Family Search for PF04219 (DUF413)

Running HMMer for PF04219

PF04219 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.

VK055_3211 DUF413 domain-containing protein from Klebsiella pneumoniae subsp. pneumoniae
Aligns to 10:99 / 112 (80.4%), covers 97.8% of PF04219, 135.8 bits

• A systematic analysis of hypermucoviscosity and capsule reveals distinct and overlapping genes that impact Klebsiella pneumoniae fitness
  Mike, PLoS pathogens 2021
  • “...DNA replication, transcription, and RNA biology ( VK055_1319 , VK055_1576 , hflX , VK055_4703 , VK055_3211 , hdfR , rph , and nudH ), as well as four genes related to protein biology ( yebR , VK055_2441 , leuC , and surA ) and one related...”
  • “...into six categories: (1) hmv low /CPS low ( uvrY , galU , rfaH , VK055_3211 , arnD , wza ), (2) hmv WT /CPS low ( pgm ), (3) hmv WT /CPS high ( hha , aceE , purA , smpB , pta2 ), (4)...”

DDA3937_RS20185 DUF413 domain-containing protein from Dickeya dadantii 3937
Aligns to 10:99 / 112 (80.4%), covers 97.8% of PF04219, 134.1 bits

• Cell-length heterogeneity: a population-level solution to growth/virulence trade-offs in the plant pathogen Dickeya dadantii
  Cui, PLoS pathogens 2019
  • “...tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA DDA3937_RS06285 -1.80 0.05 tRNA tRNA-Leu DDA3937_RS02950 -1.69 0.02 DNA primase DNA primase DDA3937_RS20185 -1.67 0.04 DUF413 domain-containing protein DDA3937_RS02955 -1.66 0.01 Translation 30S ribosomal protein S21 rnpB -1.61 5E-08 RNA degradation RNase P RNA component class A ssrA -1.11 3E-07 tRNA Transfer-messenger RNA...”

YPO3903 conserved hypothetical protein from Yersinia pestis CO92
Aligns to 10:99 / 112 (80.4%), covers 97.8% of PF04219, 131.2 bits

• Tn-Seq Analysis Identifies Genes Important for Yersinia pestis Adherence during Primary Pneumonic Plague
  Eichelberger, mSphere 2020
  • “...The enriched mutants had insertions in genes that encode transcriptional regulators, chaperones, an endoribonuclease, and YPO3903, a hypothetical protein. Using single-strain infections and a transcriptional analysis, we identified a significant role for YPO3903 in Y. pestis adherence in the lung and showed that YPO3903 regulated transcript...”
  • “...of psaA had a minor effect on Y. pestis adherence in the lung, suggesting that YPO3903 regulates other adhesins in addition to psaA . By enriching for mutations in genes that regulate the expression or assembly of multiple genes or proteins, we obtained screen results indicating...”

MaoP / b3764 macrodomain Ori protein from Escherichia coli K-12 substr. MG1655 (see 5 papers)
EC958_4230 macrodomain Ori organization protein MaoP from Escherichia coli O25b:H4-ST131
NP_418213 macrodomain Ori protein from Escherichia coli str. K-12 substr. MG1655
P0ADN2 UPF0438 protein YifE from Escherichia coli (strain K12)
b3764 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 10:99 / 112 (80.4%), covers 97.8% of PF04219, 129.7 bits

• Novel genes associated with enhanced motility of Escherichia coli ST131
  Kakkanat, PloS one 2017
  • “...4902 - 5.28 - EC958_1930 nlpC b1708 5.28 Endopeptidase, P60 family, Cell wall-associated hydrolase M EC958_4230 yifE b3764 5.23 Uncharacterized conserved protein S EC958_0600 tomB b0461 5.04 Hha toxicity attenuator - # Genes previously known to be involved in repression of motility *COG codes: K-Transcription, O-...”
• Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
  Link, Electrophoresis 1997 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...Protein 5.23/63,739.36 YifE YifL YigL YihK P0ADN2 P0ADN6 P27848 Protein Hypothetical lipoprotein Hypothetical protein Putative GTP-binding factor 6.13/13,002.38...”
• Novel genes associated with enhanced motility of Escherichia coli ST131
  Kakkanat, PloS one 2017
  • “...5.28 - EC958_1930 nlpC b1708 5.28 Endopeptidase, P60 family, Cell wall-associated hydrolase M EC958_4230 yifE b3764 5.23 Uncharacterized conserved protein S EC958_0600 tomB b0461 5.04 Hha toxicity attenuator - # Genes previously known to be involved in repression of motility *COG codes: K-Transcription, O- Posttranslational modifications,...”

STM14_4694 macrodomain Ori organization protein MaoP from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STY3707 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
t3448 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
SC3805 putative LysR type transcriptional regulator with pssR from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Aligns to 10:99 / 112 (80.4%), covers 97.8% of PF04219, 129.2 bits

• Identification of Novel Genes Mediating Survival of Salmonella on Low-Moisture Foods via Transposon Sequencing Analysis
  Jayeola, Frontiers in microbiology 2020
  • “...) NC 1.75 2.19 1.73 NC STM14_4039 ( yhcB ) ND 2.03 2.07 NC 3.88 STM14_4694 ( yifE )* 2.02 1.73 2.22 2.05 3.46 STM14_1755 ( rnfD ) 1.71 NC 1.2 NC NC STM14_4683 ( rbsR )* 1.55 1.48 1.80 1.13 1.92 STM14_4682 ( rbsK )...”
• Quantitative proteomic analysis of the Salmonella-lettuce interaction
  Zhang, Microbial biotechnology 2014
  • “...D0ZQJ3 yfcC 6.0 1.1E-03 1 Hypothetical protein STM14_3293 D0ZTU4 yfjG 4.0 1.7E-02 1 Hypothetical protein STM14_4694 D0ZMW1 yifE 2.4 1.7E-02 1 Putative type II restriction enzyme methylase subunit D0ZU54 5.5 2.2E-03 1 Hypothetical protein STM14_0428 D0ZM36 yahO 5.7 1.9E-02 2 Hypothetical protein STM14_0454 D0ZM62 psiF 3.9...”
• Top-down proteomics in health and disease: challenges and opportunities
  Gregorich, Proteomics 2014
  • “...spectra from top-down proteomics data showing switch in S-thiolation forms in the hypothetical protein YifE (STM14_4694). Fragmentation maps show the specific cysteine residue on which the switch occurs. (B) Estimated stoichiometry from intact protein mass spectra summed across the corresponding LC peak. Adapted from Ansong et...”
• Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions
  Ansong, Proceedings of the National Academy of Sciences of the United States of America 2013
  • “...S-thiolation forms in the hypothetical protein YifE (STM14_4694). Fragmentation maps show specific cysteine residue on which switch occurs. (B) Estimated...”
• In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh
  Sheikh, PLoS neglected tropical diseases 2011
  • “...putative aldehyde dehydrogenase Protein synthesis STY4360 t4067 rplW 50S ribosomal subunit protein L23 Regulatory functions STY3707 t3448 yifE conserved hypothetical protein Transport and binding proteins STY0065 t0058 oadG oxaloacetate decarboxylase gamma chain STY0123 t0110 yabJ hypothetical ABC transporter STY0636 t2276 fepD ferric enterobactin transport protein FepD...”
• In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh
  Sheikh, PLoS neglected tropical diseases 2011
  • “...aldehyde dehydrogenase Protein synthesis STY4360 t4067 rplW 50S ribosomal subunit protein L23 Regulatory functions STY3707 t3448 yifE conserved hypothetical protein Transport and binding proteins STY0065 t0058 oadG oxaloacetate decarboxylase gamma chain STY0123 t0110 yabJ hypothetical ABC transporter STY0636 t2276 fepD ferric enterobactin transport protein FepD STY2341...”
• FlbT couples flagellum assembly to gene expression in Caulobacter crescentus
  Mangan, Journal of bacteriology 1999
  • “...SC3730 SC3799 SC3800 SC3801 SC3802 SC3803 SC3804 SC3805 SC3806 SC3807 SC3808 SC3809 SC3843 Plasmids pJBZ282 pfljK::lacZ pfljK1::lacZ pfljK2::lacZ pfljK3::lacZ...”

PmVP161_1431 DUF413 domain-containing protein from Pasteurella multocida
Aligns to 10:99 / 109 (82.6%), covers 97.8% of PF04219, 128.3 bits

• Genome-Wide Investigation of Pasteurella multocida Identifies the Stringent Response as a Negative Regulator of Hyaluronic Acid Capsule Production
  Smallman, Microbiology spectrum 2022
  • “...4.34E48 0.9 ppx PmVP161_1426 Exopolyphosphatase 8.6 9.75E81 2.2 trmA PmVP161_1430 tRNA/tmRNA [uracil-C(5)]-methyltransferase 7.6 8.83E92 1.2 PmVP161_1431 PmVP161_1431 Hypothetical protein 9.2 1.14E60 2.5 tufA_1 PmVP161_1480 Elongation factor Tu 1 6.0 1.33E61 1.5 mioC PmVP161_1625 Protein MioC 3.0 0.000615 0.9 PmVP161_1628 PmVP161_1628 Hypothetical protein 7.1 7.11E94 2.2 atpB...”

HI0847 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 10:99 / 111 (81.1%), covers 96.7% of PF04219, 125.8 bits

• Identification of biofilm proteins in non-typeable Haemophilus Influenzae
  Gallaher, BMC microbiology 2006
  • “...TdcF y y HI0760 1573769 all 2924 CO Fe-S cluster protector protein - n n HI0847 1573861 all 3085 S Uncharacterized BCR - n y HI1034 1574067 1 3 4 1666 S Uncharacterized BCR - y y HI1168 68057915 all 2926 S Uncharacterized BCR - y...”
• Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
  Kolker, Nucleic acids research 2004
  • “...addition, seven of these genes (HI0017, HI0119, HI0315, HI0700, HI0847, HI1053 and HI1349) were predicted by Karlin et al. (33) to be highly expressed based on...”
  • “...genes from the original list: HI0246, HI0668, HI0700, HI0847, HI1168, HI1236 and HI1709. For two more, HI0370 and HI1681, a conserved gene neighborhood (e.g....”

PMI3296 hypothetical protein from Proteus mirabilis HI4320
Aligns to 10:99 / 112 (80.4%), covers 97.8% of PF04219, 125.6 bits

• Transcriptome of Proteus mirabilis in the murine urinary tract: virulence and nitrogen assimilation gene expression
  Pearson, Infection and immunity 2011
  • “...PMI1504 PMI0118 PMI3064 PMI3065 PMI3061 PMI2544 PMI3057 PMI3296 PMI0418 PMI0861 PMI1039 PMI2784 PMI1898 PMI3622 PMI1034 PMI0114 PMI1828 PMI1488 PMI3364 PMI2833...”
• The high-affinity phosphate transporter Pst in Proteus mirabilis HI4320 and its importance in biofilm formation
  O'May, Microbiology (Reading, England) 2009
  • “...factor Frr, the oligoRNase Orn and two hypothetical proteins (PMI3296 and PMI3715). As expected, the PstS protein was expressed only in the DpstA mutant (Fig....”

VPA0040 conserved hypothetical protein from Vibrio parahaemolyticus RIMD 2210633
Aligns to 12:101 / 117 (76.9%), covers 100.0% of PF04219, 122.2 bits

• Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment
  García, BMC microbiology 2017
  • “...0 Putrescine transporter VPA1635 3652 16 8.4 0 Ornithine decarboxylase, initial enzyme in polyamine synthesis VPA0040 679 9 6.7 1.5E - 289 Hypothetical protein VP0061 330 7 6.0 4.1E - 130 Multidrug transmembrane resistance signal peptide protein VPA0475 1764 5 8.8 6.1E - 228 Hypothetical protein...”

VCA1021 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 12:101 / 119 (75.6%), covers 100.0% of PF04219, 120.6 bits

• RNApredator: fast accessibility-based prediction of sRNA targets
  Eggenhofer, Nucleic acids research 2011
  • “...lmo085 lmo0850 NF(NF) 31(NF) NC_002505 V.c. MicX vca0620 vca0620 NF(34) 48(7) NC_002505 V.c. Qrr1 luxO vca1021 NF(NF) 196(44) NC_002505 V.c. Qrr1 vca0939 vca0939 NF(NF) 5(NF) NC_002505 V.c. Qrr2 luxO vca0620 NF(NF) 12(NF) NC_002505 V.c. Qrr2 vca0939 vca0939 NF(NF) 3(NF) NC_002505 V.c. Qrr3 vca0939 vca0939 NF(NF) 4(NF)...”

Or search for genetic data about PF04219 in the Fitness Browser