Family Search for PF04363 (DUF496)

Running HMMer for PF04363

PF04363 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.

YPTB1571 hypothetical protein from Yersinia pseudotuberculosis IP 32953
YPO1560 conserved hypothetical protein from Yersinia pestis CO92
Aligns to 9:101 / 105 (88.6%), covers 100.0% of PF04363, 156.9 bits

• IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
  Miller, PLoS pathogens 2014
  • “...protein 2.1 YPTB0449 hypothetical protein 3.3 YPTB0458 putative exported protein 2.2 YPTB1093 hypothetical protein 3.6 YPTB1571 hypothetical protein 2.1 YPTB2255 putative exported protein 2.3 YPTB2277 hypothetical protein 2.6 YPTB2496 hypothetical protein 2.8 YPTB3109 hypothetical protein 4.1 a ORF IDs are derived from the Y. pseudotuberculosis IP...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...0.671 (0.044) YPTB1499 YPO1483 hypothetical protein 1.491 (0.029) YPTB1504 YPO1487 conserved hypothetical protein 2.062 (0.005) YPTB1571 YPO1560 conserved hypothetical protein 1.34 (0.036) YPTB1640 (hpaD) YPO1764 3.4-dihydroxyphenylacetate 2.3-dioxygenase 0.625 (0.046) YPTB1729 YPO1858 putative exported protein 0.704 (0.037) YPTB1901 or1366 conserved hypothetical protein 1.511 (0.01) YPTB1902 YPO1882 conserved...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(0.044) YPTB1499 YPO1483 hypothetical protein 1.491 (0.029) YPTB1504 YPO1487 conserved hypothetical protein 2.062 (0.005) YPTB1571 YPO1560 conserved hypothetical protein 1.34 (0.036) YPTB1640 (hpaD) YPO1764 3.4-dihydroxyphenylacetate 2.3-dioxygenase 0.625 (0.046) YPTB1729 YPO1858 putative exported protein 0.704 (0.037) YPTB1901 or1366 conserved hypothetical protein 1.511 (0.01) YPTB1902 YPO1882 conserved hypothetical...”

YeeX / b2007 DUF496 domain-containing protein YeeX from Escherichia coli K-12 substr. MG1655 (see 4 papers)
NP_416511 PTS system regulator TmaR from Escherichia coli str. K-12 substr. MG1655
b2007 conserved protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 8:100 / 109 (85.3%), covers 100.0% of PF04363, 154.8 bits

• Small genes/gene-products in Escherichia coli K-12.
  Wasinger, FEMS microbiology letters 1998 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Protein disorder is positively correlated with gene expression in Escherichia coli
  Paliy, Journal of proteome research 2008
  • “...from this list: putative -helix protein YeeX (b2007), putative outer membrane protein SlyB (b1641), and DNA-binding protein HU-beta (b0440). Some important...”
  • “...accB rpoZ atpC atpD atpF nusG groS groL b1237 b1641 b2007 b2416 b2904 b3169 b3255 b3649 b3731 b3732 b3736 b3982 b4142 b4143 0.46 0.43 0.49 0.65 0.46 0.50 0.77...”
• Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
  Mariño-Ramírez, Journal of bacteriology 2004
  • “...b1299 b1359 b1547 b1606 b1669 b1800 b1853 b1834 b1970 b2007 b2101 b2157 b2160 b2245 b2249 b2291 b2294 b2355 b2360 b2398 b2399 b2427 b2443 b2450 b2561 b2556...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b1725 b1778 b1783 b1816 b1869 b1870 b1871 b1953 b1955 b2007 b2080 b2098 b2112 b2122 b2127 b2135 b2299 b0305 b0358 b0458 b0485 b0572 b0573 b0581 b0600 b0607...”
  • “...b1667 b1678 b1725 b1778 b1783 b1816 b1869 b1870 b1871 b1953 b1955 b2007 b2080 b2098 b2112 b2122 b2127 b2135 b2299 2.2 2.2 3.5 2.6 3.5 2.6 2.7 2.1 6.8 5.3 2.2...”

SF2067 putative alpha helix protein from Shigella flexneri 2a str. 301
Aligns to 30:122 / 131 (71.0%), covers 100.0% of PF04363, 154.4 bits

• Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella flexneri
  Ye, Journal of clinical microbiology 2010
  • “...SF1137 SF1494 SF1495 SF1496 SF1497 SF1498 SF1881 SF2066 SF2067 SF2133 SF2135 SF2136 SF2137 SF2463 SF2611 SF2718 SF3737 SF3738 SF3739 SF3744 SF3745 SF4175 a b...”

P67605 UPF0265 protein YeeX from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
STY2264 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
Aligns to 8:100 / 111 (83.8%), covers 100.0% of PF04363, 153.6 bits

• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...yecF Unclassified -9.069 0.706 ND ND ND ND ND ND 6.772 1.342 UPF0265 protein YeeX P67605 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...”
• Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm
  Chin, BMC genomics 2017
  • “...and motility protein A 3.3313 5.00E-05 0.001837 cspC Cold shock-like protein CspC 3.34324 5.00E-05 0.001837 STY2264 Hypothetical protein 3.38655 5.00E-05 0.001837 dps DNA protection during starvation protein 3.42148 5.00E-05 0.001837 STY4154 DNA-binding protein 3.45538 0.00085 0.015693 ecnB Entericidin B 3.5082 5.00E-05 0.001837 STY0800 Hypothetical protein 3.80587...”
  • “.... Typhi biofilm genesis. In the down-regulated group, only 2 genes were identified; STY1854 and STY2264 . NCBI BLAST showed that STY2264 was an ortholog of the gene yeeX , found in Salmonella enterica subsp. enterica serovar Typhimurium strain YU15. The gene STY1854 was identified to...”

VCA0741 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 1:93 / 106 (87.7%), covers 100.0% of PF04363, 149.3 bits

• RadD Contributes to R-Loop Avoidance in Sub-MIC Tobramycin
  Negro, mBio 2019
  • “...VC1759 Prophage integrase 1.1 1.3 8 (0.001) 1.6 VCA0032 Unknown 2.8 1.4 5.6 (2.20E04) 1.5 VCA0741 Unknown 1.8 2.2 5 (0.008) 1.3 VCA0654 scrR Carbohydrate metabolism 1.6 2.1 4.9 (5.80E05) 1.2 VC0099 glpG Protease 1.3 1.6 4.8 (3.70E06) 1.5 VC1824 Carbohydrate metabolism 1.3 1.7 4.5 (0.004)...”

M892_24630 DUF496 family protein from Vibrio campbellii ATCC BAA-1116
Aligns to 1:93 / 104 (89.4%), covers 100.0% of PF04363, 144.6 bits

• Vibrio campbellii hmgA-mediated pyomelanization impairs quorum sensing, virulence, and cellular fitness
  Wang, Frontiers in microbiology 2013
  • “...Hypothetical protein 3.42E-05 1.09 0.40 2.73 S M892_13325 Hypothetical protein 4.02E-07 3.90 1.96 1.99 S M892_24630 Hypothetical protein 7.09E-04 0.78 0.23 3.39 S M892_05410 Putative serine protein kinase 5.29E-06 2.33 0.44 5.30 T M892_10150 Universal stress protein 1.95E-04 2.37 1.25 1.90 T M892_12235 Cyclic AMP receptor...”

HD1377 conserved hypothetical protein from Haemophilus ducreyi 35000HP
Aligns to 9:101 / 111 (83.8%), covers 97.8% of PF04363, 137.9 bits

• Comparative proteomic analysis of the Haemophilus ducreyi porin-deficient mutant 35000HP::P2AB
  Davie, Journal of bacteriology 2009
  • “...RpoD RpmF HD0776 PutP ArgH RecB HD1190 HD1219 RarA Kgd HD1377 MoaE HD1400 Pta ManB MukB Rnc AceF GroEL GroES RpmI RpoB NusG HD1887 OmpP2B LspA2 AceE CafA HD1654...”
  • “...groEL frdA nudH rluB suhB secB rpoD putP argH recB HD1190 HD1377 HD1400 mukB aceE cafA HD1654 imp uup nusG 4.0 2.5 5.5 1.0 2.0 0.4 1.7 0.06 2.2 0.3 2.1 0.7...”

HI1168 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 9:101 / 114 (81.6%), covers 98.9% of PF04363, 130.3 bits

• Identification of biofilm proteins in non-typeable Haemophilus Influenzae
  Gallaher, BMC microbiology 2006
  • “...- n y HI1034 1574067 1 3 4 1666 S Uncharacterized BCR - y y HI1168 68057915 all 2926 S Uncharacterized BCR - y y HI1333 1574791 All 1534 J Predicted RNA-binding protein containing KH domain, possibly ribosomal protein - N N HI1349 1574811 All 783...”
• Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
  Kolker, Nucleic acids research 2004
  • “...from the original list: HI0246, HI0668, HI0700, HI0847, HI1168, HI1236 and HI1709. For two more, HI0370 and HI1681, a conserved gene neighborhood (e.g....”

PM0836 unknown from Pasteurella multocida subsp. multocida str. Pm70
Aligns to 9:101 / 112 (83.0%), covers 98.9% of PF04363, 124.9 bits

• Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS)
  Bossé, Animal diseases 2021
  • “...NAD(P)H nitroreductase; insertion likely disrupts transcription of degQ e This protein shares 100% identity with PM0836 (Genbank accession AAK02920) which was reported to be in vivo expressed (Hunt et al. 2001 ) f Insertion located 57 bases upstream of the start of atpI (MIDG3277_1814); insertion likely...”
• In vivo-expressed genes of Pasteurella multocida
  Hunt, Infection and immunity 2001
  • “...dehydrogenase PM0221 Thiol-disulfide interchange protein c b PM0836 PM1135 PM0272 PM0514 PM0271 PM1256 PM0027 PM0704 and PM705 PM1968 PM0951 PM0554 PM1444...”

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