Family Search for PF05974 (DUF892)

PF05974 hits 48 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

RLV_7281 ferritin-like domain-containing protein from Rhizobium leguminosarum bv. viciae
Aligns to 6:163 / 165 (95.8%), covers 99.4% of PF05974, 215.1 bits

• Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells
  Durán, Molecular & cellular proteomics : MCP 2021
  • “...Chr phosphoenolpyruvate carboxykinase [ATP] 2.24 92 49 RLV_7109 Chr NAD-dependent succinate-semialdehyde DH 3.24 130 39 RLV_7281 Chr YciF stress-response, ferritin-like domain containing protein 2.04 33 13 Lentil-overexpressed proteins RLV_502 pRlvA putative small heat shock protein 0.36 0 56 RLV_817 pRlvA molecular chaperone Hsp20 0.17 0 78...”

SMc00371 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
Aligns to 6:163 / 163 (96.9%), covers 100.0% of PF05974, 212.5 bits

• Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation
  Zuniga-Soto, Scientific reports 2019
  • “...Response in S . meliloti Response at early stage in E . adhaerens Function Reference SMc00371 WP_025430719.1 OV14_RS32210 pb 75% Down-regulated Down-regulated* (D3-D7) ferritin-like domain-containing protein Capela et al . 33 SMc00371 WP_025430830.1 OV14_RS32800 pb 61% Down-regulated Down-regulated* (D3-D7) ferritin-like domain-containing protein Capela et al ....”
• Role of the extracytoplasmic function sigma factor RpoE4 in oxidative and osmotic stress responses in Rhizobium etli
  Martínez-Salazar, Journal of bacteriology 2009
  • “...in R. etli, corresponding to SMc03873, SMb20094, SMc00371, SMc00885, SMc20879, SMc00063, SMb20454, and SMb21454 in S. meliloti, respectively. On the other...”
• Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions
  Yuan, Journal of bacteriology 2008
  • “...protein is 70% identical to the Sinorhizobium meliloti SMc00371 protein, 40% FIG. 3. Acid-induced genes classified into nine categories. protein protein protein...”
• An extracytoplasmic function sigma factor acts as a general stress response regulator in Sinorhizobium meliloti
  Sauviac, Journal of bacteriology 2007
  • “...smb21481 smb21572 smb21640 smb21673 smc00048 smc00063 smc00371 smc00506 smc00665 smc00795 smc00796 smc00800 smc00885 smc00931 smc01140 smc01266 smc01267...”
  • “...smb20007 (katC) smb20094 smb20227 (ndiA1) smb21484 (rpoE5) smc00371 smc00885 smc01504 smc01505 smc03873 (rpoH2) 6.2 (1.1) 21.4 (14.5) 29.5 (13.9) 36.7 (23.7)...”
• Role of the regulatory gene rirA in the transcriptional response of Sinorhizobium meliloti to iron limitation
  Chao, Applied and environmental microbiology 2005
  • “...SMc00062 SMc00086 SMc00136 SMc00235 SMc00301 SMc00338 SMc00371 SMc00401 SMc00402 SMc00512 SMc00537 Expression ratiob Gene and/or description IRON REGULATION...”

MAFF_RS18965 ferritin-like domain-containing protein from Mesorhizobium japonicum MAFF 303099
Aligns to 10:167 / 168 (94.0%), covers 99.4% of PF05974, 208.2 bits

• Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence
  Yuan, Frontiers in microbiology 2021
  • “...113-2GL002109 blr7089 MCHK_RS17580 SM2011_RS03405 Nodule senescence 113-2GL002468 bll6756 MAFF_RS00585 SM2011_RS21450 Nodule senescence 113-2GL003340 113-2GL001478 bll7648,bll5866 MAFF_RS18965 MCHK_RS27010 Nitrogen fixation 113-2GL003434 blr5774 MCHK_RS17320 Nitrogen fixation 113-2GL003840 bll5412 MAFF_RS02150 MCHK_RS09810 SM2011_RS21190 Early stages of nodule development 113-2GL003842 bll5410 MAFF_RS02160 MCHK_RS09820 SM2011_RS21200 Early stages of nodule development 113-2GL003843 bll5409...”

C6B940 Uncharacterized protein from Rhizobium leguminosarum bv. trifolii (strain WSM1325)
Aligns to 8:165 / 168 (94.0%), covers 98.7% of PF05974, 207.9 bits

• Physiological changes in rhizobia after growth in peat extract may be related to improved desiccation tolerance
  Casteriano, Applied and environmental microbiology 2013 (secret)

blr6172 blr6172 from Bradyrhizobium japonicum USDA 110
Aligns to 1:158 / 165 (95.8%), covers 98.7% of PF05974, 207.4 bits

• Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures
  Lardi, International journal of molecular sciences 2016
  • “...unknown protein 4.7 blr2132 unknown protein 6.7 blr2140 hypothetical protein 4.2 blr2505 hypothetical protein 4.3 blr6172 hypothetical protein 4.7 blr7321 hypothetical protein 4.3 blr7327 hypothetical protein 6.0 bsr1749 hypothetical protein 4.4 Intracellular trafficking, secretion, and vesicular transport blr1813 RhcJ protein rhcJ 5.7 blr1819 RhcR protein rhcR...”

NGR_RS29265 ferritin-like domain-containing protein from Sinorhizobium fredii NGR234
Aligns to 6:163 / 163 (96.9%), covers 100.0% of PF05974, 207.3 bits

• RpuS/R Is a Novel Two-Component Signal Transduction System That Regulates the Expression of the Pyruvate Symporter MctP in Sinorhizobium fredii NGR234
  Ramos, Frontiers in microbiology 2022
  • “...pobA 4.04 t 41 hydroxybenzoate hydroxylase Transport pNGR234b NGR_RS05295 4.09 DUF2934 domain-containing protein Unknown pNGR234b NGR_RS29265 4.22 Ferritin-like domain-containing protein Stress Chromosome NGR_RS05300 4.36 CBS domain-containing protein Regulation pNGR234b NGR_RS06710 4.36 CerR family C-terminal domain-containing protein Regulation pNGR234b NGR_RS09255 4.65 DctP family TRAP transporter solute-binding subunit...”

RPA3943 conserved hypothetical protein from Rhodopseudomonas palustris CGA009
Aligns to 10:167 / 168 (94.0%), covers 99.4% of PF05974, 205.4 bits

• Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris
  Oshlag, Applied and environmental microbiology 2020
  • “...3-Oxoacyl-ACP reductase 5.52* 1.20 rpa4285 Malonic semialdehyde reductase 5.51* 1.73 rpa3565 l,d -Transpeptidase 5.39 2.17* rpa3943 Ferritin-like domain-containing protein 5.09* 0.55* rpa4394 Isocitrate lyase 5.05* 6.21* rpa3308 Ferritin-like domain-containing protein 5.03 1.12 rpa0320 4-Coumaroyl-homoserine lactone synthase 5.00 6.71* rpa1089 Hypothetical protein 4.99 1.32 rpa0214 Hypothetical protein...”

