Family Search for PF04474 (DUF554)

PF04474 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.

CLJU_c32170 DUF554 domain-containing protein from Clostridium ljungdahlii DSM 13528
Aligns to 2:222 / 239 (92.5%), covers 99.5% of PF04474, 262.6 bits

• Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii
  Philipps, Biotechnology for biofuels 2019
  • “...detail, revealing that the cassette had integrated within a gene encoding a putative membrane protein (CLJU_c32170) at position 3523326. An analytical PCR confirmed the integration at this position and loss of the plasmid backbone (Additional file 3 : Figure S3). Whole-genome sequencing was carried out to...”

lmo0793 similar to conserved hypothetical protein from Listeria monocytogenes EGD-e
LMOf2365_0810 hypothetical protein from Listeria monocytogenes str. 4b F2365
Aligns to 4:228 / 233 (96.6%), covers 99.5% of PF04474, 251.7 bits

• Comparison between Listeria sensu stricto and Listeria sensu lato strains identifies novel determinants involved in infection
  Schardt, Scientific reports 2017
  • “...NPQTN specific sortase B; surface protein transpeptidase involved in anchoring of SvpA and Hbp1 COG4509 lmo0793 Putative transport protein COG1811 svpA / hbp2 (lmo2185), hbp1 (lmo2186) NPQTN cell wall anchored proteins with similarity to IsdA, IsdC of Staphylococcus aureus 93 ; heme-binding NEAT domain associated with...”
• Transcriptomic Analysis of Listeria monocytogenes in Response to Bile Under Aerobic and Anaerobic Conditions
  Chakravarty, Frontiers in microbiology 2021
  • “...Drug resistance transporter, EmrB/QacA family 4.7 LMOf2365_0930 Putative membrane protein 5.0 LMOf2365_0967 Putative transporter 5.1 LMOf2365_0810 Putative membrane protein 5.6 LMOf2365_1721 Cation efflux family protein 6.4 LMOf2365_0588 Magnesium transporter, CorA family 6.5 LMOf2365_0701 ABC transporter, ATP-binding protein 7.1 lmrB-2 LMOf2365_2560 Lincomycin resistance protein LmrB 7.3 LMOf2365_1695...”

GAH_01290 DUF554 domain-containing protein from Geoglobus ahangari
Aligns to 2:220 / 230 (95.2%), covers 99.1% of PF04474, 241.8 bits

• The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T)
  Manzella, Standards in genomic sciences 2015
  • “...of alternative compounds. In addition, we identified a gene in this region of the genome (GAH_01290) coding for an uncharacterized channel protein, which could potentially function as a nitrate transport protein. The presence of genes encoding both nitrate reductase proteins (NarGHIJ and NirA) combined with the...”

YDFK_BACSU / P96689 Uncharacterized membrane protein YdfK from Bacillus subtilis (strain 168) (see paper)
Aligns to 2:220 / 229 (95.6%), covers 99.5% of PF04474, 233.2 bits

ECs3842 putative transport protein from Escherichia coli O157:H7 str. Sakai
Aligns to 3:228 / 235 (96.2%), covers 99.5% of PF04474, 226.2 bits

• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...b2435 b3967 b1252 b3343 b2527 ECs1853 ECs4872 ECs3255 ECs3842 b2375 b2966 b1280 b3943 ECs3100 ECs5032 b4050 b2211 EC no. (O157:H7) b no. (K-12) Replication,...”

YqgA / b2966 DUF554 domain-containing protein YqgA from Escherichia coli K-12 substr. MG1655
b2966 predicted inner membrane protein from Escherichia coli str. K-12 substr. MG1655
Q46831 Uncharacterized protein YqgA from Escherichia coli (strain K12)
Aligns to 3:228 / 235 (96.2%), covers 99.5% of PF04474, 226.2 bits

• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...b1252 b3343 b2527 ECs1853 ECs4872 ECs3255 ECs3842 b2375 b2966 b1280 b3943 ECs3100 ECs5032 b4050 b2211 EC no. (O157:H7) b no. (K-12) Replication, recombination,...”
• Inactivation of efflux pumps abolishes bacterial biofilm formation
  Kvist, Applied and environmental microbiology 2008
  • “...b no. Change (fold) during biofilm formationa 83972 VR50 b2966 b3710 b3242 b1053 b3241 b2170 b4141 b1596 b0842 39.45 11.46 24.78 8.82 30.89 7.42 8.96 3.62 6.86...”
• Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine
  Hancock, Infection and immunity 2007
  • “...yhcN yqgA rydB sgaB c2436 c2424 b2583 c3859 b3710 b3238 b2966 b4430 b4194 19.8 19.6 19.0 18.9 18.3 17.3 17.2 17.1 16.5 1,196 1,408 1,863 3,664 1,862 5,790 1,010...”
• Co-translational protein aggregation and ribosome stalling as a broad-spectrum antibacterial mechanism
  Khodaparast, Nature communications 2025 (no snippet)

SBOV31771 DUF554 domain-containing protein from Salmonella enterica subsp. enterica serovar Bovismorbificans str.
Aligns to 3:228 / 235 (96.2%), covers 99.5% of PF04474, 219.0 bits

• Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi
  Bronowski, PLoS neglected tropical diseases 2013
  • “...of 3476 contains a ROD inserted at a t-RNA(Phe) -downstream of the CDS homologue to SBOV31771 in the 3114 strain-, showing high sequence homology to the SPI-7 of the human restricted pathogen S. Typhi CT18 ( Figure 1 , Figure S3 ). SPI-7 is a large...”

DR1630 conserved hypothetical protein from Deinococcus radiodurans R1
Aligns to 8:251 / 258 (94.6%), covers 98.6% of PF04474, 200.5 bits

• A novel OxyR sensor and regulator of hydrogen peroxide stress with one cysteine residue in Deinococcus radiodurans
  Chen, PloS one 2008
  • “...protein 4.642973 0.000548 DR2453 P-type ATPase metal efflux 4.543941 0.00816 DR0533 Predicted protein 4.380241 0.001366 DR1630 Conserved transport protein 4.305581 0.012968 DR1583 Conserved membrane protein 4.254401 0.000343 DR1200 Predicted protein 4.061794 0.003261 DR2385 Phenylacetic acid degradation protein PaaB 4.044868 0.000759 DR0746 Predicted protein 4.032291 0.00016 DR2208...”

lp_1684 integral membrane protein from Lactobacillus plantarum WCFS1
lp_1684 DUF554 domain-containing protein from Lactiplantibacillus plantarum WCFS1
Aligns to 3:231 / 241 (95.0%), covers 100.0% of PF04474, 194.8 bits

• Transcriptional analysis of the molecular mechanism underlying the response of Lactiplantibacillus plantarum to lactic acid stress conditions
  Jang, Heliyon 2023
  • “...(Lactic acid-control) Product ENSG ID eggNOG ID log2FC p-value q (FDR) log2FC p-value q (FDR) lp_1684 4.98 7.90E-31 8.12E-29 6.14 1.77E-44 2.53E-42 membrane protein lp_1684 COG1811 accA2 5.11 1.59E-72 2.04E-69 6.01 8.24E-93 1.06E-89 acetyl-CoA carboxyl transferase lp_1680 COG0825 accD2 5.19 4.50E-64 2.31E-61 5.99 7.62E-80 3.92E-77 acetyl-CoA...”
  • “...oxoacyl-ACP reductase (lp_1674), oxoacyl-ACP synthase (lp_1675, lp_1671), acyl-CoA hydrolase (lp_1686), and membrane proteins (lp_3177, lp_2949, lp_1684). Interestingly, the expression of lactate racemization-related genes (lp_0105, lp_0104, lp_0106, and lp_1017) increased only following dl -lactic acid treatment ( Table 1 ). The results of the transcriptome analysis were...”
• Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide stress tolerance
  Stevens, Applied and environmental microbiology 2010
  • “...2.49 2.16 Hypothetical protein lp_0199 lp_0291 lp_1098 lp_1684 lp_3256 lp_3353 lp_0199 lp_0291 lp_1098 lp_1684 lp_3256 lp_3353 Unknown Oxidoreductase Unknown...”

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