Family Search for PF04222 (DUF416)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

PF04222 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.

YjaG / b3999 DUF416 domain-containing protein YjaG from Escherichia coli K-12 substr. MG1655 (see 2 papers)
Aligns to 5:193 / 196 (96.4%), covers 99.5% of PF04222, 279.1 bits

STMMW_41221 YjaG family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
STM4169 putative cytoplasmic protein from Salmonella typhimurium LT2
t3462 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
SEN3955 hypothetical protein from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Aligns to 5:193 / 196 (96.4%), covers 100.0% of PF04222, 276.1 bits

• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis
  Fong, Microbial genomics 2023
  • “...Putative aldolase D7795_04494 SEN3868 P125109_04397 STMMW_40431 STM4078 1.13 yjaG Conserved hypothetical protein D7795_04594 SEN3955 P125109_04498 STMMW_41221 STM4169 1.06 dgkA Diacylglycerol kinase D7795_04646 SEN4005 P125109_04550 STMMW_41861 STM4236 1.53 yjfI Conserved hypothetical protein D7795_04792 SEN4136 P125109_04696 STMMW_43141 STM4370 1.59 yjfO Putative exported protein D7795_04801 SEN4145 P125109_04705 STMMW_43231 STM4379...”
• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis
  Fong, 2022
• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis
  Fong, Microbial genomics 2023
  • “...aldolase D7795_04494 SEN3868 P125109_04397 STMMW_40431 STM4078 1.13 yjaG Conserved hypothetical protein D7795_04594 SEN3955 P125109_04498 STMMW_41221 STM4169 1.06 dgkA Diacylglycerol kinase D7795_04646 SEN4005 P125109_04550 STMMW_41861 STM4236 1.53 yjfI Conserved hypothetical protein D7795_04792 SEN4136 P125109_04696 STMMW_43141 STM4370 1.59 yjfO Putative exported protein D7795_04801 SEN4145 P125109_04705 STMMW_43231 STM4379 1.24...”
• Exploring the Prevalence of Antimicrobial Resistance in Salmonella and commensal Escherichia coli from Non-Traditional Companion Animals: A Pilot Study
  Marco-Fuertes, Life (Basel, Switzerland) 2024 (no snippet)
• Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis
  Fong, Microbial genomics 2023
  • “...2.93 yneB Putative aldolase D7795_04494 SEN3868 P125109_04397 STMMW_40431 STM4078 1.13 yjaG Conserved hypothetical protein D7795_04594 SEN3955 P125109_04498 STMMW_41221 STM4169 1.06 dgkA Diacylglycerol kinase D7795_04646 SEN4005 P125109_04550 STMMW_41861 STM4236 1.53 yjfI Conserved hypothetical protein D7795_04792 SEN4136 P125109_04696 STMMW_43141 STM4370 1.59 yjfO Putative exported protein D7795_04801 SEN4145 P125109_04705...”

MHA_2723 DUF416 family protein from Mannheimia haemolytica PHL213
Aligns to 4:193 / 196 (96.9%), covers 100.0% of PF04222, 265.7 bits

• Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
  Reddy, BMC bioinformatics 2012
  • “...510 Alternate Start MHA_2666 2591266 2592276 1011 336 - 2591266 2592360 1095 364 Alternate Start MHA_2723 2659955 2660545 591 196 - 2659955 2660692 738 245 Alternate Start P reviously annotated gene locus, length and strand specificity. Observed locus based on RNA-Seq expression along with gene length...”

NT01EI_0182 hypothetical protein from Edwardsiella ictaluri 93-146
Aligns to 5:193 / 196 (96.4%), covers 100.0% of PF04222, 260.2 bits

• Transposon mutagenesis and identification of mutated genes in growth-delayed Edwardsiella ictaluri
  Kalindamar, BMC microbiology 2019
  • “...enzyme (NAD-ME) 2.00E-72 64 Eis002 NT01EI_1721 PTS system, mannose/fructose/sorbose family, IIB component 2.00E-106 32 Eis004 NT01EI_0182 Hypothetical protein 7.00E-57 26 Eis006 NT01EI_0085 ATP-dependent DNA helicase Rep 2.00E-114 46 Eis009 NT01EI_1236 Coproporphyrinogen III oxidase, aerobic 6.00E-32 24 Eis011 NT01EI_3690 ABC transporter, periplasmic amino acid binding protein 1.00E-74...”

YPTB0296 hypothetical protein from Yersinia pseudotuberculosis IP 32953
Aligns to 5:193 / 196 (96.4%), covers 100.0% of PF04222, 254.1 bits

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...0.001) 0.681 (0.008) YPTB0196 or0133 conserved hypothetical protein 3.061 (< 0.001) YPTB0219 YPO3816A 1.383 (0.046) YPTB0296 YPO3732 conserved hypothetical protein 0.558 (< 0.001) YPTB0378 YPO0323 conserved hypothetical protein 1.483 (0.016) YPTB0454 YPO3522 conserved hypothetical protein 1.472 (0.03) YPTB0478 YPO3498 conserved hypothetical protein 0.734 (0.038) YPTB0506 or0367...”

VC0268 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 32:221 / 222 (85.6%), covers 99.5% of PF04222, 252.2 bits

• Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains
  Miller, Applied and environmental microbiology 2007
  • “...VC0269 to VC0270 transformed into Sa5Y using primers in VC0268, an intervening gene present in Sa5Y but not in VCXB21, and VC0271. (F) Probes VC1280 to VC1286...”
  • “...apparently replaced the intervening segment found between ORFs VC0268 and VC0271 in the Sa5Y recipient strain. Independent mapping showed that Sa5Y contains 9...”
• Serogroup conversion of Vibrio cholerae in aquatic reservoirs
  Blokesch, PLoS pathogens 2007
  • “...VchoM_01000822 (homolog to VC0265), 0821 = VchoM_01000821 (homolog to VC0267), 0820 = VchoM_01000820 (homolog to VC0268), 0819 = VchoM_01000819 (homolog to VC0271). About 15% of the Kan R transformants (approximating a transformation frequency of 2.2 10 6 ) exhibited the same opaque colony morphotype as O139...”

NP_667836 hypothetical protein from Yersinia pestis KIM
YPO3732 conserved hypothetical protein from Yersinia pestis CO92
Aligns to 5:193 / 196 (96.4%), covers 100.0% of PF04222, 252.0 bits

• Extensive antibody cross-reactivity among infectious gram-negative bacteria revealed by proteome microarray analysis
  Keasey, Molecular & cellular proteomics : MCP 2009
  • “...co-regulated protein, NP_667380 + 0140 UDP- N -glucosamine 1- carboxyvinyltransferase, NP_667483 + 0498 Hypothetical protein, NP_667836 + 0838 Putative dehydrogenase, NP_668172 + 1012 Putative oxidoreductase, NP_668342 + 1028 ATP-dependent specificity component of clpP, NP_668358 + 1029 DNA-binding ATP-dependent protease La, NP_668359 + 1038 Putative LRP-like transcriptional...”
• Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling
  Ansong, Current topics in microbiology and immunology 2013
  • “...genes that showed correlated expression, but were located farther away from the biosynthetic cluster, were YPO3732 and YPO2055. 5 Host Perspective During infection, pathogens attempt to hijack resources from the host, while host cells attempt to limit the materials available for pathogen reproduction and virulence. The...”
  • “...(panel B) in the fab pathway (panel A) are shown including putative fabI candidates YPO1954, YPO3732, and YPO2055. Each column represents ratio of 37C/26C across time (1 h, 2 h, 4 h, 8 h). The color scale ranges from green (total low relative abundance) to red...”
• An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
  Charusanti, BMC systems biology 2011
  • “...function as FabI. Other genes showing correlated expression but located farther away from YPO1597-YPO1601 are YPO3732 and YPO2055. Pathway analysis and model simulations led to the hypothesis that YP CO92 cannot utilize rhamnose and melibiose due to a missing sink reaction and perturbed gene regulation, respectively,...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...0.681 (0.008) YPTB0196 or0133 conserved hypothetical protein 3.061 (< 0.001) YPTB0219 YPO3816A 1.383 (0.046) YPTB0296 YPO3732 conserved hypothetical protein 0.558 (< 0.001) YPTB0378 YPO0323 conserved hypothetical protein 1.483 (0.016) YPTB0454 YPO3522 conserved hypothetical protein 1.472 (0.03) YPTB0478 YPO3498 conserved hypothetical protein 0.734 (0.038) YPTB0506 or0367 conserved...”

HSM_0565 hypothetical protein from Haemophilus somnus 2336
HSM_0565 DUF416 family protein from Histophilus somni 2336
Aligns to 4:193 / 196 (96.9%), covers 100.0% of PF04222, 252.0 bits

• Identification and initial characterization of Hfq-associated sRNAs in Histophilus somni strain 2336
  Subhadra, PloS one 2023
  • “...631711 187 Y - HSM_0021 HSM_0022 ND This work HS53 658121 658225 105 Y - HSM_0565 HSM_0566 ND This work HS54 672117 672270 154 Y Y HSM_0578 HSM_0027 ND This work HS55 674011 674147 137 Y - HSM_0028 HSM_0029 ND This work HS62 764367 764500 134...”

SO_3458 conserved hypothetical protein from Shewanella oneidensis MR-1
Aligns to 6:197 / 199 (96.5%), covers 99.5% of PF04222, 245.1 bits

• Analysis of the BarA/UvrY two-component system in Shewanella oneidensis MR-1
  Binnenkade, PloS one 2011
  • “...identified in other species. SO_3457 is likely transcribed in an operon with the downstream gene SO_3458, predicted to encode a conserved hypothetical protein of 199 amino acids. 10.1371/journal.pone.0023440.g001 Figure 1 Domain organization of S. oneidensis MR-1 BarA (SO_3457; upper panel) and UvrY (SO_1860, lower panel). White...”

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