Family Search for PF04393 (DUF535)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF04393 hits 29 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
YPTB1389 putative virulence factor from Yersinia pseudotuberculosis IP 32953
YPO1363 putative virulence factor from Yersinia pestis CO92
y2816 putative enzyme from Yersinia pestis KIM
Aligns to 32:312 / 315 (89.2%), covers 99.3% of PF04393, 344.0 bits
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...(0.005) YPTB1297 YPO1261 conserved hypothetical protein 0.659 (0.014) YPTB1387 YPO1361 putative membrane protein 1.593 (0.003) YPTB1389 YPO1363 putative virulence factoR 0.632 (0.043) YPTB1422 YPO1397 conserved hypothetical protein (pseudogene. inframe deletion) 1.803 (0.012) YPTB1432 YPO1408 putative exported protein 0.671 (0.044) YPTB1499 YPO1483 hypothetical protein 1.491 (0.029) YPTB1504...”
- A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim
Feldman, Molecular biology and evolution 2016 - “...spr Outer membrane lipoprotein (Murein hydrolase) 1530658 C A AGA to ATA R to I YPO1363 Virulence factor 1609461 a T C ACA to GCA T to A YPO1417 Ironsulfur binding protein 1754708 C T CCA to CTA P to L YPO1539 galU UTP-glucose-1-phosphate uridylyltransferase 2352174...”
- Comparative Global Gene Expression Profiles of Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant at Flea and Human Body Temperatures
Galindo, Comparative and functional genomics 2010 - “...system component 66.9 Other functions y0223 cold shock-like protein cspI Response to cold shock 68.7 YPO1363 putative virulence factor Pathogenesis 34.8 y0815 superoxide dismutase precursor (Cu-Zn) sodC Resistance to reactive oxygen species 18.2 Unknown functions various genes (y3398, YPO0130, 0198, 1087, 1560, 1996, 2153, 2854, and...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPTB1297 YPO1261 conserved hypothetical protein 0.659 (0.014) YPTB1387 YPO1361 putative membrane protein 1.593 (0.003) YPTB1389 YPO1363 putative virulence factoR 0.632 (0.043) YPTB1422 YPO1397 conserved hypothetical protein (pseudogene. inframe deletion) 1.803 (0.012) YPTB1432 YPO1408 putative exported protein 0.671 (0.044) YPTB1499 YPO1483 hypothetical protein 1.491 (0.029) YPTB1504 YPO1487...”
- Characterization of phagosome trafficking and identification of PhoP-regulated genes important for survival of Yersinia pestis in macrophages
Grabenstein, Infection and immunity 2006 - “...hypothetical protein, pagP YPO1559, hypothetical protein YPO1363, putative virulence factor, somA YPO0164, putative membrane receptor protein hypothetical...”
- “...YPO2421 YPO2422 YPO2420 YPO2292 YPO2419 YPO1715 YPO2174 YPO1363 YPO2418 YPO1635 YPO1659 YPO2417 YPO1559 y0838 YPO2416 YPO3352 y3284 YPO3351 YPO2449 y0447 y0840...”
- Role of the PhoP-PhoQ gene regulatory system in adaptation of Yersinia pestis to environmental stress in the flea digestive tract
Vadyvaloo, Microbiology (Reading, England) 2015 - “...C 1.3 12.5 19.4 6.1 y2563 pagP Lipid A acylation; palmitoyltransferase 1.1 20.4 46.6 9.9 y2816 virK -like virulence factor (1.5) 17.4 28.5 24.9 y2858 Membrane protein (1.9) 5.4 7.0 2.9 * Linked genes. Gene not annotated in Y. pestis KIM (YPO number indicates Y. pestis...”
- Characterization of phagosome trafficking and identification of PhoP-regulated genes important for survival of Yersinia pestis in macrophages
Grabenstein, Infection and immunity 2006 - “...to create insertions in ORFs (y2124 and y2816) using an EZ::TN KAN-2 transposon kit (Epicenter). Alternatively, the kanamycin resistance cassette (kan)...”
- “...into suicide vector pSB890 (25) using either BamHI (y2124, y2816, and pagP) or SmaI (mgtC) restriction sites. To create an in-frame deletion mutation in ugd,...”
YbjX / b0877 DUF535 domain-containing protein YbjX from Escherichia coli K-12 substr. MG1655 (see 4 papers)
Aligns to 47:326 / 330 (84.8%), covers 99.3% of PF04393, 342.2 bits
c1012 Hypothetical protein ybjX from Escherichia coli CFT073
Aligns to 47:326 / 330 (84.8%), covers 99.3% of PF04393, 341.6 bits
ECs0963 putative enzyme from Escherichia coli O157:H7 str. Sakai
Z1112 putative enzyme from Escherichia coli O157:H7 EDL933
Aligns to 47:326 / 330 (84.8%), covers 99.3% of PF04393, 341.1 bits
STM0940 Homolog of virK from Salmonella typhimurium LT2
Aligns to 39:318 / 322 (87.0%), covers 98.9% of PF04393, 335.5 bits
KPN_02355 putative enzyme from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Aligns to 34:314 / 322 (87.3%), covers 99.3% of PF04393, 334.1 bits
STM2781 virulence gene; homologous sequence to virK in Shigella from Salmonella typhimurium LT2
NP_461707 virK-like protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Aligns to 29:306 / 309 (90.0%), covers 99.3% of PF04393, 320.9 bits
SC2712 virulence gene; homologous sequence to virK in Shigella from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Aligns to 29:306 / 309 (90.0%), covers 99.3% of PF04393, 320.3 bits
Ent638_1394 protein of unknown function DUF535 from Enterobacter sp. 638
Aligns to 35:314 / 318 (88.1%), covers 98.9% of PF04393, 311.8 bits
CP0237 VirK, required for proper localization of IcsA (VirG) at the surface of bacteria from Shigella flexneri 2a str. 301
Aligns to 25:301 / 316 (87.7%), covers 98.6% of PF04393, 305.5 bits
pWR501_0252 virulence factor VirK from Shigella flexneri 5a str. M90T
Aligns to 25:301 / 316 (87.7%), covers 98.6% of PF04393, 305.4 bits
- RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Vergara-Irigaray, BMC genomics 2014 - “...2.00 -2.21 pWR501_0250 shf peptidoglycan deacetylase 1.24 -3.42 -1.30 pWR501_0251 rfbU glycosiltransferase 1.21 -1.65 -1.16 pWR501_0252 virK virulence protein 1.15 -2.16 -1.03 pWR501_0039 parA plasmid segregation protein 1.13 pWR501_0253 msbB acyltransferase 1.07 -3.03 -1.08 pWR501_0074 sepA secreted protease -1.12 1.34 1.52 pWR501_0177 hypothetical protein -1.55 1.04...”
Ent638_2409 protein of unknown function DUF535 from Enterobacter sp. 638
Aligns to 31:311 / 313 (89.8%), covers 99.3% of PF04393, 302.4 bits
ESA_02187 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
Aligns to 31:309 / 313 (89.1%), covers 98.6% of PF04393, 301.2 bits
pCoo045 VirK from Escherichia coli
Aligns to 25:301 / 316 (87.7%), covers 98.6% of PF04393, 297.7 bits
NTHI0592 hypothetical protein from Haemophilus influenzae 86-028NP
Aligns to 23:290 / 291 (92.1%), covers 98.9% of PF04393, 295.3 bits
HI0461 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Q57144 Uncharacterized protein HI_0461 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Aligns to 23:290 / 291 (92.1%), covers 98.9% of PF04393, 294.9 bits
- Modified lipooligosaccharide structure protects nontypeable Haemophilus influenzae from IgM-mediated complement killing in experimental otitis media
Langereis, mBio 2012 - “...of variance and the Tukey post hoc test. (D to G) Complement resistance of Rd (HI0461) (D), 86-028NP (NTHI0592) (E), 3655 (CGSHi3655_02894) (F), and 1521062 (G) was determined with 10% (Rd), 20% (3655), or 40% (86-028NP and 1521062) serum, respectively ( n = 3). Statistical significance...”
- Genetic analysis of a pyocin-resistant lipooligosaccharide (LOS) mutant of Haemophilus ducreyi: restoration of full-length LOS restores pyocin sensitivity
Filiatrault, Journal of bacteriology 2001 - “...encodes a putative homolog to a hypothetical protein (HI0461) of H. influenzae, the gene encoding an argininosuccinate synthase homolog, and a change in the...”
- “...a conserved hypothetical membrane protein of H. influenzae (HI0461) (14) and N. meningitidis (30) (Fig. 2 [top]). These results suggest that the chromosomal DNA...”
- Systematic identification of essential genes by in vitro mariner mutagenesis
Akerley, Proceedings of the National Academy of Sciences of the United States of America 1998 - “...primer in lane 2), (b) HI1658, (c) HI0911, (d) HI0905, (e) HI0461, ( f ) same primer as in (c), and (g) HI0456. Identification of essential genes that have no...”
- Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
Shahbaaz, PloS one 2013 - “...P44675 Yes Cellular process 7. P43990 Yes Cellular process 8. P44693 Yes Cellular process 9. Q57144 Yes Cellular process 10. P44733 Yes Cellular process 11. P44740 Yes Yes 12. P44023 Yes Yes 13. Q57523 Yes Yes 14. P44038 Yes Cellular process 15. P44041 Yes Information and...”
R2866_0112 VirK/YbjX family protein from Haemophilus influenzae R2866
Aligns to 23:290 / 291 (92.1%), covers 98.9% of PF04393, 294.6 bits
- Panel 4: Report of the Microbiology Panel
Barenkamp, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery 2017 - “...resistance in NTHi from the ME, correlating with decreased binding of IgM. 55 NTHi gene R2866_0112 had a role in complement resistance: gene deletion altered the LOS and increased IgM binding and complement-mediated lysis. In a mouse model, the R2866_0112 mutant was less virulent. The group...”
- Binding of human factor H to outer membrane protein P5 of non-typeable Haemophilus influenzae contributes to complement resistance
Langereis, Molecular microbiology 2014 - “...complement ( Table 1 ), indicating that these genes contribute to resistance to complement-mediated killing. R2866_0112 was found to contribute most significantly to survival of NTHi strain R2866 in the presence of active complement, which was in accordance with our previous genome-wide mariner transposon mutants screen...”
- “...P -value Gene locus Gene name Product HI-NHS NHS 19 239 186 104.2 21 7.0E-39 R2866_0112 Hypothetical protein 1 813 25 72.2 12 5.0E-28 R2866_1237 ompP5 Outer membrane protein P5 12 248 240 51.0 15 1.6E-13 R2866_1822 lgtF UDP-glucose-lipooligosaccharide beta 14 glucosyltransferase 50 115 1 099...”
- Modified lipooligosaccharide structure protects nontypeable Haemophilus influenzae from IgM-mediated complement killing in experimental otitis media
Langereis, mBio 2012 - “...ear, which correlated with decreased binding of IgM. We identified a crucial role for the R2866_0112 gene in complement resistance. Deletion of this gene altered the lipooligosaccharide (LOS) composition of the bacterium, which increased IgM binding and complement-mediated lysis. In a novel mouse model of coinfection...”
- “...This decreased susceptibility correlated with decreased binding of IgM to the bacterium. Expression of the R2866_0112 gene is essential for modifying the LOS structure, which prevents binding of IgM and confers bacterial resistance to complement-mediated killing, similar to our observation in clinical isolates. Finally, using a...”
CGSHi3655_02894 hypothetical protein from Haemophilus influenzae 3655
Aligns to 23:290 / 291 (92.1%), covers 98.9% of PF04393, 292.3 bits
VPA0243 putative virK protein from Vibrio parahaemolyticus RIMD 2210633
Aligns to 25:301 / 304 (91.1%), covers 97.9% of PF04393, 288.9 bits
- Transcriptomic Analysis of Vibrio parahaemolyticus Reveals Different Virulence Gene Expression in Response to Benzyl Isothiocyanate
Song, Molecules (Basel, Switzerland) 2019 - “...parahaemolyticus . Genes related to virulence, including tdh , fliI , VPA0318 , VP1057 , VPA0243 and VPA0202 were downregulated under BITC treatment in the RNA sequencing data as shown in Table 3 . Therefore, the six genes mentioned above were selected for validation using qPCR....”
- “...as it dropped to 0.08 with BITC treatment. Additionally, the expression levels of VPA0202 , VPA0243 , VP1057 , fliI and VPA0318 were decreased compared with sample C_BITC. Significant downregulation in the expression of sample Q_BITC relative to sample C_BITC was exhibited in the qPCR results....”
VC1317 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 23:295 / 306 (89.2%), covers 98.9% of PF04393, 281.1 bits
R2866_1281 VirK/YbjX family protein from Haemophilus influenzae R2866
Aligns to 21:284 / 288 (91.7%), covers 97.9% of PF04393, 272.7 bits
- Binding of human factor H to outer membrane protein P5 of non-typeable Haemophilus influenzae contributes to complement resistance
Langereis, Molecular microbiology 2014 - “...identified for which a role in complement resistance was not established previously ( lapB [ R2866_1281 ] and clpB [ R2866_1533 ]). Interestingly, gene R2866_1237 , coding for outer membrane protein P5 (OmpP5) (also known as OmpA), was shown to have a prominent role in resistance...”
- “...shows the power of this genome-wide screening technique. The role for the genes lapB ( R2866_1281 ) or clpB ( R2866_1533 ) in resistance to complement-mediated killing is currently not known. The R2866 WT strain bound substantial levels of C3 as detected by flow cytometry and...”
APL_0453 hypothetical protein from Actinobacillus pleuropneumoniae L20
Aligns to 16:280 / 288 (92.0%), covers 99.3% of PF04393, 271.7 bits
APP7_0385 hypothetical protein from Actinobacillus pleuropneumoniae serovar 7 str. AP76
APL_0363 hypothetical protein from Actinobacillus pleuropneumoniae L20
Aligns to 19:287 / 290 (92.8%), covers 97.5% of PF04393, 256.6 bits
- Role of (p)ppGpp in Viability and Biofilm Formation of Actinobacillus pleuropneumoniae S8
Li, PloS one 2015 - “...= 2.26), capsule polysaccharide export protein (APP7_1644, log 2 = 2.01) and autotransporter serine protease (APP7_0385, log 2 = 4.03), which are involved in persistence in the upper respiratory tract; the fimbrial biogenesis protein (APP7_0937, log 2 = 2.96; APP7_0938, log 2 = 1.38), tight adherence...”
- malT knockout mutation invokes a stringent type gene-expression profile in Actinobacillus pleuropneumoniae in bronchoalveolar fluid
Lone, BMC microbiology 2009 - “...identified by RT-PCR DD studies. These included genes encoding protein synthesis and hypothetical proteins (APL_068, APL_0363, and APL_0367), in addition to a cell surface protein, LamB (Figure 1 ). Homologs (>99% DNA identity) of the 3 hypothetical proteins are present in all the serotypes of A....”
NMY220_1280 VirK/YbjX family protein from Neisseria meningitidis NM220
NMA1569 hypothetical membrane protein from Neisseria meningitidis Z2491
Aligns to 21:287 / 310 (86.1%), covers 97.5% of PF04393, 243.1 bits
PP3138, PP_3138 VirK domain protein from Pseudomonas putida KT2440
Aligns to 16:297 / 333 (84.7%), covers 98.9% of PF04393, 240.3 bits
- Colony morphology and transcriptome profiling of Pseudomonas putida KT2440 and its mutants deficient in alginate or all EPS synthesis under controlled matric potentials
Gulez, MicrobiologyOpen 2014 - “...in the WT (Table 2 ). No other exopolysaccharide gene was differentially expressed, except for PP_3138 in the Pea operon which was downregulated. In contrast, Nielsen etal. ( 2011 ) observed upregulation of pea and bcs genes, although not to the extent of alginate genes. This...”
- “...O-acetyltransferase, putative 0.71 1.01 N/A PP_3137 Glycosyl transferase, group 2 family protein 0.42 0.69 N/A PP_3138 VirK domain protein 1.65 1.78 N/A PP_3139 Glycosyl transferase, group 1 family protein 0.41 0.56 N/A PP_3140 Glycosyl transferase, group 2 family protein 0.26 0.09 N/A PP_3141 Glycosyl transferase, WecB/TagA/CpsF...”
- Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440
Fernández, Antimicrobial agents and chemotherapy 2012 - “...PP2694 (M) PP2695 (M) PP2723 (M) PP2821 PP2936 PP2943 PP3138 (M) PP3155 (M) PP3214 PP3297 PP3316 PP3455 (M) PP3797 (M) PP4671 PP4810 PP5066 (M) PP5087 pqqC...”
Cj1069 hypothetical protein Cj1069 from Campylobacter jejuni subsp. jejuni NCTC 11168
Aligns to 16:282 / 288 (92.7%), covers 98.2% of PF04393, 219.6 bits
- The Periplasmic Chaperone Network of Campylobacter jejuni: Evidence that SalC (Cj1289) and PpiD (Cj0694) Are Involved in Maintaining Outer Membrane Integrity
Taylor, Frontiers in microbiology 2017 - “...deletion mutants in genes encoding both known and predicted chaperones ( cj0596 , cj0694 , cj1069 , cj1228c , and cj1289 ) using NCTC 11168H as the parental strain. These mutants were characterized using a range of assays to determine effects on growth, agglutination, biofilm formation,...”
- “...Phenotypes of Mutants in Candidate Periplasmic Chaperone Genes The effects of removal of Cj0596 (PEB4), Cj1069 (VirK) and Cj1228 (HtrA) have been previously studied in mutants made in different parental wild-type backgrounds ( Novik et al., 2009 ; Rathbun et al., 2009 ; Boehm et al.,...”
- Characterization of a Campylobacter jejuni VirK protein homolog as a novel virulence determinant
Novik, Infection and immunity 2009 - “...mutant was mapped to the CJJ81176_1087 open reading frame (Cj1069 in the C. jejuni NCT 11168 reference strain), which encodes a protein with very significant...”
- “...mutant that mapped to the CJJ81176_1087 open reading frame (Cj1069 in the reference strain NCTC 11168), which encodes a homolog of the VirK family of proteins...”
CJJ81176_1087 hypothetical protein from Campylobacter jejuni subsp. jejuni 81-176
Aligns to 16:282 / 288 (92.7%), covers 97.9% of PF04393, 214.5 bits
P32181 Membrane protein LapB from Mannheimia haemolytica
Aligns to 18:225 / 225 (92.4%), covers 76.5% of PF04393, 190.3 bits
I5G01_10980 DUF535 family protein from Klebsiella pneumoniae
Aligns to 36:290 / 302 (84.4%), covers 86.5% of PF04393, 151.0 bits
Or search for genetic data about PF04393 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory