Family Search for PF09922 (DUF2154)

PF09922.9 hits 9 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

lmo1020 similar to B. subtilis YvqF protein (NCBI ptt file) from Listeria monocytogenes EGD-e
Aligns to 122:234 / 237 (47.7%), covers 100.0% of PF09922, 126.0 bits

• Regulation of LiaRS-dependent gene expression in bacillus subtilis: identification of inhibitor proteins, regulator binding sites, and target genes of a conserved cell envelope stress-sensing two-component system
  Jordan, Journal of bacteriology 2006
  • “...liaIH (first gene lin0953/Lmo0954) and liaFSR (lin1019/ Lmo1020) are organized in two independent transcriptional units, as noted above (Fig. 3A)....”
  • “...1049151 18.22 TAgGACTcAAGTtgTAGgtgAA 18.95 TCcGACTaAAGTagTAGgctAt lmo0954 lmo1020 102 120 lmo0954/0955; homologous to liaIH lmo1020 to -1022; homologous to...”
• The LisRK signal transduction system determines the sensitivity of Listeria monocytogenes to nisin and cephalosporins
  Cotter, Antimicrobial agents and chemotherapy 2002
  • “...and a gene encoding a protein of unknown function (lmo1020, yvqF, or tcdsorf1). While mutation of llkinD has not been achieved, it was found that the most...”

lin1019 similar to B. subtilis YvqF protein (NCBI ptt file) from Listeria innocua Clip11262
Aligns to 122:234 / 237 (47.7%), covers 100.0% of PF09922, 125.1 bits

• Regulation of LiaRS-dependent gene expression in bacillus subtilis: identification of inhibitor proteins, regulator binding sites, and target genes of a conserved cell envelope stress-sensing two-component system
  Jordan, Journal of bacteriology 2006
  • “...TAgGACTcAAGTtgTAGgtgAA 18.49 TCcGACTaAAGTagTAGAgAtt 18.34 TAtGcCTttAGTCcTAtgAAAA Lin0953 Lin1019 Lin1043 103 121 95 Lin0953/0954; homologous to liaIH Lin1019 to...”

spr0342 Conserved hypothetical protein (NCBI ptt file) from Streptococcus pneumoniae R6
Aligns to 114:229 / 232 (50.0%), covers 100.0% of PF09922, 119.3 bits

• The pneumococcal cell envelope stress-sensing system LiaFSR is activated by murein hydrolases and lipid II-interacting antibiotics
  Eldholm, Journal of bacteriology 2010
  • “...the pneumococcal system also contains a third component (spr0342) corresponding to LiaF. Our results show that CbpD, together with LytA and LytC, activates the...”
  • “...a promoter deletion analysis. Promoter fragments upstream of spr0342 were transcriptionally fused to lacZ, using the promoter-probe vector pPPP2 (14) (see Table...”

LIAF_BACSU / O32199 Protein LiaF from Bacillus subtilis (strain 168) (see 6 papers)
NP_391190 LiaR negative effector LiaF from Bacillus subtilis subsp. subtilis str. 168
Aligns to 126:238 / 241 (46.9%), covers 100.0% of PF09922, 119.2 bits

• disruption phenotype: Upregulates expression of liaI which in turn induces the liaRS two-component regulatory system.
• Stoichiometry and perturbation studies of the LiaFSR system of Bacillus subtilis.
  Schrecke, Molecular microbiology 2013 (PubMed)
  • GeneRIF: Transcription and translation initiation combined indicate a LiaF:LiaS:LiaR ratio of 18:4:1.

SACOL1944 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus COL
SA1702 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus N315
SAV1886 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus Mu50
USA300HOU_1882 hypothetical membrane protein (RefSeq) from Staphylococcus aureus subsp. aureus USA300_TCH1516
Aligns to 119:230 / 233 (48.1%), covers 100.0% of PF09922, 105.6 bits

• BACTERIAL VACCINE COMPONENTS FROM STAPHYLOCOCCUS AUREUS AND USES THEREOF
  MALOUIN, 2011
• Different bacterial gene expression patterns and attenuated host immune responses are associated with the evolution of low-level vancomycin resistance during persistent methicillin-resistant Staphylococcus aureus bacteraemia
  Howden, BMC microbiology 2008
  • “...number of these cell wall genes were also down regulated in pair 5 (SACOL1066, SACOL1943, SACOL1944, SACOL2116, SACOL2571). Figure 2 Heat map analysis of cell wall genes . Heat map analysis of "core cell wall genes" and additional cell wall genes which have been commonly shown...”
• Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association
  Alam, Genome biology and evolution 2014
  • “...Katayama et al. (2009) ; Cui et al. (2009) ; Gardete et al. (2012) yvqF SA1702 Uncharacterized protein Y220C Gardete et al. (2012) agrA SA1844 Accessory gene regulator A a The list consists of gene identified by comparative whole-genome and candidate gene sequencing studies. For a...”
  • “...and ntree = 10,000. From this result, six significant features (rpoB H481, SA0017, SA1659, SA0617, SA1702, and SA1700) were selected for a second iteration of the classifier, using mytry = 4 and ntree = 10,000 parameters. The second classifier ( etest_rf_pred2 ) was then used to...”
• Serine/threonine phosphatase Stp1 contributes to reduced susceptibility to vancomycin and virulence in Staphylococcus aureus
  Cameron, The Journal of infectious diseases 2012
  • “...including the ABC transporter permease vraG [32]; yvqF (SA1702) [7], which is a member of the vraSR operon; and the DNA-dependent RNA polymerase subunit...”
  • “...transporter permease ABC transporter, defense 633 SNP Ala580Val SA1702 SA2047 yvqF rplC Protein of the VraSR operon 50S ribosomal protein L3 Cell wall/outer...”
• Whole genome sequencing and complete genetic analysis reveals novel pathways to glycopeptide resistance in Staphylococcus aureus
  Renzoni, PloS one 2011
  • “...LiaS, a putative S. aureus VraS ortholog. B. subtilis LiaF is syngenic to S. aureus SA1702, and mutations in SA1702 have also been reported to affect glycopeptide resistance [17] , [38] . Indeed, a recent report suggests that S. aureus SA1702/YvqF and VraS directly interact lending...”
• Site-specific mutation of Staphylococcus aureus VraS reveals a crucial role for the VraR-VraS sensor in the emergence of glycopeptide resistance
  Galbusera, Antimicrobial agents and chemotherapy 2011
  • “...of missense mutations mapping in vraS, vraR, or SA1702 (16, 32-34, 52). How missense mutations such as VraS-I5N modify VraRS-dependent signaling and gene...”
• Genetic changes associated with glycopeptide resistance in Staphylococcus aureus: predominance of amino acid substitutions in YvqF/VraSR
  Kato, The Journal of antimicrobial chemotherapy 2010
  • “...encoding a two-component histidine kinase sensor; and SA1702 (also called yvqF, located immediately upstream of vraS), encoding a conserved hypothetical...”
• Reduced vancomycin susceptibility in Staphylococcus aureus, including vancomycin-intermediate and heterogeneous vancomycin-intermediate strains: resistance mechanisms, laboratory detection, and clinical implications
  Howden, Clinical microbiology reviews 2010
  • “...mutations to arise was a nucleotide change in SA1702 (strain N315 locus tag nomenclature), resulting in a predicted amino acid substitution (H164R). SA1702 is...”
  • “...promoters. It is possible that the H164R mutation of SA1702 has led to the upregulation of vraR, the liaR ortholog in S. aureus. In support of this...”
• 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
  • “...3.9 2.5 2.5 rplT SA1725 50S ribosomal protein L20 sa_c2926s2487_at * 3.2 5 30 rplU SA1702 50S ribosomal protein L21 sa_c4872s4181_at * 2.6 15 stable rplV SA2234 50S ribosomal protein L22 sa_c10192s8875_a_at 3.7 5 30 rplW SA2237 50S ribosomal protein L23 sa_c4852s4158_at * 2.4 15 stable...”
  • “...19.5 2.5 2.5 rplT SA1725 50S ribosomal protein L20 sa_c2926s2487_at * 4.4 5 15 rplU SA1702 50S ribosomal protein L21 sa_c4872s4181_at * 3.7 15 15 rplV SA2234 50S ribosomal protein L22 sa_c4852s4158_at * 4.1 15 15 rplX SA2228 50S ribosomal protein L24 sa_c7511s6531_a_at * 5.9 15...”
• Genetic analysis of factors affecting susceptibility of Bacillus subtilis to daptomycin
  Hachmann, Antimicrobial agents and chemotherapy 2009
  • “...homolog LiaH. S. aureus harbors the liaFSR orthologs SA1702 and vraSR (35). When testing for daptomycin susceptibility, Muthaiyan et al. observed an increased...”
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• A multidrug ABC transporter with a taste for GTP
  Orelle, Scientific reports 2018
  • “...exhibited similar sequence identities with Sav1866 and MsbA (about 30% for each Pat protein with Sav1886, and 27 and 31% for PatA and PatB, respectively, with MsbA), but due to higher atomic resolution (3.4 versus 3.7), the Sav1866 structure 2ONJ was proposed to be the unique...”
• Two ABCB4 point mutations of strategic NBD-motifs do not prevent protein targeting to the plasma membrane but promote MDR3 dysfunction
  Degiorgio, European journal of human genetics : EJHG 2014
  • “...a homodimeric bacterial transporter. Both MDR3 and Sav1886 show significant homology of sequence (35% identical residues, spanning 578 amino-acid positions) and...”
  • “...molecules present in the bacterial multidrug ABC transporter Sav1886 from S. aureus (PDB: 2hyd).3 The multiple sequence alignment of amino-acid stretches from...”
• Structural evolution of the ABC transporter subfamily B
  Flanagan, Evolutionary bioinformatics online 2007
  • “...amino acid sequences including the eukaryotic ABC transporter subfamily B and bacterial orthologs of the Sav1886 protein from S. aureus were used in this analysis. Eukaryotic sequences were downloaded from the National Center for Biotechnology Informations Homologene database ( www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene ). Clusters of homologous protein sequences...”
  • “...B6, 83488; B7, 3175; B8, 5203; B9, 10491; B10, 6474; B11, 74509. Bacterial orthologs of Sav1886 were identified in the IMG database ( http://img.jgi.doe.gov/ ) ( Markowitz et al. 2006 ) of pre-computed clusters of best pair-wise BLAST alignments (ortholog cluster 7683, 37 sequences). The sequence...”
• A mutation in the PP2C phosphatase gene in a Staphylococcus aureus USA300 clinical isolate with reduced susceptibility to vancomycin and daptomycin
  Passalacqua, Antimicrobial agents and chemotherapy 2012
  • “...mutation was Pro174Ser replacement in a hypothetical gene (USA300HOU_1882) that is located just upstream of, and potentially in an operon with, the regulatory...”

SPy1623 conserved hypothetical protein (NCBI ptt file) from Streptococcus pyogenes M1 GAS
Aligns to 132:228 / 228 (42.5%), covers 83.3% of PF09922, 103.3 bits

• Large-scale identification of serotype 4 Streptococcus pneumoniae virulence factors
  Hava, Molecular microbiology 2002 (secret)

llmg_1650 putative secreted protein (NCBI) from Lactococcus lactis subsp. cremoris MG1363
Aligns to 79:188 / 191 (57.6%), covers 78.9% of PF09922, 58.1 bits

• Efficient overproduction of membrane proteins in Lactococcus lactis requires the cell envelope stress sensor/regulator couple CesSR
  Pinto, PloS one 2011
  • “...protein; Regulation of lysozyme resistance 5.60 5.3*10 7 llmg_1156/yneG Putative transcriptional repressor 5.79 6.2*10 5 llmg_1650 Putative membrane protein 3.08 9.4*10 7 llmg_1649/cesS Two-component system sensor (histidine kinase) 2.35 5.0*10 5 llmg_1648/cesR Two-component system regulator 2.75 8.5*10 7 llmg_1647 Putative hydrolase from the Cof-subfamily 2.04 2.1*10...”

LBA0404 hypothetical protein (RefSeq) from Lactobacillus acidophilus NCFM
Aligns to 151:248 / 252 (38.9%), covers 62.3% of PF09922, 35.3 bits

• Microarray analysis of a two-component regulatory system involved in acid resistance and proteolytic activity in Lactobacillus acidophilus
  Azcarate-Peril, Applied and environmental microbiology 2005
  • “...found LBA0352 hypothetical protein LBA0402 unknown LBA0404 hypothetical protein LBA1495 putative fibrinogen-binding protein LBA1611 surface protein fmtB LBA1690...”

NP_722171 hypothetical protein from Streptococcus mutans UA159
Aligns to 127:224 / 228 (43.0%), covers 68.4% of PF09922, 32.0 bits

• The hdrRM operon of Streptococcus mutans encodes a novel regulatory system for coordinated competence development and bacteriocin production.
  Okinaga, Journal of bacteriology 2010
  • GeneRIF: HdrM antagonizes the function of HdrR.
• Genetic characterization of the hdrRM operon: a novel high-cell-density-responsive regulator in Streptococcus mutans.
  Merritt, Microbiology (Reading, England) 2007 (PubMed)
  • GeneRIF: Part of a two-gene operon induced by conditions of high cell density. Putative membrane protein that functions together SMU.1854. Referred to as "hdrM".