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NCBI: 10-JUN-2013
⊟Summary[edit | edit source]
- organism: Staphylococcus aureus COL
- locus tag: SACOL2054 [new locus tag: SACOL_RS10750 ]
- pan locus tag?: SAUPAN005333000
- symbol: rpoF
- pan gene symbol?: sigB
- synonym:
- product: RNA polymerase sigma factor SigB
⊟Genome View[edit | edit source]
⊟Gene[edit | edit source]
⊟General[edit | edit source]
- type: CDS
- locus tag: SACOL2054 [new locus tag: SACOL_RS10750 ]
- symbol: rpoF
- product: RNA polymerase sigma factor SigB
- replicon: chromosome
- strand: -
- coordinates: 2121192..2121962
- length: 771
- essential: unknown other strains
⊟Accession numbers[edit | edit source]
- Gene ID: 3237972 NCBI
- RefSeq: YP_186870 NCBI
- BioCyc: see SACOL_RS10750
- MicrobesOnline: 913531 MicrobesOnline
⊟Phenotype[edit | edit source]
Share your knowledge and add information here. [edit]
⊟DNA sequence[edit | edit source]
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721ATGGCGAAAGAGTCGAAATCAGCTAATGAAATTTCACCTGAGCAAATTAACCAATGGATT
AAAGAACACCAAGAAAATAAGAATACAGATGCACAGGATAAGTTAGTTAAACATTACCAA
AAACTAATTGAGTCATTGGCATATAAATATTCTAAAGGACAATCACATCACGAAGATTTA
GTTCAAGTTGGTATGGTTGGTTTAATAGGTGCCATAAATAGATTCGATATGTCCTTTGAA
CGGAAGTTTGAAGCCTTTTTAGTACCTACTGTAATCGGTGAAATCAAAAGATATCTACGA
GATAAAACTTGGAGTGTACATGTTCCGAGACGTATTAAAGAAATTGGGCCAAGAATCAAA
AAAGTGAGCGATGAACTAACCGCTGAATTAGAGCGTTCACCTTCTATCAGTGAAATAGCT
GATCGATTAGAAGTCTCAGAAGAAGAAGTGTTAGAAGCAATGGAAATGGGACAAAGTTAT
AATGCGTTAAGTGTTGATCATTCCATTGAAGCTGATAAAGATGGTTCAACTGTTACGCTA
TTAGATATTATGGGGCAACAAGATGACCATTATGACTTAACTGAAAAACGTATGATTTTA
GAAAAAATATTACCTATATTATCTGATCGCGAACGAGAAATCATACAATGTACGTTTATT
GAAGGATTGAGTCAAAAAGAGACAGGTGAGCGTATCGGTTTAAGTCAAATGCATGTATCA
CGACTTCAGAGAACGGCAATTAAGAAATTACAAGAAGCAGCACATCAATAG60
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⊟Protein[edit | edit source]
⊟General[edit | edit source]
- locus tag: SACOL2054 [new locus tag: SACOL_RS10750 ]
- symbol: RpoF
- description: RNA polymerase sigma factor SigB
- length: 256
- theoretical pI: 5.645
- theoretical MW: 29443.3
- GRAVY: -0.616016
⊟Function[edit | edit source]
- TIGRFAM: RNA polymerase sigma-B factor (TIGR02941; HMM-score: 485.3)and 30 moreRNA polymerase sigma-70 factor, sigma-B/F/G subfamily (TIGR02980; HMM-score: 303.8)Cellular processes Sporulation and germination RNA polymerase sigma-F factor (TIGR02885; HMM-score: 179.8)Transcription Transcription factors RNA polymerase sigma-F factor (TIGR02885; HMM-score: 179.8)Cellular processes Sporulation and germination RNA polymerase sigma-G factor (TIGR02850; HMM-score: 145.1)Transcription Transcription factors RNA polymerase sigma-G factor (TIGR02850; HMM-score: 145.1)RNA polymerase sigma factor, sigma-70 family (TIGR02937; HMM-score: 138.1)RNA polymerase sigma factor, FliA/WhiG family (TIGR02479; HMM-score: 119.6)RNA polymerase sigma factor, cyanobacterial RpoD-like family (TIGR02997; HMM-score: 92.6)Transcription Transcription factors RNA polymerase sigma factor RpoD (TIGR02393; HMM-score: 81.4)Cellular processes Sporulation and germination RNA polymerase sigma-K factor (TIGR02846; HMM-score: 69.9)Transcription Transcription factors RNA polymerase sigma-K factor (TIGR02846; HMM-score: 69.9)Cellular processes Adaptations to atypical conditions alternative sigma factor RpoH (TIGR02392; HMM-score: 67.8)Transcription Transcription factors alternative sigma factor RpoH (TIGR02392; HMM-score: 67.8)Cellular processes Adaptations to atypical conditions RNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 65.4)Transcription Transcription factors RNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 65.4)Cellular processes Sporulation and germination RNA polymerase sigma-E factor (TIGR02835; HMM-score: 63)Transcription Transcription factors RNA polymerase sigma-E factor (TIGR02835; HMM-score: 63)RNA polymerase sigma-70 factor, Bacteroides expansion family 1 (TIGR02985; HMM-score: 47)RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1 (TIGR02984; HMM-score: 35.8)Cellular processes Sporulation and germination RNA polymerase sigma-H factor (TIGR02859; HMM-score: 35.1)Transcription Transcription factors RNA polymerase sigma-H factor (TIGR02859; HMM-score: 35.1)RNA polymerase sigma-70 factor, TIGR02952 family (TIGR02952; HMM-score: 34)RNA polymerase sigma factor, SigZ family (TIGR02959; HMM-score: 26.3)RNA polymerase sigma-70 factor, sigma-E family (TIGR02983; HMM-score: 23.3)RNA polymerase sigma factor, TIGR02999 family (TIGR02999; HMM-score: 21.2)Cellular processes Sporulation and germination RNA polymerase sigma-I factor (TIGR02895; HMM-score: 19.7)Transcription Transcription factors RNA polymerase sigma-I factor (TIGR02895; HMM-score: 19.7)RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family (TIGR02989; HMM-score: 18.8)RNA polymerase sigma-70 factor, Myxococcales family 1 (TIGR03001; HMM-score: 16.2)RNA polymerase sigma factor RpoE (TIGR02939; HMM-score: 13.7)
- TheSEED :
- RNA polymerase sigma factor SigB
Regulation and Cell signaling Quorum sensing and biofilm formation Biofilm formation in Staphylococcus RNA polymerase sigma factor SigBand 2 more - PFAM: HTH (CL0123) Sigma70_r3; Sigma-70 region 3 (PF04539; HMM-score: 64.1)Sigma70_r4; Sigma-70, region 4 (PF04545; HMM-score: 62.8)Sigma70_r2; Sigma-70 region 2 (PF04542; HMM-score: 61.7)and 16 moreSigma70_r4_2; Sigma-70, region 4 (PF08281; HMM-score: 26.5)Sigma70_ECF; ECF sigma factor (PF07638; HMM-score: 23)GerE; Bacterial regulatory proteins, luxR family (PF00196; HMM-score: 21.9)HTH_16; Helix-turn-helix domain (PF12645; HMM-score: 21.6)HTH_23; Homeodomain-like domain (PF13384; HMM-score: 19.8)HTH_3; Helix-turn-helix (PF01381; HMM-score: 16.8)IF2_N; Translation initiation factor IF-2, N-terminal region (PF04760; HMM-score: 16.7)HTH_Tnp_1; Transposase (PF01527; HMM-score: 16.6)HTH_38; Helix-turn-helix domain (PF13936; HMM-score: 16.3)KORA; TrfB plasmid transcriptional repressor (PF16509; HMM-score: 16.1)HTH_37; Helix-turn-helix domain (PF13744; HMM-score: 15)HTH_AsnC-type; AsnC-type helix-turn-helix domain (PF13404; HMM-score: 14.8)HTH_31; Helix-turn-helix domain (PF13560; HMM-score: 14.8)HTH_24; Winged helix-turn-helix DNA-binding (PF13412; HMM-score: 13.6)HTH_28; Helix-turn-helix domain (PF13518; HMM-score: 13)HTH_Crp_2; Crp-like helix-turn-helix domain (PF13545; HMM-score: 12.3)
⊟Structure, modifications & cofactors[edit | edit source]
⊟Localization[edit | edit source]
- PSORTb: Cytoplasmic
- Cytoplasmic Score: 9.97
- Cytoplasmic Membrane Score: 0
- Cellwall Score: 0.01
- Extracellular Score: 0.02
- Internal Helices: 0
- LocateP: Intracellular
- Prediction by SwissProt Classification: Cytoplasmic
- Pathway Prediction: No pathway
- Intracellular possibility: 1
- Signal peptide possibility: -1
- N-terminally Anchored Score: 1
- Predicted Cleavage Site: No CleavageSite
- SignalP: no predicted signal peptide
- SP(Sec/SPI): 0.007397
- TAT(Tat/SPI): 0.000536
- LIPO(Sec/SPII): 0.000631
- predicted transmembrane helices (TMHMM): 0
⊟Accession numbers[edit | edit source]
⊟Protein sequence[edit | edit source]
- MAKESKSANEISPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQEAAHQ
⊟Experimental data[edit | edit source]
- experimentally validated: PeptideAtlas
- protein localization: Cytoplasmic [3] [4] [5]
- quantitative data / protein copy number per cell: 118 [6]
- interaction partners:
SACOL1513 (hup) DNA-binding protein HU [7] (data from MRSA252) SACOL1102 (pdhA) pyruvate dehydrogenase complex E1 component subunit alpha [7] (data from MRSA252) SACOL1103 (pdhB) pyruvate dehydrogenase complex E1 component subunit beta [7] (data from MRSA252) SACOL1104 (pdhC) branched-chain alpha-keto acid dehydrogenase E2 [7] (data from MRSA252) SACOL1105 (pdhD) dihydrolipoamide dehydrogenase [7] (data from MRSA252) SACOL0584 (rplA) 50S ribosomal protein L1 [7] (data from MRSA252) SACOL1257 (rplS) 50S ribosomal protein L19 [7] (data from MRSA252) SACOL1702 (rplU) 50S ribosomal protein L21 [7] (data from MRSA252) SACOL2213 (rpoA) DNA-directed RNA polymerase subunit alpha [7] (data from MRSA252) SACOL0588 (rpoB) DNA-directed RNA polymerase subunit beta [7] (data from MRSA252) SACOL0589 (rpoC) DNA-directed RNA polymerase subunit beta' [7] (data from MRSA252) SACOL2120 (rpoE) DNA-directed RNA polymerase subunit delta [7] (data from MRSA252) SACOL2055 (rsbW) serine-protein kinase RsbW [7] (data from MRSA252) SACOL0405 MATE efflux family protein [7] (data from MRSA252) SACOL1099 hypothetical protein [7] (data from MRSA252)
⊟Expression & Regulation[edit | edit source]
⊟Operon[edit | edit source]
- MicrobesOnline: rpoF < rsbW < rsbV < rsbU
⊟Regulation[edit | edit source]
- regulator: SigB* (activation) regulon
⊟Transcription pattern[edit | edit source]
- S.aureus Expression Data Browser: data available for NCTC8325
⊟Protein synthesis (provided by Aureolib)[edit | edit source]
⊟Protein stability[edit | edit source]
- half-life: no data available
⊟Biological Material[edit | edit source]
⊟Mutants[edit | edit source]
⊟Expression vector[edit | edit source]
⊟lacZ fusion[edit | edit source]
⊟GFP fusion[edit | edit source]
⊟two-hybrid system[edit | edit source]
⊟FLAG-tag construct[edit | edit source]
⊟Antibody[edit | edit source]
⊟Other Information[edit | edit source]
You are kindly invited to share additional interesting facts.
⊟Literature[edit | edit source]
⊟References[edit | edit source]
- ↑ 1.0 1.1 Markus Bischoff, Paul Dunman, Jan Kormanec, Daphne Macapagal, Ellen Murphy, William Mounts, Brigitte Berger-Bächi, Steven Projan
Microarray-based analysis of the Staphylococcus aureus sigmaB regulon.
J Bacteriol: 2004, 186(13);4085-99
[PubMed:15205410] [WorldCat.org] [DOI] (P p) - ↑ 2.0 2.1 Jan Pané-Farré, Beate Jonas, Konrad Förstner, Susanne Engelmann, Michael Hecker
The sigmaB regulon in Staphylococcus aureus and its regulation.
Int J Med Microbiol: 2006, 296(4-5);237-58
[PubMed:16644280] [WorldCat.org] [DOI] (P p) - ↑ Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
PLoS One: 2009, 4(12);e8176
[PubMed:19997597] [WorldCat.org] [DOI] (I e) - ↑ Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
J Proteome Res: 2011, 10(4);1657-66
[PubMed:21323324] [WorldCat.org] [DOI] (I p) - ↑ Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
The Staphylococcus aureus proteome.
Int J Med Microbiol: 2014, 304(2);110-20
[PubMed:24439828] [WorldCat.org] [DOI] (I p) - ↑ Daniela Zühlke, Kirsten Dörries, Jörg Bernhardt, Sandra Maaß, Jan Muntel, Volkmar Liebscher, Jan Pané-Farré, Katharina Riedel, Michael Lalk, Uwe Völker, Susanne Engelmann, Dörte Becher, Stephan Fuchs, Michael Hecker
Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis.
Sci Rep: 2016, 6;28172
[PubMed:27344979] [WorldCat.org] [DOI] (I e) - ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 Artem Cherkasov, Michael Hsing, Roya Zoraghi, Leonard J Foster, Raymond H See, Nikolay Stoynov, Jihong Jiang, Sukhbir Kaur, Tian Lian, Linda Jackson, Huansheng Gong, Rick Swayze, Emily Amandoron, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Osvaldo Santos-Filho, Peter Axerio-Cilies, Kendall Byler, William R McMaster, Robert C Brunham, B Brett Finlay, Neil E Reiner
Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus.
J Proteome Res: 2011, 10(3);1139-50
[PubMed:21166474] [WorldCat.org] [DOI] (I p)
⊟Relevant publications[edit | edit source]
Jan Pané-Farré, Beate Jonas, Konrad Förstner, Susanne Engelmann, Michael Hecker
The sigmaB regulon in Staphylococcus aureus and its regulation.
Int J Med Microbiol: 2006, 296(4-5);237-58
[PubMed:16644280] [WorldCat.org] [DOI] (P p)Jan Pané-Farré, Beate Jonas, Steven W Hardwick, Katrin Gronau, Richard J Lewis, Michael Hecker, Susanne Engelmann
Role of RsbU in controlling SigB activity in Staphylococcus aureus following alkaline stress.
J Bacteriol: 2009, 191(8);2561-73
[PubMed:19201800] [WorldCat.org] [DOI] (I p)