Family Search for PF04287 (DUF446)

Running HMMer for PF04287

PF04287 hits 8 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

YqcC / b2792 DUF446 domain-containing protein YqcC from Escherichia coli K-12 substr. MG1655 (see 4 papers)
b2792 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 6:103 / 109 (89.9%), covers 99.0% of PF04287, 118.3 bits

• The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
  Frick-Cheng, mBio 2020
  • “...YghG 3.3 b2971 yifK Putative transporter YifK 3.6 b3795 yqcC DUF446 domain-containing protein YqcC 2.5 b2792 yqgF Ribonuclease H-like domain-containing nuclease 2.3 b2949 yqiA Esterase YqiA 2.3 b3031 a FC, fold change. TABLE2 Top 30 genes differentially downregulated in human patients and mice Gene Annotation Log...”
• DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli
  DeLisa, Journal of bacteriology 2001
  • “...4.0 b2792 ................................................................................... 3.9 yebG...”

Z4108 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
Aligns to 6:103 / 109 (89.9%), covers 99.0% of PF04287, 118.1 bits

• Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People's Republic of China
  Wang, Infection and immunity 1992
  • “...3 3 3 3 3 strains Z4047 Z4110 Z4048 Z4022 Z4107 Z4108 Z4023 Z4105 Z4090 Z4095 Z4094 Z4057 Z4060 Z4015 Z4746 Z4753 Z4063 Z4064 Z4055 Z4083 B40 B256 B373 B473...”
  • “...Z4752, Z4061 Z4755 Z4049, Z4741 Z4068 Z4072 Z4022 Z4107 Z4108 Z4023 Z4105, B499 Z4090, Z4114 Z4093 Z4111 Z4095 Z4094 Z4057 Z4060 Z4015 Z4746 Z4753 Z4063, Z4067,...”

SO_1619 conserved hypothetical protein from Shewanella oneidensis MR-1
Aligns to 6:102 / 107 (90.7%), covers 96.9% of PF04287, 117.9 bits

• Analysis of the BarA/UvrY two-component system in Shewanella oneidensis MR-1
  Binnenkade, PloS one 2011
  • “...S. oneidensis MR-1 this study crsB1csrB2 in-frame deletion of the gene region between SO_1617 and SO_1619 encoding CsrB1 and CsrB2 separated by SO_1616 encoding a transposase S 198 MR-1, tagged with eGfp in a mini-Tn 7 construct, Cm r [66] SO_1860 gfp SO_1860, tagged with eGfp...”

t2874 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
Aligns to 6:103 / 109 (89.9%), covers 99.0% of PF04287, 115.8 bits

• Methicillin-Resistant Staphylococcus aureus (MRSA) in Different Food Groups and Drinking Water
  González-Machado, Foods (Basel, Switzerland) 2024
  • “...V (3) -Vegetables: ST59 (3), ST1 (1) and ST7 (1) t437 (3), t114 (1) and t2874 (1) SCC mec IVa (3), IVd (1) and not detected (1) [ 64 ] 397 samples comprised of 16 different raw leafy vegetables from selected wet markets May 2015March 2016...”

EAM_2712 hypothetical protein from Erwinia amylovora ATCC 49946
Aligns to 6:103 / 107 (91.6%), covers 100.0% of PF04287, 114.1 bits

• The RNA-binding protein CsrA plays a central role in positively regulating virulence factors in Erwinia amylovora
  Ancona, Scientific reports 2016
  • “...genome was located about 200 bases downstream of EAM_2713 gene and 79 bases upstream of EAM_2712 gene ( Supplementary Fig. S1 ). The non-coding csrB mRNA transcript is 455 nucleotides long and contains 31 GGA motifs, which are essential for CsrA binding 46 47 . The...”

HI1436 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Q57152 Uncharacterized protein HI_1436 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Aligns to 4:100 / 106 (91.5%), covers 99.0% of PF04287, 113.5 bits

• Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae
  Shahbaaz, 3 Biotech 2015
  • “...HP HI1317 10. NC_000907.1 950703 NP_439541.1 O86237 HP HI1388.1 11. NC_000907.1 950784 NP_439587.1 Q57152 HP HI1436 12. NC_000907.1 950455 NP_439742.1 P44268 HP HI1600 13. NC_000907.1 950796 NP_439799.1 P52606 HP HI1657 Materials and methods Sequence retrieval Extensive analysis of H. influenzae genome shows 1,657 proteins which are...”
• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...HP HI1434 949657 P45202 Cys-tRNAPro/Cys-tRNACysdeacylaseybaK 23.0 HP HI1435 950339 P44197 tRNApseudouridine synthase C 231. HP HI1436 950784 Q57152 RNA pseudouridine synthase C 232. HP HI1454 950340 P44202 Cytochrome C biogenesis protein transmembrane region 233. HP HI1462 950787 P45217 Outer membrane efflux porinTdeA 234. HP HI1469 949595...”
• Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae
  Shahbaaz, 3 Biotech 2015
  • “...NP_439468.1 P44160 HP HI1317 10. NC_000907.1 950703 NP_439541.1 O86237 HP HI1388.1 11. NC_000907.1 950784 NP_439587.1 Q57152 HP HI1436 12. NC_000907.1 950455 NP_439742.1 P44268 HP HI1600 13. NC_000907.1 950796 NP_439799.1 P52606 HP HI1657 Materials and methods Sequence retrieval Extensive analysis of H. influenzae genome shows 1,657 proteins...”
  • “...bioinformatics tools. The predicted models of P44506, P44641, P46494, P44827, Q57151, P44094, P45104, P71373, P44160, Q57152, P44268, P52606 show significant validation score on SAVES server. The outcomes of structural analysis for each protein are described here, separately. HP P44506 HP P44506 is localized in the cytoplasm...”
• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...949657 P45202 Cys-tRNAPro/Cys-tRNACysdeacylaseybaK 23.0 HP HI1435 950339 P44197 tRNApseudouridine synthase C 231. HP HI1436 950784 Q57152 RNA pseudouridine synthase C 232. HP HI1454 950340 P44202 Cytochrome C biogenesis protein transmembrane region 233. HP HI1462 950787 P45217 Outer membrane efflux porinTdeA 234. HP HI1469 949595 P44205 molybdenum...”

SF5M90T_2595 YqcC family protein from Shigella flexneri 5a str. M90T
Aligns to 6:103 / 109 (89.9%), covers 99.0% of PF04287, 112.6 bits

• RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
  Vergara-Irigaray, BMC genomics 2014
  • “...b log2FC WT no O 2 /O 2 fnr /WT no O 2 csrB syd/ SF5M90T_2595 protein-binding sRNA 360 4.97 csrC yihi/yihA protein-binding sRNA 245 3.38 a sRNAs are arranged in descending order in relation to Log2 of Fold Change values of WT no O 2...”

VSAL_I0712 YqcC family protein from Aliivibrio salmonicida LFI1238
VSAL_I0712 hypothetical protein from Vibrio salmonicida LFI1238
Aligns to 6:102 / 106 (91.5%), covers 98.0% of PF04287, 112.6 bits

• Differential expression profiling of ΔlitR and ΔrpoQ mutants reveals insight into QS regulation of motility, adhesion and biofilm formation in Aliivibrio salmonicida
  Khider, BMC genomics 2019
  • “...genes encoding methyl-accepting chemotaxis proteins were also downregulated such as VSAL_I2193 , VSAL_I0799 at LCD, VSAL_I0712 at HCD and VSAL_II1022 at both low and high cell densities (Additional file 8 : Table S9). In contrast to rpoQ transcriptome ( rpoQ/ wt), the litR transcription profiling (...”

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