Family Search for PF09836 (DUF2063)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF09836 hits 31 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
MCA3109 hypothetical protein from Methylococcus capsulatus str. Bath
Aligns to 10:96 / 252 (34.5%), covers 98.8% of PF09836, 98.1 bits
PA14_21590 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
Aligns to 5:90 / 244 (35.2%), covers 98.8% of PF09836, 96.0 bits
PA3282 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 5:90 / 244 (35.2%), covers 98.8% of PF09836, 96.0 bits
BP2926 conserved hypothetical protein from Bordetella pertussis Tohama I
Aligns to 2:94 / 251 (37.1%), covers 97.6% of PF09836, 93.3 bits
SMb20528 HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
Aligns to 17:108 / 266 (34.6%), covers 94.0% of PF09836, 90.6 bits
LF41_2295 putative DNA-binding domain-containing protein from Lysobacter dokdonensis DS-58
Aligns to 7:93 / 248 (35.1%), covers 100.0% of PF09836, 88.0 bits
- Genome sequence of Lysobacter dokdonensis DS-58(T), a gliding bacterium isolated from soil in Dokdo, Korea
Kwak, Standards in genomic sciences 2015 - “...5, 23S rRNA (guanosine-2-O-)-methyltransferase (LF41_2292); 6, permease (LF41_2293); 7, ribonuclease T (LF41_2294); 8, hypothetical protein (LF41_2295); 9, DUF692 domain containing protein (LF41_2296); 10, hypothetical protein (LF41_2297); 11, phosphate transport system regulatory protein (LF41_2298); 12, phosphate transport ATP-binding protein (LF41_2299); 13, phosphate transport system permease protein (LF41_2300);...”
PGA1_c21020 component of stress sensing system with PGA1_c21010 (DUF692) from Phaeobacter inhibens BS107
Aligns to 3:95 / 251 (37.1%), covers 97.6% of PF09836, 85.7 bits
- mutant phenotype: PFam PF09836.5 (DUF2063). Conserved cofitness and pleiotropic phenotypes
B158DRAFT_1334 component of chlorite stress sensing system with PGA1_c21010 (DUF692) from Kangiella aquimarina DSM 16071
Aligns to 12:98 / 261 (33.3%), covers 100.0% of PF09836, 84.0 bits
- mutant phenotype: PFam PF09836.5 (DUF2063). conserved specific phenotype and conserved cofitness
PA4105 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 7:93 / 251 (34.7%), covers 100.0% of PF09836, 83.1 bits
- Genome-Wide Mapping Reveals Complex Regulatory Activities of BfmR in Pseudomonas aeruginosa
Fan, Microorganisms 2021 - “...handful of BfmR targets (e.g., bfmRS operon, pa4103 - pa4104 operon, pa4107 - pa4106 - pa4105 operon, rhlR , and phdA ) have been identified so far [ 11 , 18 ]. In this study, we used high-throughput methods to identify BfmR targets. We showed at...”
- “...of the BfmR regulon and includes known target genes such as pa4103 , pa4104 , pa4105 , pa4106 , and pa4107 (Data set 2). Functional analyses indicate that those BfmR-targeted genes are involved in different biological processes including oxidative phosphorylation (e.g., cyoABCDE operon), metabolism (e.g., phhABC...”
- Within-Host Evolution of the Dutch High-Prevalent Pseudomonas aeruginosa Clone ST406 during Chronic Colonization of a Patient with Cystic Fibrosis
van, PloS one 2016 - “...superfamily, PA4104 is a hypothetical gene encoding a polypeptide with similarities to the DoxX superfamily, PA4105 and PA4106 are hypothetical genes encoding DUF 2063 and DUF 692 superfamily protein, respectively. EfhP is the gene originally named PA4107. Arrows indicate direction of transcription. Besides differences in colony...”
- A novel signal transduction pathway that modulates rhl quorum sensing and bacterial virulence in Pseudomonas aeruginosa
Cao, PLoS pathogens 2014 - “...than 10-fold. Interestingly, these 7 genes, including PA4100 , bfmR , PA4103 , PA4104 , PA4105 , PA4106 , and PA4107 , are located at or near the bfmRS ( PA4101 - PA4102 ) loci ( Figure S2A , Table S2 in Text S1 ). These...”
- “...that PA4103 and PA4104 are organized into PA4103 operon ( PA4103 - PA4104 ) while PA4105 , PA4106 and PA4107 are organized into PA4107 operon ( PA4107 - PA4106 - PA4105 ) ( www.pseudomonas.com ). Among these genes, PA4100 encodes a dehydrogenase of unknown function, and...”
- A Pseudomonas aeruginosa EF-hand protein, EfhP (PA4107), modulates stress responses and virulence at high calcium concentration
Sarkisova, PloS one 2014 - “...aeruginosa PAO1, suggests that it is operonic with two genes encoding hypothetical proteins PA4106 and PA4105. These proteins contain the DUF692 and DUF2063 domains, respectively, with PA4106 having structural similarity to sugar isomerases, and PA4105 having structural similarity to a predicted transcriptional regulator from Neisseria gonorrhoeae...”
MIM_c31290 DNA-binding domain-containing protein from Advenella mimigardefordensis DPN7
Aligns to 9:101 / 259 (35.9%), covers 96.4% of PF09836, 81.9 bits
- Proteomic analysis of organic sulfur compound utilisation in Advenella mimigardefordensis strain DPN7T
Meinert, PloS one 2017 - “...correspondig to the locus tags: MIM_c31270, putative membrane protein; MIM_c31280, putative membrane protein, DoxX family; MIM_c31290, hypothetical protein; MIM_c31300, hypothetical protein; MIM_c31310, hypothetical protein; MIM_c31320, methylisocitrate lyase; MIM_c31330, putative AcnD-accessory protein PrpF; MIM_c31340, Fe/S-dependent 2-methylisocitrate dehydratase; MIM_c31350, 2-methylcitrate synthase; MIM_c31360, transcriptional regulator, XRE family ; MIM_c31370,...”
CC3256 hypothetical protein from Caulobacter crescentus CB15
Aligns to 6:95 / 254 (35.4%), covers 98.8% of PF09836, 80.5 bits
- Extracytoplasmic function (ECF) sigma factor σF is involved in Caulobacter crescentus response to heavy metal stress
Kohler, BMC microbiology 2012 - “...genes down-regulated in sigF mutant cells relative to the parental strain (CC2748, CC2905, CC2906, CC3255, CC3256 and CC3257) (Table 1 ). Interestingly, close inspection of probes corresponding to the upstream region from CC2906 and CC3255 suggested that these regions are also down-regulated in sigF mutant cells...”
- “...4.904 NA NA NA CC3255 280 DUF692 protein of unknown function 4.783 4.697 1.123 5.820 CC3256 254 DUF2063 protein of unknown function 3.311 NA NA NA CC3257 150 2 DoxX protein of DoxX family 2.644 2.473 2.879 5.352 a according to CMR ( Comprehensive Microbial Resource...”
- Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus
Hu, Journal of bacteriology 2005 - “...is a dose response. Four genes (CC3254, CC3255, CC3256, and CC3257) consecutively located on the chromosome were commonly upregulated under cadmium, chromate,...”
Rmet_4683 DNA-binding domain-containing protein from Cupriavidus metallidurans CH34
Aligns to 7:98 / 258 (35.7%), covers 98.8% of PF09836, 80.2 bits
PP0991 conserved hypothetical protein from Pseudomonas putida KT2440
Aligns to 7:93 / 257 (33.9%), covers 100.0% of PF09836, 76.0 bits
CC2905 hypothetical protein from Caulobacter crescentus CB15
Aligns to 5:92 / 261 (33.7%), covers 98.8% of PF09836, 74.8 bits
- Extracytoplasmic function (ECF) sigma factor σF is involved in Caulobacter crescentus response to heavy metal stress
Kohler, BMC microbiology 2012 - “...found only six genes down-regulated in sigF mutant cells relative to the parental strain (CC2748, CC2905, CC2906, CC3255, CC3256 and CC3257) (Table 1 ). Interestingly, close inspection of probes corresponding to the upstream region from CC2906 and CC3255 suggested that these regions are also down-regulated in...”