XC_3753 hypothetical protein from Xanthomonas campestris pv. campestris str. 8004
Aligns to 5:162 / 168 (94.0%), covers 99.4% of PF05974, 200.6 bits

• Co-regulation of Iron Metabolism and Virulence Associated Functions by Iron and XibR, a Novel Iron Binding Transcription Factor, in the Plant Pathogen Xanthomonas
  Pandey, PLoS pathogens 2016
  • “...mutant strain with the deletion of entire cluster of bacterioferritin-related protein encoding genes XC_3752 , XC_3753 and XC_3754 ); 2. fhuE XC_0925 , double deletion mutant in the receptors for non-vibrioferrin mediated ferric iron uptake encoding genes ( XC_0924 and XC_0925 ); and 3. fecR (...”
  • “...periplasmic iron dicitrate sensor [ 33 ]. The bacterioferritin-related protein encoding genes ( XC_3752 , XC_3753 and XC_3754 ) and the genes encoding the ferric iron uptake proteins ( XC_0924 and XC_ 0925) are regulated by both xibR and low-iron condition, whereas, the expression of fecR...”

RPA3308 ycfI, putative structural proteins from Rhodopseudomonas palustris CGA009
Aligns to 10:168 / 169 (94.1%), covers 99.4% of PF05974, 197.6 bits

• Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris
  Oshlag, Applied and environmental microbiology 2020
  • “...l,d -Transpeptidase 5.39 2.17* rpa3943 Ferritin-like domain-containing protein 5.09* 0.55* rpa4394 Isocitrate lyase 5.05* 6.21* rpa3308 Ferritin-like domain-containing protein 5.03 1.12 rpa0320 4-Coumaroyl-homoserine lactone synthase 5.00 6.71* rpa1089 Hypothetical protein 4.99 1.32 rpa0214 Hypothetical protein 4.92* 0.66* rpa4220 l,d -Transpeptidase 4.92 0.68 rpa4286 Dioxygenase 4.90* 2.03...”

Atu5278 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 5:161 / 166 (94.6%), covers 97.5% of PF05974, 195.6 bits

• Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions
  Yuan, Journal of bacteriology 2008
  • “...protein genes Atu2203 Atu2249 Atu2257 Atu2272 Atu4768 Atu4499 Atu5278 Atu5516 0.99 1.05 1.03 1.43 1.12 1.03 1.15 1.43 Conserved Conserved Conserved Conserved...”
  • “...a gene encoding a putative nonheme catalase, KatN (Atu5278). It is known that in Streptococcus mutans, E. coli, and Lactococcus lactis, acidic conditions (pH...”

2gyqA / Q6N4M9 Ycfi, a putative structural protein from rhodopseudomonas palustris.
Aligns to 10:161 / 162 (93.8%), covers 94.3% of PF05974, 194.7 bits

• Ligands: fe (iii) ion; zinc ion (2gyqA)

SENTW_1469 ferritin-like domain-containing protein from Salmonella enterica subsp. enterica serovar Weltevreden str.
STM1729 putative cytoplasmic protein from Salmonella typhimurium LT2
t1641 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
Aligns to 5:163 / 167 (95.2%), covers 99.4% of PF05974, 189.1 bits

• Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
  Brankatschk, Microbial biotechnology 2014
  • “...Protein of unknown function yebV SENTW_1340 15.38 Uncharacterized protein yiaK SENTW_3767 9.61 Putative protein yciF SENTW_1469 11.99 Unknown function ygaT (csiD) SENTW_2877 19.85 Hypothetical protein tctA SENTW_2876 10.62 Unknown function yqeF SENTW_3132 4.61 Putative acyltransferase TPX SENTW_1534 6.12 Putative thiol peroxidase ybdL SENTW_0580 4.55 Putative aminotransferase...”
• Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses
  Karavolos, BMC genomics 2008
  • “...multidrug/protein/lipid transport system 1.7 STM1586 putative periplasmic protein, similar to E. coli putative receptor 1.7 STM1729, yciF putative cytoplasmic protein 1.7 B Adrenaline Downregulated genes KEGG annotation Product Fold change Transport and metabolism STM2299, yfbG ( pmrI ) transformylase 0.4 STM1935, ftn cytoplasmic ferritin 0.4 STM2297,...”
• A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
  Perkins, PLoS genetics 2009
  • “...regulon. The four remaining genes were slsA (t3757), hyaA (t1458) and hypothetical genes t1459 and t1641 that are discussed below. Importantly, we confirmed that these genes were differentially expressed in the ompR mutant by a further method, quantitative PCR assays (data not shown). Many of the...”

SEN1305 hypothetical protein from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Aligns to 5:163 / 167 (95.2%), covers 99.4% of PF05974, 186.6 bits

• Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism
  Martinez-Sanguiné, Infection and immunity 2021 (secret)

4eruA / A0A0F6B221 Crystal structure of putative cytoplasmic protein, ycif bacterial stress response protein from salmonella enterica
Aligns to 6:159 / 159 (96.9%), covers 96.2% of PF05974, 185.4 bits

• Ligand: magnesium ion (4eruA)

ECs1654 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 5:163 / 166 (95.8%), covers 98.7% of PF05974, 183.8 bits

• Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts
  Crozier, Frontiers in microbiology 2016
  • “...(n/a) 2.87 NS NS NS ECs1653 x Citrobacter freundii CFNIH1 (95) -15.29 9.20 NS -13.23 ECs1654 x Citrobacter freundii CFNIH1 (94) -32.08 8.79 NS -71.95 ECs1655 Citrobacter freundii CFNIH1 (94) -18.13 8.85 NS -8.21 ECs2304 Shigella dysenteriae Sd197 (99) 12.97 20.21 NS -3.27 ECs2473 x Escherichia...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs1441 ECs1488 ECs1490 ECs1576 ECs1588 ECs1593 ECs1612 ECs1654 ECs1655 ECs1691 ECs1760 ECs1763 ECs1771 ECs1775 ECs1823 ECs1824 ECs1829 ECs1830 ECs1831 ECs1845...”

Z1923 unknown protein encoded by prophage CP-933X from Escherichia coli O157:H7 EDL933
Aligns to 7:165 / 168 (94.6%), covers 98.7% of PF05974, 183.7 bits

• Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
  Sharma, BMC microbiology 2017
  • “...encoded by bacteriophage Bp-933W 4.12 0.01 Z1922 Hypothetical protein encoded by bacteriophage CP-933X 2.23 0.03 Z1923 Hypothetical protein encoded by bacteriophage CP-933X 2.38 0.04 intO Z2036 Integrase for bacteriophage CP-933O 1.26 0.01 coxT Z2970 Regulator for prophage CP-933T +4.42 0.04 Z2971 Phage CP-933T encoded hypothetical protein...”
• Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933
  Dong, BMC genomics 2009
  • “...Putative ABC transporter Z0608 55 Putative outer membrane protein Z1504 93 Unknown Z1629 117 Unknown Z1923 64 Prophage CP-933X protein Z1924 137 Prophage CP-933X protein Z2296 57 Unknown Z2297 254 Unknown Z2298 55 Unknown Z3624 64 D-fructokinase Z3625 139 Sucrose hydrolase Z4874 60 Unknown Z5000 48...”
  • “...Putative enzyme (prophage CP-933N) Z1922 9.9 0.8 4.8 0.2 35 O-Island 52 Unknown (prophage CP-933X) Z1923 8.9 1.0 2.9 0.1 64 O-Island 52 Unknown (prophage CP-933X) Z1924 11.1 0.9 4.0 0.2 137 O-Island 52 Unknown (prophage CP-933X) Z2048 4.1 0.2 2.3 0.1 3 O-Island 57 Unknown...”

