain and a C-terminal oligomerization or effector domain. 39...”
- A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria
McKenzie, Journal of bacteriology 2012 - “...sugar MSMEG_4655 MSMEG_4656 MSMEG_4657 MSMEG_4658 MSMEG_4659 MSMEG_4660 MSMEG_4661 MSMEG_4662 MSMEG_4663 MSMEG_4664 MSMEG_4665 MSMEG_4666 MSMEG_5057 MSMEG_5058...”
- GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
Vindal, BMC genomics 2007 - “...MSMEG_0874 FadR 234 MSMEG_4121 FadR 229 MSMEG_0895 FadR 247 MSMEG_4140 MocR 508 MSMEG_2323 MocR 534 MSMEG_4659 HutC 245 MSMEG_1117 FadR 239 MSMEG_5174 YtrA 121 MSMEG_1227 HutC 274 MSMEG_5201 FadR 254 MSMEG_1317 FadR 229 MSMEG_5375 FadR 230 MSMEG_1572 MocR 470 MSMEG_5630 HutC 245 MSMEG_1995 FadR 241 MSMEG_5731...”
- “...- - - - - YdhC MSMEG_4140 - - - - - - - YcnF MSMEG_4659 Rv0792c MAP0628c Mb0816c Mvan_4015 - - MUL_0525 YvoA MSMEG_5174 Rv1152 MAP2632c Mb1183 Mvan_4569 - - MUL_0993 YtrA MSMEG_5201 Rv3060c MAP2347 Mb3086c Mvan_4590 - Mkms_4157 MUL_3832 - MSMEG_5630 - MAP3505c -...”
cg3202 GntR family regulatory protein from Corynebacterium glutamicum ATCC 13032
43% identity, 24% coverage
- Physiological Response of Corynebacterium glutamicum to Indole
Walter, Microorganisms 2020 - “...putative phenol 2-monooxygenase 2.08 cg3169 pck phosphoenolpyruvate carboxykinase (GTP) 2.00 cg3195 putative flavin-containing monooxygenase 1.60 cg3202 farR transcriptional regulator. GntR-family 1.88 cg3226 putative MFS-type L-lactate permease 2.05 cg3303 putative PadR-family transcriptional regulator 2.26 cg3327 dps starvation-inducible DNA-binding protein 1.85 cg3367 ABC-type multidrug transport system, ATPase 1.72...”
- Deciphering the Adaptation of Corynebacterium glutamicum in Transition from Aerobiosis via Microaerobiosis to Anaerobiosis
Lange, Genes 2018 - “...by homologous recombination with pJUL zur This study C. glutamicum farR Markerless deletion of FarR (cg3202) by homologous recombination with pJUL farR This study C. glutamicum ripA Markerless deletion RipA (cg1120) by homologous recombination with pJUL ripA This study C. glutamicum cg2648 Markerless deletion of cg2648...”
- “...zur (cg2502), pK19 mobsacB ::(Flank1-Flank2), Kan R This study pJUL farR For deletion of farR (cg3202), pK19 mobsacB ::(Flank1-Flank2), Kan R This study pJUL ripA For deletion of ripA (cg1120), pK19 mobsacB ::(Flank1-Flank2), Kan R This study pJULcg2648 For deletion of cg2648, pK19 mobsacB ::(Flank1-Flank2), Kan...”
- Single-Domain Peptidyl-Prolyl cis/trans Isomerase FkpA from Corynebacterium glutamicum Improves the Biomass Yield at Increased Growth Temperatures
Kallscheuer, Applied and environmental microbiology 2015 - “...Relative mRNA level (JVO1 fkpA vs JVO1) cg3219 cg3202 cg2114 cg2613 cg0967 cg3255 cg2113 cg2500 cg1003 cg1568 cg1164 cg2833 cg0973 cg2182 cg1853 cg2181 cg1606...”
- Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032
Mentz, BMC genomics 2013 - “...( cg2627) the transcriptional activator of the ketoadipate metabolism genes [ 53 ], FarR ( cg3202 ) a transcriptional regulator involved in nitrogen metabolism [ 54 ], and two members of the HTH_3-family ( cg1392; cg2040 ). Bioinformatic analysis of sequence and structural conservation of trans...”
GmuR / VIMSS728558 GmuR regulator of Glucomannan utilization (repressor) from Bacillus licheniformis DSM 13
41% identity, 27% coverage
DSY2275 hypothetical protein from Desulfitobacterium hafniense Y51
44% identity, 26% coverage
NagQ / VIMSS2205600 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Rhizobium leguminosarum bv. viciae 3841
42% identity, 26% coverage
Mvan_5874 UbiC transcription regulator-associated domain protein from Mycobacterium vanbaalenii PYR-1
37% identity, 30% coverage
SCO1716 gntR-family transcriptional regulator from Streptomyces coelicolor A3(2)
38% identity, 27% coverage
- Structure and regulatory targets of SCO3201, a highly promiscuous TetR-like regulator of Streptomyces coelicolor M145
Xu, Biochemical and biophysical research communications 2014 (PubMed)- “...for the promoter regions of 5 regulators (SCO1716, SCO1950, SCO3367, SCO4009 and SCO5046), a putative histidine phosphatase (SCO1809), an acetyltransferase...”
- “...TetR-family protein SCO1417 Putative GntR-family regulatory protein SCO1716 Possible GntR family transcriptional regulator (2nd gene of an operon of 3 genes...”
- Cloning and characterization of the pyrrolomycin biosynthetic gene clusters from Actinosporangium vitaminophilum ATCC 31673 and Streptomyces sp. strain UC 11065
Zhang, Antimicrobial agents and chemotherapy 2007 - “...(BAC76515), 54/44 SCO1715 (CAB50930), 83/75 SCO1716 (CAB50931), 81/70 MvanDRAFT_5628 Bcep18194_C7158 (AAB06202), 69/56 Formate dehydrogenase Flavin adenine...”
PdhR / VIMSS6935293 PdhR regulator of Pyruvate metabolism, effector Pyruvate (repressor) from Shewanella baltica OS155
50% identity, 24% coverage
Q9I041 Probable transcriptional regulator from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA14_27900 putative transcriptional regulator from Pseudomonas aeruginosa UCBPP-PA14
PA2802 probable transcriptional regulator from Pseudomonas aeruginosa PAO1
50% identity, 27% coverage
EP10_000465 GntR family transcriptional regulator from Geobacillus icigianus
43% identity, 27% coverage
- The Transcriptomic Response of Cells of the Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation
Peltek, International journal of molecular sciences 2024 - “...EP10_001940), of the gene responsible for negative regulation of the transport and utilization of N-acetylglucosamine (EP10_000465) [ 24 ], the operon encoding the system of transport and utilization of fructose (EP10_002551, EP10_002552, and EP10_002553), a lactic-acid synthesis gene (EP10_003019), and genes of enzymes related to the...”
- “...and of the gene coding for the negative regulator of transport and utilization of N-acetylglucosamine (EP10_000465) (promoting inhibition of the utilization of N-acetylglucosamine as a carbon source [ 24 ], thereby allowing this compound to be redirected to the synthesis of the main component of the...”
D0Z05_15530 transcriptional regulator LldR from Enterobacter hormaechei
43% identity, 24% coverage
AraR / VIMSS64456 AraR regulator of Arabinose utilization, effector Arabinose (repressor) from Bacillus halodurans C-125
Q9KBQ0 Arabinose metabolism transcriptional repressor from Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
41% identity, 17% coverage
PdhR / VIMSS7700630 PdhR regulator of Pyruvate metabolism, effector Pyruvate (repressor) from Tolumonas auensis DSM 9187
48% identity, 24% coverage
KP1_5297 putative GntR-family transcriptional repressor for L-lactate utilization from Klebsiella pneumoniae NTUH-K2044
43% identity, 24% coverage
M28_Spy0522 transcriptional regulator, GntR family from Streptococcus pyogenes MGAS6180
42% identity, 27% coverage
PdhR / VIMSS4632354 PdhR regulator of Pyruvate metabolism, effector Pyruvate (repressor) from Moritella sp. PE36
52% identity, 22% coverage
TM0766 / VIMSS7084055 TM0766 regulator of Hypothetical ABC transporter (repressor) from Thermosipho melanesiensis BI429
40% identity, 60% coverage
BH0651 transcriptional regulator (GntR family) from Bacillus halodurans C-125
Q9KF35 Transcriptional regulator (GntR family) from Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
37% identity, 59% coverage
PHNR_SALTY / Q7CR30 Putative transcriptional regulator of 2-aminoethylphosphonate degradation operons from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
PhnR / VIMSS147806 PhnR regulator of Phosphonate utilization; 2-aminoethylphosphonate utilization, effector 2-aminoethylphosphonate (repressor) from Salmonella typhimurium LT2
STM0430 2-aminoethylphosphonate transport, repressor from Salmonella typhimurium LT2
42% identity, 28% coverage
- A Salmonella Regulator Modulates Intestinal Colonization and Use of Phosphonoacetic Acid
Elfenbein, Frontiers in cellular and infection microbiology 2017 - “...2015 ). This gene shares 29.2% sequence similarity and 45.1% amino acid identity with PhnR (STM0430; Sievers et al., 2011 ). We hypothesized that STM3602 might regulate one or both of the phosphonate utilization loci in STm. We characterized the survival and growth of the STM3602...”
- “...Salmonella lacks the gene phnF but has a putative regulator of phosphonate utilization, phnR ( STM0430 ). STM3602 has 45.1% amino acid identity with PhnR (Sievers et al. 2011). The GC content of STM3602 and phnR differ substantially (49 and 59%, respectively), consistent with recent acquisition...”
YidP / b3684 putative DNA-binding transcriptional regulator YidP from Escherichia coli K-12 substr. MG1655 (see 5 papers)
yidP / RF|NP_418139 uncharacterized HTH-type transcriptional regulator yidP from Escherichia coli K12 (see 2 papers)
b3684 predicted DNA-binding transcriptional regulator from Escherichia coli str. K-12 substr. MG1655
P31453 Uncharacterized HTH-type transcriptional regulator YidP from Escherichia coli (strain K12)
39% identity, 27% coverage
GamR / VIMSS726383 GamR regulator of Glucosamine utilization, effector Glucosamine-6-phosphate (repressor) from Bacillus licheniformis DSM 13
38% identity, 27% coverage
F3P16_RS11440 UTRA domain-containing protein from Acinetobacter baumannii
42% identity, 29% coverage
PdhR / VIMSS3564242 PdhR regulator of Pyruvate metabolism, effector Pyruvate (repressor) from Aeromonas salmonicida subsp. salmonicida A449
48% identity, 24% coverage
CDR20291_1936 GntR-family transcriptional regulator from Clostridium difficile R20291
CD2023 GntR-family transcriptional regulator from Clostridium difficile 630
CDR20291_1936 GntR family transcriptional regulator from Clostridioides difficile R20291
41% identity, 59% coverage
- Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms
Slater, Scientific reports 2019 - “...CDR20291_1716 1.3143654 thiol peroxidase 9 CDR20291_1717 1.110872 hypothetical protein 10 CDR20291_1934 1.5456229 hypothetical protein 11 CDR20291_1936 1.3368874 GntR family transcriptional regulator 12 CDR20291_1937 1.3736945 ABC transporter ATP-binding protein 13 CDR20291_2389 1.2619709 competence protein 14 CDR20291_2830 1.11333 ribonucleoside-diphosphate reductase subunit alpha 15 CDR20291_2928 1.7538156 PTS system transporter...”
- Control of Clostridium difficile Physiopathology in Response to Cysteine Availability
Dubois, Infection and immunity 2016 - “...(fur) CD3176 (sigL) Intron CD0278 Intron CD2065 Intron CD2023 Intron CD3176 Intron CD2602 Intron CD1594 (cysK) Antisense CD3029 (malY) Resistance Cmr Tmr Cmr...”
- “...as several regulators of unknown function (CD2065, CD0278, and CD2023 [Table 1]). As described in Fig. S1 in the supplemental material, primers were designed to...”
