Family Search for PF04341 (DUF485)

PF04341 hits 27 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

AZOBR_RS02935 small component of pyruvate transporter (yjcH-like) from Azospirillum brasilense Sp245
Aligns to 9:97 / 100 (89.0%), covers 98.9% of PF04341, 125.6 bits

• mutant phenotype: Specifically important for pyruvate utilization. 54% identical to E. coli yjcH.

PFLU1813 hypothetical protein from Pseudomonas fluorescens SBW25
Aligns to 10:99 / 103 (87.4%), covers 98.9% of PF04341, 121.9 bits

• Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation
  Sepulveda, Frontiers in microbiology 2017
  • “..., Gm r This work ES06 acs pSRKgm -acs , Gm r This work ES07 pflu1813 This work ES08 actP This work ES09 pflu5625 This work ES10 0110 This work ES11 pflu1813 pflu5625 This work ES12 pflu1813 0110 This work ES13 actP pflu5625 This work ES14...”
  • “...work pK18mobSacB-acs Deletion of acs , Km r , SacB This work pK18mobSacB-pflu1813 Deletion of pflu1813 , Km r , SacB This work pK18mobSacB-actP Deletion of actP , Km r , SacB This work pK18mobSacB-pflu5625 Deletion of pflu5625 , Km r , SacB This work pK18mobSacB-pflu0110...”

PS417_08860 small component of pyruvate transporter (yjcH-like) from Pseudomonas simiae WCS417
Aligns to 10:99 / 103 (87.4%), covers 98.9% of PF04341, 121.6 bits

• mutant phenotype: Specifically important for pyruvate utilization. 59% identical to E. coli yjcH.

Cp1002B_2057 DUF485 domain-containing protein from Corynebacterium pseudotuberculosis
Aligns to 22:109 / 113 (77.9%), covers 97.8% of PF04341, 119.5 bits

• In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis
  Araújo, PeerJ 2020
  • “...Cp1002B_1949 D9Q9H4 Bax1-inhibitor protein Cp1002B_1975 D9Q9E9 Sulfolipid-1-addressing protein SfLAP Cp1002B_1992 D9Q9D3 Substrate-binding periplasmic ABC lipoprotein Cp1002B_2057 D9Q971 TcpE family protein Cp1002B_2072 D9Q956 Cell wall synthesis potein CwsA Cp1002B_2078 D9Q950 Actinobacterial holin-X protein, holin superfamily III Determination of virulence potential of target molecules Among some auxiliary tools...”

D9Q971 DUF485 domain-containing protein from Corynebacterium pseudotuberculosis (strain C231)
Aligns to 22:109 / 113 (77.9%), covers 97.8% of PF04341, 119.5 bits

• In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis
  Araújo, PeerJ 2020
  • “...D9Q9H4 Bax1-inhibitor protein Cp1002B_1975 D9Q9E9 Sulfolipid-1-addressing protein SfLAP Cp1002B_1992 D9Q9D3 Substrate-binding periplasmic ABC lipoprotein Cp1002B_2057 D9Q971 TcpE family protein Cp1002B_2072 D9Q956 Cell wall synthesis potein CwsA Cp1002B_2078 D9Q950 Actinobacterial holin-X protein, holin superfamily III Determination of virulence potential of target molecules Among some auxiliary tools used,...”

PP1742 conserved hypothetical protein from Pseudomonas putida KT2440
Aligns to 10:99 / 103 (87.4%), covers 98.9% of PF04341, 118.7 bits

• PpoR is a conserved unpaired LuxR solo of Pseudomonas putida which binds N-acyl homoserine lactones
  Subramoni, BMC microbiology 2009
  • “...PP2335 citrate synthase 12.097 3. PP1743 acetate permease 9.109 4. PP4621 homogentisate 1,2-dioxygenase 7.574 5. PP1742 hypothetical protein 7.057 6. PP4064 isovaleryl-CoA dehydrogenase 6.120 7. PP4065 3-methylcrotonyl-CoA carboxylase, beta subunit, putative 6.042 8. PP0882 dipeptide ABC transporter, periplasmic dipeptide-binding protein 5.896 9. PP4402 2-oxoisovalerate dehydrogenase, beta...”

Pf1N1B4_3672 small component of pyruvate transporter (yjcH-like) from Pseudomonas fluorescens FW300-N1B4
Aligns to 10:99 / 103 (87.4%), covers 98.9% of PF04341, 118.1 bits

• mutant phenotype: Specifically important for pyruvate utilization. 62% identical to E. coli yjcH.

Pf6N2E2_5848 small component of pyruvate transporter (yjcH-like) from Pseudomonas fluorescens FW300-N2E2
Aligns to 10:99 / 103 (87.4%), covers 98.9% of PF04341, 114.9 bits

• mutant phenotype: Important for pyruvate utilization. 58% identical to E. coli yjcH.

blr4114 blr4114 from Bradyrhizobium japonicum USDA 110
Aligns to 8:96 / 100 (89.0%), covers 98.9% of PF04341, 114.6 bits

• Growth Rate of and Gene Expression in Bradyrhizobium diazoefficiens USDA110 due to a Mutation in blr7984, a TetR Family Transcriptional Regulator Gene
  Ohkama-Ohtsu, Microbes and environments 2016
  • “...HspC2 heat shock protein 4.7 blr2767 (Fe-S)-binding protein, fixG 4.7 A blr4660 ABC transporter 4.7 blr4114 hypothetical protein 4.6 blr4115 acetate permease 4.5 blr4657 beta-glucosidase 4.5 bll6888 porin 4.4 blr7490 hypothetical protein 4.3 blr3577 dihydroxyacetone kinase subunit DhaK 4.2 B bsr2765 cbb3 oxidase subunit IV, fixQ...”
• Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1 cascade in Bradyrhizobium japonicum
  Mesa, Journal of bacteriology 2008
  • “...Hypothetical protein Hypothetical protein Hypothetical protein bll3998 blr4114 blr4174 bsr4175 blr4637 bsl4650 bll4651 blr4652 blr4955 bsl5002 56.5 62.5 46.7...”

PA3235 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 10:99 / 103 (87.4%), covers 97.8% of PF04341, 113.3 bits

• Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations
  Ruparel, Drug target insights 2023
  • “...34 PA2933 large subunit ribosomal protein L6 (rplF; 50S ribosomal protein L6) 2.96 0.0004 35 PA3235 Hypothetical protein 2.96 1.62E-10 36 PA4290 Methyl-accepting chemotaxis protein 2.96 0 37 PA0384 Hypothetical protein 2.92 0.01 38 PA3287 Hypothetical protein 2.92 5.20E-14 39 PA0848 Peroxiredoxin (alkyl hydroperoxide reductase subunit...”
  • “...208964.PA2364 1 49 PA2375 208964.PA2375 1 50 PA2666 208964.PA2666 1 51 PA2679 208964.PA2679 1 52 PA3235 208964.PA3235 1 53 PA3420 208964.PA3420 1 54 PA3441 208964.PA3441 1 55 PA3694 208964.PA3694 1 56 PA3882 208964.PA3882 1 57 PA5328 208964.PA5328 1 58 hutU 208964.PA5100 1 59 ospR 208964.PA2825 1...”
• AIDmut-Seq: a Three-Step Method for Detecting Protein-DNA Binding Specificity
  Li, Microbiology spectrum 2023
  • “...in the wild type and the erdR mutant strain under an acetate-induced growth condition. Except PA3235 , most of the tested genes exhibited increased expression when erdR was deleted ( Fig.5C ), indicating that ErdR represses the transcription of these promoters. Notably, expression of PA3235 ,...”
• Systems-Wide Dissection of Organic Acid Assimilation in Pseudomonas aeruginosa Reveals a Novel Path To Underground Metabolism
  Dolan, mBio 2022
  • “...compared with growth in MOPS-succinate. Notable proteins include those in the ORF cluster (PA3232 to PA3235, blue) containing the putative ActP transporter protein (PA3234), enzymes in the 2MCC, glyoxylate shunt and TCA cycle (brown), cytochrome oxidase components (turquoise), and enzymes involved in branched-chain amino acid catabolism...”
  • “...monocarboxylic acids have also been described ( 30 ). One cluster of ORFs (PA3232 to PA3235) was upregulated (~16 FC) during growth on propionate and encode a putative acetate permease (ActP). Indeed, PA3234 shows 80% amino acid identity to the ActP protein from Escherichia coli ,...”
• Systems-wide dissection of organic acid assimilation in Pseudomonas aeruginosa reveals a novel path to underground metabolism
  Dolan, 2022
• Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel
  Gunasekera, Applied and environmental microbiology 2017
  • “...(e.g., rubA1, rub, oprF, oprG, mexE, oprN, pvdE, PA3235, PA2779, PA3819, PA3451, PA0038, PA0276, PA3986, PA5424, PA0109, and PA2024). DNA sequence analyses of...”
  • “...corresponding Fold gene ID change Putative function category PA3235 37.04 16.14 14.03 12.84 11.22 PA3819 8.8 PA0586 PA5212 8.18 7.21 PA3451 PA1542 PA0038 PA1728...”
• Development of a Novel Method for Analyzing Pseudomonas aeruginosa Twitching Motility and Its Application to Define the AmrZ Regulon
  Xu, PloS one 2015
  • “...studies shared multiple genes, such as the DGC-encoding gene gcbA , and hypothetical genes PA0102, PA3235, etc. ( S2 Table ). However, there were significant differences between these two studies. First, growth conditions were dissimilar in these two studies. We and others have shown that pilA...”
• ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa
  Jones, PLoS pathogens 2014
  • “...11.66 3.31 hypothetical protein (no prediction) PA5138 10.23 4.20 predicted ABC-type amino acid transport/signal transduction PA3235 9.18 6.49 predicted membrane protein PA4222 9.09 7.13 ABC transporter ATP-binding protein PA4677 8.96 5.99 predicted dipeptidase fleQ 8.05 3.00 transcriptional regulator FleQ PA3234 7.63 3.88 acetate permease pchG 7.13...”
  • “...did not suggest a common mechanism ( Figure 4A ). However, with the exception of PA3235 , each of the directly AmrZ-repressed promoters observed contained an AmrZ binding site from 100 to +15 relative to the transcription start site ( Figure 4B ). This implies that...”
• Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis
  Folsom, BMC microbiology 2010
  • “...226 2020 2-keto-3-deoxy-6-phosphogluconate aldolase PA3186-3190 oprB 68 1936 glucose uptake PA3205 16 1033 hypothetical protein PA3235 101 2118 conserved hypothetical protein PA3309 33 1076 O 2 universal stress protein PA3369-3371 196 3302 hypothetical proteins PA3412 163 3772 Cu probable transcriptional regulator PA3415 225 2682 probable dihydrolipoamide...”
• More

y0509 hypothetical protein from Yersinia pestis KIM
Aligns to 10:99 / 103 (87.4%), covers 97.8% of PF04341, 113.0 bits

• Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division
  Fukuto, Infection and immunity 2010
  • “...levels of transcription of Y0052 (yopB), y0464 (fadB), y0509, y0655, y0850, y1895 (yfeC), y2316, y3120, and y3553 were determined by quantitative reverse...”
  • “...y1607 y0655 y2882 y1189 y1041 y0310 y1607 YPO1423a y3555 y0509 y0016 y0463 y0655 y1821 y2881 y2125 y3804 y2236 y0015 YPO3681 y3836 y2591 50S ribosomal protein...”

cg0952 putative integral membrane protein from Corynebacterium glutamicum ATCC 13032
Aligns to 22:109 / 113 (77.9%), covers 100.0% of PF04341, 112.6 bits

• The MarR-Type Regulator MalR Is Involved in Stress-Responsive Cell Envelope Remodeling in Corynebacterium glutamicum
  Hünnefeld, Frontiers in microbiology 2019
  • “...et al., 2005 ), and several (secreted) membrane proteins of unknown function (cg0623, cg0636, cg0879, cg0952, cg1578, cg1910, and cg3322). The most distinct downregulation was observed for the malE gene, encoding the malic enzyme which catalyzes the decarboxylation of malate to pyruvate. Pyruvate itself is a...”
• Function of L-Pipecolic Acid as Compatible Solute in Corynebacterium glutamicum as Basis for Its Production Under Hyperosmolar Conditions
  Pérez-García, Frontiers in microbiology 2019
  • “...permease subunit -1.3 -0.2 cg0935 Conserved hypothetical protein -0.4 -1.3 rpf1 RPF-protein precursor 0.9 -0.4 cg0952 Putative integral membrane protein -0.9 -0.3 betP Na + /glutamate symporter -1.2 -0.7 cg1091 Hypothetical protein -1.6 -1.0 cg1091 Hypothetical protein -1.6 -1.0 cg1109 Hypothetical protein -0.3 -1.1 cg1279 Putative...”
• The copper-deprivation stimulon of Corynebacterium glutamicum comprises proteins for biogenesis of the actinobacterial cytochrome bc₁-aa₃ supercomplex
  Morosov, The Journal of biological chemistry 2018
  • “...ppmA tagA1 cg0133 cg0759 cg0760 cg0762 cg0899 cg0924 cg0952 cg0953 cg1293 cg1836 cg2403a cg2406a cg2546 cg2557 cg2836 cg2837 cg3022 cg3195 cg3335 a prpD2 prpB2...”
• Single-Domain Peptidyl-Prolyl cis/trans Isomerase FkpA from Corynebacterium glutamicum Improves the Biomass Yield at Increased Growth Temperatures
  Kallscheuer, Applied and environmental microbiology 2015
  • “...cg0121 (0.48), cg0922 (0.47), cg1577 (0.46), cg0924 (0.45), cg0952 (0.42), cg3124 (0.34), cg2336 (0.32), cg1332 (0.28), cg2438 (0.27). are sublethal for C....”
• Identification and characterization of a bacterial transport system for the uptake of pyruvate, propionate, and acetate in Corynebacterium glutamicum
  Jolkver, Journal of bacteriology 2009
  • “...The mctC gene is preceded by and cotranscribed with cg0952, a locus encoding a small membrane protein, and the transcription of the cg0952-mctC operon is under...”
  • “...of promoter-reporter fusions. The intergenic region between cg0952 and cg0951 (i.e., the cg0952-mctC promoter region; 477 bp; fragment mctCP) and the...”
• Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
  Follmann, BMC genomics 2009
  • “...component 0 -0.14 -2.35 - -0.8 - 3.3 4.0 - 1.8 1.0 - DtxR 21 cg0952 o mctB putative monocarboxylate transporter subunit 2 -2.55 -1.32 - 0.5 - 2.4 4.7 4.1 - 2.1 -0.6 RamA, RamB 22 cg0953 o mctC monocarboxylate transporter 13 -2.44 -1.01 -...”
  • “...0 -1.09 -0.61 4.6 5.0 4.3 - - - -0.7 - - LexA, PdxR 40 cg0952 o mctB putative monocarboxylate transporter subunit 2 -2.55 -1.32 - 0.5 - 2.4 4.7 4.1 - 2.1 -0.6 41 cg0953 o mctC monocarboxylate transporter 13 -2.44 -1.01 - 3.0 -0.2...”
• A proteomic study of Corynebacterium glutamicum AAA+ protease FtsH
  Lüdke, BMC microbiology 2007
  • “...to the wild type, NADH dehydrogenase ( ndh ), a putative integral membrane protein ( cg0952 ) and the ATPase component of an ABC-type sugar transport system ( msiK ) were down-regulated by a factor of 0.5 (data not shown). Comparison of cytoplasmic protein profiles In...”

NBC2815_03739 DUF485 domain-containing protein from Xanthomonas fragariae
Aligns to 13:101 / 105 (84.8%), covers 98.9% of PF04341, 111.6 bits

• Transcriptome analysis of Xanthomonas fragariae in strawberry leaves
  Puławska, Scientific reports 2020
  • “...chemotaxis sensory transducer) and phuR_2 (coding for a hemin receptor) were the most upregulated, while NBC2815_03739 (coding for the adhesion protein XadA) and genes of proteins involved in LPS biosynthesis, WxcD, WxcE and WxcO, were the most downregulated in planta . The downregulation of LPS synthesis...”

STM4274 putative inner membrane protein from Salmonella typhimurium LT2
Aligns to 10:99 / 104 (86.5%), covers 97.8% of PF04341, 110.5 bits

• Repression of Salmonella enterica phoP expression by small molecules from physiological bile
  Antunes, Journal of bacteriology 2012
  • “...PSLT046 STM2190 STM2799 STM1292 STM0730 STM3321 STM1742 STM3033 STM4274 STM4126 ORF04918 Fold regulation cyoC cyoE dppA phoH fimI lpdA acnB 10.36 7.02 4.55 4.46...”

STY4472 putative membrane protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
t4180 putative membrane protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
Aligns to 10:99 / 104 (86.5%), covers 97.8% of PF04341, 110.5 bits

• Genetic Markers in S. Paratyphi C Reveal Primary Adaptation to Pigs
  Nair, Microorganisms 2020
  • “...1: torC , ratC , STY4541, STY2432, STY1834, STY1781; 2: slrP and fliB ; 3: STY4472, STY4044, STY1408, STY1353. Figure 3 Distribution of disrupted pathways. Annotated UpSet plot of shared and unique disrupted pathways. Number of genes disrupted in pathways given above the columns (includes multiple...”
• Genomic dissection of travel-associated extended-spectrum-beta-lactamase-producing Salmonella enterica serovar typhi isolates originating from the Philippines: a one-off occurrence or a threat to effective treatment of typhoid fever?
  Hendriksen, Journal of clinical microbiology 2015
  • “...deletion of 144 kb between sequence positions 4358279 (STY4472) and 4502238 (STY4635) was absent in isolate 11073567 relative to the CT18 reference genome (see...”
• Comparison of Salmonella enterica Serovars Typhi and Typhimurium Reveals Typhoidal Serovar-Specific Responses to Bile
  Johnson, Infection and immunity 2018
  • “...1.57 fadA t3316 3-Ketoacyl-CoA thiolase 7.66 2.88 1.57 actP t4179 Acetate permease 3.41 1.58 1.27 t4180 Hypothetical protein 3.44 1.72 1.32 acs t4181 Acetyl-CoA synthetase 3.91 2.11 1.31 acnA t1625 Aconitate hydratase 3.18 1.81 1.59 argT t0509 Lysine-arginine-ornithine-binding periplasmic protein 3.36 2.29 1.33 argD t1182 Bifunctional...”

SCO1823 integral membrane protein from Streptomyces coelicolor A3(2)
Aligns to 31:118 / 124 (71.0%), covers 98.9% of PF04341, 110.2 bits

• Transcriptomic analysis of Streptomyces coelicolor differentiation in solid sporulating cultures: first compartmentalized and second multinucleated mycelia have different and distinctive transcriptomes
  Yagüe, PloS one 2013
  • “...3 SCO5655 Hypothetical protein 4 4.4 4.3 SCO5484 Small hydrophobic membrane protein 4.7 5.2 5.6 SCO1823 Hypothetical protein 1.2 3.9 2.1 SCO0932 Hypothetical protein 1.8 3.5 2.8 SCO6795 Hypothetical protein 2.5 3.4 2.5 SCO5249 Nucleotide-binding protein 2.9 3.2 2.4 SCO6797 ATP/GTP binding protein 2.2 3 2.2...”

b4068 required for glycolate transport, with actP from Escherichia coli BW25113
YjcH / b4068 DUF485 domain-containing inner membrane protein YjcH from Escherichia coli K-12 substr. MG1655 (see 2 papers)
b4068 conserved inner membrane protein involved in acetate transport from Escherichia coli str. K-12 substr. MG1655
Aligns to 10:99 / 104 (86.5%), covers 97.8% of PF04341, 109.7 bits

• mutant phenotype: PFam PF04341.8 (DUF485). This gene is specifically important for glycolate utilization and is conserved cofit with actP.
• Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes
  Skippington, Genome biology and evolution 2012
  • “...yahO b0329 omrA 20 Variable Incongruent No dppB b3543 omrA 27 Core Incongruent No yjcH b4068 omrA 24 Variable Congruent No dppF b3540 omrA 27 Core Incongruent No fimA b4314 omrA 2 Variable N < 4 N < 4 ykgC b0304 omrA 21 Variable Incongruent No...”
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...b2658 b2672 b2809 b2856 b2857 b3099 b3170 b3184 b3260 b3512 b4068 b4126 b4127 Change in expression (fold) SdiA vs no SdiA SdiA1E11 vs SdiA 6.5 5.3 5.3 9.2 5.3...”
• A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli
  Ernst, PLoS computational biology 2008
  • “...CysB b2762, cysH 1 1 Confirmed with direct binding evidence in Salmonella typhimurium [67] PhoB b4068, yjcH 1 NagC b2677, proV 1 FhlA b1924, fliD 1 LexA b1061, dinI 1 Yes Yes Gel shift assay and site-directed mutagenesis [68] ; ChIP-chip evidence [12] OxyR b4367, fhuF...”
• Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
  González, Journal of bacteriology 2006
  • “...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 b1927 b2092...”

ECs_5050 inner membrane protein from Escherichia coli O157:H7 str. Sakai
UTI89_C4658 hypothetical protein YjcH from Escherichia coli UTI89
ECs5050 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 10:99 / 104 (86.5%), covers 97.8% of PF04341, 109.7 bits

• Antibacterial efficacy interference of the photocatalytic TiO₂ nanoparticle and the lytic bacteriophage vb_EcoS_bov25_1D on the Enterohaemorragic Escherichia coli strain Sakai
  Steinbach, Heliyon 2024
  • “...EscT protein_coding 915450 2,18352571 ECs_5082 phnI ribophosphonate triphosphate synthase complex catalytic subunit protein_coding 914254 2,18786512 ECs_5050 yjcH inner membrane protein protein_coding 914283 2,19153537 ECs_3605 cysN sulfate adenylyltransferase subunit 1 protein_coding 914673 2,19495958 ECs_3999 tdcR threonine dehydratase operon activator protein protein_coding 916156 2,21958706 ECs_4580 escU T3SS structure...”
• Plasmid parB contributes to uropathogenic Escherichia coli colonization in vivo by acting on biofilm formation and global gene regulation
  Song, Frontiers in molecular biosciences 2022 (no snippet)
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...yjbR 2.21 2 ECs5213 cybC 2.20 2 ECs5049 actP 4.17 2 ECs5222 pyrB -2.95 1 ECs5050 yjcH 3.78 2 ECs5253 O157 2.70 2 ECs5089 phnB 4.22 2 ECs5332 yjjG 3.09 2 ECs5109 yjdJ 3.07 2 a Genes with "O157" indicate that these are O157-specific ORFs. Expression...”

PP_3273 conserved hypothetical protein from Pseudomonas putida KT2440
Aligns to 10:98 / 102 (87.3%), covers 97.8% of PF04341, 108.3 bits

• Light Response of Pseudomonas putida KT2440 Mediated by Class II LitR, a Photosensor Homolog
  Sumi, Journal of bacteriology 2020 (secret)

A1S_3301 hypothetical protein from Acinetobacter baumannii ATCC 17978
DJ41_3173 DUF485 domain-containing protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Aligns to 10:98 / 110 (80.9%), covers 96.6% of PF04341, 102.7 bits

• Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells
  Rumbo-Feal, PloS one 2013
  • “...acetyl-CoA hydrolase/transferase 3.42 0.96 A1S_3297 outer membrane protein 1.17 3.80 A1S_3300 acetate permease 17.44 1.23 A1S_3301 hypothetical protein 5.77 0.52 A1S_3303 hypothetical protein 5.78 0.47 A1S_3309 acetyl-CoA synthetase 4.17 1.96 A1S_3328 pyruvate dehydrogenase subunit E1 0.50 0.92 A1S_3350 hypothetical protein 0.38 0.89 A1S_3402 arginase/agmatinase/formimionoglutamate hydrolase 3.72...”
• Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing
  Camarena, PLoS pathogens 2010
  • “...A1S_2148 3.4 0.105 Acetyl-CoA synthetase, COG0365 A1S_1577 23 0.066 flavoprotein involved in K+ transport COG2072 A1S_3301 4.1 0.107 Predicted membrane protein, COG3162 2.1 A1S_2710 2.5 0.076 Type II Citrate synthase(gltA) A1S_0179 3.1 0.121 Predicted flavodoxin, COG0655 A1S_3008 4.8 0.115 acetyl-CoA carboxylase, COG4799 A1S_0359 3.9 0.108 Predicted...”
• Role of EmaSR in Ethanol Metabolism by Acinetobacter baumannii
  Shu, International journal of molecular sciences 2022
  • “...TCA cycle. In analyzing highly differential gene clusters of the EmaSR and EmaR upregulated transcriptomes, DJ41_3173 , DJ41_3174 and the neighboring genes of EmaSR encoded genes were observed to have reduced expression levels in the SR mutant ( Figure 5 D). Another gene cluster that demonstrated...”
  • “...self-regulate transcription, which is consistent with the features of most TCS. Transcriptome data demonstrated that DJ41_3173 and DJ41_3174 in the neighboring regions of emaSR were upregulated by EmaSR ( Table S1 , Figure 1 A). DJ41 _3174 has been annotated as having solute transporter function for...”

GSU2353 conserved hypothetical protein from Geobacter sulfurreducens PCA
Aligns to 12:99 / 102 (86.3%), covers 97.8% of PF04341, 93.9 bits

• Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens
  Leang, Journal of bacteriology 2005
  • “...GSU0988 GSU0990 GSU0996 GSU1339 GSU1943 GSU1994 GSU2353 GSU2780 GSU3079 GSU3080 GSU3081 GSU3084 GSU3085 Hypothetical Hypothetical Hypothetical Hypothetical...”

PD1295 conserved hypothetical protein from Xylella fastidiosa Temecula1
Aligns to 14:102 / 106 (84.0%), covers 98.9% of PF04341, 90.2 bits

• Characterization of regulatory pathways in Xylella fastidiosa: genes and phenotypes controlled by gacA
  Shi, Applied and environmental microbiology 2009
  • “...fimbrial protein gene PD1926, and hypothetical protein gene PD1295 were positively regulated by gacA in X. fastidiosa. Several genes were negatively regulated...”
  • “...of hsf, cvaC (PD0216), fimbrial protein gene PD1926, and PD1295 in the gacA mutant and higher expression levels of gumC (Fig. 2). Detection of rRNA at similar...”
• Characterization of regulatory pathways in Xylella fastidiosa: genes and phenotypes controlled by algU
  Shi, Applied and environmental microbiology 2007
  • “...compared to the wild type, and the PD0521 and PD1295 RNAs were slightly increased in the algU::nptII mutant. Validation of microarray data. To validate the...”
  • “...algR, algH, mucD, ompW, cvaC (PD0216), PD0521, and PD1295 was validated by RT-PCR (Fig. 1). Forty-three genes were differentially expressed in the algU::nptII...”

PP_2796 conserved hypothetical protein from Pseudomonas putida KT2440
Aligns to 10:99 / 107 (84.1%), covers 97.8% of PF04341, 88.6 bits

• Identification and characterization of levulinyl-CoA synthetase from Pseudomonas citronellolis, which differs phylogenetically from LvaE of Pseudomonas putida
  Habe, AMB Express 2019
  • “...72 Unknown DFU485 domain-containing protein Pseudomonas citronellolis 100 WP_074983811 Hypothetical protein Pseudomonas putida KT2440 31 PP_2796 (LvaF) PCLA_07r0387 a 531 Levulinyl-CoA synthetase Long-chain fatty acid-CoA ligase Pseudomonas citronellolis 99 WP_074983808 Medium-chain fatty acid-CoA ligase Pseudomonas putida KT2440 39 35 PP_0763, PP_2795 (LvaE) PCLA_07r0389 a 624 Levulinate...”

PCLA_07r0386, WP_074983811 DUF485 domain-containing protein from Pseudomonas citronellolis
Aligns to 16:105 / 109 (82.6%), covers 97.8% of PF04341, 87.9 bits

• Identification and characterization of levulinyl-CoA synthetase from Pseudomonas citronellolis, which differs phylogenetically from LvaE of Pseudomonas putida
  Habe, AMB Express 2019
  • “...symporter (ActP) Pseudomonas citronellolis 99 WP_074983813 Acetate permease (ActP-II) Pseudomonas putida KT2440 64 PP_2797 (LvaG) PCLA_07r0386 a 72 Unknown DFU485 domain-containing protein Pseudomonas citronellolis 100 WP_074983811 Hypothetical protein Pseudomonas putida KT2440 31 PP_2796 (LvaF) PCLA_07r0387 a 531 Levulinyl-CoA synthetase Long-chain fatty acid-CoA ligase Pseudomonas citronellolis 99...”
  • “...LvaR from P . putida KT2440 (Table 2 ). In addition, within the cluster, ORF PCLA_07r0386 (a homologue of a DUF485 domain-containing protein homologue; 72 amino acids) encoded a product with 35 to 39% identity with a hypothetical protein that clustered with the putative membrane protein...”
  • “...putida KT2440 64 PP_2797 (LvaG) PCLA_07r0386 a 72 Unknown DFU485 domain-containing protein Pseudomonas citronellolis 100 WP_074983811 Hypothetical protein Pseudomonas putida KT2440 31 PP_2796 (LvaF) PCLA_07r0387 a 531 Levulinyl-CoA synthetase Long-chain fatty acid-CoA ligase Pseudomonas citronellolis 99 WP_074983808 Medium-chain fatty acid-CoA ligase Pseudomonas putida KT2440 39 35...”

DBX28_14830 DUF485 domain-containing protein from Pseudomonas aeruginosa
Aligns to 10:99 / 107 (84.1%), covers 97.8% of PF04341, 86.5 bits

• Integrated Comparative Genomic Analysis and Phenotypic Profiling of Pseudomonas aeruginosa Isolates From Crude Oil
  Xu, Frontiers in microbiology 2020
  • “...DBX28_14820 3158054 3158206 CDS amino acid permease 1SD DBX28_14825 3158284 3159942 CDS cation acetate symporter DBX28_14830 3159939 3160262 CDS DUF485 domain-containing protein DBX28_14835 3160319 3161968 CDS acyl-CoA synthetase DBX28_14840 3162052 3162819 CDS SDR family NAD(P)-dependent oxidoreductase + 1SD DBX28_14845 3162819 3163991 CDS acyl-CoA dehydrogenase DBX28_14850 3164042...”

BAS1517 conserved hypothetical protein from Bacillus anthracis str. Sterne
Aligns to 21:106 / 113 (76.1%), covers 97.8% of PF04341, 86.2 bits

• Identification of CodY targets in Bacillus anthracis by genome-wide in vitro binding analysis
  Château, Journal of bacteriology 2013
  • “...BAS1316 (hisG) BAS1376* BAS1377 BAS1384 BAS1512* BAS1517 BAS1573 BAS1713 BAS1713 BAS1718 BAS1763 BAS1820 BAS1825* BAS1825*/BAS1826 BAS1853* BAS1866 BAS1873...”

RHA1_ro02848 hypothetical protein from Rhodococcus sp. RHA1
Aligns to 11:94 / 97 (86.6%), covers 92.1% of PF04341, 46.2 bits

• Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria
  Gao, Microbiology and molecular biology reviews : MMBR 2012
  • “...RHA1_ro01170 RHA1_ro02067 RHA1_ro02254 RHA1_ro02467 RHA1_ro02848 RHA1_ro04046 RHA1_ro04254 RHA1_ro05348 RHA1_ro05515 RHA1_ro05936 RHA1_ro05750 YP_700261.1...”

Or search for genetic data about PF04341 in the Fitness Browser