Family Search for PF11162 (DUF2946)

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

PF11162 hits 23 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

PP_4837 conserved hypothetical protein from Pseudomonas putida KT2440
Aligns to 22:138 / 143 (81.8%), covers 99.2% of PF11162, 90.6 bits

• Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation
  Dabrowska, International journal of molecular sciences 2020
  • “...H 21.89 26.41 17.42 nd PP_2745 nd universal stress protein family 78.71 28.68 26.75 nd PP_4837 nd hypothetical protein 6.24 6.21 7.98 nd PP_5735 nd hypothetical protein 63.74 12.6 55.31 nd ijms-22-00152-t002_Table 2 Table 2 List of genes showing statistically significant upregulation detected in all analyzed...”

PaeAG1_01361 DUF2946 domain-containing protein from Pseudomonas aeruginosa
Aligns to 12:149 / 153 (90.2%), covers 100.0% of PF11162, 87.3 bits

• Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach
  Molina-Mora, Scientific reports 2020
  • “...15 1.03 1.49 Turquoise Transcription machinery RNA polymerase sigma factor RpoS COL CIP AZM Cu PaeAG1_01361 DR97_4078 19 -1.22 -1.48 Brown Uncharacterized protein PaeAG1_02250 rpmF (PA2970) 22 -1.17 -1.39 Brown Ribosome Ribosomal protein L32; Belongs to the bacterial ribosomal protein bL32 family CIP H 2 O...”

DR97_4078 DUF2946 domain-containing protein from Pseudomonas aeruginosa
Aligns to 12:149 / 153 (90.2%), covers 100.0% of PF11162, 87.0 bits

• Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach
  Molina-Mora, Scientific reports 2020
  • “...1.03 1.49 Turquoise Transcription machinery RNA polymerase sigma factor RpoS COL CIP AZM Cu PaeAG1_01361 DR97_4078 19 -1.22 -1.48 Brown Uncharacterized protein PaeAG1_02250 rpmF (PA2970) 22 -1.17 -1.39 Brown Ribosome Ribosomal protein L32; Belongs to the bacterial ribosomal protein bL32 family CIP H 2 O 2...”

PSPPH_4466 hypothetical protein from Pseudomonas syringae pv. phaseolicola 1448A
Aligns to 46:166 / 171 (70.8%), covers 100.0% of PF11162, 86.3 bits

• Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola
  Sistrom, PloS one 2015
  • “..."PSPPH_1388 (amino acid ABC transporter, periplasmic amino acid-binding protein)" 6 1 141653 141921 Deletion 269 PSPPH_4466 (hypothetical protein) 259583 259844 Deletion 262 PSPPH_0408 (hypothetical protein) 2 127 Deletion 126 PSPPH_4902 (molybdenum-pterin binding domain-containing protein) 14090 14090 SNP 1 G C PSPPH_0186 (citrate transporter) 159 1 PSPPH_0187...”

BP2923 putative lipoprotein from Bordetella pertussis Tohama I
Aligns to 17:142 / 145 (86.9%), covers 100.0% of PF11162, 84.8 bits

• Metabolic Sensing of Extracytoplasmic Copper Availability via Translational Control by a Nascent Exported Protein
  Öztürk, mBio 2023
  • “...is located in the SSN cluster 15. For example, CruR from Bordetella pertussis (encoded by bp2923 ), located in SSN cluster 1 ( Fig.6C ), was recently identified as an upstream ORF (uORF) that post-transcriptionally regulates the production of a TonB-like transporter. However, in the presence...”
• Post-transcriptional regulation by copper with a new upstream Open Reading Frame
  Roy, 2022
• Posttranscriptional Regulation by Copper with a New Upstream Open Reading Frame
  Roy, mBio 2022
  • “...of copper, the entire operon is transcribed and translated. Perception of copper by the nascent bp2923 -coded protein via its conserved CXXC motif triggers Rho-dependent transcription termination between the first and second genes by relieving translation arrest on a conserved C-terminal RAPP motif. Homologs of bp2923...”
  • “...three genes form an operon, as shown by RT-PCR on the IGR ( Fig.S1 ). bp2923 encodes a putative 145-residue-long protein of unknown function of the DUF2946 Pfam protein family, predicted to be exported. This family is characterized by two conserved sequence motifs, CXXC (where X...”
• A Mutation Upstream of the rplN-rpsD Ribosomal Operon Downregulates Bordetella pertussis Virulence Factor Production without Compromising Bacterial Survival within Human Macrophages
  Novák, mSystems 2020
  • “...3.0 NS ND NS ND BP3671 Glycosyl transferase family protein 2.9 NS ND NS ND BP2923 Lipoprotein 2.8 NS ND NS ND BP3497 Hypothetical protein 2.8 P/A NS ND BP3627 rplX 50S ribosomal protein L24 2.8 NS ND NS ND BP3440 Putative exported protein 2.8 2.6...”
• Differentially expressed genes in Bordetella pertussis strains belonging to a lineage which recently spread globally
  de, PloS one 2014
  • “...sulfate BP1112 bipA outer membrane ligand binding protein Om 3.3 * 4.4 ** 3.1 1.0 BP2923 lipoprotein Un 3.9 * 4.9 * 1.3 1.6 BP0713 membrane protein (Pseudogene) Un 3.8 * 4.1 * 1.6 1.8 BP0468 AsnC-family transcriptional regulator C 1.4 3.7 * 2.5 1.0 1.1...”

AO356_08325 predicted copper homeostasis protein from Pseudomonas fluorescens FW300-N2C3
Aligns to 7:131 / 134 (93.3%), covers 99.2% of PF11162, 77.1 bits

• mutant phenotype: PFam PF11162.4 (DUF2946). conserved cofit with TonB-dependent copper receptor (AO356_08330), and cofit with copper chaperone CopZ (AO356_08320)

KPNJ2_01377 DUF2946 domain-containing protein from Klebsiella pneumoniae 30684/NJST258_2
Aligns to 16:145 / 152 (85.5%), covers 100.0% of PF11162, 76.0 bits

• Iron Acquisition and Siderophore Release by Carbapenem-Resistant Sequence Type 258 Klebsiella pneumoniae
  Holden, mSphere 2018
  • “...59.7 2.7 13.6 40.0 6.6 20.6 50.4 10.6 31.3 66.2 30.5 58.2 45.0 1.6 5.11E05 KPNJ2_01377 Hypothetical protein 12.0 14.4 17.8 1.8 25.3 18.5 15.6 29.6 28.5 14.9 31.1 28.5 0.7 15.2 22.6 1.7 1.59E04 KPNJ2_01378 Sulfite reductase (NADPH) flavoprotein alpha-component 9.2 45.6 90.6 4.6 104.2...”

BPSS1743 putative exported protein from Burkholderia pseudomallei K96243
Aligns to 10:128 / 131 (90.8%), covers 100.0% of PF11162, 71.5 bits

• A genetic programming approach for Burkholderia pseudomallei diagnostic pattern discovery
  Yang, Bioinformatics (Oxford, England) 2009
  • “...* BPSS1544 BPSL1902 * + + BPSS0065 BPSS0663 + + BPSS1743 + + BPSS0893 + BPSL2615 BPSL1902 * BPSL2096 BPSS1525 + BPSL1661 BPSS1532 BPSS2331 * BPSL2096 BPSL3228 +...”
  • “...BPSL2615 BPSS2194 + BPSL1661 * BPSS1778 BPSS0663 + BPSL1317 BPSS0933 * BPSS1743 + + BPSS1525 + + BPSL2520 + BPSL2096 + + * = 0.8 : BPSL2615 BPSL1902 * BPSS0477...”

AO353_13585 predicted copper homeostasis protein from Pseudomonas fluorescens FW300-N2E3
Aligns to 9:131 / 133 (92.5%), covers 100.0% of PF11162, 59.1 bits

• mutant phenotype: PFam PF11162.4 (DUF2946). conserved cofit with TonB-dependent copper receptor (AO353_13570) and perhaps with copper chaperone CopZ (AO353_13580)

PA3786 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 9:127 / 129 (92.2%), covers 100.0% of PF11162, 58.9 bits

• In vitro and in vivo screening for novel essential cell-envelope proteins in Pseudomonas aeruginosa
  Fernández-Piñar, Scientific reports 2015
  • “...PAO1. Surprisingly, we obtained a deletion mutant in six genes of interest (PA0517, PA1645, PA1981, PA3786, PA4485 and PA5126; Table 2 ), including all the genes encoding proteins with unpredictable function. This evidence clearly rules out that these genes are strictly essential for P. aeruginosa growth...”
  • “...the detergent SDS ( Fig. 2 ). In contrast, the remaining genes (PA0517, PA1645, PA1981, PA3786, PA4485 and PA5126) appeared to be dispensable for P. aeruginosa growth in vitro and for cell envelope stability ( Figs 1 and 2 ). This finding is in line with...”

PA14_15110 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
Aligns to 9:127 / 129 (92.2%), covers 100.0% of PF11162, 57.8 bits

• In vitro and in vivo screening for novel essential cell-envelope proteins in Pseudomonas aeruginosa
  Fernández-Piñar, Scientific reports 2015
  • “...Extracellular Hypothetical protein 648 PA2614 lolA PA14_30310 Yes No Periplasm Periplasmic chaperone LolA 627 PA3786 PA14_15110 No 1 (N-terminal, inout orientation) 5 IM Hypothetical protein 390 PA4460 lptH PA14_57920 Yes No Periplasm LPS transport protein LptA 527 PA4485 PA14_58210 Yes 6 No OM 7 Conserved hypothetical...”
• Contribution of Veillonella parvula to Pseudomonas aeruginosa-mediated pathogenicity in a murine tumor model system
  Pustelny, Infection and immunity 2015
  • “...PA14_09340 PA14_56620 PA14_55580 PA14_09270 PA14_19700 PA14_15110 PA14_53300 PA14_39420 PA14_28950 PA14_62100 PA14_09210 PA14_38580 PA14_62350 PA14_09300...”

PFL_0651 conserved hypothetical protein from Pseudomonas fluorescens Pf-5
Aligns to 9:130 / 132 (92.4%), covers 100.0% of PF11162, 50.7 bits

• Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors
  Garbeva, The ISME journal 2011
  • “...SEQ_ID Gene description Possible function Pfl_0360 Pfl_0651 Urocanate hydratase Response regulator receiver domain protein (CheY) Chemotaxis sensory transducer,...”

AZOBR_RS30660 DUF2946 family protein from Azospirillum baldaniorum
Aligns to 17:134 / 137 (86.1%), covers 95.8% of PF11162, 49.8 bits

• Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions
  Koul, BMC genomics 2020
  • “...Cyclic di-GMP-II riboswitch AbSp_308 AZOBR_RS37495 scch1500.1 Chlorobium chlorochromatii CaD3 36.2 0.021 100 Regulatory element AbSp_345 AZOBR_RS30660 ssme817.1 Sinorhizobium meliloti 1021 36.2 0.019 100 cis-encoded antisense RNA AbSp_93 AZOBR_RS24525 seco498.1 Escherichia coli K12 MG1655 50.1 7.00E-07 96 Trans-encoded antisense RNA AbSp_2 AZOBR_RS36450 RF0000 -NA 63.1 1.20E-14 100...”

bll4882 bll4882 from Bradyrhizobium japonicum USDA 110
Aligns to 14:125 / 128 (87.5%), covers 98.3% of PF11162, 48.8 bits

• Copper starvation-inducible protein for cytochrome oxidase biogenesis in Bradyrhizobium japonicum
  Serventi, The Journal of biological chemistry 2012
  • “...the B. japonicum genome displayed an increased expression: bll4882 to bll4878; supplemental Table S3). For reasons that will become evident from subsequent...”
  • “...(fold-change <-2) are listed. ORF name bll4881 bll4882 bll4880 bll4879 bll4878 bll4815 blr4931 bll4814 bsr4821 bll5511 bll4816 bll2208 bll2209 bsl2212 bll2210...”

PA0433 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 21:143 / 144 (85.4%), covers 97.5% of PF11162, 42.5 bits

• The secondary metabolite hydrogen cyanide protects Pseudomonas aeruginosa against sodium hypochlorite-induced oxidative stress
  da, Frontiers in microbiology 2023
  • “...1 g/mL NaOCl PAO1 WT 9.288 0.875 7.946 0.874 PA14 WT 8.115 0.983 7.310 0.912 PA0433 PA0433 PW1792 9.110 0.503 7.682 3.079 PA14_05630 7.952 0.268 7.624 1.822 PA0434 PA0434 PW1793 9.074 0.311 6.904 4.3 PA14_05640 8.051 0.323 6.828 2.660 PA0435 PA0435 PW1795 9.452 0.502 7.005 4.078...”
• Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
  Valzano, Microbiology spectrum 2022
  • “...IS492_31815 PA5541 PA14_73070 pyrC2 Zinc-independent paralog of dihydroorotase PyrC (pyrimidine biosynthesis) + 3.1E09 1.0 IS492_02205 PA0433 PA14_05630 Hypothetical protein (unknown function, DUF2946 domain-containing protein) 1.3E03 0.7 IS492_02210 PA0434 PA14_05640 TBDR for which the siderophore has not been identified 1.5E28 1.7 IS492_02430 PA0478 PA14_06250 fiuC GNAT family...”
• Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
  Rahmani-Badi, Frontiers in microbiology 2015
  • “...PA3450 Cell cycle ftsHZY, gidA, mreB, cafA, mind Hypothetical proteins PA0089, PA0193, PA0333, PA0338, PA0429, PA0433, PA0581, PA0754, PA0841, PA0935, PA0939, PA0979, PA0982, PA1016, PA1096, PA1149, PA1167, PA1367, PA1571, PA1814, PA1925, PA2137, PA2189, PA2412, PA2464, PA2506, PA2651, PA2659, PA2689, PA2771, PA2780, PA2829, PA2842, PA2958, PA2971, PA3070,...”
• Effect of anaerobiosis and nitrate on gene expression in Pseudomonas aeruginosa
  Filiatrault, Infection and immunity 2005
  • “...phasec PA0024 PA0025 PA0049 PA0149 PA0179 PA0200 PA0430 PA0433 PA0447 PA0471 PA0472 PA0586 PA0587 PA0747 PA0792 PA0802 PA0836 PA0918 PA0930 PA0997 PA0998 PA0999...”
• Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis
  Schuster, Journal of bacteriology 2003
  • “...together. The expression patterns of a representative quorum-repressed gene, PA0433, are shown in Fig. 3. A curiousity is that these genes are expressed at low...”
  • “...the FIG. 3. Transcript abundance of the quorum-repressed gene PA0433 in wild-type P. aeruginosa (black line), in the receptor mutant (orange line), and in the...”
• Insertions of the transposon Tn1 into the Pseudomonas aeruginosa chromosome
  Krishnapillai, Genetics 1981
  • “...PA043 1 (R18) PA0431 (R18) PA0432(R18) PA043Z(R18) PAO433(R18) PA0433 (R18) PA0434(R18) PA0434(R18) PA0435 ( R l 8) PA0435 (R18) PA0435 (R18) PA0436(R18)...”
  • “...transconjugant a t 37O, but transpositions from PA0432, PA0433, PA0435, PA0436, PA0437 and PA0438 were not detectable (< 10-O). The Sa::Tnl derivatives were...”

IS492_02205 DUF2946 domain-containing protein from Pseudomonas aeruginosa
Aligns to 15:137 / 138 (89.1%), covers 97.5% of PF11162, 42.4 bits

• Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
  Valzano, Microbiology spectrum 2022
  • “...1.6 IS492_31815 PA5541 PA14_73070 pyrC2 Zinc-independent paralog of dihydroorotase PyrC (pyrimidine biosynthesis) + 3.1E09 1.0 IS492_02205 PA0433 PA14_05630 Hypothetical protein (unknown function, DUF2946 domain-containing protein) 1.3E03 0.7 IS492_02210 PA0434 PA14_05640 TBDR for which the siderophore has not been identified 1.5E28 1.7 IS492_02430 PA0478 PA14_06250 fiuC GNAT...”

PA14_05630 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
Aligns to 21:143 / 144 (85.4%), covers 97.5% of PF11162, 42.3 bits

• The secondary metabolite hydrogen cyanide protects Pseudomonas aeruginosa against sodium hypochlorite-induced oxidative stress
  da, Frontiers in microbiology 2023
  • “...7.946 0.874 PA14 WT 8.115 0.983 7.310 0.912 PA0433 PA0433 PW1792 9.110 0.503 7.682 3.079 PA14_05630 7.952 0.268 7.624 1.822 PA0434 PA0434 PW1793 9.074 0.311 6.904 4.3 PA14_05640 8.051 0.323 6.828 2.660 PA0435 PA0435 PW1795 9.452 0.502 7.005 4.078 PA14_05650 8.162 0.38 7.520 1.772 PA2299 PA2299...”
• Activity of N-Acetylcysteine Alone and in Combination with Colistin against Pseudomonas aeruginosa Biofilms and Transcriptomic Response to N-Acetylcysteine Exposure
  Valzano, Microbiology spectrum 2022
  • “...PA5541 PA14_73070 pyrC2 Zinc-independent paralog of dihydroorotase PyrC (pyrimidine biosynthesis) + 3.1E09 1.0 IS492_02205 PA0433 PA14_05630 Hypothetical protein (unknown function, DUF2946 domain-containing protein) 1.3E03 0.7 IS492_02210 PA0434 PA14_05640 TBDR for which the siderophore has not been identified 1.5E28 1.7 IS492_02430 PA0478 PA14_06250 fiuC GNAT family N...”

CC1775 hypothetical protein from Caulobacter crescentus CB15
Aligns to 14:131 / 134 (88.1%), covers 98.3% of PF11162, 40.1 bits

• Analysis of the Caulobacter crescentus Zur regulon reveals novel insights in zinc acquisition by TonB-dependent outer membrane proteins
  Mazzon, BMC genomics 2014
  • “...CC0027 PKHD-type hydroxylase (2OG-Fe(II) oxygenase superfamily) 0.31 CC0711 feoA Ferrous iron transport protein A 0.45 CC1775 Hypothetical protein (DUF2946 domain) 0.37 CC1776 Transcriptional regulator (GntR family) 0.48 CC1777 sodA Superoxide dismutase, Fe-Mn family 0.23 CC1778 TonB-dependent receptor 0.44 CC1780 ThiJ/PfpI protease family protein 0.50 CC1782 Hypothetical...”
• A caulobacter crescentus extracytoplasmic function sigma factor mediating the response to oxidative stress in stationary phase
  Alvarez-Martinez, Journal of bacteriology 2006
  • “...11, 2017 by University of California, Berkeley CC1039 CC1775 CC1777 CC1839 CC2906 CC3255 CC3257 CC3572 RTPCRb Gene product a 1843 1844 ALVAREZ-MARTINEZ ET AL....”

Achr_23750 DUF2946 domain-containing protein from Azotobacter chroococcum NCIMB 8003
Aligns to 14:124 / 124 (89.5%), covers 99.2% of PF11162, 37.7 bits

• Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)
  Robson, PloS one 2015
  • “...pAcX50f and will be discussed under that heading. A second cluster of 10 chromosomal genes (Achr_23750 to 23660) encodes a relatively small non-ribosomal peptide synthetase and several multidrug-resistance efflux pumps all of which show greatest identity to orthologs from the -proteobacterial species Pseudogulbenkia . Two of...”

PXO_RS17240 DUF2946 family protein from Xanthomonas oryzae pv. oryzae PXO99A
Aligns to 12:142 / 145 (90.3%), covers 99.2% of PF11162, 37.2 bits

• PXO_RS20535, Encoding a Novel Response Regulator, Is Required for Chemotactic Motility, Biofilm Formation, and Tolerance to Oxidative Stress in Xanthomonas oryzae pv. oryzae
  Antar, Pathogens (Basel, Switzerland) 2020
  • “...2.21 Hypothetical protein PXO_RS06905 2.22 Membrane protein PXO_RS14325 2.24 Hypothetical protein PXO_RS23085 2.28 Hypothetical protein PXO_RS17240 2.29 DUF2946 domain-containing protein PXO_RS25705 2.29 Hypothetical protein PXO_RS23540 2.29 Hypothetical protein PXO_RS23950 2.34 Hypothetical protein PXO_RS20635 2.48 Methylisocitrate lyase PXO_RS16940 2.50 DUF378 domain-containing protein PXO_RS06660 2.59 MerC domain-containing protein...”

XOO3404 hypothetical protein from Xanthomonas oryzae pv. oryzae KACC10331
Aligns to 35:165 / 168 (78.0%), covers 99.2% of PF11162, 36.0 bits

• A thiadiazole reduces the virulence of Xanthomonas oryzae pv. oryzae by inhibiting the histidine utilization pathway and quorum sensing
  Liang, Molecular plant pathology 2018 (secret)

Nwi_2630 conserved hypothetical protein from Nitrobacter winogradskyi Nb-255
Aligns to 12:139 / 141 (90.8%), covers 98.3% of PF11162, 30.1 bits

• Phylogenomics and signature proteins for the alpha proteobacteria and its main groups
  Gupta, BMC microbiology 2007
  • “...Hypothetical Nwi_2577 YP_319182 Hypothetical Nwi_1512 YP_318125 Hypothetical Nwi_2588 13 YP_319193 Hypothetical Nwi_1581 3 YP_318194 Hypothetical Nwi_2630 YP_319235 Hypothetical Nwi_1582 YP_318195 Hypothetical Nwi_2676 YP_319281 Hypothetical Nwi_1586 YP_318199 Dihydrofolate reductase Nwi_2677 3 YP_319282 Hypothetical Nwi_1649 1,3 YP_318262 Hypothetical Nwi_2769 YP_319374 Hypothetical Nwi_1674 YP_318287 Hypothetical Nwi_2789 1 YP_319394 Hypothetical...”

Pden_4445 hypothetical protein from Paracoccus denitrificans PD1222
Aligns to 23:136 / 139 (82.0%), covers 100.0% of PF11162, 24.4 bits

• Copper control of bacterial nitrous oxide emission and its impact on vitamin B12-dependent metabolism
  Sullivan, Proceedings of the National Academy of Sciences of the United States of America 2013
  • “...genes was being Fig. 5. Growth characteristics of Pden_4445- PD2304, pcuC- PD2305, and senC2- PD2306 strains in anaerobic batch culture conditions in Cu-H media...”
  • “...plays a pivotal role in anaerobic Cu-metabolism, encoded by Pden_4445, 4444 (here we term pcuC), and 4443 (here we term senC2). Pden_4445 encodes a hypothetical...”

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