SMb21464 putative transcriptional regulator, gntR family protein from Sinorhizobium meliloti 1021
40% identity, 28% coverage
Z5031 transcriptional regulator from Escherichia coli O157:H7 EDL933
39% identity, 24% coverage
DVU2953 transcriptional regulator, GntR family from Desulfovibrio vulgaris Hildenborough
35% identity, 14% coverage
LldR / b3604 DNA-binding transcriptional dual regulator LldR from Escherichia coli K-12 substr. MG1655 (see 5 papers)
NP_418061 DNA-binding transcriptional dual regulator LldR from Escherichia coli str. K-12 substr. MG1655
P0ACL7 Putative L-lactate dehydrogenase operon regulatory protein from Escherichia coli (strain K12)
b3604 DNA-binding transcriptional repressor from Escherichia coli str. K-12 substr. MG1655
39% identity, 24% coverage
- Lactate utilization is regulated by the FadR-type regulator LldR in Pseudomonas aeruginosa.
Gao, Journal of bacteriology 2012 - Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli.
Aguilera, Journal of bacteriology 2008 - GeneRIF: These results are consistent with the hypothesis that LldR has a dual role, acting as a repressor or an activator of lldPRD operon.
- A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2
Chakraborty, Applied and environmental microbiology 2021 (secret) - The Two-Component Monooxygenase MeaXY Initiates the Downstream Pathway of Chloroacetanilide Herbicide Catabolism in Sphingomonads
Cheng, Applied and environmental microbiology 2017 - “...dehydratase O09174 AKV10929 49 63 Transcriptional regulator P0ACL7 30 WP_018684803 50 Q0S811 30 WP_048575098 P27137 KMS51534 67 29 100 B8NKI4 WP_048574811...”
- Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery
Neusser, BMC genomics 2010 - “...transcriptional regulator b3319 rplD 0.63 50S ribosomal protein L4 b1526 yneJ 0.62 predicted transcriptional regulator b3604 lldR 0.62 transcriptional repressor b1320 ycjW 0.61 predicted transcriptional regulator b1328 ycjZ 0.60 predicted transcriptional regulator b3604 lldR 0.57 transcriptional repressor b1014 putA 0.54 fused DNA-binding transcriptional repressor b1334 fnr...”
- Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms
Wang, The ISME journal 2009 - “...-protein trpB b1261 1.6 Tryptophan synthase, -protein Carbohydrate metabolism lldP b3603 3.0 L-lactate permease lldR b3604 2.5 Transcriptional regulator lldD b3605 2.3 L-lactate dehydrogenase sdhA b0723 1.9 Succinate dehydrogenase, flavoprotein subunit sdhB b0724 1.9 Succinate dehydrogenase, iron sulfur protein sdhC b0721 1.7 Succinate dehydrogenase, cytochrome b556...”
- The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...0.9 17.04 1 0.86 0.54 2.38 1 0.58 0.53 0.65 This work L-lactate permease lldR b3604 lldPRD 1 29.89 0.79 15.07 1 0.07 0.13 0.33 1 0.73 0.54 0.86 This work transcriptional regulator lldD b3605 lldPRD 1 12.6 0.79 7.63 1 0.21 0.15 0.56 1 0.68...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...b3544 2.5 2.7 Dipeptide transport protein lldP lldR lldD b3603 b3604 b3605 2 2.5 3.1 2.6 3.5 2 L-Lactate glpK b3926 2.3 4.4 Glycerol kinase glpF b3927 2.9 4.9...”
- Rapid identification and mapping of insertion sequences in Escherichia coli genomes using vectorette PCR
Zhong, BMC microbiology 2004 - “...sequence (Fig. 2 ). Three additional IS3 elements were found at b0805 ( IS3 -b), b3604 ( IS3 -e), b4242 ( IS3 -f). IS4 One IS4 was located based on flanking sequences amplified from both sides. No additional IS4 insertions were found. IS5 Primers IS5 -A...”
- “...1642 P P IS3 -d 3427623 b3280 - 953 646 P P IS3 -e 3776882 b3604 - 1435 935* P P P IS3 -f 4466303 b4242 - 640 935* P P P IS5 -a 1102866 b1040-b1041 + 365 400 P P IS30 -a 4115565 b3927 -...”
- Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
Mariño-Ramírez, Journal of bacteriology 2004 - “...ybaD ybaO ybbN ybcW ybdB ybdG ybeZ ybgC ybgF b3633 b3604 b0179 b0889 b1517 b1512 b2463 b1620 b4037 b4346 b4119 b3929 b3939 b0349 b0783 b4351 b0091 b2733 b2286...”
- Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
Pomposiello, Journal of bacteriology 2001 - “...b2090 b2095 b0720 b3212 b2947 b3510 b3509 b2237 b1732 b3604 b3603 b4129 b1817 b1818 b1531 b1532 b1530 b3028 b3601 b0578 b1482 b4376 b1897 b0932 b0903 b1014...”
A0A0R2I605 HTH gntR-type domain-containing protein from Carnobacterium divergens DSM 20623
42% identity, 14% coverage
AgaR / VIMSS2059626 AgaR regulator of N-acetylgalactosamine utilization, effector N-acetylgalactosamine (repressor) from Streptococcus sanguinis SK36
42% identity, 28% coverage
NagQ / VIMSS2775968 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Reinekea sp. MED297
45% identity, 25% coverage
MMB18_RS11700 histidine utilization repressor from Burkholderia contaminans
41% identity, 29% coverage
NagQ / VIMSS3411617 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Silicibacter TM1040
42% identity, 27% coverage
CD0652 GntR-family transcriptional regulator from Clostridium difficile 630
41% identity, 59% coverage
I35_RS10875 histidine utilization repressor from Burkholderia cenocepacia H111
41% identity, 29% coverage
- Transcriptional Response of Burkholderia cenocepacia H111 to Severe Zinc Starvation
Barnett, British journal of biomedical science 2023 - “...ABC transporter substrate-binding protein 3.449536319 6.4E17 I35_RS16055 Amino acid ABC transporter ATP-binding protein 3.362442596 8.91E17 I35_RS10875 Histidine utilization repressor 3.330074112 0.0000992 I35_RS01035 Phenylacetic acid degradation protein 3221187039 0.001583599 I35_RS10870 Urocanate hydratase 3.121275534 0.010056873 I35_RS28525 Carbonate dehydratase 3.090073095 3.69E61 I35_RS01040 Phenylacetate-CoA oxygenase subunit PaaB 3.088767817 0.002296074 I35_RS13375...”
SE1039_RS08735 PSM export ABC transporter transcriptional regulator PmtR from Staphylococcus equorum
38% identity, 52% coverage
Tsac_0038 GntR family transcriptional regulator from Thermoanaerobacterium saccharolyticum JW/SL-YS485
40% identity, 27% coverage
lmo2241 similar to transcriptional regulators (GntR family) from Listeria monocytogenes EGD-e
LMRG_01591 hypothetical protein from Listeria monocytogenes 10403S
36% identity, 56% coverage
- A novel RofA-family transcriptional regulator, GadR, controls the development of acid resistance in Listeria monocytogenes
Wu, mBio 2023 - “...shift in carbon metabolism during growth in acidic conditions. Expression of multiple transcriptional regulators (e.g., lmo2241 , lmo2551 , lmo0815 , and lmo2494 ) was also affected, and these might be partially responsible for the SigB-independent differentially regulated genes (Table S2). The identification of GadR as...”
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...protein L21 3.22 0.00 LMRG_01435 lmo1535 LMRG_01435-LMRG_01436 YebC/PmpR family DNA-binding transcriptional regulator 2.25 0.00 LMRG_01591 lmo2241 LMRG_01591-LMRG_01593 Transcriptional regulator, GntR family 2.25 0.00 LMRG_01669 lmo2163 LMRG_01669-LMRG_01673 Myo-inositol 2-dehydrogenase 1, Oxidoreductase 2.21 0.00 LMRG_01810 lmo2438 ClbS/DfsB family four-helix bundle protein 2.97 0.00 LMRG_01955 lmo2741 LMRG_01955-LMRG_01957 Multidrug-efflux transporter,...”
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...ribosomal protein L21 3.22 0.00 LMRG_01435 lmo1535 LMRG_01435-LMRG_01436 YebC/PmpR family DNA-binding transcriptional regulator 2.25 0.00 LMRG_01591 lmo2241 LMRG_01591-LMRG_01593 Transcriptional regulator, GntR family 2.25 0.00 LMRG_01669 lmo2163 LMRG_01669-LMRG_01673 Myo-inositol 2-dehydrogenase 1, Oxidoreductase 2.21 0.00 LMRG_01810 lmo2438 ClbS/DfsB family four-helix bundle protein 2.97 0.00 LMRG_01955 lmo2741 LMRG_01955-LMRG_01957 Multidrug-efflux...”
DvMF_1994 / VIMSS8501261 DvMF_1994 regulator of Carbohydrate metabolism from Desulfovibrio vulgaris str. Miyazaki F
42% identity, 27% coverage
PP1697 transcriptional regulator, GntR family from Pseudomonas putida KT2440
41% identity, 21% coverage
LldR / VIMSS150974 LldR regulator of Lactate utilization, effector L-lactate (activator/repressor) from Salmonella typhimurium LT2
STM3693 putative transcriptional regulator for lct operon (GntR family) from Salmonella typhimurium LT2
43% identity, 24% coverage
BCAM0966 GntR family regulatory protein from Burkholderia cenocepacia J2315
39% identity, 24% coverage
SM_b20758 putative transcriptional regulator, GntR or ArsR family protein from Sinorhizobium meliloti 1021
35% identity, 30% coverage
- Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis
Taboada-Castro, Frontiers in bioinformatics 2024 - “...and SMa2287; four LacI family TFs: SM_b20667, SM_b21187, SM_b21272, and SMa0078; four ArsR family TFs: SM_b20758, SM_b21008, SM_b21576, and SM_b21601; two AraC family TFs: SM_b21419 and SM_b21559; two TetR family TFs: SMa1726 and SMa2387; one ROK family member: SMa 2004; one MerR family gene: SMA1705; one...”
- “...group enumerated with 0 was constituted of the carbonphosphorus lyase SM_b20759, the ArsR family TF SM_b20758, and the propionyl-CoA carboxylase subunit beta SM_b20755. One of the numerous groups of neighbor genes was the 111 group numerated from 473 to 487; it contains ABC transporter permease SMc02160,...”
PA1142 probable transcriptional regulator from Pseudomonas aeruginosa PAO1
44% identity, 29% coverage
NagQ / VIMSS7175194 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Marinomonas sp. MWYL1
38% identity, 28% coverage
SCO4215 GntR-family regulatory protein from Streptomyces coelicolor A3(2)
43% identity, 26% coverage
- Effects of carbon ion beam-induced mutagenesis for the screening of RED production-deficient mutants of Streptomyces coelicolor JCM4020
Yanagisawa, PloS one 2022 - “...8 Mt 202004 5,148,481 G>T UTR 4,727,540 352G>T Glu118* N GntR family transcriptional regulator JCM4020_43460 SCO4215 100.0 4,593,233 C>A UTR 4,565,012 1316_1317insG Val440>FS F membrane protein (SarA) JCM4020_41980 SCO4069 100.0 9 Mt 202007 6,013,594 22 T>C Ser8Pro M two-component system response regulator JCM4020_55720 SCO5455 100.0 4,593,233...”
- Genome-Wide Mutagenesis Links Multiple Metabolic Pathways with Actinorhodin Production in Streptomyces coelicolor
Xu, Applied and environmental microbiology 2019 - “...), SCO2832 , SCO2987 ( ohrR ), SCO3269 , SCO3571 , SCO3981 , SCO4118 , SCO4215 , SCO4358 , and SCO5351 , and eight ACT downmodulators, SCO1728 , SCO2179 , SCO2686 , SCO3008 , SCO3579 ( wblA ), SCO3664 , SCO4426 ( afsR ), and SCO5803...”
- “...gene complementation 36 pHXZ108 pMT3 harboring SCO4025 , for gene complementation 36 pHXZ109 pMT3 harboring SCO4215 , for gene complementation 36 pHXZ110 pMT3 harboring SCO4358 , for gene complementation This work pHXZ111 pMT3 harboring SCO4892 , for gene complementation This work pHXZ114 pMT3 harboring SCO6265 ,...”
- Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance
Szafran, Frontiers in microbiology 2019 - “...Regulators sco3435 14 1.72 1.58 Transcriptional regulator sco4214 2429 -6.55 -6.60 AbaA-like regulatory protein xlnR sco4215 820 -2.05 -2.20 GntR family transcriptional regulator sco4671 21 2.31 2.08 LysR family transcriptional regulator sco4673 56 3.20 2.35 DeoR family transcriptional regulator sco5656 2804 -1.80 -2.15 Transcriptional regulator lexA...”
- Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
Rebets, Frontiers in microbiology 2018 - “...0.4 21 2.7 29 0.9 12885 SCO5100 GntR1 30 1.8 35 0.9 34 2.7 17315 SCO4215 GntR2 32 0.4 34 0.4 34 3.7 18945 SCO3864 GntR3 33 0.4 34 0.4 34 3.3 04375 SCO6974 GntR4 30 2.3 34 0.4 31 2.3 Effect of Sigma Factor Gene...”
- Large-Scale Transposition Mutagenesis of Streptomyces coelicolor Identifies Hundreds of Genes Influencing Antibiotic Biosynthesis
Xu, Applied and environmental microbiology 2017 - “...harboring SCO3664 pMT3 harboring SCO4025 pMT3 harboring SCO4215 pMT3 harboring SCO5264 pMT3 harboring SCO6118 pMT3 harboring SCO6265 pMT3 harboring SCO7733 77...”
- Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism
Guyet, BMC microbiology 2014 - “...catcccgccg 5.08 -30 2.653 s. m. SCO3971 SLI4220 SGR3620 tggccggtac 7.78 -465 1.631 u. f. SCO4215 SLI4452 - xlnR gatgaggccg 3.74 -294 1.964 r. SCO5240 SLI5531 SGR2274 wblE tgtcccgatc 5.99 -170 2.246 u. f. SCO5862 SLI6134 SGR1670 cutR tggccgaaaa 7.69 -99 1.927 r. SCO6009 SLI6398 SGR1498...”
LMOf2365_2274 transcriptional regulator, GntR family from Listeria monocytogenes str. 4b F2365
36% identity, 56% coverage
BMEII0370 HISTIDINE UTILIZATION REPRESSOR from Brucella melitensis 16M
37% identity, 30% coverage
KSF55_06595 PLP-dependent aminotransferase family protein from Lactiplantibacillus pentosus
39% identity, 15% coverage
DR0265 histidine utilization repressor HutC, putative from Deinococcus radiodurans R1
44% identity, 24% coverage
- Identification of new genes contributing to the extreme radioresistance of Deinococcus radiodurans using a Tn5-based transposon mutant library
Dulermo, PloS one 2015 - “...analyses also point out a new transcriptional regulator belonging to the GntR family, encoded by DR0265 , and a predicted RNase belonging to the newly described Y family, both contributing to the extreme radioresistance of D . radiodurans . Altogether, this work has revealed new cell...”
- “...performed an initial characterization of three previously undescribed radiosensitive mutants inactivated for loci DR0007 , DR0265 and DR2462 . Results and Discussion Construction of a Tn 5 -based transposon mutant library in D . radiodurans To generate a collection of mutants in D . radiodurans ,...”
Ccel_1263 FadR/GntR family transcriptional regulator from Ruminiclostridium cellulolyticum H10
40% identity, 32% coverage
TreR / VIMSS2180048 TreR regulator of Trehalose utilization, effector Trehalose-6-phosphate (repressor) from Leuconostoc mesenteroides mesent. 8293
41% identity, 27% coverage
Atu3252 transcriptional regulator, GntR family from Agrobacterium tumefaciens str. C58 (Cereon)
43% identity, 29% coverage
- A peptidoglycan N-deacetylase specific for anhydroMurNAc chain termini in Agrobacterium tumefaciens
Gilmore, The Journal of biological chemistry 2024 - “...gene annotated as the GntR-family regulator of hexuronate transporter and metabolism exuR ( 15 ) (Atu3252) and an unannotated MarR-family transcriptional regulator (Atu4504). The tRNA adenosine dimethylallytransferase MiaA (Atu2039) showed as having an increased number of Tn insertions compared with the WT strain suggesting that its...”
- A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Budnick, Scientific reports 2020 - “..., atu5118 , atu0484 , atu0828 , atu1296 , atu2187 , atu2350 , atu2384 , atu3252 , atu4782 , atrA , atrB , avhB1 , and chvE . Surprisingly, we determined that the A. tumefaciens rVtlR protein did not interact with any of these promoter regions...”
DR_0265 GntR family transcriptional regulator from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
44% identity, 27% coverage
- Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species
Lim, FEMS microbiology reviews 2019 - “...Others DdrI 1 1 1 1 1 1 1 1 1 1 1 DR_0171 1 DR_0265 1 2 2 1 1 2 1 1 1 1 See the legend to Table 2 . Regulators of DNA repair system The metallopeptidase/repressor pair IrrE/DdrO Based on the currently...”
- “...understanding how it directly or indirectly regulates gene expression in D. radiodurans requires further work. DR_0265 is another predicted DNA-binding transcription factor (GntR family). Its contribution to radiation resistance has been found after screening transposon mutants (Dulermo etal. 2015 ). The target genes for DR_0265 are...”
- Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria
Thiaville, Molecular microbiology 2015 - “...(EC 6.3.2.4) -2.7 3.15E-02 0.232 DR_1074 (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase (EC 4.2.1.-) -2.7 4.27E-04 0.284 DR_0265 Predicted transcriptional regulator of N-Acetylglucosamine utilization, GntR family -2.8 5.32E-03 1 DR_1082 Ribosomal subunit interface protein -2.9 1.25E-04 0.922 DR_2033 Glutamine synthetase type III, GlnN (EC 6.3.1.2) -3.3 1.24E-04 1...”
BC3792 Transcriptional regulator, GntR family from Bacillus cereus ATCC 14579
BMB171_C3461, BMB171_RS18795 GntR family transcriptional regulator from Bacillus thuringiensis BMB171
38% identity, 27% coverage
- Correction: SecDF as Part of the Sec-Translocase Facilitates Efficient Secretion of Bacillus cereus Toxins and Cell Wall-Associated Proteins
, PloS one 2014 - “...protein 0.06 2.9E-07 BC3790 Nucleoside transport ATP-binding protein 0.11 3.5E-05 BC3791 Nucleoside-binding protein 0.06 1.7E-06 BC3792 Transcriptional regulator, GntR family 0.09 1.4E-05 BC4405 Protein translocase subunit SecDF 0.13 1.0E-05 BC4831 ABC transporter ATP-binding protein 6.68 3.9E-08 BC5117 ABC transporter permease protein 0.11 1.6E-06 BC5118 ABC transporter...”
- SecDF as part of the Sec-translocase facilitates efficient secretion of Bacillus cereus toxins and cell wall-associated proteins
Vörös, PloS one 2014 - “...protein 0.06 2.9E-07 BC3790 Nucleoside transport ATP-binding protein 0.11 3.5E-05 BC3791 Nucleoside-binding protein 0.06 1.7E-06 BC3792 Transcriptional regulator, GntR family 0.09 1.4E-05 BC4405 Protein translocase subunit SecDF 0.13 1.0E-05 BC4831 ABC transporter ATP-binding protein 6.68 3.9E-08 BC5117 ABC transporter permease protein 0.11 1.6E-06 BC5118 ABC transporter...”
- Assessment of CcpA-mediated catabolite control of gene expression in Bacillus cereus ATCC 14579
van, BMC microbiology 2008 - “...under the apparent control of the transcriptional regulator encoded by the also higher expressed ymfC (BC3792), for both the regulator and the yuf -operon putative CRE-sites could be identified (see Additional file 2 ). Interestingly, expression of two putative operons with an apparent function in catabolism...”
- NupR Responding to Multiple Signals Is a Nucleoside Permease Regulator in Bacillus thuringiensis BMB171
Qin, Microbiology spectrum 2022 - “...NupR are marked in green, red, deep blue, blue, and brown, respectively. 3461 to 3457, BMB171_C3461 (NupR/NagR), BMB171_C3460 (nucleoside-binding protein), BMB171_C3459 (nucleoside transport ATP-binding protein), and BMB171_C3458-3457 (nucleoside transport system permease protein), respectively. (C) Effects of the mutants in transcription factor CcpA/ComK/PurR conservative binding site on...”
- “...5.397 GGAGGTCAAACGTCTAATGA Pro BMB171_RS26735 Bacillolysin 1.452 AGTGGTATGACAACTCAAAA Pro BMB171_RS26950 HAD superfamily hydrolase 1.707 AATAGTAAGACATCAAACCT Pro BMB171_RS18795 GntR family transcriptional regulator CGACCTCTGATGTAAGACTT Pro BMB171_RS26765 Collagen adhesion protein 5.91 AAAGGTCTGATATCATTCTT Pro BMB171_RS26545 Uracil phosphoribosyltransferase 6.51 CGAAGTAAGACAACTGACGA Pro BMB171_RS20290 Uracil permease 7.54 ACAGGTCTGACGTCTATCGT CDS b BMB171_RS00930 Diadenylate cyclase 2.39...”
PdhR / VIMSS10254524 PdhR regulator of Pyruvate metabolism, effector Pyruvate (repressor) from Edwardsiella tarda EIB202
ETAE_0658 pyruvate dehydrogenase complex repressor from Edwardsiella tarda EIB202
48% identity, 24% coverage
LldR / VIMSS7532440 LldR regulator of Lactate utilization, effector L-lactate (repressor) from Desulfomicrobium baculatum DSM 4028
41% identity, 27% coverage
NagQ / VIMSS1251569 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Jannaschia sp. CCS1
42% identity, 27% coverage
SERP1478 transcriptional regulator, GntR family from Staphylococcus epidermidis RP62A
F1613_RS11065 PSM export ABC transporter transcriptional regulator PmtR from Staphylococcus epidermidis
38% identity, 54% coverage
- Toxin Mediates Sepsis Caused by Methicillin-Resistant Staphylococcus epidermidis
Qin, PLoS pathogens 2017 - “...- SERP0095 trans-sulfuration enzyme family protein -8.77 - SERP2196 MarR family transcriptional regulator -8.64 - SERP1478 GntR family transcriptional regulator -8.26 - SERP2003 amino acid ABC transporter ATP-binding protein -7.99 - SERP2187 hypothetical protein -7.65 - SERP2195 alpha keto acid dehydrogenase complex, E3 component, lipoamide dehydrogenase...”
- “...- SERP0473 hypothetical protein -5.46 -1.31 -4.17 - SERP1474 hypothetical protein -5.27 -11.93 2.26 - SERP1478 GntR family transcriptional regulator -4.32 -11.37 2.63 - SERP2158 amino acid permease -3.75 -3.27 -1.14 - SERP0944 ThiJ/PfpI family protein -3.71 -1.71 -2.16 trpG SERP0938 anthranilate synthase component II -3.65...”
- Genome-wide transcription response of Staphylococcus epidermidis to heat shock and medically relevant glucose levels
Benjamin, Frontiers in microbiology 2024 - “...( Supplementary Table S2 ). We also observed downregulation of other transcription regulators including rsp., F1613_RS11065 (GntR family transcription regulator), and pyrR by 5.5-, 4.6-, and 4.1-fold, respectively ( Supplementary Table S2 ). Sixteen hypothetical proteins and 23 uncharacterized genes (39 total) were also downregulated under...”
SPy1285 / VIMSS3591554 SPy1285 regulator of Transport (repressor) from Streptococcus suis 05ZYH33
42% identity, 53% coverage
SMb20441 putative transcriptional regulator protein from Sinorhizobium meliloti 1021
42% identity, 26% coverage
- Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome
Mauchline, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...reporter fusion revealed a constitutive promoter upstream of SMb20441 (GntRtype regulator), but no expression was obtained on cloning the region upstream of...”
- “...the promoter for a large transcript, including SMb20441, SMb20442 (SBP), SMb20443 (small permease), SMb20444 (large permease), SMb20445 (putative alcohol...”
- The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti
Finan, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...GntR-like genes were apparent (e.g., SMb20106, SMb20129, and SMb20441). In addition to the above regulators, we have identified four rpoE-like genes encoding...”
DASR_STRGR / Q8VV01 HTH-type transcriptional repressor DasR from Streptomyces griseus (see paper)
45% identity, 26% coverage
- function: Global regulator that is part of the nutrient-sensing system. In the absence of glucosamine 6-P (GlcN6P), represses the phosphotransferase system (PTS) specific for the uptake of N- acetylglucosamine (PTSNag), and genes involved in the metabolism of chitin, as well as several genes involved in development, thereby linking carbon availability to morphogenesis (By similarity). Regulates the dasABC transport operon involved in glucose-related morphogenesis. Essential for development (PubMed:11741848).
SCO3264 gntR-family regulator from Streptomyces coelicolor A3(2)
38% identity, 26% coverage
- Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
Romero-Rodríguez, BMC microbiology 2016 - “...ScoZm comparison, the four genes encoding regulatory proteins that showed stimulation belonged to the GntR (SCO3264, SCO3986), LuxR families (SCO4261) and a transcriptional activator (SCO6288) (Additional file 1 : Table S2). The two regulators belonging to the GntR family, the SCO3264, and SCO3986, were highly overexpressed...”
- “...transcriptional factors have been previously described. The in silico prediction of the putative targets of SCO3264 has revealed a large set of sensitive genes involved in primary and secondary metabolism. Actually, in a S. coelicolor SCO3264 mutant constructed in our lab, a premature and high-level production...”
SG0466 pyruvate dehydrogenase complex repressor from Sodalis glossinidius str. 'morsitans'
48% identity, 24% coverage
O31761 Uncharacterized HTH-type transcriptional regulator YmfC from Bacillus subtilis (strain 168)
42% identity, 27% coverage
PdhR / b0113 DNA-binding transcriptional dual regulator PdhR from Escherichia coli K-12 substr. MG1655 (see 5 papers)
PdhR / P0ACL9 Transcription factor PdhR (repressor) from Escherichia coli K12 MG1655 (see 2 papers)
P0ACL9 Pyruvate dehydrogenase complex repressor from Escherichia coli (strain K12)
NP_414655 DNA-binding transcriptional dual regulator PdhR from Escherichia coli str. K-12 substr. MG1655
b0113 transcriptional regulator of pyruvate dehydrogenase complex from Escherichia coli str. K-12 substr. MG1655
ECs0117 transcriptional regulator for pyruvate dehydrogenase complex from Escherichia coli O157:H7 str. Sakai
48% identity, 24% coverage
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...no.b Descriptionb pI/MW Theoreticalc Experimentald P0ACL9 Pyruvate dehydrogenase complex repressor 6.04/29,425.47 PdxB P05459 Erythronate-4-phosphate...”
- Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility.
Anzai, Microbial genomics 2020 - GeneRIF: Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility.
- PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli.
Ogasawara, Journal of bacteriology 2007 - GeneRIF: Study suggests that PdhR is a master regulator for controlling the formation of not only the PDH complex but also the respiratory electron transport system.
- PdhR, the pyruvate dehydrogenase repressor, does not regulate lipoic acid synthesis.
Feng, Research in microbiology - GeneRIF: These data show that PdhR plays no physiological role in regulation of lipA expression.
- An integrated approach to reconstructing genome-scale transcriptional regulatory networks
Imam, PLoS computational biology 2015 - “...25 1 14.2 1.9 12.9 13.3 b1014 (PutA) 2 13.3 100 20 50 33.3 50 b0113 (PdhR) 42 10.7 7.1 71.4 11.9 100 14 b0020 (NhaR) 7 10.5 28.5 50 14.3 100 14.3 b3702 (DnaA) 12 6.8 33.3 10 16.7 3.5 16.7 b3912 (CpxR) 63 6.6...”
- Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding
Myers, PLoS genetics 2013 - “...[18] 3,654,924 hdeD b3511 Acid-Resistance Membrane Protein 1 43.5 + + None [18] 121,987 pdhR-aceEF-lpdA b0113 Pyruvate Dehydrogenase 1 50.5 + [29] [140] 770,404 cydAB b0733 Cytochrome bd -1 Terminal Oxidase 1 53.5 + + [50] [141] 3,654,924 hdeAB-yhiD b3510 Acid-Resistance Proteins 1 126.5 + +...”
- Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
King, Applied and environmental microbiology 2010 - “...ECs3371 ECs4239 ECs0117 ECs1043 ECs2137 b2509 b3397 b0113 b0959 b1530 Replication, recombination, and repair ECs0528 ECs0668 ECs0965 b0475 b0630 b0879 ECs0154...”
- A PhoQ/P-regulated small RNA regulates sensitivity of Escherichia coli to antimicrobial peptides
Moon, Molecular microbiology 2009 - “...Descriptions Fold change Fold change Fold change Fold change Exp 1 Exp2 Exp1 Exp2 pdhR b0113 2.2 1.1 8.5 5.6 transcriptional regulator for pyruvate dehydrogenase complex rhlE b0797 2.6 1.8 2.7 2.2 putative ATP-dependent RNA helicase ycaD b0898 2.6 1.3 2.2 2.0 Putative MFS transporter aroA...”
- Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine
Hancock, Infection and immunity 2007 - “...rplK iscR rseA yceD ryhB Z5401 b0990 b3703 b3336 c4228 b0113 b3983 b2531 b2572 b1088 b4451 Z5401 5S rRNA 23S rRNA 16S rRNA 10Sa RNA (tmRNA); tags incomplete...”
- Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
Ren, Applied and environmental microbiology 2005 - “...1.7 0.0189 1.1 nrdE b2675 1.4 0.0807 1.5 0.0143 1.5 pdhR b0113 1.3 0.0114 2.0 0.0373 1.3 yhgJ b3419 1.2 0.0509 1.4 0.0256 1.0 yhgK b3420 1.3 0.0847 1.6 0.0016...”
- Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity
Weber, Journal of bacteriology 2005 - “...b3515 gadX b3516 gem pdhR rssB wrbA yiaG yjdC b1285 b0113 b1235 b1004 b3555 b4135 Transport and membrane (20) artM artP blc eutH gabP mscL potF rssA ugpB ugpC...”
- Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
Pomposiello, Journal of bacteriology 2001 - “...b0096 b4034 b4035 b0168 b1531 b0086 b0578 b2281 b2279 b0113 b4025 b1101 b1658 b3317 b3319 b3305 b3985 b3318 b3312 b3314 b3321 b3316 b0724 b3908 b4062 b0729...”
- Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
King, Applied and environmental microbiology 2010 - “...not present in COGs Transcription ECs3371 ECs4239 ECs0117 ECs1043 ECs2137 b2509 b3397 b0113 b0959 b1530 Replication, recombination, and repair ECs0528 ECs0668...”
- Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
Bergholz, Applied and environmental microbiology 2009 - “...recA 1.47 0.71 0.85 0.96 1.11 Energy metabolism ECs0117 ECs0512 ECs1054 ECs1487 ECs1862 ECs2002 ECs2056 ECs2078 ECs2132 ECs2239 ECs2511 ECs2583 ECs3346 ECs3527...”
SMa0402 putative GntR-type regulator from Sinorhizobium meliloti 1021
39% identity, 30% coverage
NagQ / VIMSS2036665 NagQ regulator of N-acetylglucosamine utilization, effector N-acetylglucosamine (repressor) from Ralstonia eutropha H16
H16_A0310 GntR family transcriptional regulator from Cupriavidus necator H16
H16_A0310 transcriptional regulator, GntR-family from Ralstonia eutropha H16
42% identity, 28% coverage
BruAb2_0306 HutC, histidine utilization repressor from Brucella abortus biovar 1 str. 9-941
BAB2_0308 Bacterial regulatory protein, GntR family from Brucella melitensis biovar Abortus 2308
WP_002967218 histidine utilization repressor from Brucella abortus
37% identity, 30% coverage
S0112 transcriptional regulator for pyruvate dehydrogenase complex from Shigella flexneri 2a str. 2457T
48% identity, 24% coverage
SPA0155 pyruvate dehydrogenase complex repressor from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
t0157 pyruvate dehydrogenase complex repressor from Salmonella enterica subsp. enterica serovar Typhi Ty2
T_RS00790 pyruvate dehydrogenase complex transcriptional repressor PdhR from Salmonella enterica subsp. enterica serovar Choleraesuis str.
48% identity, 24% coverage
NH13_02010 GntR family transcriptional regulator from Lactobacillus acidophilus
46% identity, 27% coverage
SPD_1829 transcriptional regulator, GntR family protein from Streptococcus pneumoniae D39
SP_2020 GntR family transcriptional regulator from Streptococcus pneumoniae TIGR4
SP_RS10220 GntR family transcriptional regulator from Streptococcus pneumoniae
41% identity, 26% coverage
- Identification of Streptococcus pneumoniae genes associated with hypothiocyanous acid tolerance through genome-wide screening
Shearer, Journal of bacteriology 2023 (secret) - Association of symptomatic upper respiratory tract infections with the alteration of the oropharyngeal microbiome in a cohort of school children in Côte d'Ivoire
Missa, Frontiers in microbiology 2024 - “...CDC-R TCGTGCGTTTTAATTCCAGCT lytA - CDC-Probe TGCCGAAAACGCTTGATACAGGGAG ROX BHQ2 SP_2020_ F TAAACAGTTTGCCTGTAGTCG Tavares et al., 2019 SP_2020 _R CCCGGATATCTCTTTCTGGA SP_2020_ Probe AACCTTTGTTCTCTCTCGTGGCAGCTCAA Cy5 BHQ2 H. influenzae HelS -F CCGGGTGCGGTAGAATTTAATAA Arjarquah et al., 2022 HelA -R CTGATTTTTCAGTGCTGTCTTTGC Hel - Probe ACAGCCACAACGGTAAAGTGTTCTACG FAM BHQ1 2.7 RNA extraction Ribonucleic acid...”
- The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults
Boelsen, mSphere 2020 - “...( 38 ) (TIGR4 NCBI reference sequence, NC_003028 ; locus tag, SP_RS10220; old locus tag, SP_2020), also referred to as SP2020 ( 19 , 29 ), used forward primer (5-AGTTTGCCTGTAGTCGAATGA-3), reverse primer (5-TTTGAGCTGCCACGAGAG-3) and the probe (5-6-carboxyfluorescein [FAM]-AAACGTGGGCAGGGAACCTTTGTT-BHQ1-3) concentrations of 300nM, 100nM, and 200nM, respectively. No-template...”
- Identification of Streptococcus pneumoniae by a real-time PCR assay targeting SP2020
Tavares, Scientific reports 2019 - “...(SP_1937, nt 1840405 to 1841361), TIGR4 piaB (SP_1033, nt 974409 to 975428) or TIGR4 SP2020 (SP_2020, nt 1925563 to 1926291). Comparisons between TIGR4 complete genome and the hit contigs were performed by Double ACT v2 and visualized using Artemis Comparison Tool (ACT). Multilocus sequence analysis (MLSA)...”
- “...(SP_1937, nt 1840405 to 1841361), TIGR4 piaB (SP_1033, nt 974409 to 975428) and TIGR4 SP2020 (SP_2020, nt 1925563 to 1926291). Ethics statement The study was conducted in accordance with the European Statements for Good Clinical Practice and the declaration of Helsinki of the World Health Medical...”
- Identification of Virulence-Associated Properties by Comparative Genome Analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, Three S. oralis Subspecies, and S. infantis
Kilian, mBio 2019 - “...in association with various operons, such as PTS (SP_0246/7, SP_0306, SP_0330, SP_0473, SP_1856, SP_1899, and SP_2020), ABC transporters (SP_0716, SP_1057, SP_1433, SP_1821, SP_1920, SP_2088/90, and SP_2172), teichoic acid biosynthesis (SP_1942), type II restriction-modification system (SP_1936), tryptophan synthesis (SP_1809), ion transport (SP_1227), oxidoreductase (SP_0789), thioredoxin (SP_1774), lipoprotein...”
- The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults
Boelsen, mSphere 2020 - “...transcriptional regulator gene bguR ( 38 ) (TIGR4 NCBI reference sequence, NC_003028 ; locus tag, SP_RS10220; old locus tag, SP_2020), also referred to as SP2020 ( 19 , 29 ), used forward primer (5-AGTTTGCCTGTAGTCGAATGA-3), reverse primer (5-TTTGAGCTGCCACGAGAG-3) and the probe (5-6-carboxyfluorescein [FAM]-AAACGTGGGCAGGGAACCTTTGTT-BHQ1-3) concentrations of 300nM, 100nM,...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 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