XCV2099 hypothetical protein from Xanthomonas campestris pv. vesicatoria str. 85-10
XAC2155 conserved hypothetical protein from Xanthomonas axonopodis pv. citri str. 306
Aligns to 3:158 / 169 (92.3%), covers 98.7% of PF05974, 178.9 bits

• Identification of 17 HrpX-regulated proteins including two novel type III effectors, XOC_3956 and XOC_1550, in Xanthomonas oryzae pv. oryzicola
  Xue, PloS one 2014
  • “...XCV4357 (92%) XCC4117 (86%) Xrp8 hypothetical protein XOC_2462 (100%) N a N N XAC2155 (91%) XCV2099 (91%) XCC2020 (86%) Xrp9 hypothetical protein XOC_1951 (100%) PXO_00529 (98%) XOO2357 (99%) XOO2488 (96%) XAC2517 (96%) XCV2699 (92%) XCC2382 (84%) Xrp10 hypothetical protein XOC_0560 100%) PXO_04113 (90%) XOO3892 (91%) XOO4113...”
• Diffusible signal factor (DSF)-mediated quorum sensing modulates expression of diverse traits in Xanthomonas citri and responses of citrus plants to promote disease
  Li, BMC genomics 2019
  • “...families (XAC3753 and XAC3754). Interestingly, the genes encoding stress-induced protein (XAC2156) and Ferritin-like di-iron-carboxylate protein (XAC2155) were upregulated by DSF/Rpf mediated QS and possibly involved in the adaptation of Xac to the host environment. The genes encoding putative GH18_chitinase-like glycosyl hydrolase (XAC3073) and GT2 family glycosyltransferase...”
  • “...Locus tag Log 2 Fold Change (Wt/ rpfF ) Homologue [Bacterial species] Identity (%) c XAC2155 1.36 ferritin-like domain-containing protein [ Xanthomonas group] 99 XAC2156 1.97 stress-induced protein [ X. phaseoli ] 98 XAC3073 1.01 GH18_chitinase-like glycosyl hydrolase [ X. citri ] 99 XAC3533 1.23 glycosyltransferase,...”
• Identification of 17 HrpX-regulated proteins including two novel type III effectors, XOC_3956 and XOC_1550, in Xanthomonas oryzae pv. oryzicola
  Xue, PloS one 2014
  • “...XAC4251 (92%) XCV4357 (92%) XCC4117 (86%) Xrp8 hypothetical protein XOC_2462 (100%) N a N N XAC2155 (91%) XCV2099 (91%) XCC2020 (86%) Xrp9 hypothetical protein XOC_1951 (100%) PXO_00529 (98%) XOO2357 (99%) XOO2488 (96%) XAC2517 (96%) XCV2699 (92%) XCC2382 (84%) Xrp10 hypothetical protein XOC_0560 100%) PXO_04113 (90%) XOO3892...”
• Evolutionary history of the plant pathogenic bacterium Xanthomonas axonopodis
  Mhedbi-Hajri, PloS one 2013
  • “...( xac3768, xcv1954 ), adhesins ( fhaB1 , fhaB2 ), sensors ( xac0852 , xac2152, xac2155, xac3050 , xac3498 , xac4062 ), and T3Es ( avrXccA2 , xopC1, xopE1, xopF2, xopJ5, xopL, xopP, xopAJ, xopAF ). Discussion Our analyses based on coalescence and Bayesian clustering approaches...”

PA2184 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 3:158 / 169 (92.3%), covers 98.7% of PF05974, 178.4 bits

• MoaB1 Homologs Contribute to Biofilm Formation and Motility by Pseudomonas aeruginosa and Escherichia coli
  Kaleta, Journal of bacteriology 2023
  • “...mutant to wild-type levels. Moreover, MoaB1 was found to interact with other conserved biofilm-associated proteins, PA2184 and PA2146, as well as the sensor-kinase SagS. However, despite the interaction, MoaB1 failed to restore SagS-dependent expression of brlR encoding the transcriptional regulator BrlR, and inactivation of moaB1 or...”
• A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
  Kaleta, NPJ biofilms and microbiomes 2022
  • “...n.d. PA2313::IS WT-like Susceptible WT-like PA2313 1.7541094 n.d. PA2184::IS WT-like ( hyper ) Susceptible Susceptible PA2184 3.5862951 n.d. PA3915::IS Reduced WT-like Susceptible PA3915 16.111408 n.d. PA0048::IS Reduced WT-like WT-like PA0048 10.477965 2.84 PA4913::IS Reduced WT-like WT-like PA4913 3.1685878 3.83 PA5033::IS Reduced WT-like WT-like PA5033 5.2524326 n.d....”
  • “...PA0048, PA0602, PA0918, PA2114, PA2146, PA3236, PA3915, PA4909, PA4913, PA5033, and PA5421, while inactivation of PA2184 coincided with hyperbiofilm formation. A summary of the biofilm architecture formed by the mutant strains analyzed in this study is given in Table 1 . It is of interest to...”
• Analysis of the Pseudomonas aeruginosa regulon controlled by the sensor kinase KinB and sigma factor RpoN
  Damron, Journal of bacteriology 2012
  • “...PA2175 PA2176 PA2178 PA2179 PA2180 PA2181 PA2182 PA2183 PA2184 PA2185 PA2186 PA2187 PA2188 PA2190 PA2192 Gene RpoN-Dependent KinB Regulon of P. aeruginosa TABLE...”
  • “...NS, nonsignificant. to the transcriptome analyses, PA2169, PA2171, PA2184, and PA2190 were upregulated in the kinB mutant (Table 4) and repressed in the PAO1...”
• A eukaryotic-type signalling system of Pseudomonas aeruginosa contributes to oxidative stress resistance, intracellular survival and virulence
  Goldová, BMC genomics 2011
  • “...3.05 0.032 HP 8.3 4.2 6.6 4.2 PA2181 2.99 0.001 HP 5.3 2.6 3.7 2.8 PA2184 5.62 0.007 CHP 7.6 4.9 5.1 5.0 PA2187 3.01 0.038 HP 7.2 3.4 5.6 3.9 PA2188 2.14 0.032 Pr. alcohol dehydrogenase (Zn-dependent) (Putative enzymes) 4.2 2.8 3.1 2.8 PA2192 2.72...”
• Effects of antibiotics on quorum sensing in Pseudomonas aeruginosa
  Skindersoe, Antimicrobial agents and chemotherapy 2008
  • “...PA2163 PA2165 PA2166 PA2167 PA2170 PA2171 PA2176 PA2178 PA2184 PA2190 PA2193 PA2194 PA2195 PA2300 PA2302 PA2069 PA2137 PA2139 PA2141 PA2142 PA2143 PA2144 PA2146...”
• Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
  Waite, BMC genomics 2006
  • “...GeneChip microarrays (Affymetrix), genes from four different clusters (PA0020, cluster 8; fliE , cluster 6; PA2184, cluster 1; PA5555, cluster 4) representing different transcriptional profiles were examined by qRT-PCR. This was performed on RNA samples taken from 4 conditions (LP planktonic culture, SP planktonic culture, 8...”
  • “...(qRT-PCR) transcription profiles . A) PA0020 (array cluster 8), B) fliE (array cluster 6), C) PA2184 (array cluster 1), D) PA5555 (array cluster 4). X-axis labels (expression conditions) LP, LP planktonic culture; SP, SP planktonic culture; 8, 8 hr biofilm; 48, 48 hr biofilm. Microarray results...”
• Transcriptome analysis of Pseudomonas aeruginosa growth: comparison of gene expression in planktonic cultures and developing and mature biofilms
  Waite, Journal of bacteriology 2005
  • “...reverse transcriptase PCR of four genes (fliE, PA0020, PA2184, and PA5555) was used to provide independent verification of the microarray results (data not...”
  • “...PA2136 PA2140 PA2149 PA2155 PA2168 PA2179 PA2181 PA2184 PA2186 PA2188 PA2718 PA3460 PA3461 PA3540 PA4570 PA4870 PA4877 PA5460 Hypothetical protein Hypothetical...”
• Screening for quorum-sensing inhibitors (QSI) by use of a novel genetic system, the QSI selector
  Rasmussen, Journal of bacteriology 2005
  • “...PA2168 PA2169 PA2170 PA2171 PA2172 PA2174 PA2175 PA2176 PA2184 PA2187 PA2190 PA2191 PA2198 PA2225 PA2226 PA2244 PA2245 PA2250 PA2251 PA2272 PA2277 PA2278 PA2296...”

7tmvA / A0A0H3GMY9 Crystal structure of a putative structural protein from klebsiella pneumoniae
Aligns to 3:159 / 159 (98.7%), covers 97.5% of PF05974, 177.1 bits

• Ligand: zinc ion (7tmvA)

YciF / b1258 DUF892 domain-containing protein YciF from Escherichia coli K-12 substr. MG1655 (see 9 papers)
YCIF_ECOLI / P21362 Protein YciF from Escherichia coli (strain K12) (see paper)
b1258 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
NP_415774 DUF892 domain-containing protein YciF from Escherichia coli str. K-12 substr. MG1655
Aligns to 5:163 / 166 (95.8%), covers 99.4% of PF05974, 176.7 bits

• subunit: Homodimer.
• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...body P-ring formation protein FlgA 225.3 6.0 b1886 tar Methyl-accepting chemotaxis protein Tar 1507.2 6.0 b1258 yciF DUF892 domain-containing protein YciF 27.2 6.0 b1566 flxA Qin prophage protein FlxA 402.2 6.0 b1887 cheW Chemotaxis protein CheW 345.4 6.0 b2378 lpxP Palmitoleoyl acyltransferase 422.4 5.9 b1073 flgB...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
  González, Journal of bacteriology 2006
  • “...ydcV b3717 b1511 b2252 b3143 b4217 b1160 b1257 b3690 b0513 b1258 b0329 b4068 b1443 yncG spf yjcO ymgB ymgC yeaQ amyA gatC b1454 b3864 b4078 b1166 b1167 b1795...”
• Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity
  Weber, Journal of bacteriology 2005
  • “...b0643 b0707 b0753 b0767 b0865 b1003 b1050 b1188 b1164 b1258 b1259 b1341 b1547 b1614 b1783 b1784 b1847 b1999 b2080 b2086 b2602 b2660 b2672 b2665 Putative...”
• Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis
  Tani, Proceedings of the National Academy of Sciences of the United States of America 2002
  • “...b1739 b1896 b1897 b3506 b1646 b1519 b1197 b3519 b1004 b0329 b1188 b1258 3.2 4.4 10.4 7.2 4.9 3.1 3.6 6.7 2.2 15.7 4.9 13.0 2.4 Prior association with Lrp (6...”
• Escherichia coli stress protein YciF: expression, crystallization and preliminary crystallographic analysis.
  Liu, Acta crystallographica. Section D, Biological crystallography 2004 (PubMed)
  • GeneRIF: expression, crystallization and preliminary crystallographic analysis of Escherichia coli stress protein YciF
• Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant.
  Yoshida, Molecular & general genetics : MGG 1993 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...P0A915 Outer membrane protein W 6.03/22,927.83 P21362 P0AB55 P0AFR4 P76034 5.47/18,597.16 5.19/10,602.04 5.97/23,211.76 5.99/27,602.61 YdaA YdbC YdbH Q6SJ49...”
• Identification of RpoS (sigma(S))-regulated genes in Salmonella enterica serovar typhimurium
  Ibanez-Ruiz, Journal of bacteriology 2000
  • “...P39169 (YgaU), P31677 (OtsA), P77391 (YeaG), P21179 (KatE), P21362 (YciF), and P29013 (YcgB). AF213176, and otsA has been previously shown to be regulated by...”

Z2554 putative structural proteins from Escherichia coli O157:H7 EDL933
ECs1830 putative structural proteins from Escherichia coli O157:H7 str. Sakai
Aligns to 5:163 / 166 (95.8%), covers 99.4% of PF05974, 176.7 bits

• Rapid detection of porins by matrix-assisted laser desorption/ionization-time of flight mass spectrometry
  Hu, Frontiers in microbiology 2015
  • “...study KP1 Z2110 TEM-1, SHV-11, CTX-M-14, DHA-1 4 2 32 Cai et al. (2012) KP2 Z2554 TEM-1, SHV-11, CTX-M-14 0.5 8 16 Cai et al. (2012) KP3 Z4 IMP-4, TEM-1, SHV-1 32 32 256 Cai et al. (2012) KP4 Z5 IMP-4, TEM-1, SHV-12 1 1 2...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs1760 ECs1763 ECs1771 ECs1775 ECs1823 ECs1824 ECs1829 ECs1830 ECs1831 ECs1845 ECs2000 ECs2019 ECs2020 ECs2085 ECs2144 Exponential phase/ stationary phasec...”

EC042_RS07285 ferritin-like domain-containing protein from Escherichia coli 042
Aligns to 5:163 / 166 (95.8%), covers 99.4% of PF05974, 176.5 bits

• Overexpression of the third H-NS paralogue H-NS2 compensates fitness loss in hns mutants of the enteroaggregative Escherichia coli strain 042
  Prieto, Scientific reports 2020
  • “...6.6 EC042_RS10355 (GGDEF domain-containing protein) 249.9 7.5 EC042_RS20290 (glutamate decarboxylase alpha subunit GadA) 247.8 37.6 EC042_RS07285 (ferritin-like domain-containing protein) 245.6 8.0 EC042_RS22730 (hypothetical protein) 243.5 3.4 EC042_RS13790 (fimbrial protein) 235.5 4.2 EC042_RS08620 (acid stress response transcriptional regulator YdeO) 226.4 7.1 EC042_RS12365 (DUF2314 domain-containing protein) 223.0 6.4...”

SMb20091 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
F7XJ33 Uncharacterized protein from Sinorhizobium meliloti (strain SM11)
Aligns to 3:158 / 168 (92.9%), covers 99.4% of PF05974, 176.2 bits

• Most Sinorhizobium meliloti Extracytoplasmic Function Sigma Factors Control Accessory Functions
  Lang, mSphere 2018
  • “...S. meliloti ( 21 ), its overexpression revealed only a single putative target: expression of SMb20091, encoding a conserved hypothetical protein, increased 1.7-fold ( Fig.2 ; Data Set S1 ). While RpoE2 also activates expression of SMb20091, we believe this is an indirect effect because SMb20091...”
• Proteomic alterations explain phenotypic changes in Sinorhizobium meliloti lacking the RNA chaperone Hfq
  Barra-Bily, Journal of bacteriology 2010
  • “...12, 2017 by University of California, Berkeley SMb20091 SMb20428 SMb21176 SMb21181 Reference(s) identifying protein(s) VOL. 192, 2010 PHENOTYPIC ALTERATIONS IN...”
• Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution.
  Liu, Scientific reports 2016
  • “...phylogeny 43 ( Fig. 6a ). Three predicted, uncharacterized proteins in the DUF892 family (A0A072C8A3, F7XJ33 and Q1QGY5) were cloned and over-expressed in wildtype E. coli containing the fluorescent iron sensor. The converted intracellular iron levels based on fluorescence measurements were markedly decreased compared to the...”
  • “...over-expression in E. coli of three predicted proteins in the DUF893 family: A0A072C8A3 (lane 3), F7XJ33 (lane 4), Q1QGY5 (lane 5). Lane 1 is no-expression control. Lane 2 is over-expression of ftnA. The over-expressed proteins have similar theoretical molecular weights with bands running close to 15kD...”

ECs1829 hypothetical protein from Escherichia coli O157:H7 str. Sakai
BHW77_15525 ferritin-like domain-containing protein from Escherichia coli
Aligns to 2:157 / 168 (92.9%), covers 97.5% of PF05974, 173.2 bits

• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs1691 ECs1760 ECs1763 ECs1771 ECs1775 ECs1823 ECs1824 ECs1829 ECs1830 ECs1831 ECs1845 ECs2000 ECs2019 ECs2020 ECs2085 ECs2144 Exponential phase/ stationary...”
• Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7
  Sharma, BMC genomics 2019
  • “...BP-4795 60 29 2,800,1432,860,221 BHW77_14595 and BHW77_14980 50.25 NC_004813 13/Enterobacteria phage BP-4795 57.4 32 2,967,2683,024,670 BHW77_15525 and BHW77_15920 50.94 NC_004813 14/Enterobacteria phage P88 24.8 18 3,361,8913,386,762 BHW77_17640 and BHW77_17830 50.31 NC_026014 15/ Escherichia virus Lambda 30.1 14 3,440,4753,470,640 BHW77_18140 and BHW77_18340 54.39 NC_001416 16/ Shigella phage...”

EC042_RS07280 ferritin-like domain-containing protein from Escherichia coli 042
Aligns to 2:157 / 168 (92.9%), covers 97.5% of PF05974, 173.0 bits

• Overexpression of the third H-NS paralogue H-NS2 compensates fitness loss in hns mutants of the enteroaggregative Escherichia coli strain 042
  Prieto, Scientific reports 2020
  • “...(locus tag) Fold change hns 25C hns 37C (A) EC042_RS07290 (general stress protein) 1137.5 9.3 EC042_RS07280 (ferritin-like domain-containing protein) 736.5 8.8 EC042_RS00760 (fimbrial protein) 718.8 4.3 EC042_RS12270 (colanic acid biosynthesis acetyltransfer WcaF) 581.7 9.8 EC042_RS12260 (GDP-L-fucose synthase WcaG) 505.7 5.4 EC042_RS24025 (cadaverine/lysine antiporter CadB) 492.4 7.0...”

XCC2020 conserved hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913
Aligns to 3:158 / 169 (92.3%), covers 98.7% of PF05974, 173.0 bits

• Identification of 17 HrpX-regulated proteins including two novel type III effectors, XOC_3956 and XOC_1550, in Xanthomonas oryzae pv. oryzicola
  Xue, PloS one 2014
  • “...XCC4117 (86%) Xrp8 hypothetical protein XOC_2462 (100%) N a N N XAC2155 (91%) XCV2099 (91%) XCC2020 (86%) Xrp9 hypothetical protein XOC_1951 (100%) PXO_00529 (98%) XOO2357 (99%) XOO2488 (96%) XAC2517 (96%) XCV2699 (92%) XCC2382 (84%) Xrp10 hypothetical protein XOC_0560 100%) PXO_04113 (90%) XOO3892 (91%) XOO4113 (90%) XAC3866...”

ECs1653 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Z1922 unknown protein encoded by prophage CP-933X from Escherichia coli O157:H7 EDL933
Aligns to 2:157 / 168 (92.9%), covers 96.9% of PF05974, 172.1 bits

• Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts
  Crozier, Frontiers in microbiology 2016
  • “...x x No highly similar BLAST hits outside Escherichia coli (n/a) 2.87 NS NS NS ECs1653 x Citrobacter freundii CFNIH1 (95) -15.29 9.20 NS -13.23 ECs1654 x Citrobacter freundii CFNIH1 (94) -32.08 8.79 NS -71.95 ECs1655 Citrobacter freundii CFNIH1 (94) -18.13 8.85 NS -8.21 ECs2304 Shigella...”
• Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
  Sharma, BMC microbiology 2017
  • “...protein for prophage CP-933H +1.43 0.03 Z1460 Hypothetical protein encoded by bacteriophage Bp-933W 4.12 0.01 Z1922 Hypothetical protein encoded by bacteriophage CP-933X 2.23 0.03 Z1923 Hypothetical protein encoded by bacteriophage CP-933X 2.38 0.04 intO Z2036 Integrase for bacteriophage CP-933O 1.26 0.01 coxT Z2970 Regulator for prophage...”
• Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933
  Dong, BMC genomics 2009
  • “...48 Putative enzyme Z1764 9.0 0.2 7.3 0.2 3 O-Island 50 Putative enzyme (prophage CP-933N) Z1922 9.9 0.8 4.8 0.2 35 O-Island 52 Unknown (prophage CP-933X) Z1923 8.9 1.0 2.9 0.1 64 O-Island 52 Unknown (prophage CP-933X) Z1924 11.1 0.9 4.0 0.2 137 O-Island 52 Unknown...”

bll3758 bll3758 from Bradyrhizobium japonicum USDA 110
Aligns to 256:414 / 431 (36.9%), covers 96.2% of PF05974, 171.4 bits

• Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae
  Chuanboon, PeerJ 2019
  • “...to associate with other protein functions such as the manganese catalase domain in the protein bll3758 from Bradyrhizobium japonicum ( Hindupur et al., 2006 ). Using the STRING software, the YciF protein has a direct interconnection with the OsmC (encoding peroxiredoxin) ( Fig. 11 ). In...”
• The crystal structure of the E. coli stress protein YciF
  Hindupur, Protein science : a publication of the Protein Society 2006
  • “...as the manganese catalase domain in the protein bll3758 from Bradyrhizobium japonicum, suggesting a functional role in protecting the cell against oxidative...”
• KatG is the primary detoxifier of hydrogen peroxide produced by aerobic metabolism in Bradyrhizobium japonicum
  Panek, Journal of bacteriology 2004
  • “...but they are not KatE homologs. Furthermore, ORF bll3758 is homologous to a nonheme catalase characterized for Salmonella serovar Typhimurium (27). We focused...”

YciE / b1257 DUF892 domain-containing protein YciE from Escherichia coli K-12 substr. MG1655 (see 5 papers)
yciE / GB|AAC74339.1 protein yciE from Escherichia coli K12 (see paper)
NP_415773 DUF892 domain-containing protein YciE from Escherichia coli str. K-12 substr. MG1655
b1257 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
BWG_1086 hypothetical protein from Escherichia coli BW2952
W8T248 DUF892 family protein from Escherichia coli
Aligns to 2:157 / 168 (92.9%), covers 97.5% of PF05974, 171.4 bits

• Expression, crystallization and preliminary crystallographic analysis of YciE, a stress protein from Escherichia coli.
  Liu, Acta crystallographica. Section D, Biological crystallography 2004 (PubMed)
  • GeneRIF: Expression, crystallization and preliminary crystallographic analysis of YciE
• Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant.
  Yoshida, Molecular & general genetics : MGG 1993 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains
  McGuire, BMC genomics 2023
  • “...putative fimbrial-like adhesin protein FS 140/356 narX b1222 sensory histidine kinase NarX FS 586/598 yciE b1257 DUF892 domain-containing protein YciE T 139/168 recE * b1350 Rac prophage; exonuclease VIII, ds DNA exonuclease, 5 3 specific FS 496/866 ydaU * b1359 Rac prophage; DUF1376 domain-containing protein YdaU...”
• Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium
  Cortés-Tolalpa, Microbial cell factories 2014
  • “...Other metabolic process 18.7104 narZ b1468 Nitrate reductase Z, subunit Other metabolic process 13.4094 yciE b1257 Conserved protein Other metabolic process 18.9020 ydiS b1699 Putative flavoprotein Other metabolic process 20.0646 ygdI b2809 Putative lipoprotein Out of OGs 15.8477 slp b3506 Starvation lipoprotein Out of OGs 16.3895...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
  González, Journal of bacteriology 2006
  • “...yciF yahO yjcH ydcV b3717 b1511 b2252 b3143 b4217 b1160 b1257 b3690 b0513 b1258 b0329 b4068 b1443 yncG spf yjcO ymgB ymgC yeaQ amyA gatC b1454 b3864 b4078 b1166...”
• YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
  Herzberg, Journal of bacteriology 2006
  • “...12.1 9.8 ORFs with unknown function hdeB b3509 9.2 b3511 b0443 b1257 b1166 b1167 b1957 9.8 5.3 4 4.3 4.3 4 nrdH thrL hdeD ybaW yciE ymgB ymgC yodC a ribosomal...”
• 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
  • “...b1111 b1112 b1128 b1145 b1168 b1178 b1195 b1205 b1256 b1257 b1273 b1285 b1321 b1333 b1376 b1378 b1414 b1446 b1454 b1586 b1598 b1667 b1678 b1725 b1778 b1783...”
• The Lack of the Essential LptC Protein in the Trans-Envelope Lipopolysaccharide Transport Machine Is Circumvented by Suppressor Mutations in LptF, an Inner Membrane Component of the Escherichia coli Transporter
  Benedet, PloS one 2016
  • “...C frameshift 156157 5253 - - Predicted divalent heavy-metal cations transporter A, B, C, D BWG_1086 yciE TA missense 388 130 AtcTtc IF Conserved protein A, B, C, D BWG_3107 insD C frameshift 346347 116 - - IS2 transposase C BWG_3693 orf CT missense 103 35...”
• Proteomics-Based Mechanistic Investigation of Escherichia coli Inactivation by Pulsed Electric Field
  Liu, Frontiers in microbiology 2019
  • “...GN=cysI 30.5 6 1.8737 0.0141 W1WPC4 Cell division protein ZapB, GN=zapB 88.6 7 1.8712 0.0026 W8T248 Protein YciE, GN=yciE 51.8 6 1.8429 0.0174 W1HGY9 6,7-dimethyl-8-ribityllumazine synthase, GN=ribH 87.2 8 1.8411 0.0024 A0A2S7HHN4 Uncharacterized protein (Fragment), GN=C5P43_35025 34.2 3 1.8367 0.0432 M9GGR7 Protein rof, GN=rof 63.3 3...”

XC_2164 hypothetical protein from Xanthomonas campestris pv. campestris str. 8004
Aligns to 3:158 / 169 (92.3%), covers 98.7% of PF05974, 171.3 bits

• Proteolysis of histidine kinase VgrS inhibits its autophosphorylation and promotes osmostress resistance in Xanthomonas campestris
  Deng, Nature communications 2018
  • “...six genes from the ChIP-seq data, XC_0690 (encoding a sugar kinase), XC_0943 (conserved hypothetical protein), XC_2164 (YciE orthologue of E. coli that is involved in osmotic stress responses) 28 , XC_3300 (outer-membrane protein) XC_3301 (oxidoreductase), and XC_3576 (outer-membrane protein), for further functional investigation. As shown in...”
  • “...inactivation of XC_0690 and XC_3576 did not have any recognizable impacts, suggesting that XC_0943 , XC_2164 , XC_3300 and XC_3301 are involved in the osmostress response. The EMSA revealed that VgrR physically bound to the promoter regions of these four genes (Fig. 8 b, c, Supplementary...”
• Co-regulation of Iron Metabolism and Virulence Associated Functions by Iron and XibR, a Novel Iron Binding Transcription Factor, in the Plant Pathogen Xanthomonas
  Pandey, PLoS pathogens 2016
  • “...Spectrometry (ICP-OES). (G and H) Relative quantification of the expression of Xanthomonas putative ferritin-like protein (XC_2164) and putative ferritin related protein (XC_2190) of Xcc grown under PS, PS + 100 M DP, and PS + 100 M DP + 100 M FeSO 4 by real-time qRT-PCR....”
  • “...Fig 4F ). Expression analysis by real-time qRT-PCR indicated that iron storage-related putative ferritin genes XC_2164 , XC_2190 and XC_3752 were down regulated in the xibR mutant compared to the in wild-type Xcc 8004 and xibR /pSSP30 under low-iron condition ( Fig 4G and 4H ;...”

UTI89_C1527 putative structural proteins from Escherichia coli UTI89
Aligns to 5:163 / 166 (95.8%), covers 98.7% of PF05974, 170.7 bits

• Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections
  García, Microbial genomics 2021
  • “...adhesin YehA Cell adhesion (N,U) 10.89 UTI89_C2825 guaA GMP synthase (glutamine-hydrolyzing) Purine metabolism (F) 10.88 UTI89_C1527 yciF Putative structural protein DNA damage (S) 10.74 UTI89_C2232 UTI89_C2232 Hypothetical protein (NI) 10.73 UTI89_C2309 rfbC dTDP-4-dehydrorhamnose 3,5-epimerase LPS biosynthesis (M) 10.65 UTI89_C3163 syd Protein Syd Regulation protein assembly (S)...”

Q1QGY5 Uncharacterized protein from Nitrobacter hamburgensis (strain DSM 10229 / NCIMB 13809 / X14)
Aligns to 3:158 / 167 (93.4%), covers 98.7% of PF05974, 170.7 bits

• Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution.
  Liu, Scientific reports 2016
  • “...( Fig. 6a ). Three predicted, uncharacterized proteins in the DUF892 family (A0A072C8A3, F7XJ33 and Q1QGY5) were cloned and over-expressed in wildtype E. coli containing the fluorescent iron sensor. The converted intracellular iron levels based on fluorescence measurements were markedly decreased compared to the no-expression control,...”
  • “...coli of three predicted proteins in the DUF893 family: A0A072C8A3 (lane 3), F7XJ33 (lane 4), Q1QGY5 (lane 5). Lane 1 is no-expression control. Lane 2 is over-expression of ftnA. The over-expressed proteins have similar theoretical molecular weights with bands running close to 15kD mark (arrows). The...”

STM1730 putative cytoplasmic protein from Salmonella typhimurium LT2
SEN1304 hypothetical protein from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Aligns to 2:157 / 168 (92.9%), covers 98.1% of PF05974, 170.2 bits

• A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis
  Chowdhury, Journal of proteome research 2009
  • “...Additional details are provides in supplementary table 4 . Proteins Count of peptides Protein descriptions STM1730 3 putative cytoplasmic protein (yciE) STM2038 2 Propanediol utilization: polyhedral bodies (pduA) STM2039 (Bait) 10 Propanediol utilization: polyhedral bodies (pudB) STM2045 1 Propanediol utilization: polyhedral bodies (pduJ) STM2323 3 NADH...”
• Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism
  Martinez-Sanguiné, Infection and immunity 2021 (secret)

A6T7L3 Uncharacterized protein from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
Aligns to 2:157 / 168 (92.9%), covers 97.5% of PF05974, 169.8 bits

• Zinc limitation in Klebsiella pneumoniae profiled by quantitative proteomics influences transcriptional regulation and cation transporter-associated capsule production
  Sukumaran, BMC microbiology 2021
  • “...ilvY Positive regulator for ilvC A6TFL0 3.945 yibQ Uncharacterized protein A6T709 4.210 KPN78578_09190 UPF0434 protein A6T7L3 4.406 yciE Uncharacterized protein A6TBM1 4.507 yohC Putative transport protein A6THH0 5.221 treR Trehalose repressor A6T810 5.363 pspB Phage shock protein B A6TAN3 5.442 chaB Cation transport regulator A6T811 5.691...”

UTI89_C1526 hypothetical protein from Escherichia coli UTI89
Aligns to 2:157 / 168 (92.9%), covers 97.5% of PF05974, 169.7 bits

• Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections
  García, Microbial genomics 2021
  • “...periplasmic chaperone YehC Cell wall organization/protein folding (N,U) 9.90 UTI89_C5118 UTI89_C5118 Hypothetical protein (NI) 9.88 UTI89_C1526 yciE DUF892 domain-containing protein (S) 9.88 UTI89_C3488 hldE Bifunctional protein HldE Carbohydrate metabolism (F) 9.82 UTI89_C4745 efp Elongation factor P Translational elongation (J) 9.78 UTI89_C4031 UTI89_C4031 Hypothetical protein (NI) 9.76...”

BPSS2221 conserved hypothetical protein from Burkholderia pseudomallei K96243
Aligns to 3:158 / 169 (92.3%), covers 98.7% of PF05974, 169.2 bits

• Global transcriptional profiling of Burkholderia pseudomallei under salt stress reveals differential effects on the Bsa type III secretion system
  Pumirat, BMC microbiology 2010
  • “...dehydrogenase domain protein BPSS1272 1.0 4.4* 0.035 Hypothetical protein BPSS2215 -1.2 7.3* 0.038 Hypothetical protein BPSS2221 1.0 3.0* 0.037 Response regulator BPSS2231 -1.4 6.4* 0.038 Hypothetical protein BPSS2232 1.1 26.6* 0.037 Hypothetical protein BPSS2240 -1.8 6.8* 0.038 Short chain dehydrogenase/oxidoreductase BPSS2242 1.0 10.0* 0.035 Glycosyltransferase family...”

Avin_11100 hypothetical protein from Azotobacter vinelandii AvOP
Aligns to 3:158 / 169 (92.3%), covers 99.4% of PF05974, 164.4 bits

• The Azotobacter vinelandii AlgU regulon during vegetative growth and encysting conditions: A proteomic approach
  Chowdhury-Paul, PloS one 2023
  • “...Encysting conditions Hemerythrin HHE cation binding protein Avin_00300 0.69 0.09 107 18 Conserved hypothetical protein Avin_11100 0.076 0.001 114 23 Conserved hypothetical protein Avin_11110 0.23 0.02 25 2.3 Acetoacetyl-CoA thiolase Avin_16380 1.194 0.22 5.7 0.77 Malto-oligosyltrehalose trehalohydrolase treZ Avin_24900 0.91 0.16 13 3.0 Encystment and alginate...”
  • “...Avin_10970 Motif GAACTAtttcggagaaagtatt.TCttA 0.9 17 LEA-1 protein lea-1 0.2 Avin_11010 18 Conserved hypothetical protein 0 Avin_11100 Motif GAACTTtcaaagatcgggcggatTCtaC 0.9 19 Conserved hypothetical protein 0.1 Avin_11110 Motif GAACTCtatccggccatgcaag.TCgtA 0.9 20 Leucyl aminopeptidase pepA 0 Avin_11650 21 MraZ-family protein mraZ 0.3 Avin_13160 22 DNA topoisomerase I topA 0...”

all0615 hypothetical protein from Nostoc sp. PCC 7120
Aligns to 15:173 / 183 (86.9%), covers 98.1% of PF05974, 163.8 bits

• Cell surface-associated proteins in the filamentous cyanobacterium Anabaena sp. strain PCC 7120
  Yoshimura, Microbes and environments 2012
  • “...positions between Met-23 and Thr-24 or between Thr-24 and Asn-25. Asr1134-, Asr4653-, Asr4319-, Asr3935-, Alr1718-, All0615-, All4201-, All4377- and All4782-derived proteins without signal peptides could be secreted by nonspecific and/or currently unknown translocation pathways ( 1 ). Earlier studies have shown that both Sec and Tat...”
  • “...resistance to acid and salt stresses ( 42 , 45 ). The protein sequence of All0615 was similar to YciF. ORF alr0114 encodes a homologue of a plant chloroplast protein Tic22 that belongs to Tic complex, a translocator of the inner membrane ( Table 3 )....”

XC_3752 hypothetical protein from Xanthomonas campestris pv. campestris str. 8004
Aligns to 5:160 / 171 (91.2%), covers 98.1% of PF05974, 157.8 bits

• Co-regulation of Iron Metabolism and Virulence Associated Functions by Iron and XibR, a Novel Iron Binding Transcription Factor, in the Plant Pathogen Xanthomonas
  Pandey, PLoS pathogens 2016
  • “...analysis by real-time qRT-PCR indicated that iron storage-related putative ferritin genes XC_2164 , XC_2190 and XC_3752 were down regulated in the xibR mutant compared to the in wild-type Xcc 8004 and xibR /pSSP30 under low-iron condition ( Fig 4G and 4H ; S9H Fig ). Growth...”
  • “...triple deletion mutant strain with the deletion of entire cluster of bacterioferritin-related protein encoding genes XC_3752 , XC_3753 and XC_3754 ); 2. fhuE XC_0925 , double deletion mutant in the receptors for non-vibrioferrin mediated ferric iron uptake encoding genes ( XC_0924 and XC_0925 ); and 3....”

XCC3681 conserved hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913
Aligns to 5:160 / 171 (91.2%), covers 98.1% of PF05974, 157.8 bits

• Heterologous expression of mycobacterial Esx complexes in Escherichia coli for structural studies is facilitated by the use of maltose binding protein fusions
  Arbing, PloS one 2013
  • “...ferritin/ferritin-like superfamily; dodecamer 2FJC-N 10.6 2.6 121 (150) 11 5 Xanthomonas campestris ; hypothetical protein XCC3681; domain of unknown function (DUF892)/ferritin-like superfamily; unknown 3HIU-A 10.6 3.0 131 (142) 7 Proteins similar to EsxGH ms (PDBid: 3Q4H; chains A and B, MSMEG_0620-MSMEG_0621) 1 Escherichia coli ; YciE;...”
  • “...(DUF892)/ferritin-like superfamily; dimer 3OGH-A 10.5 3.0 134 (145) 6 2 Xanthomonas campestris ; hypothetical protein XCC3681; domain of unknown function (DUF892)/ferritin-like superfamily; unknown 3HIU-B 10.2 3.0 135 (146) 7 3 Halobacterium salinarum ; DpsA, DPS-like protein; ferritin/ferritin-like superfamily; dodecamer 1TK6-B 9.7 3.4 132 (175) 8 4...”

XOC_2462 DUF892 family protein from Xanthomonas oryzae pv. oryzicola BLS256
Aligns to 1:150 / 161 (93.2%), covers 95.6% of PF05974, 148.9 bits

• Identification of 17 HrpX-regulated proteins including two novel type III effectors, XOC_3956 and XOC_1550, in Xanthomonas oryzae pv. oryzicola
  Xue, PloS one 2014
  • “...N Xrp7 YP_005630808 XOC_4583 9 2 7 6 1 S L N N Xrp8 YP_005628761 XOC_2462 9 6 3 6 1 G L 81/56 TTCGA-N 16 -TTCGA N Xrp9 YP_005628272 XOC_1951 11 3 8 8 0 L R 114/69 TTCGT-N 6 -TTCGA-N 25 -TTCGC -N33-TATGAT Xrp10...”
  • “...PXO_03860 (96%) XOO4170 (96%) XOO4427 (95%) XAC4251 (92%) XCV4357 (92%) XCC4117 (86%) Xrp8 hypothetical protein XOC_2462 (100%) N a N N XAC2155 (91%) XCV2099 (91%) XCC2020 (86%) Xrp9 hypothetical protein XOC_1951 (100%) PXO_00529 (98%) XOO2357 (99%) XOO2488 (96%) XAC2517 (96%) XCV2699 (92%) XCC2382 (84%) Xrp10 hypothetical...”

3oghB / A0A0H2V857 Crystal structure of ycie protein from e. Coli cft073, a member of ferritine-like superfamily of diiron-containing four-helix-bundle proteins
Aligns to 5:148 / 151 (95.4%), covers 97.5% of PF05974, 146.6 bits

• Ligands: magnesium ion; fe (iii) ion (3oghB)

Deide_13500 hypothetical protein from Deinococcus deserti VCD115
Aligns to 7:164 / 165 (95.8%), covers 97.5% of PF05974, 144.7 bits

• Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti
  de, PLoS genetics 2009
  • “...Deide_21340, Deide_11730, Deide_16050, Deide_16110, Deide_09460, Deide_01434, and Deide_15100) and more widely conserved proteins (Deide_3p01280, Deide_21050, Deide_13500, Deide_04930, and Deide_14540) of unknown function, suggesting an important role in D. deserti . The proteome data indicate that plasmids P1 and P3 are underused in our standard growth conditions...”

RC1_0834 hypothetical protein from Rhodospirillum centenum SW
Aligns to 3:158 / 170 (91.8%), covers 99.4% of PF05974, 139.5 bits

• Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development
  Dong, BMC genomics 2015
  • “...protein 6.4452 TGTGAAGCAGTTCACA 25 RC1_3787 gcyC + Gene in Operon hypothetical protein 6.08831 TGTGAAGCAGTTCACA 5 RC1_0834 yes + 202 Single Gene hypothetical protein 2.6779 GATAAAGTGGCGCACA 9 RC1_1394 cheL + Gene in Operon chemotactic signal-response protein CheL 2.13001 CCAGATATTGGTAACA 12 RC1_1693 yes 226 Single Gene phasin family...”

Smlt2538 hypothetical protein from Stenotrophomonas maltophilia K279a
Aligns to 7:162 / 173 (90.2%), covers 97.5% of PF05974, 138.6 bits

• Acquired resistance of Stenotrophomonas maltophilia to antimicrobials induced by herbicide paraquat dichloride
  Vanitshavit, PloS one 2024 (no snippet)

Q1Q5F8 Bacterioferritin from Kuenenia stuttgartiensis
Aligns to 72:146 / 158 (47.5%), covers 34.0% of PF05974, 25.7 bits

• Quantitative three-dimensional nondestructive imaging of whole anaerobic ammonium-oxidizing bacteria
  Peng, Journal of synchrotron radiation 2020
  • “...Furthermore, some iron storage proteins of Q1Q315 and Q1Q5F8, which have strong capacity to store iron, were also existing in anammoxosome. These abundant...”

BP0546 bacterioferritin from Bordetella pertussis Tohama I
Aligns to 70:189 / 189 (63.5%), covers 78.0% of PF05974, 25.6 bits

• Omics Analysis of Blood-Responsive Regulon in Bordetella pertussis Identifies a Novel Essential T3SS Substrate
  Drzmisek, International journal of molecular sciences 2021
  • “...receptors BfrB, BfrF and BfrI, TonB-dependent iron receptor BP0857, iron-binding proteins IRP1-3 and BP1139, bacterioferritin BP0546, heme uptake protein HurI as well as various ironsulfur cluster proteins including a putative regulatory protein BP1155 containing 4Fe-4S cluster. 2.3. Most of the Blood-Mediated Effects Are Lost in Liquid...”
• Transcriptional profiling of Bordetella pertussis reveals requirement of RNA chaperone Hfq for Type III secretion system functionality
  Bibova, RNA biology 2015
  • “...hfq mutant upon infection. In addition, genes involved in iron metabolism such as bhuU and BP0546 encoding hemin permease and bacterioferritin, respectively, also exhibited lower transcript levels in the hfq strain at day 12 ( Table S4 ). Within the set of genes observed to have...”

1u7mA Solution structure of a diiron protein model: due ferri(ii) turn mutant (see paper)
Aligns to 1:52 / 53 (98.1%), covers 31.4% of PF05974, 25.2 bits

• Ligand: zinc ion (1u7mA)

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