Family Search for PF13349 (DUF4097)

PF13349 hits 44 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

lmo0601 similar to cell surface protein (NCBI ptt file) from Listeria monocytogenes EGD-e
3 alignments in 52:365 / 366 (85.8%), covering up to 64.3% of PF13349, 229.4 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...”

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, 195.9 bits

• disruption phenotype: Up-regulates expression of liaI which in turn induces the liaRS two-component regulatory system.

WP_005728236 DUF4097 family beta strand repeat-containing protein from Lactobacillus crispatus
2 alignments in 46:242 / 242 (81.4%), covering up to 70.7% of PF13349, 144.4 bits

• Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil
  Oliveira, PeerJ 2021
  • “...Pyruvate oxidase [EC:1.2.3.3] ( poxL ) K00158 WP_005723618 1 1 1 1 Adhesin Putative adhesin WP_005728236 1 1 1 1 WP_005729490 1 1 1 Antimicrobial production Safety assessment of the strains for probiotic applications Features associated with safety in the four strains from Brazil are shown...”

BMD_0825 hypothetical protein (RefSeq) from Bacillus megaterium DSM319
BMD_0825 DUF4097 domain-containing protein from Priestia megaterium DSM 319
Aligns to 45:287 / 289 (84.1%), covers 99.6% of PF13349, 138.7 bits

• Construction and Application of a Plasmid-Based Signal Peptide Library for Improved Secretion of Recombinant Proteins with Priestia megaterium
  Mayer, Microorganisms 2022
  • “...pMSP4 ErfK/YbiS/YcfS/YnhG family protein (ADF37131.1) 128.2 0.815 28 SP 12 from pMSP8 Conserved hypothetical protein BMD_0825 (ADF37687.1) 125.5 0.663 23 SP 14 from pMSP3 Levanase (ADF38396.1) 124.0 0.517 29 SP 14 from pMSP3 Levanase (ADF38396.1) 119.3 0.517 29 SP 10 from pMSP3 Conserved hypothetical protein BMD_3012...”

SP_0098 hypothetical protein (RefSeq) from Streptococcus pneumoniae TIGR4
SPD_0094 hypothetical protein (NCBI) from Streptococcus pneumoniae D39
Aligns to 57:297 / 303 (79.5%), covers 99.6% of PF13349, 131.3 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 (NCBI ptt file) from Streptococcus pneumoniae R6
Aligns to 74:314 / 320 (75.3%), covers 99.6% of PF13349, 130.8 bits

• Discrimination of Streptococcus pneumoniae from viridans group streptococci by genomic subtractive hybridization
  Suzuki, Journal of clinical microbiology 2005
  • “...427 29.6 43.4 46.9 spn9828c spn14.1 spn24 spr1523 spr0087 spr1092 114 320 292 39.1 40.6 44.9 spn25.1 spr1622 512 30.0 NDd Unknown (NP_359394)...”
• Regulation of iron transport in Streptococcus pneumoniae by RitR, an orphan response regulator
  Ulijasz, Journal of bacteriology 2004
  • “...log2 PDE RitR ABC-SBP galT nirC rimM dpr spr0087 hemH mulY ABC-MSP spr0114 spr1201 ABC-SBP spr0563 PTS-EII adhE Response regulator ABC transporter,...”
  • “...by ritR spr0336 spr1620 spr1667 spr1097 spr0686 spr1430 spr0087 spr0914 spr1108 spr0750 spr0114 spr1201 spr1527 spr0563 spr0294 spr1837 8130 ULIJASZ ET AL. FIG....”

YP_001449372 hypothetical protein (RefSeq) from Streptococcus gordonii str. Challis substr. CH1
Aligns to 53:334 / 337 (83.7%), covers 96.8% of PF13349, 122.8 bits

• Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation
  Olson, BMC genomics 2013
  • “...65 Pasterurella mutocida ZP_18466110 SCRE_1851* 333 Conserved hypothetical protein 38.82 3609 100.6 28 S. gordonii YP_001449372 SCRE_1887* 229 Triose-phosphate isomerase 28.41 4057 100.0 40 Leuconostoc citreum YP_001728668 SCRE_1888 179 Conserved hypothetical protein 27.96 3880 100.0 48 Bacillus sp ZP_01723913 *Genes found in all sequenced SAG from...”

EF0797 conserved domain protein (NCBI ptt file) from Enterococcus faecalis V583
2 alignments in 60:334 / 341 (80.6%), covering up to 65.9% of PF13349, 88.5 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...”

SE1920 conserved hypothetical protein (NCBI ptt file) from Staphylococcus epidermidis ATCC 12228
Aligns to 124:267 / 267 (53.9%), covers 59.8% of PF13349, 78.8 bits

• Mapping the pathways to staphylococcal pathogenesis by comparative secretomics
  Sibbald, Microbiology and molecular biology reviews : MMBR 2006
  • “...32470549b 32470583 SE0583 SE0627 SE0828 SE1020 SE1500 SE1575 SE1628 SE1883 SE1920 SE2142 SE2152 SE2197 SE2201 SE2373 SE2398 P601 P607 P517 P202 S T A I S A V V...”

SERP1470 hypothetical protein (NCBI) from Staphylococcus epidermidis RP62A
Aligns to 44:278 / 278 (84.5%), covers 100.0% of PF13349, 75.9 bits

• Gram-positive three-component antimicrobial peptide-sensing system
  Li, Proceedings of the National Academy of Sciences of the United States of America 2007
  • “...permease protein 0.49 0.42 0.45 SERP0573 SERP0712 SERP1470 SERP1772 SERP2170 SERP2442 SERP0971 SERP1394 SERP1395 SERP1951 SERP1952 2.05* 2.07* 2.05* 2.15* 2.07*...”

WP_005729490 DUF4097 family beta strand repeat-containing protein from Lactobacillus crispatus
Aligns to 23:225 / 225 (90.2%), covers 85.5% of PF13349, 74.7 bits

• Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil
  Oliveira, PeerJ 2021
  • “...) K00158 WP_005723618 1 1 1 1 Adhesin Putative adhesin WP_005728236 1 1 1 1 WP_005729490 1 1 1 Antimicrobial production Safety assessment of the strains for probiotic applications Features associated with safety in the four strains from Brazil are shown in Table 4 . About...”

LMRG_01762 hypothetical protein (RefSeq) from Listeria monocytogenes 10403S
Q8Y4F8 Lmo2486 protein from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
lmo2486 lmo2486 (NCBI ptt file) from Listeria monocytogenes EGD-e
Aligns to 140:350 / 403 (52.4%), covers 76.7% of PF13349, 67.3 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...”

LMOf2365_2459 PspC domain protein (NCBI) from Listeria monocytogenes str. 4b F2365
Aligns to 140:350 / 403 (52.4%), covers 76.7% of PF13349, 66.7 bits

• Contributions of a LysR Transcriptional Regulator to Listeria monocytogenes Virulence and Identification of Its Regulons.
  Abdelhamed, Journal of bacteriology 2020 (secret)

EF1753 conserved hypothetical protein (NCBI ptt file) from Enterococcus faecalis V583
Aligns to 276:529 / 533 (47.7%), covers 97.6% of PF13349, 66.2 bits

• 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...”

OG1RF_11464 daptomycin-sensing surface protein LiaX from Enterococcus faecalis OG1RF
Aligns to 276:529 / 533 (47.7%), covers 97.6% of PF13349, 66.1 bits

• Comprehensive analysis of phospholipids and glycolipids in the opportunistic pathogen Enterococcus faecalis
  Rashid, PloS one 2017
  • “...Polymorphisms (SNPs) in the DapR strains Dap21 and Dap22. Strain Gene/locus cls1 (OG1RF_10364) cls2 (OG1RF_11324) OG1RF_11464 OG1RF_11507 OG1RF_11901 Dap21 Mutation type Substitution - Frameshift Frameshift - Mutation location R267C - 272 19 - Dap22 Mutation type - Substitution Frameshift Nonsense Inframe insertion Mutation location - P181H...”

LGG_00914 hypothetical protein (RefSeq) from Lactobacillus rhamnosus GG
LGG_00914 daptomycin-sensing surface protein LiaX from Lacticaseibacillus rhamnosus GG
Aligns to 247:492 / 496 (49.6%), covers 75.1% of PF13349, 64.3 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...”

O34628 Uncharacterized protein YvlB from Bacillus subtilis (strain 168)
Aligns to 107:361 / 365 (69.9%), covers 93.2% of PF13349, 61.5 bits

• Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops
  Urrutia-Irazabal, eLife 2021
  • “...Accession Description LogFC P37474 Transcription-repair-coupling factor GN=mfd 7.887 O34863 UvrABC system protein A GN=uvrA 6.127 O34628 Uncharacterised protein YvlB GN=yvlB 5.779 Q795Q5 Uncharacterised membrane protein YttA GN=yttA 3.735 O34942 ATP-dependent DNA helicase RecG GN=recG 3.304 Q06796 50S ribosomal protein L11 GN=rplK 3.269 P20429 DNA-directed RNA polymerase...”

SO_3842 conserved hypothetical protein (NCBI ptt file) from Shewanella oneidensis MR-1
Aligns to 40:221 / 318 (57.2%), covers 76.7% of PF13349, 60.5 bits

• Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation
  Gupta, Genome research 2007
  • “...from the N-terminal portion of conserved hypothetical protein SO_3842. The peptide breakage before the starred residue is produced when the signal peptide is...”

LMRG_01761 hypothetical protein (RefSeq) from Listeria monocytogenes 10403S
Aligns to 162:417 / 420 (61.0%), covers 84.7% of PF13349, 60.3 bits

• PASTA kinase-dependent control of peptidoglycan synthesis via ReoM is required for cell wall stress responses, cytosolic survival, and virulence in Listeria monocytogenes
  Kelliher, PLoS pathogens 2021
  • “...clpC C246587A Q512K ATPase subunit of Clp protease Lmrg_00741 oatA C1277896T Silent Peptidoglycan o -acetyltransferase Lmrg_01761 G2516839A Silent DUF-containing protein Lmrg_01723 mreB G2557908GA Frameshift, premature stop codon Rod shape-determining protein Lmrg_01945 G2789642A A241T ATP-binding subunit of multidrug efflux pump Shading represents SNPs in genes involved in...”
• Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
  Boonmee, Frontiers in microbiology 2019
  • “...LMRG_01622 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...”
• PrfA-like transcription factor gene lmo0753 contributes to L-rhamnose utilization in Listeria monocytogenes strains associated with human food-borne infections
  Salazar, Applied and environmental microbiology 2013
  • “...LMRG_01676 LMRG_01269 LMRG_01809 LMRG_01908 LMRG_02074 LMRG_01761 LMRG_00606 LMRG_01655 LMRG_01915 LMRG_02072 LMRG_00868 LMRG_02225 LMRG_02073 LMRG_01886...”

Q8Y4F7 Lmo2487 protein from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
lmo2487 similar to B. subtilis YvlB protein (NCBI ptt file) from Listeria monocytogenes EGD-e
Aligns to 162:417 / 420 (61.0%), covers 84.7% of PF13349, 60.3 bits

• 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...”
• 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 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...”
• Interference of components of the phosphoenolpyruvate phosphotransferase system with the central virulence gene regulator PrfA of Listeria monocytogenes
  Mertins, Journal of bacteriology 2007
  • “...similar to B. subtilis YvlC protein; lmo2486, unknown; lmo2487, similar to B. subtilis YvlB protein; lmo1001, similar to B. subtilis protein YkvS; ptsH, PTS...”
• More

SA1740 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus N315
MW1867 hypothetical protein (NCBI ptt file) from Staphylococcus aureus subsp. aureus MW2
Aligns to 45:280 / 280 (84.3%), covers 100.0% of PF13349, 58.3 bits

• Regulation of hemolysin expression and virulence of Staphylococcus aureus by a serine/threonine kinase and phosphatase
  Burnside, PloS one 2010
  • “...Pathogenicity protein, putative 2 MH era GTP-binding protein Era - small molecule interactions 1 MH SA1740 Two component DNA-binding regulator, PhoP 1 MH rot Virulence factor regulator protein 3 MH fumC Fumarate hydratase, class II - TCA cycle 2 MH pcrA PcrA protein - DNA replication,...”
• 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
  • “...sa_c10143s10555cv_s_at 7.9 2.5 15 N315-SA1804 putative transcriptional regulator Signal transduction sa_c3083s2636_a_at 2.4 2.5 2.5 phoP SA1740 alkaline phosphatase synthesis transcriptional regulatory protein sa_c8744s7687_a_at 14.7 15 15 SA1759 universal stress protein family Posttranslational modification, protein turnover, chaperone sa_c8485s7447_a_at 3.5 2.5 15 SA0872 OsmC/Ohr family protein sa_c3196s2743_a_at 3.5...”
• Staphylococcus aureus Virulence Affected by an Alternative Nisin A Resistance Mechanism.
  Kawada-Matsuo, Applied and environmental microbiology 2020 (secret)

D2S332 DUF4097 domain-containing protein from Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / JCM 9101 / NCIMB 13204 / VKM B-1734 / 4k)
Aligns to 26:273 / 276 (89.9%), covers 67.9% of PF13349, 57.2 bits

• Familial syndromic esophageal atresia maps to 2p23-p24.
  Celli, American journal of human genetics 2000

LACR_2166 hypothetical protein (NCBI) from Lactococcus lactis subsp. cremoris SK11
llmg_2164 hypothetical protein (NCBI) from Lactococcus lactis subsp. cremoris MG1363
Aligns to 115:360 / 370 (66.5%), covers 85.9% of PF13349, 55.2 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...”

SPy2174 hypothetical protein (NCBI ptt file) from Streptococcus pyogenes M1 GAS
Aligns to 51:359 / 359 (86.1%), covers 100.0% of PF13349, 54.7 bits

• Determination of the relationship between group A streptococcal genome content, M type, and toxic shock syndrome by a mixed genome microarray
  Vlaminckx, Infection and immunity 2007
  • “...DpiB Malate-sodium symport NAD-dependent malic enzyme SpyM3_1329 Spy2174 SpyM3_1331 SpyM3_1330 prtf-1 SPy1046 sfb SPy1107 malP SPy1110 oadA citE citF citX...”
• Regulation of SpeB in Streptococcus pyogenes by pH and NaCl: a model for in vivo gene expression
  Loughman, Journal of bacteriology 2006
  • “...spy2033 spy2037 speB spy2040 spy2041 spy2050 spy2051 spy2174 spy2169 spy2170 spy2193 Putative function Hypothetical protein Putative PTS IID (mannose specific)...”

Spy49_1783 hypothetical protein (RefSeq) from Streptococcus pyogenes NZ131
Aligns to 51:357 / 357 (86.0%), covers 100.0% of PF13349, 53.2 bits

• Genome-wide screening of potential RNase Y-processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131
  Chen, MicrobiologyOpen 2019
  • “...(streptopain)/streptococcal pyrogenic exotoxin B (SpeB) operon_842 + Spy49_1781 Hypothetical protein Spy49_1781 Spy49_1782 Hypothetical protein Spy49_1782 Spy49_1783 Hypothetical protein Spy49_1783 John Wiley & Sons, Ltd 3.6 FolC1 The folC1 gene encodes dihydrofolate/folylpolyglutamate synthase (DHFS/FPGS), which is involved in folate synthesis and intracellular retention (Bognar, Osborne, & Shane,...”

EDAG_01115 daptomycin-sensing surface protein LiaX from Enterococcus faecium D344SRF
Aligns to 266:518 / 522 (48.5%), covers 96.8% of PF13349, 52.1 bits

• Involvement of the Eukaryote-Like Kinase-Phosphatase System and a Protein That Interacts with Penicillin-Binding Protein 5 in Emergence of Cephalosporin Resistance in Cephalosporin-Sensitive Class A Penicillin-Binding Protein Mutants in Enterococcus faecium
  Desbonnet, mBio 2016
  • “...was a protein of unknown function that we have designated P 5 AP (Pbp5-associated protein) (EDAG_01115 [protein identifier {ID} EFD09967 from the genome of E.faecium D344SRF]) referred to in the mass spectrometry data set as H8LA73_H8LA73_ENTFU from the E.faecium strain Aus0004 closed genome used as a...”

XCC1308 conserved hypothetical protein (NCBI ptt file) from Xanthomonas campestris pv. campestris str. ATCC 33913
Aligns to 33:291 / 294 (88.1%), covers 90.0% of PF13349, 52.0 bits

• Insights into the extracytoplasmic stress response of Xanthomonas campestris pv. campestris: role and regulation of {sigma}E-dependent activity
  Bordes, Journal of bacteriology 2011
  • “...Cell envelope XCC0539 XCC2266 XCC3925 Unknown function XCC1308 XCC0401 1.49 (NC_003902: 32909643290833, minus strandc) XCC3224 XCC1244 XCC0944 XCC3226 XCC3798...”

SACE_3262 hypothetical protein (RefSeq) from Saccharopolyspora erythraea NRRL 2338
Aligns to 21:276 / 282 (90.8%), covers 85.1% of PF13349, 50.8 bits

• Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain
  Peano, Microbial cell factories 2012
  • “...SACE_3102 1249 Frameshift (+G 338/339) Unknown function SACE_3186 392 Missense (R390S) Unknown function (tpcl cluster) SACE_3262 282 Frameshift (+C 434/435) Insertion between Unknown function SACE 3264: Unknown secreted protein. SACE_3264 117 SACE 3572 and SACE 3573 SACE 3572: Unknown secreted protein. SACE 3573: Unknown function SACE_3748...”

YP_702564 hypothetical protein (NCBI) from Rhodococcus sp. RHA1
Aligns to 10:279 / 281 (96.1%), covers 83.9% of PF13349, 48.7 bits

• Identification and characterization of the biosynthetic gene cluster of polyoxypeptin A, a potent apoptosis inducer
  Du, BMC microbiology 2014
  • “...DSM 43021 70/78 plyZ 79 YP_001612061 LysR family transcriptional regulator Sorangium cellulosum 65/77 orf11 287 YP_702564 Hypothetical protein Rhodococcus jostii RHA1 56/73 orf14742 170 YP_002777514 Hypothetical protein ROP_03220 Rhodococcus opacus B4 51/63 a Numbers are in amino acids. Upstream of the ply gene cluster, three genes,...”

AMED_1127 DUF4097 family beta strand repeat-containing protein from Amycolatopsis mediterranei U32
Aligns to 20:219 / 220 (90.9%), covers 70.7% of PF13349, 47.1 bits

• Identification and functional analysis of a nitrate assimilation operon nasACKBDEF from Amycolatopsis mediterranei U32
  Shao, Archives of microbiology 2011 (PubMed)
  • “...to the protein coding genes of AMED_1121 to AMED_1127. These genes were co-transcribed as an operon, concomitantly repressed by ammonium while activated with...”

ROP_29250 hypothetical protein (RefSeq) from Rhodococcus opacus B4
Aligns to 12:279 / 281 (95.4%), covers 79.1% of PF13349, 46.5 bits

• Identification and characterization of the biosynthetic gene cluster of polyoxypeptin A, a potent apoptosis inducer
  Du, BMC microbiology 2014
  • “...orf11 ) and orf14742 encode proteins with similarities to LysR family transcriptional regulator, hypothetical protein ROP_29250 and hypothetical protein ROP_03220. To prove that the genes beyond this cluster are not related to PLY biosynthesis, we inactivated orf1 and orf11 . The resulting mutants have no effect...”

YPO1174 hypothetical protein (NCBI ptt file) from Yersinia pestis CO92
2 alignments in 4:182 / 309 (57.9%), covering up to 30.1% of PF13349, 45.0 bits

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB1085 YPO2592 putative membrane protein 0.609 (0.015) YPTB1161 YPO1126 putative exported protein 0.596 (0.004) YPTB1215 YPO1174 hypothetical protein 1.527 (0.047) YPTB1222 YPO1181 putative membrane protein 0.697 (0.032) YPTB1227 YPO1186 conserved hypothetical protein 0.634 (0.005) YPTB1297 YPO1261 conserved hypothetical protein 0.659 (0.014) YPTB1387 YPO1361 putative membrane protein...”
• Application of high-density array-based signature-tagged mutagenesis to discover novel Yersinia virulence-associated genes
  Karlyshev, Infection and immunity 2001
  • “...YPO3004 YPO3099 YPO2532 YPO2712 YPO2440 YPO2287a YPO1108 YPO1174 YPO1186 YPO1382 (promoter region) YPO1987 YPO1994 YPO2174 YPO0054 YPO0337 YPO0702 59 (98) NS...”

Smlt3512 hypothetical protein (RefSeq) from Stenotrophomonas maltophilia K279a
Aligns to 35:290 / 293 (87.4%), covers 94.8% of PF13349, 44.1 bits

• σ^P-NagA-L1/L2 Regulatory Circuit Involved in ΔompA_299-356-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...”

LSA0512 Hypothetical protein (NCBI) from Lactobacillus sakei subsp. sakei 23K
Aligns to 218:487 / 491 (55.0%), covers 59.8% of PF13349, 43.9 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...”

M3FS09 Lipoprotein from Streptomyces bottropensis ATCC 25435
Aligns to 131:288 / 291 (54.3%), covers 58.2% of PF13349, 40.4 bits

• Proteomic Reference Map and Comparative Analysis between Streptomyces griseus S4-7 and wbiE2 Transcription Factor-Mutant Strain
  Kim, The plant pathology journal 2020
  • “...Chlorite dismutase W9FXT2 27845/5.90 68 491 16 8 - +1.96 - Stress response 19 Lipoprotein M3FS09 30955/5.06 31 38 6 0 +2.44 - - Transport/Virulence 20 Electron transfer flavoprotein subunit alpha A0A087JXW9 32481/4.97 44 666 8 8 - +3.13 +1.95 Transport 21 Proteasome subunit alpha G0Q7E7...”

Q8N0U4 Protein FAM185A from Homo sapiens
Aligns to 205:364 / 392 (40.8%), covers 47.4% of PF13349, 37.2 bits

• Salivary proteome signatures in the early and middle stages of human pregnancy with term birth outcome.
  Dey, Scientific reports 2020
  • “...0.000 0.002 1 P84090 Enhancer of rudimentary homolog ERH 1.61 3.13 1.94 0.000 0.000 1 Q8N0U4 Protein FAM185A FAM185A 0.72 1.06 1.47 0.021 0.075 1 P78417 Glutathione S-transferase omega-1 GSTO1 0.48 1.20 2.49 0.000 0.002 1 P16402 Histone H1.3 HIST1H1D 1.32 3.84 2.92 0.007 0.030 1...”

PG0419 hypothetical protein (NCBI) from Porphyromonas gingivalis W83
Aligns to 60:277 / 301 (72.4%), covers 81.9% of PF13349, 36.8 bits

• 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 (RefSeq) from Porphyromonas gingivalis ATCC 33277
Aligns to 45:256 / 286 (74.1%), covers 81.5% of PF13349, 36.4 bits

• The Porphyromonas gingivalis ferric uptake regulator orthologue binds hemin and regulates hemin-responsive biofilm development
  Butler, PloS one 2014
  • “...3.3E-04 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...”

FRAAL2567 hypothetical protein (NCBI) from Frankia alni ACN14a
Aligns to 15:278 / 280 (94.3%), covers 75.1% of PF13349, 35.8 bits

• 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...”

CG8187 uncharacterized protein from Drosophila melanogaster
Aligns to 48:346 / 376 (79.5%), covers 77.9% of PF13349, 35.5 bits

• 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...”

XOO2060 hypothetical protein (NCBI) from Xanthomonas oryzae pv. oryzae KACC10331
Aligns to 81:276 / 278 (70.5%), covers 50.2% of PF13349, 34.8 bits

• Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper
  Potnis, BMC genomics 2011
  • “...311018 XOO2886 - XOO2906 XOO3286 - XOO3319 / Xoo PXO99A XOO0245 - XOO0270 XOO2029 - XOO2060 / Xoc BLS256 XOC2523 - XOC2545 XOC1309 - XOC1370 / Xg / / / Xcc ATCC33913 / / / Xcc 8004 / / / Xca 756C / / / Xalb...”

XAC1545 conserved hypothetical protein (NCBI ptt file) from Xanthomonas axonopodis pv. citri str. 306
Aligns to 38:271 / 272 (86.0%), covers 61.8% of PF13349, 32.5 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...”

PF1074 hypothetical protein (NCBI ptt file) from Pyrococcus furiosus DSM 3638
Aligns to 8:213 / 214 (96.3%), covers 64.7% of PF13349, 31.5 bits

• Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins
  Weinberg, Journal of bacteriology 2005
  • “...(4.2) 2.6 1.0 (6.2) Unknown PF1072 PF1073 PF1074 [Conserved hypothetical protein] [Conserved hypothetical protein] [Conserved hypothetical protein] 0 4 0 3.7...”
  • “...PF1270, and PF1973) or increase even further (PF0190 and PF1074). The latter include two adjacent ORFs (PF0324 and PF0325) up-regulated by 20-fold after 5 h and...”

CD1347 hypothetical protein (RefSeq) from Clostridium difficile 630
Aligns to 55:234 / 356 (50.6%), covers 56.2% of PF13349, 29.3 bits

• Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species
  Adams, Antimicrobial agents and chemotherapy 2015
  • “...helices (RhaT family; E value, 2.04e3), and CD1347 encodes a predicted membrane protein with a single N-terminal transmembrane helix. No intergenic...”

Or search for genetic data about PF13349 in the Fitness Browser