Family Search for PF13349 (DUF4097)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF13349 hits 49 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
LIAG_BACSU / O32200 Protein LiaG from Bacillus subtilis (strain 168) (see 6 papers)
Aligns to 48:290 / 290 (83.8%), covers 100.0% of PF13349, 229.8 bits
- disruption phenotype: Up-regulates expression of liaI which in turn induces the liaRS two-component regulatory system.
- Moving toward a better understanding of the model bacterial predator Bdellovibrio bacteriovorus
Caulton, Microbiology (Reading, England) 2023 - “...(PDB code 1DAB); the Bacillus subtilis stress response protein LiaG (Alphafold model for Uniprot entry O32200); and a putative adhesin from Bacteroides fragilis (PDB code 3PET). ( b ) A more clear-cut equivalence: Left, Alphafold model of the pilin-like Bd0115 (Uniprot entry Q6MRG9). Right, Bd0115 and...”
lmo0601 similar to cell surface protein from Listeria monocytogenes EGD-e
3 alignments in 52:365 / 366 (85.8%), covering up to 67.1% of PF13349, 199.3 bits
- Structure-based molecular characterization of the LltR transcription factor from Listeria monocytogenes
Kim, Biochemical and biophysical research communications 2022 (PubMed)- “...(lmo0599 ) and two hypothetical transmembrane proteins (lmo0600 and lmo0601 ) was identified [11 ]. Strikingly, a deletion of the first gene, lmo0599 , resulted...”
- PadR-type repressors controlling production of a non-canonical FtsW/RodA homologue and other trans-membrane proteins
Hauf, Scientific reports 2019 - “...The lmo0599 operon contains two additional genes coding for the hypothetical trans-membrane proteins lmo0600 and lmo0601 . A striking phenotype of the lmo0599 mutant is its impaired growth at refrigeration temperature. In light of these and other results we suggest that Lmo0599 should be renamed and...”
- “...lmo0599 LltR, PadR-like transcriptional repressor 150.649.7 4.410 05 lmo0600 DUF1700 containing hypothetical protein 118.034.3 0.0001 lmo0601 DUF4097 containing hypothetical protein 106.823.8 4.810 5 lmo0602 hypothetical protein, N-acetyltransferase domain 12.79.1 0.0011 lmo0954 LiaI phage shock protein 3.81.1 0.0024 lmo2487 DUF4097 containing hypothetical protein 3.10.7 0.0072 lmo0955 LiaH...”
BMD_0825 DUF4097 domain-containing protein from Priestia megaterium DSM 319
BMD_0825 hypothetical protein from Bacillus megaterium DSM319
Aligns to 45:287 / 289 (84.1%), covers 99.6% of PF13349, 159.3 bits
SP_0098 hypothetical protein from Streptococcus pneumoniae TIGR4
SPD_0094 hypothetical protein from Streptococcus pneumoniae D39
Aligns to 57:297 / 303 (79.5%), covers 99.6% of PF13349, 151.8 bits
- Genome-wide identification of Streptococcus pneumoniae genes essential for bacterial replication during experimental meningitis
Molzen, Infection and immunity 2011 - “...identified three clusters of seemingly unrelated genes: SP_0098, SP_0099, and SP_0101, encoding a putative cyanate transporter and hypothetical proteins;...”
- “...3.0 5.0 0.3 2.5 Hypothetical SP_0029 SP_0067 SP_0098 SP_0099 SP_0198 SP_0276 SP_0279 SP_0552 SP_0649 SP_0748 SP_0822 SP_1025 SP_1059 SP_1465 SP_1635 SP_1931...”
- S1 Domain RNA-Binding Protein CvfD Is a New Posttranscriptional Regulator That Mediates Cold Sensitivity, Phosphate Transport, and Virulence in Streptococcus pneumoniae D39
Sinha, Journal of bacteriology 2020 (secret) - TprA/PhrA Quorum Sensing System Has a Major Effect on Pneumococcal Survival in Respiratory Tract and Blood, and Its Activity Is Controlled by CcpA and GlnR
Motib, Frontiers in cellular and infection microbiology 2019 - “...are less accentuated in mannose than galactose. The notably downregulated genes on mannose included SPD_0093, SPD_0094, and SPD_0095. These genes code for hypothetical proteins of unknown function, and are highly conserved in the fully sequenced pneumococcal genomes (Liu et al., 2017 ). Haas et al. (...”
- NADH-Mediated Gene Expression in Streptococcus pneumoniae and Role of Rex as a Transcriptional Repressor of the Rex-Regulon
Afzal, Frontiers in microbiology 2018 - “...mg/ml NADH. D39 tag a Function b Ratio c Upregulated genes spd_0093 Hypothetical protein 3.6 spd_0094 Hypothetical protein 2.6 spd_0095 Hypothetical protein 2.0 spd_0474 Hypothetical protein 1.8 spd_0475 CAAX amino terminal protease family protein 1.7 spd_0526 Fructose-1,6-bisphosphate aldolase, class II, Fba 1.9 spd_1004 Glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent,...”
- Transcriptional Repressor PtvR Regulates Phenotypic Tolerance to Vancomycin in Streptococcus pneumoniae
Liu, Journal of bacteriology 2017 - “...a cluster of four genes with unknown functions (SPD_0093, SPD_0094, SPD_0095, and SPD_0096 in type 2 strain D39 and SP0097, SP0098, SP0099, and SP0100 in type 4...”
- “...PadR family transcriptional regulator, whereas SPD_0093 (354 aa), SPD_0094 (303 aa), and SPD_0095 (197 aa) are described as hypothetical proteins. Based on our...”
- Niacin-mediated Gene Expression and Role of NiaR as a Transcriptional Repressor of niaX, nadC, and pnuC in Streptococcus pneumoniae
Afzal, Frontiers in cellular and infection microbiology 2017 - “...niacin . D39 tag a Function b Ratio c UPREGULATED GENES spd_0093 Hypothetical protein 3.1 spd_0094 Hypothetical protein 2.8 spd_0095 Hypothetical protein 2.4 spd_0474 Hypothetical protein 4.6 spd_0475 CAAX amino terminal protease family protein 3.5 spd_0526 Fructose-1,6-bisphosphate aldolase, class II, Fba 1.5 spd_0976 Redox-sensitive transcriptional regulator...”
- Pneumococcal galactose catabolism is controlled by multiple regulators acting on pyruvate formate lyase
Al-Bayati, Scientific reports 2017 - “...IIC component 2.4 SPD_0068 PTS system, IID component 2.7 SPD_0069 PTS system, IIA component 1.9 SPD_0094 Hypothetical protein 2.3 SPD_0095 Hypothetical protein 2 SPD_0128 MutT/nudix family protein 2.3 SPD_0145 Hypothetical protein 2 SPD_0148 Ransporter, major facilitator family protein 2.8 SPD_0149 Hypothetical protein 2.2 SPD_0308 ATP-dependent Clp...”
- Suppression of a deletion mutation in the gene encoding essential PBP2b reveals a new lytic transglycosylase involved in peripheral peptidoglycan synthesis in Streptococcus pneumoniae D39
Tsui, Molecular microbiology 2016 - “...phosphorylase, Pnp/Udp family protein 1.8 6.8 E-06 spd_0093 c membrane protein, putative 3.3 7.1 E-12 spd_0094 c conserved hypothetical protein 3.3 6.2 E-13 spd_0095 c conserved hypothetical protein 2.9 2.6 E-13 spd_0096 c transcriptional regulator, PadR family protein 2.7 3.2 E-07 spd_0308 ClpL, ATP-dependent Clp protease...”
- The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
Yadav, PloS one 2015 - “...2.9 (0.04) SPD_0935 Tn5252, Orf 9 protein 3.0 (0.05) SPD_0023 conserved hypothetical protein 2.2 (0.05) SPD_0094 conserved hypothetical protein 1.4 (0.02) SPD_0668 conserved hypothetical protein 2.2 (0.05) SPD_0796 conserved hypothetical protein 1.5 (0.03) SPD_0829 conserved hypothetical protein 4.0 (0.05) SPD_0831 conserved domain protein 7.3 (0.03) SPD_0923...”
- More
spr0087 Hypothetical protein from Streptococcus pneumoniae R6
Aligns to 74:314 / 320 (75.3%), covers 99.6% of PF13349, 151.4 bits
YP_001449372 hypothetical protein from Streptococcus gordonii str. Challis substr. CH1
Aligns to 53:334 / 337 (83.7%), covers 90.7% of PF13349, 117.3 bits
SM12261_RS08945 DUF4097 family beta strand repeat-containing protein from Streptococcus mitis NCTC 12261
Aligns to 57:303 / 315 (78.4%), covers 99.2% of PF13349, 113.5 bits
WP_005728236 DUF4097 family beta strand repeat-containing protein from Lactobacillus crispatus SJ-3C-US
Aligns to 46:216 / 242 (70.7%), covers 70.3% of PF13349, 103.2 bits
EF0797 conserved domain protein from Enterococcus faecalis V583
2 alignments in 60:334 / 341 (80.6%), covering up to 63.8% of PF13349, 81.5 bits
- E. faecalisacquires resistance to antimicrobials and insect immunity via common mechanisms
Wadhawan, 2022 - Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species
Adams, Antimicrobial agents and chemotherapy 2015 - “...histidine kinase LiaS Fe-S cluster binding subunit EF0797 hypothetical protein EF1027 MprF2 EF1797 hypothetical protein (DrmA) Intergenic region downstream of...”
- “...449delA (565/608) M110I G170V L52P A29T N150fs EF2912c EF1109 EF0797 EF1027 MprF2 EF1797 DrmA 31-bp del NA EF1367 a Boldface indicates that the gene or pathway...”
- The cell wall-targeting antibiotic stimulon of Enterococcus faecalis
Abranches, PloS one 2014 - “...and 60 min time points. Among those 19 genes, 4 genes encoding hypothetical proteins (EF0026, EF0797, EF1533 and EF3245) were inactivated and the respective mutant strains characterized in relation to antibiotic tolerance and virulence in the Galleria mellonella model. The phenotypes obtained for two of these...”
- “...coding for hypothetical proteins that are unique to enterococci or closely Gram-positive bacteria (EF0026, EF0708, EF0797, EF1258, EF1533 and EF3245) for subsequent mutational analysis. 10.1371/journal.pone.0064875.t001 Table 1 Genes upregulated by Ampicilin (Amp), Bacitracin (Bac), Cep (Cephalotin) and Vancomycin (Van) 30 or 60 min after exposure. Gene...”
WP_005729490 DUF4097 family beta strand repeat-containing protein from Lactobacillus crispatus
Aligns to 23:225 / 225 (90.2%), covers 85.4% of PF13349, 80.7 bits
SERP1470 hypothetical protein from Staphylococcus epidermidis RP62A
Aligns to 44:278 / 278 (84.5%), covers 100.0% of PF13349, 76.8 bits
SE1920 conserved hypothetical protein from Staphylococcus epidermidis ATCC 12228
Aligns to 52:267 / 267 (80.9%), covers 99.6% of PF13349, 75.7 bits
LMRG_01762 hypothetical protein from Listeria monocytogenes 10403S
Q8Y4F8 Lmo2486 protein from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
lmo2486 lmo2486 from Listeria monocytogenes EGD-e
Aligns to 140:349 / 403 (52.1%), covers 78.9% of PF13349, 69.2 bits
- Mutant and Recombinant Phages Selected from In Vitro Coevolution Conditions Overcome Phage-Resistant Listeria monocytogenes
Peters, Applied and environmental microbiology 2020 (secret) - Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705
Melian, Frontiers in microbiology 2021 - “...octaprenyltransferase mo1677/menA Q8Y6K7 Precorrin-3 methylase lmo1197/cbiF Q8Y7S4 Uncharacterized Hypothetical protein lmo2209 Q8Y567 Hypothetical protein lmo2486 Q8Y4F8 Hypothetical protein lmo1466 Q8Y746 Hypothetical protein lmo2843 Q8Y3J2 Hypothetical protein lmo0391 Q8Y9X6 Hypothetical protein lmo0111 Q8YAK7 Hypothetical protein lmo2502 Q8Y4E4 Hypothetical protein lmo0584 Q8Y9E6 Hypothetical protein lmo1452 P53434 Interaction of...”
- Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705
Melian, Frontiers in microbiology 2021 - “...1,4-dihydroxy-2-naphthoate octaprenyltransferase mo1677/menA Q8Y6K7 Precorrin-3 methylase lmo1197/cbiF Q8Y7S4 Uncharacterized Hypothetical protein lmo2209 Q8Y567 Hypothetical protein lmo2486 Q8Y4F8 Hypothetical protein lmo1466 Q8Y746 Hypothetical protein lmo2843 Q8Y3J2 Hypothetical protein lmo0391 Q8Y9X6 Hypothetical protein lmo0111 Q8YAK7 Hypothetical protein lmo2502 Q8Y4E4 Hypothetical protein lmo0584 Q8Y9E6 Hypothetical protein lmo1452 P53434 Interaction...”
- Exploring Listeria monocytogenes Transcriptomes in Correlation with Divergence of Lineages and Virulence as Measured in Galleria mellonella
Lee, Applied and environmental microbiology 2019 (secret) - Interference of components of the phosphoenolpyruvate phosphotransferase system with the central virulence gene regulator PrfA of Listeria monocytogenes
Mertins, Journal of bacteriology 2007 - “...protein; lmo2485, similar to B. subtilis YvlC protein; lmo2486, unknown; lmo2487, similar to B. subtilis YvlB protein; lmo1001, similar to B. subtilis protein...”
LGG_00914 hypothetical protein from Lactobacillus rhamnosus GG
LGG_00914 daptomycin-sensing surface protein LiaX from Lacticaseibacillus rhamnosus GG
Aligns to 245:492 / 496 (50.0%), covers 98.4% of PF13349, 68.9 bits
- Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG
Koskenniemi, Molecular & cellular proteomics : MCP 2011 - “...matchedd LGG_00031 LGG_00238 LGG_02913 LGG_00534 LGG_00914 LGG_01820 LGG_00984 LGG_02239 LGG_01295 LGG_01367 LGG_01478 LGG_01652 LGG_01820 LGG_02239 LGG_01821...”
- “...No. of peptides matchedd LGG_00252 LGG_00740 LGG_00914 LGG_00914 LGG_00914 LGG_01820 LGG_00934 LGG_00936 LGG_01062 LGG_01181 LGG_01416 LGG_01181 LGG_01416...”
- Variability of Genetic Characters Associated with Probiotic Functions in Lacticaseibacillus Species
Rossi, Microorganisms 2022 - “...acid (LTA) synthase LGG_00830, a polysaccharide biosynthesis transport protein LGG_00851, the LiaX daptomycin-sensing surface protein LGG_00914, a PspC domain-containing protein that in Staphylococcus mutans mediates biofilm formation in vivo [ 19 ], a toxin immunity protein LGG_01002, a lipopolysaccharide assembly protein LGG_01366, a fibronectin binding protein...”
- “...in L. rhamnosus GG Anti-inflammatory protein LGG_02734 b Bile salt hydrolase LGG_00501 * Biofilm formation LGG_00914; LGG_01827 Cell wall anchored proteins with LPXTG domain LGG_00434 b,f ; LGG_00578 c,d,e ; LGG_00584 Fibrinogen binding LGG_01590 c,d,e,f ; LGG_02282 b Fibronectin binding LGG_0005 a,b ; LGG_01450 Fucose utilization...”
LMOf2365_2459 PspC domain protein from Listeria monocytogenes str. 4b F2365
Aligns to 140:348 / 403 (51.9%), covers 78.9% of PF13349, 68.5 bits
LMRG_01761 hypothetical protein from Listeria monocytogenes 10403S
Aligns to 163:417 / 420 (60.7%), covers 84.1% of PF13349, 68.2 bits
lmo2487 similar to B. subtilis YvlB protein from Listeria monocytogenes EGD-e
Q8Y4F7 Lmo2487 protein from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Aligns to 163:417 / 420 (60.7%), covers 84.1% of PF13349, 68.2 bits
- Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin
Pinilla, Data in brief 2022 - “...rRNA at the A site Q48762 lmo0234 lmo0234 Nis / LNis Hypothetical protein; RNAse Q8Y4F7 lmo2487 lmo2487 Nis / LNis Annotation not available Q48754 lmo1388 tcsA Nis / LNis CD4+ T-cell stimulating antigen P66352 lmo2607 rpsK Nis / LNis 30S ribosomal protein S11; located on the...”
- Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection
Fischer, Genome research 2022 - “...( ackA , ltaS , oppD , oppF , sipZ , sod , smpB , lmo2487 ) ( Bonnemain et al. 2004 ; Gravesen et al. 2004 ; Archambaud et al. 2006 ; Gueriri et al. 2008 ; Webb et al. 2009 ; Mraheil et al....”
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...lmo2210 Hypothetical protein 18.59 0.00 LMRG_01630 lmo2202 fabH LMRG_01630-LMRG_01631 3-oxoacyl-[acyl-carrier-protein] synthase, KASIII 2.05 0.00 LMRG_01761 lmo2487 Hypothetical protein 2.14 0.00 LMRG_01976 lmo2720 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases, YtcI homolog 4.32 0.00 LMRG_02011 lmo0911 Hypothetical protein 2.43 0.00 LMRG_02071 lmo0972 dltC dltABCD , LMRG_02074 D-alanyl carrier protein...”
- PadR-type repressors controlling production of a non-canonical FtsW/RodA homologue and other trans-membrane proteins
Hauf, Scientific reports 2019 - “...5 lmo0602 hypothetical protein, N-acetyltransferase domain 12.79.1 0.0011 lmo0954 LiaI phage shock protein 3.81.1 0.0024 lmo2487 DUF4097 containing hypothetical protein 3.10.7 0.0072 lmo0955 LiaH phage shock protein 2.60.6 0.0027 lmo1637 putative ABC transporter, permease protein 2.50.2 0.0003 lmo0047 putative lipoprotein 2.40.4 0.0029 lmo1636 putative ABC transporter,...”
- Protein level identification of the Listeria monocytogenes sigma H, sigma L, and sigma C regulons
Mujahid, BMC microbiology 2013 - “...consensus promoter, suggesting direct transcriptional regulation by H . In addition, the coding gene for Lmo2487, one of these 15 proteins, is in an operon with lmo2485, which was previously reported to be positively regulated by H , even though no upstream H consensus promoter was...”
- “...conductance mechanosensitive channel protein mscL Cellular processes Adaptations to atypical conditions tttcac atcgcagttagatgttt tatact SigmaA Lmo2487 1.65 hypothetical protein lmo2487 Hypothetical proteins Conserved N/A N/A Lmo2614 2.05 50S ribosomal protein L30 rpmD Protein synthesis Ribosomal proteins: synthesis and modification ttgatt actacccctaacccgtg tataat SigmaA Lmo2621 1.63 50S...”
- Assessing the contributions of the LiaS histidine kinase to the innate resistance of Listeria monocytogenes to nisin, cephalosporins, and disinfectants
Collins, Applied and environmental microbiology 2012 - “...noted previously that the expression of liaS, lmo2229, and lmo2487 is reduced in the nisin-resistant LO28lisK mutant (8), yet the expression of these three loci...”
- “...deleting liaS on the expression of liaS, lmo2229, and lmo2487 during logarithmic growth in both the LO28 and lisK backgrounds. Although the expression of liaS...”
- Listeria monocytogenes grown at 7° C shows reduced acid survival and an altered transcriptional response to acid shock compared to L. monocytogenes grown at 37° C
Ivy, Applied and environmental microbiology 2012 - “...lmo2293 lmo2295 lmo2296 lmo2362 lmo2363 lmo2408 lmo2409 lmo2484 lmo2487 lmo2625 (rplP) lmo2630 (rplW) lmo2632 (rplC) lmo2633 (rpsJ) 5 min 15 min 5 min 15...”
- TelA contributes to the innate resistance of Listeria monocytogenes to nisin and other cell wall-acting antibiotics
Collins, Antimicrobial agents and chemotherapy 2010 - “...site. f Primers are 5 to 3. b c (lmo2487) are all upregulated in spontaneously nisin-resistant L. monocytogenes strains (16). Here the screening of a mariner...”
- More
- Proteomic dataset of Listeria monocytogenes exposed to sublethal concentrations of free and nanoencapsulated nisin
Pinilla, Data in brief 2022 - “...16S rRNA at the A site Q48762 lmo0234 lmo0234 Nis / LNis Hypothetical protein; RNAse Q8Y4F7 lmo2487 lmo2487 Nis / LNis Annotation not available Q48754 lmo1388 tcsA Nis / LNis CD4+ T-cell stimulating antigen P66352 lmo2607 rpsK Nis / LNis 30S ribosomal protein S11; located on...”
OG1RF_11464 daptomycin-sensing surface protein LiaX from Enterococcus faecalis OG1RF
Aligns to 277:529 / 533 (47.5%), covers 97.6% of PF13349, 66.5 bits
LIAX_ENTFA / Q834B6 Putative adhesin domain-containing protein LiaX; Daptomycin-sensing surface protein LiaX from Enterococcus faecalis (strain ATCC 700802 / V583) (see paper)
EF1753 conserved hypothetical protein from Enterococcus faecalis V583
Aligns to 277:529 / 533 (47.5%), covers 97.6% of PF13349, 66.5 bits
- function: Involved in cell membrane remodeling, perhaps acting by negative modulation of the liaFSR and liaXYZ gene clusters, thereby regulating content and localization of anionic phospholipids (PubMed:31818937). Binds to the antibiotic daptomycin (DAP) and to cationic antimicrobial peptides, such as human LL-37, perhaps functioning as a sensor that activates the cell envelope stress response (PubMed:31818937).
disruption phenotype: Deletion in the OG1RF strain causes anionic phospholipids to be redistributed away from the division septum; during exponential growth, there are increases in phosphatidylglycerol (PG), decreases in cardiolipin, with no change in lysyl-PG (PubMed:31818937). Confers resistance to the antibiotic daptomycin (DAP) in the OG1RF strain (PubMed:31818937). Resistant to killing of the OG1RF strain by human cathelicidin LL-37 (PubMed:31818937). Deletion in the OG1RF strain increases virulence in nematode C.elegans infection model (PubMed:31818937). - Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis
Gilmore, mBio 2020 - “...0.000 (>0.10) 0.000 (>0.10) 0.000 (>0.10) 0.490 (>0.10) 0.214 (>0.10) 0.065 (>0.10) 0.289 (>0.10) SAW_01705 EF1753 LiaX Important 0.053 0.138 (>0.10) 0.000 (>0.10) 0.096 (>0.10) 0.008 (>0.10) 0.000 (>0.10) 0.000 (>0.10) 0.000 (>0.10) 0.101 (>0.10) 0.000 (>0.10) 0.000 (>0.10) a Light shading indicates response regulators of...”
- “...EF0397, EF0990, EF1043, EF1146, EF2923, and EF3061 (all Fitness Critical) and EF1195, EF1316, EF1724, EF1752, EF1753, EF2606, and EF3086 (Fitness Important) ( Data Set S1 ). Most encode unknown functions, whereas EF0394, EF0397, EF1043, EF1752, EF1753, and EF3061 appear to be extracellular or associated with the...”
- Chlorhexidine Induces VanA-Type Vancomycin Resistance Genes in Enterococci
Bhardwaj, Antimicrobial agents and chemotherapy 2016 - “...vancomycin response regulator EF1533 EF2698 EF2697 EF2477 EF1006 EF1753 EF1752 EF1751 EF0026 EF3027 EF0932 10.5 9.8d 35.8 11.9 15.9 69.0 32.0 31.1 52.6 19.9...”
- Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species
Adams, Antimicrobial agents and chemotherapy 2015 - “...mutations in the yvlB homologue in E. faecalis, EF1753, are present in daptomycin-resistant E. faecalis strains (22, 35). Finally, L. plantarum ftsH mutant and...”
- Enterococcus faecalis Glycolipids Modulate Lipoprotein-Content of the Bacterial Cell Membrane and Host Immune Response
Theilacker, PloS one 2015 - “...protein family lipoprotein EF1416 1.201 Glucose-6-phosphate isomerase cytoplasmic EF2697 1.159 Conserved domain protein cell membrane EF1753 1.141 Uncharacterized protein cytoplasmic EF1045 1.111 6-phosphofructokinase cytoplasmic EF0761 1.097 Amino acid ABC transporter. amino acid binding permease protein cell membrane EF2496 1.085 Lipoprotein lipoprotein EF0685 1.082 Foldase protein PrsA...”
- The cell wall-targeting antibiotic stimulon of Enterococcus faecalis
Abranches, PloS one 2014 - “...7.46 38.96 13.64 21.61 EF1587 nudix family phosphohydrolase 2.82 2.61 22.39 11.86 6.7 15.45 19.3 EF1753 hypothetical protein 4.40 3.95 25.31 18.40 3.74 10.2 11.63 18.16 EF1814 EmbR/QcaA drug resistance transporter 6.01 8.05 7.86 14.35 14.55 EF2784 hypothetical protein 2.66 17.35 12.3 4.95 4.93 EF2892 hypothetical...”
- “...of a DNA-binding domain. Initially, we attempted to generate deletions in EF0026, EF0708, EF0797, EF1533, EF1753 and EF3245. However, we were unable to confirm mutations of EF0708 and EF1258, suggesting that these genes may perform an essential role for cell viability, or that we did not...”
- Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance
Miller, Antimicrobial agents and chemotherapy 2013 - “...observed a frameshift mutation at position Ile-390 in YvlB (EF1753) of a DAP-resistant E. faecalis variant (10). As none of the adaptive mutations in LiaFSR...”
- “...et al. (10) observed mutations in cls, yvlB (denoted EF1753), and drmA (denoted EF1797). In E. faecium, Munita et al. (50) demonstrated the importance of...”
- Genetic basis for daptomycin resistance in enterococci
Palmer, Antimicrobial agents and chemotherapy 2011 - “...653/1446 cardiolipin synthetase EF0782, rpoN 296/1314 EF1753, conserved 1168/1602 hypothetical protein EF1753, conserved 1168/1602 hypothetical protein EF1797,...”
- “...interest (EF0224 rpsE, EF0243 brnQ, EF0631, EF0782 rpoN, EF1753, EF1797, EF2698) using each of the strains (control, DAP-A, DAP-B, DAP-C) as templates....”
- Characterizing vancomycin-resistant Enterococcus strains with various mechanisms of daptomycin resistance developed in an in vitro pharmacokinetic/pharmacodynamic model
Steed, Antimicrobial agents and chemotherapy 2011 - “...Two gene clusters (EF2694 to EF2701 and EF1751 to EF1753) associated with cell membrane proteins and the phage shock protein C were found to be upregulated in...”
O34628 Uncharacterized protein YvlB from Bacillus subtilis (strain 168)
Aligns to 107:360 / 365 (69.6%), covers 89.0% of PF13349, 65.0 bits
MW1867 hypothetical protein from Staphylococcus aureus subsp. aureus MW2
SA1740 hypothetical protein from Staphylococcus aureus subsp. aureus N315
Aligns to 45:280 / 280 (84.3%), covers 100.0% of PF13349, 62.4 bits
LACR_2166 hypothetical protein from Lactococcus lactis subsp. cremoris SK11
llmg_2164 hypothetical protein from Lactococcus lactis subsp. cremoris MG1363
Aligns to 115:366 / 370 (68.1%), covers 98.8% of PF13349, 62.2 bits
- Proteomic analyses to reveal the protective role of glutathione in resistance of Lactococcus lactis to osmotic stress
Zhang, Applied and environmental microbiology 2010 - “...clpE LACR_1027 LACR_0578 8.6 1.7 3.2 NC Hypothetical protein LACR_2166 RNA-binding protein 2.4 1.7 NC LACR_2311 NC 1.7 NC LACR_2166 LACR_2289 3.9 NC NC 2.7 5.6...”
- Cell wall homeostasis in lactic acid bacteria: threats and defences
Martínez, FEMS microbiology reviews 2020 - “...(S. Kulakauskas, unpublished). Also, special attention should be paid to the lactococcal yth -operon (or llmg_2164 llmg_2163 ). Notably, this operon is among the highest up-regulated after treatment with Lcn972 and protects cells from its antimicrobial activity (Martnez etal . 2007 ; Roces etal . 2009...”
- Transcriptional response of Lactococcus lactis during bacterial emulsification
Tarazanova, PloS one 2019 - “...llmg_1115 XpaC-like protein 4.3 3.6e-7 S. Function unknown llmg_2163 K llmg_2163 hypothetical protein 18.4 1.4e-13 llmg_2164 llmg_2164 hypothetical protein 18.4 2.3e-11 llmg_1659 llmg_1659 hypothetical protein 11.3 4.6e-14 llmg_1572 mycA hypothetical protein 5.7 1.5e-8 llmg_0590 llmg_0590 hypothetical protein 4.9 2.1e-3 llmg_1263 llmg_1263 hypothetical protein 4.3 2.1e-6 llmg_1029...”
- Refining the Pneumococcal Competence Regulon by RNA Sequencing
Slager, Journal of bacteriology 2019 - “...homolog CesR ( 15 , 95 ) as follows: llmg_0165, llmg_0169, llmg_1115, llmg_1155, llmg_1650, and llmg_2164. Cappable-seq ( 60 ) was used to identify L. lactis TSSs (S. B. van der Meulen and O. P. Kuipers, unpublished data). Importantly, we did not use the standard 0-order...”
- Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs
van, Frontiers in microbiology 2017 - “...5 min. Among the highest upregulated genes are those of an operon ( llmg_2163 - llmg_2164 ) specifying a putative stress-responsive transcriptional regulator with a PspC domain (Llmg_2163). Both genes are ~10-fold upregulated; it was also induced upon overproduction in L. lactis of the membrane protein...”
- “...after exposure to the bacteriocin Lcn972 (Martnez et al., 2007 ). A deletion mutant of llmg_2164 was shown to be very sensitive to NaCl (Roces et al., 2009 ). In E. coli , the psp operon is induced after application of various types of stresses including...”
- Stress Physiology of Lactic Acid Bacteria
Papadimitriou, Microbiology and molecular biology reviews : MMBR 2016 - “...Lc. lactis against Lcn972, while a mutant lacking llmg_2164 suffered from a low resistance to high temperature and salinity (443). The llmg_1155/spxB gene...”
- Efficient overproduction of membrane proteins in Lactococcus lactis requires the cell envelope stress sensor/regulator couple CesSR
Pinto, PloS one 2011 - “...transporter ATP-binding and permease protein 1.83 3.7*10 5 llmg_1918 Putative membrane protein 2.55 2.9*10 4 llmg_2164 Putative uncharacterized protein 12.87 3.9*10 10 llmg_2163 Putative stress-responsive transcriptional regulator 11.88 2.5*10 9 llmg_2420 Putative uncharacterized protein 1.29 9.7*10 3 llmg_2477 Lysine-specific permease 2.91 6.3*10 6 A full-genome DNA...”
- “...Figure 3 ). Similar data was obtained using a lacZ fusion to the promoter of llmg_2164 , another CesSR regulon member (data not shown). 10.1371/journal.pone.0021873.g003 Figure 3 The CesSR response is proportional to, and follows in time, the level of production of BcaP-GFP-H6. The level of...”
SO_3842 conserved hypothetical protein from Shewanella oneidensis MR-1
2 alignments in 40:316 / 318 (87.1%), covering up to 76.8% of PF13349, 61.8 bits
M7W_985 daptomycin-sensing surface protein LiaX from Enterococcus faecium ATCC 8459 = NRRL B-2354
Aligns to 266:518 / 522 (48.5%), covers 89.4% of PF13349, 59.6 bits
D2S332 Putative adhesin domain-containing protein from Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / JCM 9101 / NCIMB 13204 / VKM B-1734 / 4k)
Aligns to 116:273 / 276 (57.2%), covers 58.5% of PF13349, 56.9 bits
XCC1308 conserved hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913
Aligns to 36:291 / 294 (87.1%), covers 84.1% of PF13349, 56.2 bits
YP_702564 hypothetical protein from Rhodococcus sp. RHA1
Aligns to 11:279 / 281 (95.7%), covers 83.3% of PF13349, 53.4 bits
ROP_29250 hypothetical protein from Rhodococcus opacus B4
Aligns to 12:279 / 281 (95.4%), covers 80.5% of PF13349, 49.6 bits
SACE_3262 hypothetical protein from Saccharopolyspora erythraea NRRL 2338
Aligns to 20:276 / 282 (91.1%), covers 70.3% of PF13349, 48.3 bits
LSA0512 Hypothetical protein from Lactobacillus sakei subsp. sakei 23K
Aligns to 230:487 / 491 (52.5%), covers 83.3% of PF13349, 48.0 bits
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...lsa0418 Hypothetical protein -0.8 LSA0464 lsa0464 Hypothetical protein -0.6 LSA0470 lsa0470 Hypothetical protein 0.9 0.7 LSA0512 lsa0512 Hypothetical protein -0.6 LSA0515 lsa0515 Hypothetical integral membrane protein -0.5 LSA0536 lsa0536 Hypothetical protein 0.7 LSA0716 lsa0716 Hypothetical protein 0.6 LSA0752 lsa0752 Hypothetical protein 0.5 0.6 LSA0757 lsa0757 Hypothetical...”
AMED_1127 DUF4097 family beta strand repeat-containing protein from Amycolatopsis mediterranei U32
Aligns to 14:219 / 220 (93.6%), covers 70.3% of PF13349, 48.0 bits
Smlt3512 hypothetical protein from Stenotrophomonas maltophilia K279a
Aligns to 35:290 / 293 (87.4%), covers 98.0% of PF13349, 48.0 bits
- σP-NagA-L1/L2 Regulatory Circuit Involved in ΔompA299-356-Mediated Increase in β-Lactam Susceptibility in Stenotrophomonas maltophilia
Li, Microbiology spectrum 2022 - “...any homology to the anti- factor. However, interestingly, we noticed that the genes (Smlt3513 and Smlt3512) downstream of rpoP encode a 177-aa and a 293-aa hypothetical protein, respectively. The rpoP , Smlt3513, and Smlt3512 genes have the same orientation. RpoP and Smlt3513 genes have a 4-bp...”
- “...Based on this observation, we speculate that rpoP-Smlt3513-Smlt3512 may form an operon and Smlt3513 and Smlt3512 may participate in the PG stress signal transduction from the periplasm into cytoplasm and then activate the cytoplasmic P . The genetic indications presented here lead to a model in...”
SPy2174 hypothetical protein from Streptococcus pyogenes M1 GAS
Aligns to 51:359 / 359 (86.1%), covers 100.0% of PF13349, 47.7 bits
SLUN_RS38415 DUF4097 family beta strand repeat-containing protein from Streptomyces lunaelactis
Aligns to 10:278 / 278 (96.8%), covers 90.2% of PF13349, 47.5 bits
- Lunaemycins, New Cyclic Hexapeptide Antibiotics from the Cave Moonmilk-Dweller Streptomyces lunaelactis MM109T
Martinet, International journal of molecular sciences 2023 - “...SLUN_RS38410 WP_108155188.1 Lun1 177 TmcL, hypothetical protein, ,-epoxyketone BGC of Streptomyces chromofuscus (CUX96959.1) 64/100 Unknown SLUN_RS38415 WP_108155189.1 Lun2 278 DUF4097 family beta strand repeat-containing protein, ,-epoxyketone BGC of Streptomyces chromofuscus (CUX96960.1) 48/100 Unknown SLUN_RS38420 WP_108155190.1 Lun3 416 Cytochrome P450, streptovaricin BGC of Streptomyces spectabilis (ASZ00144.1) 61/97...”
YPO1174 hypothetical protein from Yersinia pestis CO92
2 alignments in 4:182 / 309 (57.9%), covering up to 39.8% of PF13349, 47.0 bits
Spy49_1783 hypothetical protein from Streptococcus pyogenes NZ131
Aligns to 51:357 / 357 (86.0%), covers 100.0% of PF13349, 45.5 bits
SLUN_RS38540 DUF4097 family beta strand repeat-containing protein from Streptomyces lunaelactis
Aligns to 12:274 / 286 (92.0%), covers 73.6% of PF13349, 42.2 bits
YPTB1215 hypothetical protein from Yersinia pseudotuberculosis IP 32953
Aligns to 95:182 / 309 (28.5%), covers 27.6% of PF13349, 40.7 bits
PG_RS01865 head GIN domain-containing protein from Porphyromonas gingivalis W83
Aligns to 45:262 / 286 (76.2%), covers 82.1% of PF13349, 40.3 bits
PG0419 hypothetical protein from Porphyromonas gingivalis W83
Aligns to 60:276 / 301 (72.1%), covers 82.1% of PF13349, 40.1 bits
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...I SAM-dependent rRNA methyltransferase, 35 exonuclease domain-containing protein 2, DUF5063 domain-containing protein 1.4 0.168 PG_RS01865 PG0419 DUF2807 domain-containing protein 1.7 0.026 PG_RS01945 PG0437 Polysaccharide biosynthesis/export family protein 1.5 0.056 PG_RS02085 PG0469 Hypothetical protein 2.3 0.007 PG_RS02165 PG0487 IS 4 -like element IS1598 family transposase 87.1 0...”
- Porphyromonas gingivalis Sphingolipid Synthesis Limits the Host Inflammatory Response
Rocha, Journal of dental research 2020 (secret) - A putative TetR regulator is involved in nitric oxide stress resistance in Porphyromonas gingivalis
Boutrin, Molecular oral microbiology 2016 - “..., PG1190 , PG0195 , PG0421 and PG1546 ) and down regulated (e.g. PG0214-18 , PG0419 , PG0914 , PG1718 and PG1320 ) for both mutants in comparison to the wild-type. Transcriptome analysis of FLL460 under NO stress indicated that 5 percent of the genes were...”
- “...from the FLL460, FLL461 and complemented FLL460 strains. Genes involved in NO-stress response are PG1181, PG0419, PG0914, PG1053, PG1240, PG0893 and PG1237 . Genes encoding sigma factors and sigma factors-related proteins are PG0214-8, PG1827, PG0162, PG0985, PG1318 and PG1660 . Table 1 List of plasmids and...”
- Oxantel disrupts polymicrobial biofilm development of periodontal pathogens
Dashper, Antimicrobial agents and chemotherapy 2014 - “...Upregulated genes PG0192 PG0193 PG0214 PG0215 PG0217 PG0218 PG0419 PG0593 PG0613 PG0614 PG0927 PG0985 PG0986 PG0987 PG1314 PG1315 PG1316 PG1579 PG1584 PG1625...”
- The Porphyromonas gingivalis ferric uptake regulator orthologue binds hemin and regulates hemin-responsive biofilm development
Butler, PloS one 2014 - “...PGN_1503 PG0465 har Fur family transcriptional regulator Inorganic ion transport and metabolism 0.15 1.8E-13 PGN_1548 PG0419 - hypothetical protein Unknown 0.53 1.1E-03 2.59 PGN_1622 PG0339 - hypothetical protein Unknown 0.64 1.7E-03 1.83 1.27 PGN_1791 PG1858 - flavodoxin FldA Energy production and conversion 0.60 7.1E-04 15.25 1.34...”
- Gene expression in Porphyromonas gingivalis after contact with human epithelial cells
Hosogi, Infection and immunity 2005 - “...PG0506 rgpB Arg-gingipain B Pathogenesis ND 4.37 6.54 PG0419 PG0686 Conserved hypothetical Conserved hypothetical Unknown 4.4 3.86 2.91 14.43 2.62 19.1 PG0434...”
PGN_1548 hypothetical protein from Porphyromonas gingivalis ATCC 33277
Aligns to 45:261 / 286 (75.9%), covers 82.1% of PF13349, 39.9 bits
CG8187 uncharacterized protein from Drosophila melanogaster
Aligns to 182:348 / 376 (44.4%), covers 41.5% of PF13349, 38.8 bits
- Mitochondrial remodelling is essential for female germ cell differentiation and survival
Monteiro, PLoS genetics 2023 - “...and 60C for 30 s. Results were normalized to the mean of value obtained of CG8187, CG2698 and Und. Gene knockdown was normalized to the relative expression level in mCherry knockdown embryos. Results were calculated using the following formula: Ct = 2^-(CtRNAi Ct mCherry RNAi ),...”
- Mitochondrial fragmentation drives selective removal of deleterious mtDNA in the germline
Lieber, Nature 2019 - “...to verify amplification specificity. Results were normalized to the mean value obtained for three genes (CG8187; CG2698; Und) with invariant expression in a range tissues and developmental stages, as revealed by publicly available transcriptome data 42 . Data were analyzed using unpaired one-tailed t tests. For...”
- piRNA-mediated regulation of transposon alternative splicing in the soma and germ line
Teixeira, Nature 2017 - “...to the mean value obtained for three control genes (CG7939 [Rp49, also known as RpL32]; CG8187; CG8269 [Dmn]) with invariant expression in a range of tissues and developmental stages, as previously described 38 . For splicing analysis on gel, PCR reactions were performed in RT-qPCR-normalized cDNA...”
- ATP synthase promotes germ cell differentiation independent of oxidative phosphorylation
Teixeira, Nature cell biology 2015 - “...amplification specificity. Results were normalized to the mean value obtained for three genes (CG7939 [Rp49]; CG8187; CG8269 [Dmn]) with invariant expression in a range tissues and developmental stages, as revealed by publicly available transcriptome data 38 . Gene knockdown was represented relative to expression level in...”
Q8N0U4 Protein FAM185A from Homo sapiens
Aligns to 206:351 / 392 (37.2%), covers 47.2% of PF13349, 38.4 bits
M3FS09 Lipoprotein from Streptomyces bottropensis ATCC 25435
Aligns to 147:288 / 291 (48.8%), covers 59.3% of PF13349, 38.3 bits
FRAAL2567 hypothetical protein from Frankia alni ACN14a
Aligns to 13:278 / 280 (95.0%), covers 93.9% of PF13349, 37.0 bits
- Frankia alni Carbonic Anhydrase Regulates Cytoplasmic pH of Nitrogen-Fixing Vesicles
Pujic, International journal of molecular sciences 2023 - “...in Fumarate-Fed Cells Relative to Propionate-Fed Cells Gene Functional description Tfold FRAAL4675 Acyl-CoA transferase 11.5 FRAAL2567 Protein of unknown function 8.5 FRAAL3063 Branched-chain amino acid ABC transporter 7.4 FRAAL1390 C4-dicarboxylate transporter 6.83 FRAAL3378 Protein of unknown function 6.8 FRAAL0382 CoA-transferase 6.35 FRAAL6022 Gamma-aminobutyraldehyde dehydrogenase 6 FRAAL4493...”
- The PEG-responding desiccome of the alder microsymbiont Frankia alni
Ghedira, Scientific reports 2018 - “...glycol (PEG)-induced proteins of F. alni . Response mechanism Protein Product Tfold Membrane transport proteins FRAAL2567 Putative autotransporter adhesion 5.67 FRAAL2549 Secondary metabolite secretion ATP-binding transport 4.80 FRAAL1420 Nitrate/sulfonate ATP-binding (ABC) transporter 2.89 FRAAL2085 Trk system potassium uptake protein TrkA 1.65 Intracellular osmolytes concentration FRAAL0095 Osmotic-stress...”
- “...Psi-Blast approach.). Among re-annotated ORFs, several envelope-associated proteins were identified including the most up-regulated protein (FRAAL2567 (5.67)), a putative auto-transporter adhesin. These results consolidate previous data (see Table 1 ) that have evidenced the extreme importance of envelope-associated proteins in response to water stress. Functional analysis...”
XAC1545 conserved hypothetical protein from Xanthomonas axonopodis pv. citri str. 306
Aligns to 43:272 / 272 (84.6%), covers 64.2% of PF13349, 35.6 bits
- Deciphering the regulon of a GntR family regulator via transcriptome and ChIP-exo analyses and its contribution to virulence in Xanthomonas citri
Zhou, Molecular plant pathology 2017 - “...in nutrient broth (NB) medium and in planta. and XAC1545, which are located downstream of ytrA, were mutated. Mutation of XAC1547, XAC1546 and XAC1545 had no...”
- “...(YtrA regulated-operon 1) (including ytrA, nodI, XAC1546, XAC1545, XAC1544 and XAC1543), yro2 (including czcB, XAC2065 and XAC2066) and yro3 (including XAC0231...”
XOO2060 hypothetical protein from Xanthomonas oryzae pv. oryzae KACC10331
Aligns to 69:277 / 278 (75.2%), covers 62.2% of PF13349, 35.6 bits
Bd2093 hypothetical protein from Bdellovibrio bacteriovorus HD100
Q6MLC0 Putative adhesin domain-containing protein from Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)
Aligns to 36:333 / 333 (89.5%), covers 84.1% of PF13349, 31.9 bits
- Moving toward a better understanding of the model bacterial predator Bdellovibrio bacteriovorus
Caulton, Microbiology (Reading, England) 2023 - “...functions for cryptic Bdellovibrio genes. ( a ) Left, Alphafold model of the beta solenoid Bd2093 (Uniprot entry Q6MLC0, identified in Tudor et al . transposon study [ 22 ]). Right, similar protein structures (but disparate functions!), including the Legionella pneumophila Dot/Icm T4SS OMC component Dis3...”
- Isolation of predation-deficient mutants of Bdellovibrio bacteriovorus by using transposon mutagenesis
Tudor, Applied and environmental microbiology 2008 - “...serine protease JA-A10 JA-B5 JA-B8 Bd1580 Bd3170 Bd2093 Hypothetical protein Hypothetical protein Hypothetical protein JA-B9 Between Bd0542 and Bd0543 Bd1131...”
- Moving toward a better understanding of the model bacterial predator Bdellovibrio bacteriovorus
Caulton, Microbiology (Reading, England) 2023 - “...Bdellovibrio genes. ( a ) Left, Alphafold model of the beta solenoid Bd2093 (Uniprot entry Q6MLC0, identified in Tudor et al . transposon study [ 22 ]). Right, similar protein structures (but disparate functions!), including the Legionella pneumophila Dot/Icm T4SS OMC component Dis3 (PDB code 7MUD);...”
CD1347 hypothetical protein from Clostridium difficile 630
Aligns to 55:249 / 356 (54.8%), covers 59.3% of PF13349, 30.0 bits
Or search for genetic data about PF13349 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory