Family Search for PF06568 (DUF1127)
PF06568 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.
BAB1_0914 hypothetical protein (NCBI) from Brucella melitensis biovar Abortus 2308
Aligns to 3:39 / 48 (77.1%), covers 97.3% of PF06568, 61.6 bits
- Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens.
Kraus, Journal of bacteriology 2020 (secret) - A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Budnick, Scientific reports 2020 - “...tumefaciens , the gene atu1667 encodes for a small hypothetical protein that is orthologous to BAB1_0914 and BAB2_0512 in B. abortus . bab1_0914 and bab2_0512 are directly transcriptionally activated by VtlR in B. abortus , and thus, it was hypothesized that VtlR also directly activates the...”
- Characterization of Three Small Proteins in Brucella abortus Linked to Fucose Utilization.
Budnick, Journal of bacteriology 2018 - “...characterize the role of the VtlR-controlled small proteins BAB1_0914, BAB2_0512, and BAB2_0574 in the biology of B. abortus, particularly in the capacity of...”
- “...VtlR transcriptionally activates four genes, abcR2, bab1_0914 (bab_rs20300), bab2_0512 (bab_rs28790), and bab2_0574 (bab_rs29075) (12). The small regulatory RNA...”
- Molecular control of gene expression by Brucella BaaR, an IclR-type transcriptional repressor
Herrou, The Journal of biological chemistry 2018 - “...protein; bab1_0578, BetI TetR transcriptional regulator; bab1_0914, DUF1127; bab2_0548, ABC transmembrane transporter). B, genomic organization of the...”
- “...bab1_0578 (BetI TetR transcriptional regulator), bab1_0914 (DUF1127), and bab2_0548 (ABC transmembrane transporter) also showed significant differential...”
- A LysR-family transcriptional regulator required for virulence in Brucella abortus is highly conserved among the α-proteobacteria
Sheehan, Molecular microbiology 2015 - “...significantly elevated in the vtlR mutant strain. Moreover, three genes encoding putative small hypothetical proteins, bab1_0914, bab2_0512 and bab2_0574 , exhibited diminished levels in the vtlR mutant strain compared with the parental strain 2308. To confirm the regulation of these hypothetical protein-encoding genes by VtlR, northern...”
- “...( vtlR /Comp) ( Fig. 3 ). The vtlR mutant exhibited no production of the BAB1_0914, BAB2_0512, BAB2_0574 or AbcR2 RNAs. Importantly, AbcR1 production was maintained in the vtlR mutant strain compared with strain 2308. Complementation of vtlR expression in the vtlR mutant strain restored production...”
pRL110532 hypothetical protein (NCBI) from Rhizobium leguminosarum bv. viciae 3841
Aligns to 3:39 / 48 (77.1%), covers 97.3% of PF06568, 58.8 bits
SMc02051 CONSERVED HYPOTHETICAL PROTEIN (NCBI ptt file) from Sinorhizobium meliloti 1021
Aligns to 3:39 / 47 (78.7%), covers 97.3% of PF06568, 57.5 bits
- The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover
Grützner, Nucleic acids research 2021 - “...Phylobacteraceae ( 22 ) . Barnett etal. ( 24 ) found that the RSP_6037 ortholog SMc02051 (47 aa) from Sinorhizobium meliloti 1021 has a RpoHI and RpoHII responsive expression as described for the CcsR locus in Rhodobacter sphaeroides (Figure 1B ). Interestingly, a similar responsiveness was...”
- “...of the Rfam RNA family ar14. ar14 from Sinorhizobium meliloti 1021 includes the DUF1127-containing ORF SMc02051. The Cuckoo RNAs from this locus have been named NfeR (nodule formation efficiency RNA) and are expressed in root nodules and under salt stress, possibly from an RpoHI/HII-dependent promoter (...”
- ExoS/ChvI Two-Component Signal-Transduction System Activated in the Absence of Bacterial Phosphatidylcholine
Geiger, Frontiers in plant science 2021 - “...uptake ABC transporter, periplasmic solute binding protein precursor* 1.38 SMc02900 conserved hypothetical protein DUF1137 1.35 SMc02051 conserved hypothetical protein DUF1137 1.32 SMc01465 ( creA ) putative CreA protein* 1.28 SMc02052 conserved hypothetical protein DUF1137 1.27 SMc01580 conserved hypothetical protein* 1.25 SMa1831 ( ureF ) putative urease...”
- Characterization of Three Small Proteins in Brucella abortus Linked to Fucose Utilization.
Budnick, Journal of bacteriology 2018 - “...other bacteria in the Rhizobiales. These include sMc02051 in Sinorhizobium meliloti 1021, atu1667 in Agrobacterium tumefaciens C58, and rleg2_1502 in Rhizobium...”
- The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti
Pini, Molecular microbiology 2013 - “...Hypothetical protein 0.59 y (+) SMc01586 Hypothetical protein 0.75 y (+) SMc03999 Hypothetical protein 0.65 SMc02051 Conserved hypothetical protein 0.56 y SMc02052 Conserved hypothetical protein 0.56 SMc02266 Conserved hypothetical protein 0.83 y (+) SMc02900 Conserved hypothetical protein 0.96 SMc03100 Conserved hypothetical protein 0.66 SMc00458 feuP 1.48...”
- Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis
Gao, Molecular plant-microbe interactions : MPMI 2010 - “...et al. 2007 ; del Val et al. 2008 ; Valverde et al. 2008 8. SMc02051- tig 1,667,6181,667,986 <<< 2.8 sm7 (in silico) Valverde et al. 2008 9. SMc02855-SMc02856 206,784207,013 <<< 2.7 N.D. This study 10. SMc03061-SMc03062 759,133759,383 <<< 7.6 Candidate 182 (in silico) Valverde et...”
- Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011
Valverde, BMC genomics 2008 - “...1728196, 1728269 1728021 1 1 62 120248 n - smrC14 ( sm7 ) sm7' 922 SMc02051 < < < < < < NN, s70 NN 1667614 1667983 1667488 1667769 3 5 58 126 214 n <, S (1667516-1667467) sm8 301 SMc04042 < > < NN, s70...”
RSP_0557 DUF1127 domain-containing protein from Cereibacter sphaeroides 2.4.1
RSP_0557 hypothetical protein (NCBI) from Rhodobacter sphaeroides 2.4.1
Aligns to 27:63 / 70 (52.9%), covers 97.3% of PF06568, 56.7 bits
- Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions.
Spanka, International journal of molecular sciences 2021 - “...C led mainly to constant signals and only the strain harbouring the promoter fusion of RSP_0557 (positive control) showed an increasing fluorescence intensity over time ( Figure 7 C). Next, the change in fluorescence signal was categorized to visualize the trends as described above ( Figure...”
- “...= 3. Every dot represents the mean value of two technical replicates. The promoters of RSP_0557 (unpublished data) and 16S rRNA (McIntosh et al., 2019) were used as positive controls for the indicated growth conditions. Signals F/OD 660 are shown in Figure S9 F. ( D...”
- The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover
Grützner, Nucleic acids research 2021 - “...E. coli S17-1 to R. sphaeroides 2.4.1 ( 29 ). Construction of 3xFLAG-tagged CcaF1 and RSP_0557 expression strains The R. sphaeroides RSP_6037 and RSP_0557 loci were amplified by PCR of pRK6037 and pBBR0557 ( 17 ) plasmid DNA using primers CcaF1FLAG_NT_f and CcaF1FLAG_NT_r or RSP0557FLAG_NT_f and...”
- “...5 end followed by the 3xFLAG sequence at the N-terminus and the ccaF1 (RSP_6037) or RSP_0557 gene. The fragment was sub-cloned into the BamHI and EcoRI sites of the pJET1.2 cloning vector (Thermo Fisher Scientific, Waltham, MA, USA) and ligated into the pRK4352 overexpression vector (...”
- A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides.
Eisenhardt, International journal of molecular sciences 2021 - “...13). A negative control StsR was incubated together with a 100-fold molar excess of an RSP_0557 [ 23 ] in vitro transcript (lane 4). As further controls, the StsR transcript was loaded alone (lane 5) or after de and renaturation together with a 100-fold molar excess...”
- Short, Rich, and Powerful: a New Family of Arginine-Rich Small Proteins Have Outsized Impact in Agrobacterium tumefaciens.
Alakavuklar, Journal of bacteriology 2020 (secret) - Characteristics of Pos19 - A Small Coding RNA in the Oxidative Stress Response of Rhodobacter sphaeroides
Müller, PloS one 2016 - “...the sRNA itself. Reporter studies further revealed that regulation of the most affected mRNA, namely RSP_0557, by Pos19 is Hfq-dependent. Direct binding of Pos19 to Hfq was shown by co-immunoprecipitation. Physiological experiments indicated Pos19 to be involved in the balance of glutathione biosynthesis. Moreover, a lack...”
- “...rather weak, Pos19 can be co-immunoprecipitated with Hfq and relies on Hfq for regulation of RSP_0557, encoding a hypothetical protein. Regarding a Pos19 function in oxidative stress responses, it was demonstrated that it alters the intracellular GSH level most likely by affecting the mRNA level of...”
- Global analysis of photosynthesis transcriptional regulatory networks
Imam, PLoS genetics 2014 - “...protein) chr1 2042400 2043399 5.35 + RSP_0315 pucC (Light-harvesting 1 (B870) complex assembly) + 9 RSP_0557 Hypothetical protein chr1 2294400 2294599 2.2 + 10 RSP_0679 hemC (Hydroxymethylbilane synthase) chr1 2424000 2424399 2.1 + RSP_0680 hemE (Uroporphyrinogen decarboxylase) + 11 RSP_0820-RSP_6134 Cytochrome B561 chr1 2565800 2566199 2...”
- Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
Dufour, PLoS genetics 2012 - “...RSP_1219 tRNA and rRNA base modification RSP_2971 Unknown function Unknown function RSP_0151, RSP_0152, RSP_0269, RSP_0423, RSP_0557, RSP_0799, RSP_0896, RSP_1591, RSP_1956, RSP_1985, RSP_2225, RSP_2268, RSP_3075, RSP_3076, RSP_3089, RSP_3310, RSP_3329, RSP_4144, RSP_4209 Summary of the functional annotations of members of the RpoH I and RpoH II regulons in...”