- “...stress sigF Cr/WT Cr CC2748 313 Oxidored_molyb sulfite oxidase subunit YedY 2.097 4.654 2.500 2.154 CC2905 261 DUF2063 protein of unknown function 1.299 2.164 0.481 2.645 CC2906 289 DUF692 protein of unknown function 2.917 3.358 0.967 2.392 CC2907 105 1 DUF2282 predicted integral membrane protein 2.386...”
NMA0229 hypothetical protein NMA0229 from Neisseria meningitidis Z2491
Aligns to 8:91 / 248 (33.9%), covers 100.0% of PF09836, 71.8 bits
lpg2253 Hypothetical protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Aligns to 6:98 / 262 (35.5%), covers 97.6% of PF09836, 67.5 bits
NGO1945 hypothetical protein from Neisseria gonorrhoeae FA 1090
Aligns to 8:91 / 248 (33.9%), covers 100.0% of PF09836, 67.5 bits
- Full Copper Resistance in Cupriavidus metallidurans Requires the Interplay of Many Resistance Systems
Hirth, Applied and environmental microbiology 2023 - “...GigB contains a DUF2063 domain at the amino terminus, which occurs in the DNA-binding protein NGO1945 from Neisseria gonorrhoeae ( 105 ). GigT (Rmet_4682) has three or four predicted transmembrane spans and is loosely related to DoxX (COG2259), a subunit of a terminal quinol oxidase in...”
- Quantitative Proteomics of the 2016 WHO Neisseria gonorrhoeae Reference Strains Surveys Vaccine Candidates and Antimicrobial Resistance Determinants
El-Rami, Molecular & cellular proteomics : MCP 2019 - “...metabolism (NGO2056) and with unknown functions (NGO1299, NGO1945, NGO1969, NGO1970, NGO2089) were downregulated (Table VI). Finally, the cluster VII strains...”
- “...most downregulated proteins and included WHO_F_00875c, NGO1299, NGO1945, NGO1967, NGO1969, NGO1970, and NGO2089. Cluster III, IV, and V are comprised of...”
- Extracytoplasmic function (ECF) sigma factor σF is involved in Caulobacter crescentus response to heavy metal stress
Kohler, BMC microbiology 2012 - “...DUF2063 domain at their N-terminus. This domain was described to be a DNA-binding domain in NGO1945 from Neisseria gonorrhoeae [ 19 ]. NGO1945 is involved in the transcriptional regulation of msrAB , which codes for a methionine sulfoxide reductase [ 20 ]. However, in our microarray...”
- “...msrA homologs in C. crescentus (CC0994 and CC1039). Thus, we conclude that the role of NGO1945 in N. gonorrhoeae and CC2905 or CC3256 in C. crescentus is most likely different under these circumstances. To confirm results obtained in transcriptome analysis, we investigated the expression levels of...”
- The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation
Das, Acta crystallographica. Section F, Structural biology and crystallization communications 2010 - “...representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation NGO1945 Das Debanu a b Grishin Nick V. c d Kumar Abhinav a b Carlton Dennis a e Bakolitsa Constantina a f Miller Mitchell D. a b Abdubek Polat a g...”
- “...version of this article is available from Crystallography Journals Online. The crystal structure of the NGO1945 gene product from N. gonorrhoeae (UniProt Q5F5IO) reveals that the N-terminal domain assigned as a domain of unknown function (DUF2063) is likely to bind DNA and that the protein may...”
- Ecf, an alternative sigma factor from Neisseria gonorrhoeae, controls expression of msrAB, which encodes methionine sulfoxide reductase
Gunesekere, Journal of bacteriology 2006 - “...partially conserved (data not shown). The expression ratio for NGO1945, the gene located between ecf and NGO1946, was just below the 1.5-fold cutoff used in...”
- “...In addition, the genomic arrangement of NGO1944 (ecf), NGO1945, NGO1946, NGO1947, and NGO1948 suggests the possibility of cotranscription of at least some of...”
LPA_RS11585, LPC_RS11785 DNA-binding domain-containing protein from Legionella pneumophila 2300/99 Alcoy
Aligns to 6:98 / 262 (35.5%), covers 97.6% of PF09836, 67.5 bits
- The Legionella pneumophila GIG operon responds to gold and copper in planktonic and biofilm cultures
Jwanoswki, PloS one 2017 - “...(-) LPL_RS03575 796537 (+) Alcoy LPA_RS03750 813482 (-) LPA_RS03775 816859 (+) NC_014125.1 LPA_RS03755 814258 (-) LPA_RS11585 2646878 (-) LPA_RS03795 822332 (-) LPA_RS03760 815120 (-) LPA_RS11590 2647738 (-) LPA_RS03800 823152 (-) LPA_RS03765 815380 (-) LPA_RS11595 2648134 (-) LPA_RS03785 819919 (+) We surveyed the genomes of four additional...”
- “...(-) LPP_RS03660 807569 (+) Corby LPC_RS03790 827443 (-) LPC_RS03815 830819 (+) NC_009494.1 LPC_RS03795 828003 (-) LPC_RS11785 2673120 (-) LPC_RS03835 836292 (-) LPC_RS03800 829080 (-) LPC_RS11790 2673980 (-) LPC_RS03840 837112 (-) LPC_RS03805 829340 (-) LPC_RS11795 2674376 (-) LPC_RS03825 833879 (+) Lens LPL_RS03540 790101 (-) LPL_RS03565 793477 (+)...”
LPP_RS11155 DNA-binding domain-containing protein from Legionella pneumophila str. Paris
Aligns to 6:98 / 262 (35.5%), covers 97.6% of PF09836, 67.4 bits
LPL_RS11000 DNA-binding domain-containing protein from Legionella pneumophila str. Lens
Aligns to 6:98 / 262 (35.5%), covers 97.6% of PF09836, 66.5 bits
lpg2106 Hypothetical protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Aligns to 6:96 / 259 (35.1%), covers 98.8% of PF09836, 64.2 bits
- The Legionella pneumophila GIG operon responds to gold and copper in planktonic and biofilm cultures
Jwanoswki, PloS one 2017 - “...1.00E-19 85 38 Predicted inner membrane protein with a DoxX domain (PF07681) Rmet_4683 (ABF11545.1) 258 lpg2106 (YP_096119.1) 259 8.00E-16 89 22 Contains N-terminal DUF2063 domain with putative role in DNA binding and transcriptional regulation Rmet_4684 (ABF11546.1) 278 lpg2107 (YP_096120.1) 284 7.00E-72 98 40 DUF692 family of...”
- “...subunit, DoxD, but their precise function is unknown [ 26 ]. The second GIG gene, lpg2106 , encodes a 259-aa protein with an N-terminal DUF2063 domain that is predicted to function in DNA binding and transcriptional regulation [ 27 ]. The third GIG gene, lpg2107 ,...”
LPA_RS03795, LPC_RS03835 DNA-binding domain-containing protein from Legionella pneumophila str. Corby
Aligns to 6:100 / 271 (35.1%), covers 100.0% of PF09836, 63.9 bits
- The Legionella pneumophila GIG operon responds to gold and copper in planktonic and biofilm cultures
Jwanoswki, PloS one 2017 - “...(+) Alcoy LPA_RS03750 813482 (-) LPA_RS03775 816859 (+) NC_014125.1 LPA_RS03755 814258 (-) LPA_RS11585 2646878 (-) LPA_RS03795 822332 (-) LPA_RS03760 815120 (-) LPA_RS11590 2647738 (-) LPA_RS03800 823152 (-) LPA_RS03765 815380 (-) LPA_RS11595 2648134 (-) LPA_RS03785 819919 (+) We surveyed the genomes of four additional L . pneumophila...”
- “...(+) Corby LPC_RS03790 827443 (-) LPC_RS03815 830819 (+) NC_009494.1 LPC_RS03795 828003 (-) LPC_RS11785 2673120 (-) LPC_RS03835 836292 (-) LPC_RS03800 829080 (-) LPC_RS11790 2673980 (-) LPC_RS03840 837112 (-) LPC_RS03805 829340 (-) LPC_RS11795 2674376 (-) LPC_RS03825 833879 (+) Lens LPL_RS03540 790101 (-) LPL_RS03565 793477 (+) NC_006369.1 LPL_RS03545 790877...”
NMB2143 hypothetical protein from Neisseria meningitidis MC58
NMH_2155 DUF2063 domain-containing protein from Neisseria meningitidis H44/76
Aligns to 8:91 / 248 (33.9%), covers 100.0% of PF09836, 62.1 bits
LPP_RS03670 DNA-binding domain-containing protein from Legionella pneumophila str. Paris
Aligns to 6:100 / 271 (35.1%), covers 100.0% of PF09836, 60.1 bits
LPL_RS03585 DNA-binding domain-containing protein from Legionella pneumophila str. Lens
Aligns to 6:100 / 271 (35.1%), covers 100.0% of PF09836, 60.0 bits
HI1599 hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 3:88 / 232 (37.1%), covers 100.0% of PF09836, 58.8 bits
lpg0675 Hypothetical protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Aligns to 14:108 / 279 (34.1%), covers 100.0% of PF09836, 58.6 bits
NTHI1444 hypothetical protein from Haemophilus influenzae 86-028NP
Aligns to 9:94 / 238 (36.1%), covers 100.0% of PF09836, 56.5 bits
- Discovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion
Ahearn, Infection and immunity 2019 - “...operon 235 including the ORFs NTHI1440, NTHI1443, and NTHI1444 (Figure 3A) (34). Endpoint 236 reverse transcriptase-PCR with RNA isolated from strain 86-028NP...”
- “...includes the ORFs NTHI1440, NTHI1441, 247 NTHI1443, and NTHI1444. The nucleotide sequences of the NTHI1441 operon is 248 present and conserved in all publicly...”
- The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation
Das, Acta crystallographica. Section F, Structural biology and crystallization communications 2010 - “...and enteroinvasive E. coli (Suzuki et al. , 1994 ). H. influenzae homologs, such as NTHI1444 and HI1599, co-occur with hemoglobinhaptoglobin binding proteins that are virulence determinants (Seale et al. , 2006 ). Similarly, Pseudomonas aeruginosa homologs co-occur with heme-exporter protein D (a cytochrome c -type...”
LPL_RS03545 putative DNA-binding domain-containing protein from Legionella pneumophila str. Lens
Aligns to 4:98 / 259 (36.7%), covers 74.7% of PF09836, 49.2 bits
lpg0666 Hypothetical protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Aligns to 5:98 / 259 (36.3%), covers 75.9% of PF09836, 48.5 bits
LPA_RS03755, LPP_RS03630 putative DNA-binding domain-containing protein from Legionella pneumophila 2300/99 Alcoy
Aligns to 5:98 / 259 (36.3%), covers 75.9% of PF09836, 48.5 bits
- The Legionella pneumophila GIG operon responds to gold and copper in planktonic and biofilm cultures
Jwanoswki, PloS one 2017 - “...(-) LPL_RS11010 2496153 (-) LPL_RS03575 796537 (+) Alcoy LPA_RS03750 813482 (-) LPA_RS03775 816859 (+) NC_014125.1 LPA_RS03755 814258 (-) LPA_RS11585 2646878 (-) LPA_RS03795 822332 (-) LPA_RS03760 815120 (-) LPA_RS11590 2647738 (-) LPA_RS03800 823152 (-) LPA_RS03765 815380 (-) LPA_RS11595 2648134 (-) LPA_RS03785 819919 (+) We surveyed the genomes...”
- “...(-) lpg2255 2558333 (-) lpg0673 723047 (+) Paris LPP_RS03625 801134 (-) LPP_RS03650 804510 (+) NC_006368.2 LPP_RS03630 801910 (-) LPP_RS11155 2543886 (-) LPP_RS03670 809982 (-) LPP_RS03635 802772 (-) LPP_RS11160 2544746 (-) LPP_RS03675 810802 (-) LPP_RS03640 803032 (-) LPP_RS11165 2545073 (-) LPP_RS03660 807569 (+) Corby LPC_RS03790 827443 (-)...”
Or search for genetic data about PF09836 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory