Family Search for PF04340 (DUF484)

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PF04340 hits 7 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

YigA / b3810 DUF484 domain-containing protein YigA from Escherichia coli K-12 substr. MG1655 (see paper)
b3810 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 10:233 / 235 (95.3%), covers 99.1% of PF04340, 298.9 bits

• 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms
  Militello, BMC microbiology 2016
  • “...of dnaG-Ts 1.64 2.18E-03 b3409 feoB Putative ferrous iron permease with GTP-binding domain 1.62 3.37E-03 b3810 yigA DUF484 family protein, function unknown 1.57 2.66E-03 b0926 ycbK Periplasmic M15A family non-protease, function unknown 1.56 8.53E-04 b0927 ycbL Glyoxalase II homolog, function unknown 1.56 3.57E-03 b3704 rnpA RNase...”

c4731 Hypothetical protein yigA from Escherichia coli CFT073
Aligns to 10:233 / 235 (95.3%), covers 99.1% of PF04340, 295.3 bits

• ESCRT-III mediates budding across the inner nuclear membrane and regulates its integrity
  Arii, Nature communications 2018
  • “...Abcam, Cambridge, UK; 1:1000), CHMP4C (ab155668; Abcam; 1:500), lamin B1 (ab16048-100; Abcam; 1:1000) and calnexin (c4731; Sigma; 1:2000); and commercial mouse polyclonal antibodies against CHMP4A (ab67058; Abcam; 1:500). Mouse polyclonal antibodies against UL31(1:500) and rabbit polyclonal antibodies against UL34 (1:2000) were reported previously 61 . Establishment...”
• Herpes Simplex Virus 1 UL34 Protein Regulates the Global Architecture of the Endoplasmic Reticulum in Infected Cells
  Maeda, Journal of virology 2017
  • “...antibodies to CD98hc (H-300; Santa Cruz Biotechnology), calnexin (c4731; Sigma), and lamin B1 (ab16048-100; Abcam); and commercial goat polyclonal antibody to 1...”
• Role of herpes simplex virus 1 immediate early protein ICP22 in viral nuclear egress
  Maruzuru, Journal of virology 2014
  • “...Sigma) and rabbit polyclonal antibodies to calnexin (c4731; Sigma), lamin B1 (ab16048-100; Abcam), Flag (DDDDK; MBL), and VP23 (CAC-CT-HSV-UL18; CosmoBio)....”

PA5279 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 7:227 / 233 (94.8%), covers 99.6% of PF04340, 294.7 bits

• The emergence of cefiderocol resistance in Pseudomonas aeruginosa from a heteroresistant isolate during prolonged therapy
  Teran, Antimicrobial agents and chemotherapy 2024 (secret)
• Colony-morphology screening uncovers a role for the Pseudomonas aeruginosa nitrogen-related phosphotransferase system in biofilm formation
  Cabeen, Molecular microbiology 2016
  • “...to PA3699 ; hereafter 16550 ), which encodes a TetR-type DNA repressor; PA14_69700 (orthologous to PA5279 ; hereafter 69700 ), which encodes an uncharacterized GAF-domain protein; and ptsP , which encodes enzyme I of the nitrogen-regulated phosphotransferase (PTS Ntr ) system. Insertions in these genes were...”
  • “...is distinct from a role in lasR repression. The third newly identified gene, 69700 ( PA5279 in PAO1), is notable because its product inhibits biofilm formation and because it contains a crystallographically validated GAF domain of unknown function (PDB 3E98). GAF domains are generally considered small...”
• Structure of the cytoplasmic region of PelD, a degenerate diguanylate cyclase receptor that regulates exopolysaccharide production in Pseudomonas aeruginosa
  Whitney, The Journal of biological chemistry 2012
  • “...of a P. aeruginosa GAF domain of unknown function (PA5279; Protein Data Bank code 3E98) solved by the Joint Center for Structural Genomics contains an...”
  • “...region. Cartoon representation of P. aeruginosa PelD, P. aeruginosa PA5279, and H. sapiens PDE2A. For each protein, the GAF domain(s) is displayed in blue with...”
• Role of lon, an ATP-dependent protease homolog, in resistance of Pseudomonas aeruginosa to ciprofloxacin
  Brazas, Antimicrobial agents and chemotherapy 2007
  • “...PA4316 PA4422 PA4466 PA4700 PA4700 PA4756 PA4763 PA4961 PA5016 PA5208 PA5279 PA5345 a Gene name ilvD lon lon lon gbt recA xseA sbcB sbcB mrcB mrcB carB recN...”

PA14_69700 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
PA14_RS28410 DUF484 family protein from Pseudomonas aeruginosa UCBPP-PA14
Aligns to 7:227 / 233 (94.8%), covers 99.6% of PF04340, 293.4 bits

• SOS-Independent Pyocin Production in P. aeruginosa Is Induced by XerC Recombinase Deficiency
  Baggett, mBio 2021
  • “...commits only some cells to pyocin production and prevents widespread cell lysis. RESULTS Deletion of PA14_69700 results in substantial upregulation of pyocin genes. In previous work, we showed that an in-frame deletion of an uncharacterized gene, PA14_69700 (also known as PA14_RS28410 ), resulted in enhanced biofilm...”
• Colony-morphology screening uncovers a role for the Pseudomonas aeruginosa nitrogen-related phosphotransferase system in biofilm formation
  Cabeen, Molecular microbiology 2016
  • “...in biofilm formation. Our screen, which identified most known biofilm-related genes, also uncovered PA14_16550 and PA14_69700 , deletions of which abrogated and augmented biofilm formation, respectively. We also identified ptsP , which encodes enzyme I of the nitrogen-regulated phosphotransferase (PTS Ntr ) system, as being important...”
  • “...included PA14_16550 (orthologous to PA3699 ; hereafter 16550 ), which encodes a TetR-type DNA repressor; PA14_69700 (orthologous to PA5279 ; hereafter 69700 ), which encodes an uncharacterized GAF-domain protein; and ptsP , which encodes enzyme I of the nitrogen-regulated phosphotransferase (PTS Ntr ) system. Insertions in...”
• SOS-Independent Pyocin Production in P. aeruginosa Is Induced by XerC Recombinase Deficiency
  Baggett, mBio 2021
  • “...work, we showed that an in-frame deletion of an uncharacterized gene, PA14_69700 (also known as PA14_RS28410 ), resulted in enhanced biofilm formation by P. aeruginosa ( 29 ). To understand the mechanism by which 69700 deletion modulates biofilm formation, we performed transcriptomic analysis. We extracted RNA...”

VAB027_RS00575 DUF484 family protein from Vibrio cholerae
Aligns to 4:221 / 232 (94.0%), covers 99.1% of PF04340, 286.8 bits

• Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome
  Xie, International journal of genomics 2017
  • “...3504836 2589 VAB027_RS016705 3609897 3612475 2580 VC0128 xerC 122005 122940 936 VAA049_RS00590 114667 115602 936 VAB027_RS00575 114596 115531 936 VC2419 xerD 2593375 2594283 909 Complement VAA049_RS02440 498541 499449 909 VAB027_RS15355 3316085 3316993 909 Complement VC0012 dnaA 7397 8815 1419 VAA049_RS00005 38 1441 1404 VAB027_RS00005 38 1441...”

CCNA_00350 hypothetical protein from Caulobacter crescentus NA1000
Aligns to 7:225 / 226 (96.9%), covers 99.1% of PF04340, 259.5 bits

• Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus
  Lasker, Nature microbiology 2020
  • “...mRNA levels of an eyfp gene driven by the CtrA~P-regulated P 350 promoter (from the CCNA_00350 operon) integrated at 13 different sites along Caulobacter s single circular chromosome (loci L1-L13) ( Fig. 3b , Supplementary Table 4 ). Unlike most CtrA~P regulated promoters, whose activation is...”
  • “...sequence followed by the eyfp gene was synthesized using IDT gBlocks. Three versions of the CCNA_00350 promoter ( P 350 ) were used: wildtype P 350 (WT350) with a noncanonical CtrA binding site TCAA-N7-TTAA, P 350 with the consensus TTAA-N7-TTAA CtrA binding site (AT350) 81 ,...”

NJ56_05265 DUF484 domain-containing protein from Yersinia ruckeri
Aligns to 10:232 / 234 (95.3%), covers 97.8% of PF04340, 246.4 bits

• Genome Sequence of the Fish Pathogen Yersinia ruckeri SC09 Provides Insights into Niche Adaptation and Pathogenic Mechanism
  Liu, International journal of molecular sciences 2016
  • “...the Tat protein export pathway [ 67 ]. Protein translocation mediated by Tat (NJ56_01150-60 and NJ56_05265) from SC09 allows for the secretion of fully folded proteins and their chaperones, and appears to be able to mediate various stress responses and virulence. By contrast, the Sec apparatus...”

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