Family Search for PF04175 (DUF406)

PF04175 hits 10 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

ECs3226 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 3:94 / 94 (97.9%), covers 100.0% of PF04175, 125.5 bits

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...1 ECs3093 napH ferredoxin-type protein: electron transfer 3.04 un ECs3180 ackA acetate kinase 2.28 6 ECs3226 yfcZ orf, hypothetical protein 3.02 6 ECs3445 yfiD putative formate acetyltransferase 4.48 6 ECs3460 yfiA putative yhbH sigma 54 modulator 2.12 2 ECs3582 hypA pleiotrophic effects on 3 hydrogenase isozymes...”

YfcZ / b2343 DUF406 domain-containing protein YfcZ from Escherichia coli K-12 substr. MG1655 (see 3 papers)
b2343 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
P0AD33 UPF0381 protein YfcZ from Escherichia coli (strain K12)
Aligns to 3:94 / 94 (97.9%), covers 100.0% of PF04175, 125.1 bits

• A comparative genomics approach to prediction of new members of regulons
  Tan, Genome research 2001
  • “...atpIBEFHAGDC b1458 b1498-b1497 b1520 b1904 b1963-yedJ b2146-yeiA b2343 b2595-b2596-yfiA b2736-b2737 cdd deaD fadL fixAB flhDC folA galP gapA gcd glpABC gntKU1U2...”
• Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli
  Reitzer, Microbiology and molecular biology reviews : MMBR 2001
  • “...70.0 to 75.9 (from highest to lowest): yigL, ygeW, b2343, b2878, yjcB-vacB, ytfJ, crl, acrD, ptrA, clpPX, mutH, csgBA, b2878, pyrG, sohA, yehR, rmf, mscL, mdoB,...”
• Quantitative Shotgun Proteomic Analysis of Bacteria after Overexpression of Recombinant Spider Miniature Spidroin, MaSp1
  Randene, International journal of molecular sciences 2024
  • “...best candidates identified in our proteomic analysis represent uncharacterized bacterial proteins (accession numbers P0ADK0, P0ADA5, P0AD33, and P77376), which will require further investigation to elucidate their specific roles in spidroin expression ( Table 3 ). Other identified candidates with elevated protein levels are curious, such as...”
  • “...Target protein lacZ Beta-galactosidase* P00722 1.00 10 20 +OLR Lactose metabolism yfcZ UPF0381 protein YfcZ P0AD33 9.29 10 4 +14.00 Uncharacterized wzzB Chain length determinant protein P76372 5.22 10 3 +11.00 Lipopolysaccharide biosynthesis kdsB 3-deoxy-manno-octulosonate cytidylyltransferase P04951 9.18 10 3 +10.00 Lipopolysaccharide biosynthesis efeO Iron uptake...”

YPTB2638 hypothetical protein from Yersinia pseudotuberculosis IP 32953
YPO2745 conserved hypothetical protein from Yersinia pestis CO92
Aligns to 7:98 / 98 (93.9%), covers 98.9% of PF04175, 123.4 bits

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPO2510 putative exported protein 0.31 (< 0.001) YPTB2594 YPO2563 conserved hypothetical protein 0.563 (< 0.001) YPTB2638 YPO2745 conserved hypothetical protein 0.483 (0.001) YPTB2651 (lemA) YPO2732 putative exported protein 0.381 (< 0.001) YPTB2660 YPO2724 putative membrane protein 1.486 (0.038) YPTB2661 YPO2723 possible OmpA family (pseudogene. IS100 insertion)...”
• New insights into how Yersinia pestis adapts to its mammalian host during bubonic plague
  Pradel, PLoS pathogens 2014
  • “...15 YPO2337 - Regulation 16.7 10 25.4 11 YPO3025 - - 17.8 10 39.1 14 YPO2745 - - 18.9 11 37.1 15 YPO0585 - - 19.3 11 27.6 14 y4094 - - 20.5 11 17.3 10 YPO2006-YPO2008 - - 20.7 13 18.5 12 YPO1862 - -...”
• Inhibition of Yersinia pestis DNA adenine methyltransferase in vitro by a stibonic acid compound: identification of a potential novel class of antimicrobial agents
  McKelvie, British journal of pharmacology 2013
  • “...Conserved hypothetical protein 2.93E-03 1.06E-05 1.99 YPO2745 Conserved hypothetical protein 3.48E-02 7.20E-04 1.97 YPO3556 Conserved hypothetical protein...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...putative exported protein 0.31 (< 0.001) YPTB2594 YPO2563 conserved hypothetical protein 0.563 (< 0.001) YPTB2638 YPO2745 conserved hypothetical protein 0.483 (0.001) YPTB2651 (lemA) YPO2732 putative exported protein 0.381 (< 0.001) YPTB2660 YPO2724 putative membrane protein 1.486 (0.038) YPTB2661 YPO2723 possible OmpA family (pseudogene. IS100 insertion) 1.796...”

Q7CQ33 Cytoplasmic protein from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
STM2390 putative cytoplasmic protein from Salmonella typhimurium LT2
Aligns to 3:94 / 94 (97.9%), covers 100.0% of PF04175, 121.5 bits

• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...yeeX Unclassified -12.867 2.813 10.455 1.629 1.293 0.890 -0.540 0.696 8.884 1.714 Putative cytoplasmic protein Q7CQ33 yfcZ Unclassified 1.467 1.409 -0.175 0.344 0.415 1.314 -0.656 1.562 0.010 0.029 Putative cytoplasmic protein Q8ZKH3 yjbR Unclassified ND ND ND ND ND ND 7.963 1.687 ND ND Uncharacterized protein...”
• Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes
  Harvey, Infection and immunity 2011
  • “...Putative sigma N modulation factor Function unknown STM2390 STM3995 STM2697 STM4088 yfcZ yihD Putative cytoplasmic protein Putative cytoplasmic protein Phage...”

HI0400 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 4:95 / 95 (96.8%), covers 100.0% of PF04175, 119.4 bits

• Cloning of genes of nontypeable Haemophilus influenzae involved in penetration between human lung epithelial cells
  van, Infection and immunity 2000
  • “...as trpS. H. influenzae Rd contains another ORF (HI0400) with an associated deduced amino acid sequence showing 61% homology to that associated with ORF...”

VPA0419 conserved hypothetical protein from Vibrio parahaemolyticus RIMD 2210633
Q87J34 Uncharacterized protein from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Aligns to 6:95 / 99 (90.9%), covers 98.9% of PF04175, 105.7 bits

• Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175
  Singarapu, Proteins 2010
  • “...Services, Inc., A Wiley Company Hoboken 2860719 10.1002/prot.22630 Structure Notes Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175 Singarapu Kiran Kumar 1 2 Mills Jeffrey L 1 2 Xiao Rong 2...”
  • “...in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. VPA0419 yiiS PFAM 04175 structural genomics GFT NMR INTRODUCTION Protein with 83 residues, VPA0419 (residues 1799, numbered 183) (gi|81726230, SwissProt/TrEMBL ID Q87J34_VIBPA, accession number Q87J34) 1 from Vibrio parahaemolyticus and 99-residue...”
• Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175
  Singarapu, Proteins 2010
  • “...Protein with 83 residues, VPA0419 (residues 1799, numbered 183) (gi|81726230, SwissProt/TrEMBL ID Q87J34_VIBPA, accession number Q87J34) 1 from Vibrio parahaemolyticus and 99-residue protein yiiS (gi|81722782, SwissProt/TrEMBL ID Q83IT9_SHIFL, accession number Q83IT9) 2 , 3 from Shigella flexneri were selected as targets for the Protein Structure Initiative-2...”

Q9KL30 Uncharacterized protein from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Aligns to 7:96 / 100 (90.0%), covers 98.9% of PF04175, 105.0 bits

• Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data.
  Li, bioRxiv : the preprint server for biology 2023
  • “...R., Lui, J., Everett, J.K., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T., Kennedy, M.A. Q9KL30 VcR52 2KHD 10.2210/pdb2KHD/pdb 16238 2009-06-16 1100 (100) Ramelot, T.A., Cort, J.R., Wang, H., Ciccosanti, C., Jiang, M., Liu, J., Rost, B., Swapna, G.V.T., Acton, T.B., Xiao, R., Everett, J.K., Montelione,...”

YiiS / b3922 DUF406 domain-containing protein YiiS from Escherichia coli K-12 substr. MG1655 (see 5 papers)
b3922 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 3:96 / 99 (94.9%), covers 97.8% of PF04175, 101.7 bits

• Escherichia coli gene expression responsive to levels of the response regulator EvgA
  Masuda, Journal of bacteriology 2002
  • “...slp b3507 b3508 b3509 b3510 b3511 b3512 b3513 b3514 b3517 b3922 b4111 yhiF yhiD hdeB hdeA hdeD yhiE yhiU yhiV gadA yiiS proP b4113 basR b4115 yjdE Decreased...”

ECs4847 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 3:96 / 99 (94.9%), covers 97.8% of PF04175, 101.5 bits

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...glnA -5.34 1 ECs4244 yhgE -3.33 1 ECs4793 yihK -2.43 1 ECs4278 asd -2.55 1 ECs4847 yiiS 2.66 2 ECs4299 ugpB 6.46 2 ECs4869 metL -2.30 1 ECs4348 yhhG -2.67 1 ECs4884 yijP -3.62 1 ECs4398 yhjA -2.20 6 ECs4889 argH -4.04 1 ECs4399 treF 3.03...”

P44027 UPF0381 protein HI_0636 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI0636 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 5:95 / 96 (94.8%), covers 96.7% of PF04175, 100.6 bits

• Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175
  Singarapu, Proteins 2010
  • “...literature for any member of family PF04175 refers to a Haemophilus influenzae protein (Swiss-Prot ID P44027; 25% sequence identity with protein yiiS over 84 residues). This protein has been suggested to play an auxiliary role in penetration of the bacterial cells in between human epithelial cells....”
• Identification of Actinobacillus pleuropneumoniae genes important for survival during infection in its natural host
  Sheehan, Infection and immunity 2003
  • “...327 91 Unknown Unknown AAK03268 Unknown AAK02354 Unknown P44027 C4-decarboxylate transport protein homologc 0.20 1.05 0.79 0.72 4.67 3.60 0.87 2.49 0.90 0.05...”
• Identification of Actinobacillus pleuropneumoniae genes important for survival during infection in its natural host
  Sheehan, Infection and immunity 2003
  • “...B PM1184 (Pasteurella multocida) PM0270 (Pasteurella multocida) HI0636 (Haemophilus influenzae) Metabolism 10B12 10A11 33C7 17B8 35D11 26C3 4B9 Regulatory...”
• Cloning of genes of nontypeable Haemophilus influenzae involved in penetration between human lung epithelial cells
  van, Infection and immunity 2000
  • “...that contained open reading frames (ORFs) homologous to HI0636 to HI0641 of H. influenzae strain Rd and that showed an increased penetration in epithelial...”
  • “...epithelial cell line NCI-H292 were identified. ORFs HI0636 and HI0638, encoding two small proteins of unknown functions, were further investigated. The...”
• Frequent oligonucleotides and peptides of the Haemophilus influenzae genome
  Karlin, Nucleic acids research 1996
  • “...(5)-End (3) 676 963-674 3 USSc 105d (CCAA)20 orf (HI0636) 1987 677 215-677 132d 677 939-677 652d 3835 (CCAA)20 orf (HI0662) 766 705 969-705 896d 706 065-705...”

Or search for genetic data about PF04175 in the Fitness Browser