SMc02052 CONSERVED HYPOTHETICAL PROTEIN (NCBI ptt file) from Sinorhizobium meliloti 1021
Aligns to 4:39 / 47 (76.6%), covers 94.6% of PF06568, 54.8 bits
Atu1667 hypothetical protein (RefSeq) from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 32:68 / 77 (48.1%), covers 97.3% of PF06568, 54.3 bits
- A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Budnick, Scientific reports 2020 - “...VtlR in an AbcR1-independent manner. Agrobacterium tumefaciens VtlR directly activates the expression of abcR1 and atu1667 , a small hypothetical protein To further characterize the regulatory mechanism of A. tumefaciens VtlR, electrophoretic mobility shift assays (EMSAs) were employed to test for the ability of recombinantly purified...”
- “.... Figure 4 A. tumefaciens VtlR directly regulates abcR1 , encoding a small RNA, and atu1667 , encoding a small hypothetical protein. ( A ) Electrophoretic mobility shift assays (EMSAs) were carried out with recombinantly purified A. tumefaciens VtlR (rVtlR) and 32 P-radiolabeled abcR1 promoter region...”
- Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens.
Kraus, Journal of bacteriology 2020 (secret) - Characterization of Three Small Proteins in Brucella abortus Linked to Fucose Utilization.
Budnick, Journal of bacteriology 2018 - “...These include sMc02051 in Sinorhizobium meliloti 1021, atu1667 in Agrobacterium tumefaciens C58, and rleg2_1502 in Rhizobium leguminosarum bv. trifolii WSM2304....”
- 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 - “...Atu0544 Atu0896 Atu0904 Atu0955 Atu0983 Atu1031 Atu1467 Atu1637 Atu1667 Atu1975 Atu3190 Atu3321 Atu3837 Atu3838 Atu4185 1.06 1.27 1.19 1.48 1.05 1.88 1.49 1.01...”
Q2YKY2 DUF1127 domain-containing protein from Brucella abortus (strain 2308)
BAB2_0512 conserved hypothetical protein (NCBI) from Brucella melitensis biovar Abortus 2308
Aligns to 7:43 / 52 (71.2%), covers 97.3% of PF06568, 53.6 bits
- Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis.
Murugaiyan, Biomolecules 2020 - “...cytosol aminopeptidase Q2YRJ0 ATP/GTP-binding site motif A (P-loop) Q2YRN7 Uncharacterized protein Q8YBU9 Putative uroporphyrin-iii c-methyltransferase Q2YKY2 Uncharacterized protein Q2YL40 Uncharacterized protein Q2YLM7 Uncharacterized protein Downregulated in B. abortus and Upregulated in B. melitensis Q2YME1 Threonylcarbamoyl-AMP synthase Q2YNW9 Dihydroxy-acid dehydratase Q8YHA5 Glutaryl-CoA dehydrogenase Q2YP66 Zinc-containing alcohol dehydrogenase...”
- A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Budnick, Scientific reports 2020 - “...the gene atu1667 encodes for a small hypothetical protein that is orthologous to BAB1_0914 and BAB2_0512 in B. abortus . bab1_0914 and bab2_0512 are directly transcriptionally activated by VtlR in B. abortus , and thus, it was hypothesized that VtlR also directly activates the expression of...”
- “...atu1667 encodes a putative hypothetical protein that has not yet been characterized in Agrobacterium, but BAB2_0512, a homolog of Atu1667, encodes a small protein that is linked to the ability of B. abortus to utilize the sugar fucose 43 . It is unknown whether atu1667 also...”
- Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens.
Kraus, Journal of bacteriology 2020 (secret) - Characterization of Three Small Proteins in Brucella abortus Linked to Fucose Utilization.
Budnick, Journal of bacteriology 2018 - “...the role of the VtlR-controlled small proteins BAB1_0914, BAB2_0512, and BAB2_0574 in the biology of B. abortus, particularly in the capacity of the bacteria...”
- “...activates four genes, abcR2, bab1_0914 (bab_rs20300), bab2_0512 (bab_rs28790), and bab2_0574 (bab_rs29075) (12). The small regulatory RNA (sRNA) AbcR2...”
- A LysR-family transcriptional regulator required for virulence in Brucella abortus is highly conserved among the α-proteobacteria
Sheehan, Molecular microbiology 2015 - “...elevated in the vtlR mutant strain. Moreover, three genes encoding putative small hypothetical proteins, bab1_0914, bab2_0512 and bab2_0574 , exhibited diminished levels in the vtlR mutant strain compared with the parental strain 2308. To confirm the regulation of these hypothetical protein-encoding genes by VtlR, northern blot...”
- “...vtlR /Comp) ( Fig. 3 ). The vtlR mutant exhibited no production of the BAB1_0914, BAB2_0512, BAB2_0574 or AbcR2 RNAs. Importantly, AbcR1 production was maintained in the vtlR mutant strain compared with strain 2308. Complementation of vtlR expression in the vtlR mutant strain restored production of...”
BAB2_0574 conserved hypothetical protein (NCBI) from Brucella melitensis biovar Abortus 2308
Aligns to 3:39 / 45 (82.2%), covers 97.3% of PF06568, 52.6 bits
- Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens.
Kraus, Journal of bacteriology 2020 (secret) - Characterization of Three Small Proteins in Brucella abortus Linked to Fucose Utilization.
Budnick, Journal of bacteriology 2018 - “...of the VtlR-controlled small proteins BAB1_0914, BAB2_0512, and BAB2_0574 in the biology of B. abortus, particularly in the capacity of the bacteria to utilize...”
- “...genes, abcR2, bab1_0914 (bab_rs20300), bab2_0512 (bab_rs28790), and bab2_0574 (bab_rs29075) (12). The small regulatory RNA (sRNA) AbcR2 has a sibling sRNA,...”
- A LysR-family transcriptional regulator required for virulence in Brucella abortus is highly conserved among the α-proteobacteria
Sheehan, Molecular microbiology 2015 - “...the vtlR mutant strain. Moreover, three genes encoding putative small hypothetical proteins, bab1_0914, bab2_0512 and bab2_0574 , exhibited diminished levels in the vtlR mutant strain compared with the parental strain 2308. To confirm the regulation of these hypothetical protein-encoding genes by VtlR, northern blot analyses were...”
- “.../Comp) ( Fig. 3 ). The vtlR mutant exhibited no production of the BAB1_0914, BAB2_0512, BAB2_0574 or AbcR2 RNAs. Importantly, AbcR1 production was maintained in the vtlR mutant strain compared with strain 2308. Complementation of vtlR expression in the vtlR mutant strain restored production of AbcR2,...”
bsr4726 bsr4726 (NCBI ptt file) from Bradyrhizobium japonicum USDA 110
Aligns to 45:81 / 90 (41.1%), covers 97.3% of PF06568, 52.4 bits
YjiS / b4341 DUF1127 domain-containing protein YjiS from Escherichia coli K-12 substr. MG1655 (see paper)
P39390 Uncharacterized protein YjiS from Escherichia coli (strain K12)
Aligns to 18:54 / 54 (68.5%), covers 100.0% of PF06568, 50.7 bits
- Knowns and Unknowns of Vitamin B6 Metabolism in Escherichia coli.
Tramonti, EcoSal Plus 2021 - “...Fig. 3M ). In fact, the adjacent yjiS gene encodes an uncharacterized small protein (UniProt P39390). In summary, considering all the operons containing genes involved in PLP metabolism, it may be assumed that the PLP biosynthesis and salvage pathways are strictly associated with primary metabolism of...”
RSKD131_0402 hypothetical protein (RefSeq) from Rhodobacter sphaeroides KD131
Aligns to 4:40 / 50 (74.0%), covers 89.2% of PF06568, 50.3 bits
- The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover
Grützner, Nucleic acids research 2021 - “...ligated into the expression vector pRK4352 ( 28 ). The constitutive overexpression of the ccaF1 (RSKD131_0402) gene from R. sphaeroides KD131 (Primers are listed in Supplementary Table S2 ) was performed in the same way like for ccaF1 (RSP_6037) from R. sphaeroides 2.4.1, but using chromosomal...”
- “...the mutant lacking the hfq gene. The ccaf1 gene is shown in light grey, the RSKD131_0402 gene in black, CcsR RNAs in white. In plasmid pRKCcaF1mut_CcsR14 the ATG of the ccaF1 gene was changed to TGA. ( C ) Northern blots of total RNA from strains...”
Atu8161 hypothetical protein (RefSeq) from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 4:39 / 47 (76.6%), covers 94.6% of PF06568, 49.7 bits
RSP_6037 DUF1127 domain-containing protein from Cereibacter sphaeroides 2.4.1
RSP_6037 hypothetical protein (NCBI) from Rhodobacter sphaeroides 2.4.1
Aligns to 25:61 / 71 (52.1%), covers 89.2% of PF06568, 47.4 bits
- Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions.
Spanka, International journal of molecular sciences 2021 - “...CcsR1-4 RNAs are generated by processing of the 3 UTR of the ccaF1 mRNA ( RSP_6037 ) and modulate the C1 metabolism and the pyruvate dehydrogenase complex [ 17 ]. RNase E as well as the small CcaF1 protein have important roles in maturation of the...”
- “...[ 19 ]. The CcsR1-4 RNAs are derived from the 3 UTR of ccaF1 ( RSP_6037 ), which encodes a small RNA-binding protein required for the maturation of CcsR and other sRNAs [ 17 , 18 ]. It seems reasonable that all these sRNAs are under...”
- The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover
Grützner, Nucleic acids research 2021 - “...species (ROS), is reduced. The CcsR14 sRNAs are derived from the 3 UTR of the RSP_6037 mRNA (Figure 1A ). Transcription of the RSP_6037-CcsR genes is initiated at a RpoHI/RpoHII-dependent promoter ( 18 ). Figure 1. Schematic representations of the CcsR-RNA/DUF1127-protein loci in R. sphaeroides 2.4.1...”
- “...7 ) that prompted Reinkensmeier and Giegerich ( 22 ) to name them Cuckoo RNAs. RSP_6037 encodes a small protein of unknown function of 71 amino acids. Amino acids 2362 constitute a DUF1127 domain ( 18 ). More than 17,000 bacterial protein sequences with DUF1127 domains...”
- A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides.
Eisenhardt, International journal of molecular sciences 2021 - “...( Figure 5 ). The CcsR1-4 RNAs are transcribed together with an upstream gene, ccaF1 (RSP_6037). CcaF1 was recently identified as a small RNA-binding protein involved in RNA maturation and turn-over. Increased amounts of CcaF1 interfere with the maturation of the CcsR RNAs from the ccaF1...”
- Short, Rich, and Powerful: a New Family of Arginine-Rich Small Proteins Have Outsized Impact in Agrobacterium tumefaciens.
Alakavuklar, Journal of bacteriology 2020 (secret) - Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens.
Kraus, Journal of bacteriology 2020 (secret) - Characteristics of Pos19 - A Small Coding RNA in the Oxidative Stress Response of Rhodobacter sphaeroides
Müller, PloS one 2016 - “...hemoprotein subunit RSP_1943 -1.4 Sulfite reductase (ferredoxin) RSP_1944 cysG / cobA -1.3 Uroporphiryn-III C-methyltransferase/siroheme synthase RSP_6037 -1.0 Hypothetical protein Up-regulated RSP_0069 fliC 1.6 Flagellar filament protein RSP_2590 1.2 Hypothetical protein RSP_2876 coxM 1.2 Carbon monoxide dehydrogenase medium chain RSP_2877 coxL 1.5 Carbon monoxide dehydrogenase large chain...”
- “...preceded by a putative RpoH I /H II -dependent promoter. Furthermore, RSP_0557 is homologous to RSP_6037 which is transcribed as well from a RpoH I /H II -dependent promoter [ 18 ] and is also down-regulated by Pos19 over-expression ( Table 1 ). We could show...”
- A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions
Billenkamp, Journal of bacteriology 2015 - “...cotranscribed with the gene for the conserved hypothetical protein RSP_6037, a genetic arrangement described for only a few sRNAs until now. Each of the four...”
- “...with an upstream gene, encoding a hypothetical protein (RSP_6037) (20). This protein contains a conserved domain of unknown function (DUF1127). In R....”
- Thermodynamic matchers for the construction of the cuckoo RNA family
Reinkensmeier, RNA biology 2015 - “...8 showed that RSs0680a-d are co-transcribed with an upstream located, so far uncharacterized hypothetical gene, RSP_6037, and expressed under the control of an RpoH I /RpoH II dependent promoter. Besides, a terminator-like hairpin was found downstream of the sRNA cluster. In two complementing studies it could...”
- CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria.
Imam, mBio 2015 - “...CceR mutant. In addition to these known metabolic genes, CceR was bound upstream of genes (RSP_6037, RSP_6082, and RSP_7376) encoding proteins of unknown functions, which could indicate these proteins might have previously uncharacterized roles in carbon or energy metabolism. TABLE1 CceR binding sites across the R.sphaeroides...”
- “...Fructose-bisphosphate aldolase ( fbaB ) chr1 2.3 1127172 GT TGTT CGCGCT AACT TGG + 14 RSP_6037 Hypothetical protein chr1 7.1 692742 GC TGTT AGGGCA AACA TGG NA 15 RSP_6082 Hypothetical protein chr1 8.6 1642463 GT TGTT AGCGCC AACA TTC NA 16 RSP_7376 Hypothetical protein plasmidC 2.9...”
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SMc02900 CONSERVED HYPOTHETICAL PROTEIN (NCBI ptt file) from Sinorhizobium meliloti 1021
Aligns to 3:39 / 45 (82.2%), covers 94.6% of PF06568, 47.2 bits
PA5460 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 25:61 / 70 (52.9%), covers 97.3% of PF06568, 45.6 bits
- Functional Characterization of TetR-like Transcriptional Regulator PA3973 from Pseudomonas aeruginosa
Kotecka, International journal of molecular sciences 2022 - “...data, confirming a negative impact of PA3973 on the expression of PA3614 , PA5208 , PA5460 , PA5497 , and PA3972 ( Figure 3 C). To identify PA3973 binding sites in the P. aeruginosa genome, ChIP-seq analysis was performed using anti-FLAG antibodies and PA3973 cells carrying...”
- Inhibition of Pseudomonas aeruginosa swarming motility by 1-naphthol and other bicyclic compounds bearing hydroxyl groups
Oura, Applied and environmental microbiology 2015 - “...PA3969 PA4063 PA4115 PA4155 PA4220 PA4648 PA4773 PA4774 PA4916 PA5460 PA5481 a Fold change Product or functiona pilA pilB 2.0 3.0 2.3 Type 4 fimbrial precursor...”
- Contribution of stress responses to antibiotic tolerance in Pseudomonas aeruginosa biofilms
Stewart, Antimicrobial agents and chemotherapy 2015 - “...PA2386 PA2782 PA3126 PA3309 PA3572 PA4067 PA4211 PA4217 PA4236 PA4352 PA4610 PA4765 PA5427 PA5460 PA5475 ahpC hcpC 0 1 3 2 3 3 3 3 3 3 3 3 2 3 0 3 3 2 3 2 3...”
- Five new genes are important for common polysaccharide antigen biosynthesis in Pseudomonas aeruginosa
Hao, mBio 2013 - “...cotranscribed, while fragment 13 did not yield any RT-PCR product ( Fig.1 ), indicating that pa5460 is not part of the operon. Fragments 6 to 12, which cover the genes within the rmd - wbpZ cluster, all yielded positive RT-PCR results ( Fig.1B ), confirming that...”
- Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen
Crabbé, Applied and environmental microbiology 2011 - “...PA5067 PA5069 PA5078 PA5117 PA5128 PA5276 PA5316 PA5355 PA5460 PA5490 PA5491 PA5555 PA5557 PA5569 PA5570 ispB glyA3 PA4608 PA4610 PA4633 PA4671 PA4692 PA4702...”
- “...tatB PA5078 typA secB lppL rpmB glcD PA5460 cc4 PA5491 atpG atpH rnpA rpmH a Function Octaprenyl-diphosphate synthase Serine hydroxymethyltransferase...”
- Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis
Folsom, BMC microbiology 2010 - “...hypothetical protein PA5427 adhA 112 2664 O 2 alcohol dehydrogenase PA5446 7 866 hypothetical protein PA5460 118 3962 hypothetical protein PA5475 294 2787 O 2 hypothetical protein *Average Rank in drip flow biofilms (DFB) and three comparator microarray data sets (Comp. Rank) named in the Materials...”
- A distinct QscR regulon in the Pseudomonas aeruginosa quorum-sensing circuit
Lequette, Journal of bacteriology 2006 - “...PA4150 PA4152 PA4498 PA5083 PA5086 PA5349 PA5351 PA5460 PA5566 Conserved hypothetical protein Hypothetical protein pcaH; aromatic compound catabolism pcaG;...”
- Transcriptome analysis of Pseudomonas aeruginosa growth: comparison of gene expression in planktonic cultures and developing and mature biofilms
Waite, Journal of bacteriology 2005 - “...PA3460 PA3461 PA3540 PA4570 PA4870 PA4877 PA5460 Hypothetical protein Hypothetical protein Hypothetical protein Probable ferredoxin Probable hydroxylase...”
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AEX15_20730, SeKA_A4188 DUF1127 domain-containing protein from Salmonella enterica subsp. enterica serovar Kentucky
Aligns to 18:54 / 54 (68.5%), covers 100.0% of PF06568, 45.6 bits
- Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America
Haley, PloS one 2016 - “...SeKA_A0399 (tRNA-Ser) 14 type I restriction-modification system, putative inner membrane protein, hypothetical protein 10325 AEX15_20690, AEX15_20730 C SeKA_A4188, SeKA_A4198 C 15 hypothetical protein 693 AEX15_14050, AEX15_14060 SeKA_A3461, SeKA_A3465 16 hypothetical proteins, phage tail protein, oxidoreductase, transglycosylase E 25556 AEX15_11375, AEX15_11530 SeKA_A1348, SeKA_A1377 C ST Region Features...”
- “...14 type I restriction-modification system, putative inner membrane protein, hypothetical protein 10240 SeKA_A4188, SeKA_A4198 AEX15_20690, AEX15_20730 15 oxidoreductase, inner membrane metabolite transport protein, sorbitol dehydrogenase, fructose-bisphosphate aldolase, kinase. 9227 SeKA_A0714, SeKA_A0725 C AEX15_08380, AEX15_08375 C 16 putative membrane transport protein, mandelate racemase/muconate lactonizing enzyme, putative transcriptional...”
- “...14 type I restriction-modification system, putative inner membrane protein, hypothetical protein 10325 AEX15_20690, AEX15_20730 C SeKA_A4188, SeKA_A4198 C 15 hypothetical protein 693 AEX15_14050, AEX15_14060 SeKA_A3461, SeKA_A3465 16 hypothetical proteins, phage tail protein, oxidoreductase, transglycosylase E 25556 AEX15_11375, AEX15_11530 SeKA_A1348, SeKA_A1377 C ST Region Features Size A...”
- “...(tRNA-Leu), SEEK9263_16827 C 14 type I restriction-modification system, putative inner membrane protein, hypothetical protein 10240 SeKA_A4188, SeKA_A4198 AEX15_20690, AEX15_20730 15 oxidoreductase, inner membrane metabolite transport protein, sorbitol dehydrogenase, fructose-bisphosphate aldolase, kinase. 9227 SeKA_A0714, SeKA_A0725 C AEX15_08380, AEX15_08375 C 16 putative membrane transport protein, mandelate racemase/muconate lactonizing...”
VP2426 hypothetical protein (NCBI ptt file) from Vibrio parahaemolyticus RIMD 2210633
Aligns to 23:59 / 69 (53.6%), covers 97.3% of PF06568, 45.4 bits
PA2845 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 26:61 / 77 (46.8%), covers 97.3% of PF06568, 45.3 bits
PA5446 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 22:58 / 67 (55.2%), covers 97.3% of PF06568, 40.1 bits
- ECF Sigma Factor HxuI Is Critical for In Vivo Fitness of Pseudomonas aeruginosa during Infection
Cai, Microbiology spectrum 2022 - “...of MexAB-OprM efflux 2.52 1.77E-24 PA4371 Hypothetical protein 2.08 0.000157 PA5023 Hypothetical protein 2.2 0.000102 PA5446 Hypothetical protein 2 9.77E-13 a PAO1/pMMB- hxuI versus PAO1/pMMB with 1mM IPTG. RNA-seq data were generated by three biological replicates. As expected, the expression of TonB-dependent transducer hxuA was considerably...”
- The Small RNA ErsA Impacts the Anaerobic Metabolism of Pseudomonas aeruginosa Through Post-Transcriptional Modulation of the Master Regulator Anr
Ferrara, Frontiers in microbiology 2021 - “...Trunk et al., 2010 PA5027 hypothetical protein D 2.00 U U Trunk et al., 2010 PA5446 hypothetical protein D 2.17 U Trunk et al., 2010 a D, downregulation; U, upregulation b Log 2 of Fold Change (FC) calculated as ratio of expression in ersA vs. wt...”
- Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions
Yan, Journal of applied genetics 2017 - “...in the exposure to hydrogen peroxide (Chang et al. 2005 ), two genes PA5479 and PA5446 appeared in two new clusters with PAH degradation genes PA2508 and PA4121, respectively, so network analysis does penetrate into different mechanisms. Of highly up/down-regulated genes in response to oxidative stress,...”
- Step-wise loss of bacterial flagellar torsion confers progressive phagocytic evasion
Lovewell, PLoS pathogens 2011 - “...1.389032018 0.000518982 PA4843 hypothetical protein 3.123519763 6.85E-10 PA4953t MotB 0.69302142 0.014485643 PA5053 HslV 0.732046986 0.049682967 PA5446 hypothetical protein 1.010684502 0.01227902 Inherent microbiocidal activity and limited bacteria-cell contact does not provide for phagocytic resistance in non-swimming bacteria An alternative hypothesis to the cellular sensing of bacterial motility...”
- Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis
Folsom, BMC microbiology 2010 - “...2 urocanase PA5212 29 881 hypothetical protein PA5427 adhA 112 2664 O 2 alcohol dehydrogenase PA5446 7 866 hypothetical protein PA5460 118 3962 hypothetical protein PA5475 294 2787 O 2 hypothetical protein *Average Rank in drip flow biofilms (DFB) and three comparator microarray data sets (Comp....”
- “...biogenesis. Seven of the genes listed in Table 3 (PA0200, PA0409, PA0713, PA1174, PA3309, PA3572, PA5446) appear on the consensus list of gene transcripts upregulated in P. aeruginosa biofilms reported by Patell et al [ 7 ]. Biological basis of biofilm antibiotic tolerance P. aeruginosa strain...”
- Effect of anaerobiosis and nitrate on gene expression in Pseudomonas aeruginosa
Filiatrault, Infection and immunity 2005 - “...PA5168 PA5169 PA5275 PA5296 PA5304 PA5372 PA5415 PA5436 PA5446 PA5448 PA5460 PA5496 PA5553 PA5554 PA5556 PA5557 ig326671 ig4326394 ig4713098 Gene name 3772...”
- Microarray analysis of Pseudomonas aeruginosa reveals induction of pyocin genes in response to hydrogen peroxide
Chang, BMC genomics 2005 - “...receptor precursor (Transport of small molecules) PA0976 2.7 0.008 Conserved hypothetical protein (Hypothetical, unclassified, unknown) PA5446 2.7 0.048 Hypothetical protein (Hypothetical, unclassified, unknown) PA4229 ( pchC ) 2.6 0.008 Pyochelin biosynthetic protein (Transport of small molecules; Secreted Factors) PA4218 2.6 0.008 Probable transporter (Membrane proteins; Transport...”
BMEII0524 hypothetical protein (NCBI ptt file) from Brucella melitensis 16M
Aligns to 5:43 / 75 (52.0%), covers 91.9% of PF06568, 39.8 bits
Dshi_2778 hypothetical protein (RefSeq) from Dinoroseobacter shibae DFL 12
Aligns to 21:56 / 72 (50.0%), covers 70.3% of PF06568, 39.3 bits
BM28_RS13730 DUF1127 domain-containing protein from Brucella melitensis M28
Aligns to 30:68 / 100 (39.0%), covers 91.9% of PF06568, 39.0 bits
SMc00821 HYPOTHETICAL PROTEIN (NCBI ptt file) from Sinorhizobium meliloti 1021
Aligns to 29:65 / 98 (37.8%), covers 94.6% of PF06568, 37.2 bits
- Control of Bacterial Sulfite Detoxification by Conserved and Species-Specific Regulatory Circuits
Tan, Frontiers in microbiology 2019 - “...rpoE1 itself. In contrast, the genes proposed to be controlled by SmRpoE4 ( SMc04164 , SMc00821 , and SMc00108 ) were expressed at very low levels throughout and showed no variation between the Sm. meliloti WT and Sm. meliloti rpoE 4 strains, indicating that they are...”
- Sinorhizobium meliloti sigma factors RpoE1 and RpoE4 are activated in stationary phase in response to sulfite
Bastiat, PloS one 2012 - “...azu2 ) Probable pseudoazurin (blue copper protein) 2.2 ND SMc04164 Conserved hypothetical protein 5.9 9.8 SMc00821 Conserved hypothetical protein 2.2 18.0 SMc00108 Putative acetyltransferase 3.9 18.9 iii) rpoE4 deletion ( wt vs rpoE4) in the presence of thiosulfate SMc04051 ( rpoE4 ) Putative ECF sigma factor...”
- “...RpoE4. Microarray analyses of the rpoE4 -overexpressing strain showed increased transcription of SMc00108, SMc04164 and SMc00821. However, these genes were not induced by thiosulfate ( Fig. S2 ) nor did they display upstream putative RpoE4 or RpoE1 recognition sites. We concluded these are indirect effects of...”
PFWH6_RS27895 DUF1127 domain-containing protein from Pseudomonas fluorescens WH6
Aligns to 28:64 / 74 (50.0%), covers 94.6% of PF06568, 37.1 bits
PSPTO_5466 conserved hypothetical protein (NCBI ptt file) from Pseudomonas syringae pv. tomato str. DC3000
BUE60_19565 DUF1127 domain-containing protein from Pseudomonas syringae pv. actinidiae
Aligns to 26:62 / 71 (52.1%), covers 94.6% of PF06568, 36.0 bits
PP0153 conserved hypothetical protein (NCBI ptt file) from Pseudomonas putida KT2440
Aligns to 26:62 / 71 (52.1%), covers 94.6% of PF06568, 35.0 bits
Atu1847 hypothetical protein (RefSeq) from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 54:84 / 101 (30.7%), covers 78.4% of PF06568, 31.7 bits
SFHH103_00451 DUF1127 domain-containing protein from Sinorhizobium fredii HH103
Aligns to 29:65 / 98 (37.8%), covers 94.6% of PF06568, 31.2 bits
PA2031 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 26:66 / 84 (48.8%), covers 100.0% of PF06568, 30.2 bits
- Absence of 4-Formylaminooxyvinylglycine Production by Pseudomonas fluorescens WH6 Results in Resource Reallocation from Secondary Metabolite Production to Rhizocompetence.
Manning, Microorganisms 2021 - “...biosynthesis (Chou et al. 2013). The BRBH of PFWH6_RS27895 and RS27900 were a hypothetical protein (PA2031) and GntR (PA2032), respectively; unlike those in the WH6 genome, these genes are not adjacent to pauB4 in PAO1. Attempts to knockout the PFWH6_RS27895 resulted only in merodiploids suggesting its...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...Probable pyridoxamine 5-phosphate oxidase PA1927 metE 1.3 + 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase PA2030 1.6 + Hypothetical protein PA2031 1.7 + Hypothetical protein PA2062 2.4 Probable pyridoxal-phosphate dependent enzyme PA2066 1.1 1.6 + Hypothetical protein PA2067 1.4 1.8 + Probable hydrolase PA2068 2.6 1.9 + Probable major facilitator superfamily...”
- Food as a source for quorum sensing inhibitors: iberin from horseradish revealed as a quorum sensing inhibitor of Pseudomonas aeruginosa
Jakobsen, Applied and environmental microbiology 2012 - “...PA1901 PA1902 PA1903 PA1904 PA1905 PA1999 PA2000 PA2030 PA2031 PA2067 PA2069 PA2146 PA2190 PA2193 PA2194 PA2195 PA2300 PA2366 PA2384 PA2433 PA2566 PA2570 PA2588...”
- In-vivo expression profiling of Pseudomonas aeruginosa infections reveals niche-specific and strain-independent transcriptional programs
Bielecki, PloS one 2011 - “...hypothetical unknown protein. PA1060 - predicted permease, DMT superfamily. PA1856 encoding probable cytochrome oxidase subunit. PA2031 hypothetical unknown. PA2663 encoding membrane protein of unknown function. PA2664 fhp , flavohemoprotein, aerobic nitric oxide detoxification. PA2847 predicted permease. PA4147 acoR , transcriptional activator of acetoin/glycerol. PA5176 conserved hypothetical...”
- Cellular reporter screens for inhibitors of Burkholderia pseudomallei targets in Pseudomonas aeruginosa
Moir, Transactions of the Royal Society of Tropical Medicine and Hygiene 2008 - “...). Some of the responding genes appear to be in operons, for example, PA2030 and PA2031 for coaD , PA4181 and PA4182 for glmU , PA2403 through PA2410 for secA , and PA0612 through PA0648 for gyrA . Of particular note, the gyrA -depletion-responsive operon has...”
- “...Ratio Control Strain & Condition PA2030 hypothetical protein 10.59 1.23 1.33 0.45 0.73 7.4 MDM1168 PA2031 hypothetical protein 12.53 1.82 1.48 0.60 0.72 n.d. PA3361 hypothetical protein 15.68 0.20 0.44 0.14 0.64 n.d. PA4607 hypothetical protein 8.46 0.71 1.14 0.21 1.12 2.5 MDM1141 PA1471 hypothetical protein...”
- Quorum-sensing antagonistic activities of azithromycin in Pseudomonas aeruginosa PAO1: a global approach
Nalca, Antimicrobial agents and chemotherapy 2006 - “...PA5482 PA0139 d PA0586 PA0852 d,e PA1048 PA1244 PA1871e PA2031 PA2146c PA2171c PA2190 c PA2259 PA2274 PA2300 e PA2564e PA2565 PA3049 PA3478 e PA3529 d PA3533...”
- A cystic fibrosis epidemic strain of Pseudomonas aeruginosa displays enhanced virulence and antimicrobial resistance
Salunkhe, Journal of bacteriology 2005 - “...PA1896 PA1897 PA1901 PA1902 PA1903 PA1904 PA1905 PA1999 PA2000 PA2001 PA2030 PA2031 PA2066 aprI 2.6 11 3.3 osmC coxA 4.6 64 24 nuh 6.3 26 5.0 14 24 3.1 2.8 21...”
- Screening for quorum-sensing inhibitors (QSI) by use of a novel genetic system, the QSI selector
Rasmussen, Journal of bacteriology 2005 - “...PA1989 PA1999 PA2000 PA2001 PA2002 PA2013 PA2021 PA2030 PA2031 PA2035 PA2046 PA2050 PA2066 PA2067 PA2068 PA2069 PA2084 PA2086 PA2088 PA2090 PA2093 PA2110 Gene...”
- More
PA14_38260 hypothetical protein (NCBI) from Pseudomonas aeruginosa UCBPP-PA14
Aligns to 26:66 / 84 (48.8%), covers 100.0% of PF06568, 27.4 bits
Atu8135 hypothetical protein (RefSeq) from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 37:66 / 97 (30.9%), covers 51.4% of PF06568, 26.8 bits
Or search for genetic data about PF06568 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory