Family Search for PF04304 (DUF454)

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

PF04304 hits 20 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

Rmet_0221 YbaN family protein from Cupriavidus metallidurans CH34
Aligns to 20:135 / 150 (77.3%), covers 100.0% of PF04304, 146.7 bits

• Phenotypic and Genetic Characterization of Temperature-Induced Mutagenesis and Mortality in Cupriavidus metallidurans
  Van, Frontiers in microbiology 2021
  • “...-derivative of CH34 This study CH34-Km R CH34 harboring a EZ-Tn5 < KAN 2> in Rmet_0221 coding for a conserved hypothetical protein, Km R This study CH34 1009 CH34 Rmet_1009:: tet , Tc R This study CH34-TIMM R1 1009 CH34-TIMM R1 Rmet_1009:: tet , Tc R...”
  • “...C. metallidurans CH34 strain, i.e., CH34-Km R , containing a kanamycin resistance cassette in gene Rmet_0221, coding for a hypothetical protein, was used in the competition assays. The different strains, i.e., CH34-TIMM R1 , CH34-TIMM R2 , CH34 and CH34-Km R ( Table 1 ), were...”

BUE60_21160 YbaN family protein from Pseudomonas syringae pv. actinidiae
Aligns to 15:129 / 134 (85.8%), covers 100.0% of PF04304, 143.8 bits

• Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions
  Hirose, PeerJ 2020
  • “...5.7711 7.283092 0.000158 0.0261 0.73941 BUE60_13595 hypothetical protein 1.636492 5.54256 5.54256 7.34782 0.000186 0.027557 0.412538 BUE60_21160 hypothetical protein 0.130148 6.04703 6.04703 6.997812 0.00019 0.027557 0.777151 BUE60_19345 glutathione S-transferase 0 6.553643 7.982156 7.93946 0.000185 0.027557 0.497624 BUE60_15180 hypothetical protein 0.64369 6.95686 6.95686 7.415176 0.000178 0.027557 0.528899 BUE60_07695...”

YbaN / b0468 DUF454 domain-containing inner membrane protein YbaN from Escherichia coli K-12 substr. MG1655 (see 2 papers)
b0468 conserved inner membrane protein from Escherichia coli str. K-12 substr. MG1655
Z0585 putative gene 58 from Escherichia coli O157:H7 EDL933
SF5M90T_438 DUF454 family protein from Shigella flexneri 5a str. M90T
Aligns to 3:117 / 125 (92.0%), covers 99.1% of PF04304, 141.6 bits

• COLOMBOS: access port for cross-platform bacterial expression compendia
  Engelen, PloS one 2011
  • “...Fur, NrdR b4291 fecA Fe 3+ dicitrate transport protein fecABCDE + + Fur, CRP, PdhR b0468 ybaN Inner membrane protein ybaN + Predicted b0804 ybiX PKHD-type hydroxylase ybiX + Predicted; Fur dependent expression b1018 efeO UPF0409 protein efeUOB + Predicted; functional in related strain b1452 yncE...”
• A divalent ion is crucial in the structure and dominant-negative function of ID proteins, a class of helix-loop-helix transcription regulators
  Wong, PloS one 2012
  • “...constructs for expression and crystallization ID2 HLH (residues 2482) was cloned from full-length cDNA (Genecopoeia, Z0585) using Gateway (Invitrogen) as per manufacturer's instructions, into the pDONR221 vector (Invitrogen). Due to known instability issues of ID2, a C-terminal 14 amino acid long polypeptide (LKPSFLVQSGDIAS) was included to...”
• RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
  Vergara-Irigaray, BMC genomics 2014
  • “...hypothetical protein 0.81 SF5M90T_479 ybbF conserved hypothetical protein -1.19 SF5M90T_2195 rtn conserved hypothetical protein -1.50 SF5M90T_438 ybaN conserved hypothetical protein -1.73 SF5M90T_1853 conserved hypothetical protein -2.03 -2.58 SF5M90T_1647 conserved hypothetical protein -2.11 SF5M90T_983 ymcD conserved hypothetical protein -2.34 SF5M90T_4094 yjbA P-starvation inducible protein PsiE -2.51 1.69...”

BN5_1641 YbaN family protein from Pseudomonas oleovorans CECT 5344
Aligns to 14:128 / 132 (87.1%), covers 100.0% of PF04304, 141.5 bits

• Putative small RNAs controlling detoxification of industrial cyanide-containing wastewaters by Pseudomonas pseudoalcaligenes CECT5344
  Olaya-Abril, PloS one 2019
  • “...BN5_1637, FAD-dependent oxidoreductase NitH; BN5_1638, isocitrate dehydrogenase kinase/phosphatase-IDH; BN5_1639, uncharacterized protein; BN5_1640, -lactamase domain-containing protein; BN5_1641, inner membrane protein; BN5_1642, YecA family protein; BN5_1643, RNA-directed DNA polymerase; BN5_1644, uncharacterized protein; BN5_1645, RNA-directed DNA polymerase. J. BN5_1896, uncharacterized protein; BN5_1897, thiol-disulfide isomerase and thioredoxins protein; BN5_1898, 2-dehydro-3-deoxyphosphogluconate/4-hydroxy-2-oxoglutarate...”

SEET0819_09365, STM14_0567 DUF454 family protein from Salmonella enterica subsp. enterica serovar Tennessee str.
Aligns to 3:117 / 125 (92.0%), covers 99.1% of PF04304, 139.5 bits

• Integrative DNA methylome and transcriptome analysis reveals DNA adenine methylation is involved in Salmonella enterica Typhimurium response to oxidative stress
  Zhang, Microbiology spectrum 2023
  • “...transcriptome and DNA methylome with a high correlation R value ID Name R P Description STM14_0567 ybaN 0.90 0.016 Hypothetical protein STM14_0567 STM14_0707 ahpC 0.83 0.042 Alkyl hydroperoxide reductase subunit C STM14_0708 ahpF 0.88 0.022 Alkyl hydroperoxide reductase F52a subunit STM14_0817 potE 0.84 0.038 Putrescine transporter...”
• Whole Genome DNA Sequence Analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks
  Wilson, PloS one 2016
  • “...C->T 1659427 CP007505 coding SEET0819_07735 609 ATG->ATA M->I N + multicopper oxidase 2013944 CP007505 coding SEET0819_09365 212 CCG->CTG P->L N + hypothetical protein 266867 CP007505 coding SEET0819_01325 771 CCG->CCA P->P S + ribokinase 2745712 CP007505 coding SEET0819_12935 360 GCC->GCT A->A S + peptide ABC transporter ATP-binding...”

HD1939 conserved hypothetical protein from Haemophilus ducreyi 35000HP
Aligns to 2:117 / 130 (89.2%), covers 98.3% of PF04304, 134.4 bits

• Haemophilus ducreyi Seeks Alternative Carbon Sources and Adapts to Nutrient Stress and Anaerobiosis during Experimental Infection of Human Volunteers
  Gangaiah, Infection and immunity 2016
  • “...Operon_0515 HD1289 HD_RS05260 lrgB HD1783 HD_RS07280 HD1783 HD1939 HD_RS07950 HD1939 HD1155 HD_RS04745 lspB HD1298 HD1299 HD1301 HD1302 HD1303 HD1304 HD1305...”

VC1052 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 7:121 / 132 (87.1%), covers 100.0% of PF04304, 132.5 bits

• Preclinical evaluation of Vaxfectin-adjuvanted Vero cell-derived seasonal split and pandemic whole virus influenza vaccines
  Smith, Human vaccines & immunotherapeutics 2013
  • “...mixture of cationic lipid VC1052 and neutral co-lipid DPyPE. VC1052 [()-N-(3aminopropyl)-N,N-dimethyl-2,3-bis(cis-9-tetradecenyloxy)1-propanaminium bromide] was...”
  • “...lipid film from an equimolar chloroform solution of VC1052 and DPyPE in glass vials containing FluroTec(R) stoppers. The chloroform was evaporated under a...”
• PhoB regulates motility, biofilms, and cyclic di-GMP in Vibrio cholerae
  Pratt, Journal of bacteriology 2009
  • “...VC0724 VC0725 VC0826 VC0829 VC0831 VC1067 VC0034 VC0948 VC1052 VC1301 VC2053 VCA0079 VCA1050 Gene name 6635 6636 PRATT ET AL. J. BACTERIOL. Downloaded from...”

BQ00830 hypothetical protein from Bartonella quintana str. Toulouse
Aligns to 12:127 / 128 (90.6%), covers 99.1% of PF04304, 131.8 bits

• Bartonella quintana deploys host and vector temperature-specific transcriptomes
  Abromaitis, PloS one 2013
  • “...1.41 0.02 5.35 1.59 7 2.68 BQ00240 thioredoxin trxA 0.68 0.71 1.28 1.79 2 2.60 BQ00830 hypothetical protein 0.82 0.53 0 2.09 2 2.56 BQ07681 hypothetical protein 0.70 0.58 0 2.11 3 2.43 BQ11010 hypothetical protein 0.92 0.32 0 1.92 1 2.36 BQ09250 cold shock protein...”
  • “...8.50E-71 306837668 BQ00570 LysM domain/BON superfamily protein 2.00E-52 EHH06667.1 LysM domain/BON superfamily protein 3.00E-47 325291490 BQ00830 - - - inner membrane protein ybaN 1.70E-23 358048936 BQ02770 XRE family transcriptional regulator 4.00E-08 YP_002004972.1 conserved hypothetical protein Bartonella sp. AR 15-3 3.90E-09 319405804 BQ05030 glycosyl transferase family protein...”

APL_1806 hypothetical protein from Actinobacillus pleuropneumoniae L20
Aligns to 2:117 / 129 (89.9%), covers 97.4% of PF04304, 131.7 bits

• Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential
  Klitgaard, BMC genomics 2010
  • “...# Hemoglobin-haptoglobin-binding protein A precursor P 1.03 APL_1849 + lldD L-lactate dehydrogenase [cytochrome] C 2.04 APL_1806 - hypothetical protein S 0.98 APL_1571 + tonB1 Periplasmic protein M 1.46 APL_1570 + exbB1 Biopolymer transport protein U 2.35 APL_1569 + exbD1 Biopolymer transport protein U 1.77 APL_1568 +...”

SPO0005 YbaN family protein from Ruegeria pomeroyi DSS-3
Aligns to 2:116 / 117 (98.3%), covers 98.3% of PF04304, 128.1 bits

• Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3
  Rivers, Frontiers in microbiology 2016
  • “...No trans44 265 SPO0873 Ureidoglycolate hydrolase Nucleic acid metabolism 0.003 Yes SPO1532 Hypothetical protein 0.005 SPO0005 Hypothetical protein 0.008 SPO1350 Hypothetical protein 0.009 trans45 351 SPO3050 Hypothetical protein 0.003 SPO2852 CzcN domain-containing protein 0.003 SPO2542 Biotin/lipoate binding domain-containing protein Coenzyme metabolism 0.006 SPO2703 Hypothetical protein 0.008...”

SMb20557 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
Aligns to 1:106 / 111 (95.5%), covers 90.4% of PF04304, 127.3 bits

• The LuxR homolog ExpR, in combination with the Sin quorum sensing system, plays a central role in Sinorhizobium meliloti gene expression
  Hoang, Journal of bacteriology 2004
  • “...(alias) A C SMc02726 SMc04059 SMc04114 (pilA1) SMb20557 SMb21309 (expE6) SMc04170 SMb21310 (expE5) SMb21544 SMb20951 (exoI) SMb20391 SMb21319 (expA1) SMb21311...”

SMLT_RS19415 YbaN family protein from Stenotrophomonas maltophilia K279a
Aligns to 22:136 / 141 (81.6%), covers 99.1% of PF04304, 127.3 bits

• Putative Iron Acquisition Systems in Stenotrophomonas maltophilia
  Kalidasan, Molecules (Basel, Switzerland) 2018
  • “...Heme ABC transporter, ATPase component SMLT_RS11325 99% (K279a) Hyp1 Hypothetical protein related to heme utilization SMLT_RS19415 98% (1337) HmuU Heme ABC transporter, permease protein SMLT_RS11320 92% (K279a) HmuT Heme ABC transporter, cell surface heme and hemoprotein receptor SMLT_RS11315 97% (D457) Subsystem: Heme, hemin uptake and utilization...”

ABLAC_16850 YbaN family protein from Acinetobacter baumannii LAC-4
Aligns to 33:146 / 146 (78.1%), covers 97.4% of PF04304, 126.6 bits

• Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors
  Ou, Scientific reports 2015
  • “...analysis confirmed the presence of a hemO gene cluster in the LAC-4 genome (ABLAC_16780 to ABLAC_16850). Furthermore, comparative genomics analyses using BLASTp search + hit colocation analysis showed that 11 of the other 20 complete genomes of A. baumannii strains also contain the hemO cluster (see...”

ACICU_00880 hypothetical protein from Acinetobacter baumannii ACICU
ACICU_RS04605, DMO12_RS04720 YbaN family protein from Acinetobacter baumannii ACICU
Aligns to 33:146 / 146 (78.1%), covers 97.4% of PF04304, 126.5 bits

• New Shuttle Vectors for Gene Cloning and Expression in Multidrug-Resistant Acinetobacter Species
  Lucidi, Antimicrobial agents and chemotherapy 2018
  • “...baumannii ACICU gene cluster from the ACICU_00873 to ACICU_00880 genes) directly into pVRL1 (data not shown), supporting the potential of this plasmid in...”
• Antimicrobial Activity of Gallium Compounds on ESKAPE Pathogens
  Hijazi, Frontiers in cellular and infection microbiology 2018
  • “...bp DNA fragment encompassing eight genes of the hemO cluster of ACICU (from ACICU_00873 to ACICU_00880 locus) was obtained by PCR amplification using primers HemO_FW (5-CATTTGGTTTCCGAGTCTCG-3) and HemO_RV (5-CCATGATGCGTACCATGCA-3). The PCR product was purified by the PCR Clean-Up System (Promega) and blunt-end ligated to the SmaI...”
• Genomics of Acinetobacter baumannii iron uptake
  Artuso, Microbial genomics 2023
  • “...hphA DMO12_RS04700 Slam-dependent haemophore hsmA DMO12_RS04705 Hemophilin secretion modulator DMO12_RS04710 TonB-related protein DMO12_RS04715 Haem oxygenase DMO12_RS04720 Hypothetical protein basJ DMO12_RS13105 Acinetobactin biosynthesis isochorismate synthase basI DMO12_RS13110 Acinetobactin biosynthesis phosphopantetheinyl transferase basH DMO12_RS13115 Acinetobactin biosynthesis thioesterase barB DMO12_RS13120 Acinetobactin export ABC transporter permease/ATP-binding subunit barA DMO12_RS13125 Acinetobactin...”
• Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus
  Castro-Jaimes, Frontiers in microbiology 2020
  • “...spot 6 in the representative strains, and two of them had recombination signals (ACICU_RS04580 and ACICU_RS04605). All these data showed that A. haemolyticus can uptake hemin for iron acquisition and that the gene clusters had been integrated via recombination with neighboring genes. Regarding virulence factors characterized...”

NWMN_0112 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
SA0161 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAOUHSC_00131 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
Aligns to 2:117 / 127 (91.3%), covers 97.4% of PF04304, 126.0 bits

• Fur regulation of Staphylococcus aureus heme oxygenases is required for heme homeostasis
  Lojek, International journal of medical microbiology : IJMM 2018
  • “...isdCDEFsrtBisdG operons. The endogenous promoter for isdI was defined as the intergenic region between orfX (NWMN_0112) and aldA (NWMN_0113). However, the Fur box for isdI jis contained within the 3 region of the orfX operon, and this region was also included in the constructed promoter for...”
• Induction of virulence gene expression in Staphylococcus aureus by pulmonary surfactant
  Ishii, Infection and immunity 2014
  • “...California, Berkeley Gene no. NWMN_0093 NWMN_0095 NWMN_0112 NWMN_0207 NWMN_0221 NWMN_0223 NWMN_0224 NWMN_0225 NWMN_0232 NWMN_0233 NWMN_0245 NWMN_0246 NWMN_0360...”
• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...family protein Unkown function sa_c2968s2524_a_at 3.3 ND 2.5 SA0156 hypothetical protein sa_c3224s2774_a_at 7.8 2.5 2.5 SA0161 hypothetical protein sa_c6700s5841_a_at 2.1 2.5 2.5 SA0259 hypothetical protein sa_c7203s6269_a_at 6.5 ND 2.5 SA0445 hypothetical protein sa_c7760s6763_at * 23.5 15 30 SA0625 hypothetical protein sa_c8897s7814_a_at 6.5 ND 2.5 SA0692 hypothetical...”
• Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover
  Anderson, Journal of bacteriology 2006
  • “...putative MSSA476-SAS070 N315-SA0413 N315-SA0751 N315-SA1186 N315-SA2496 SA0161 SA0299 SA0436 SA0448 SA0497 SA0537 SA0692 SA1033 SA1372 SA1375 SA1438 SA1524...”
  • “...N315-SA1777 N315-SA1832 N315-SA2299 N315-SA0326 N315-SA0551 N315-SA1829 SA0161 SA0191 SA0215 SA0252 SA0255 SA0259 SA0314 SA0436 SA0568 SA0625 SA0641 SA0814...”
• Transcriptomic analyses reveal the potential antibacterial mechanism of citral against Staphylococcus aureus
  Liao, Frontiers in microbiology 2023
  • “...ferrochelatase SAOUHSC_02681 5.770892267 8.0905E-128 nitrate reductase subunit alpha SAOUHSC_02680 5.655444057 1.3733E-110 nitrate reductase subunit beta SAOUHSC_00131 5.423736733 3.31075E-51 YbaN family protein SAOUHSC_02679 5.263068749 3.38926E-75 respiratory nitrate reductase subunit delta SAOUHSC_02645 5.222935859 2.92178E-05 LytTR family DNA-binding domain-containing protein 3.2.3. Go functional enrichment analysis GO enrichment analysis was...”
• Functional analysis of the EsaB component of the Staphylococcus aureus Type VII secretion system
  Casabona, Microbiology (Reading, England) 2017
  • “...protein FhuA 7.0 SAOUHSC_00071 sirC 5.3 Involved in staphyloferrin B transport into the cytoplasm 4.6 SAOUHSC_00131 5.3 Putative membrane protein 6.1 SAOUHSC_02821 5.8 Putative membrane protein ns SAOUHSC_02719 6.2 ABC transporter ATP-binding protein 5.5 SAOUHSC_01920 6.3 Putative lipoprotein ns SAOUHSC_02428 htsB 6.3 Heme transport system permease...”
• Haem-iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390
  Casabona, Microbiology (Reading, England) 2017
  • “...isdI 5.7 Haem-degrading monooxygenase IsdI SAOUHSC_01086 isdF 6.1 ABC permease IsdF Fur [ 65 ] SAOUHSC_00131 6.1 Putative membrane spanning protein SAOUHSC_01088 srtB 6.2 Sortase SrtB Fur [ 65 ] SAOUHSC_01084 isdD 6.2 ATP-hydrolysing and haem-binding protein IsdD Fur [ 65 ] SAOUHSC_02432 6.2 Unknown, hypothetical...”

PP1004 conserved hypothetical protein from Pseudomonas putida KT2440
Aligns to 11:125 / 137 (83.9%), covers 100.0% of PF04304, 122.7 bits

• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

DIP2356 Putative conserved membrane protein from Corynebacterium diphtheriae NCTC 13129
Aligns to 3:120 / 125 (94.4%), covers 97.4% of PF04304, 119.1 bits

• Prediction of DtxR regulon: identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae
  Yellaboina, BMC microbiology 2004
  • “...4 DtxR-regulated genes containing the potential signal sequence Gene Product DIP0222 Diphtheria toxin DIP0109 IRP6B DIP2356 IRP4 DIP2162 ABC-type peptide transport system periplasmic component DIP0172 Putative membrane protein DIP2107 Putative integral membrane transport protein DIP0625 Haemin transporter associated protein DIP0626 ABC-type haemin transport system DIP0627 ABC-type...”

Dshi_1454 hypothetical protein from Dinoroseobacter shibae DFL 12
Aligns to 13:127 / 165 (69.7%), covers 99.1% of PF04304, 111.3 bits

• FnrL and Three Dnr Regulators Are Used for the Metabolic Adaptation to Low Oxygen Tension in Dinoroseobacter shibae
  Ebert, Frontiers in microbiology 2017
  • “...response to oxygen limitation. Beside the activation of a gene encoding a putative membrane protein (Dshi_1454) the highest log2-fold change was found for transcription of a gene encoding the outer membrane protein ( ompW ; Bouchal et al., 2010 ). On the other hand the genes...”

SH1866 hypothetical protein from Staphylococcus haemolyticus JCSC1435
Aligns to 2:117 / 128 (90.6%), covers 97.4% of PF04304, 108.2 bits

• Cigarette smoke exposure redirects Staphylococcus aureus to a virulence profile associated with persistent infection
  Lacoma, Scientific reports 2019
  • “...SH445 SH1000 umuC ::Tn; 40 SH805 SH1000 recA ::Tn; 40 SH1012 SH1000 rexB ::Tn; 40 SH1866 SH1000 dinB ::Tn; 40 SCV13 SH1000 derived Gen R SCV with auxotrophy for menadione isolated following growth in 50% CS This study Newman (ANG112) MSSA, laboratory strain isolated from human...”
• Staphylococcus aureus adapts to oxidative stress by producing H2O2-resistant small-colony variants via the SOS response
  Painter, Infection and immunity 2015
  • “...SH1000 transduced with DNA from NE1366, resulting in inactivation of catalase; Ery r This study SH1866 SH1000 dinB ::Tn SH445/pCN34 SH1000 umuC ::Tn transformed with pCN34 SH445/p umuC SH1000 umuC ::Tn transformed with p umuC USA300 LAC LAC strain of the USA300 CA-MRSA lineage 85 USA300...”

EF2922 conserved hypothetical protein from Enterococcus faecalis V583
Aligns to 3:119 / 128 (91.4%), covers 96.5% of PF04304, 100.7 bits

• Comparative genomic hybridization analysis of Enterococcus faecalis: identification of genes absent from food strains
  Lepage, Journal of bacteriology 2006
  • “...Cell envelope EF2682 EF2683 EF2684 EF2686 EF2713 EF2795 EF2922 EF2968 EF3023 EF3074 EF3075 EF3154 EF3248 EFA0047 EFB0012 PAIEF0052 e PAIEF0053 PAIEF0056 EF0501...”

Or search for genetic data about PF04304 in the Fitness Browser