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m (Text replacement - "gene Genbank" to "gene RefSeq") |
m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "") |
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__TOC__ | |||
<protect> | <protect> | ||
<aureodatabase> | <aureodatabase>annotation</aureodatabase> | ||
=Summary= | =Summary= | ||
* <aureodatabase>organism</aureodatabase> | *<aureodatabase>organism</aureodatabase> | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>pan locus</aureodatabase> | *<aureodatabase>pan locus</aureodatabase> | ||
* <aureodatabase>gene symbol</aureodatabase> | *<aureodatabase>gene symbol</aureodatabase> | ||
* <aureodatabase>pan gene symbol</aureodatabase> | *<aureodatabase>pan gene symbol</aureodatabase> | ||
* <aureodatabase>gene synonyms</aureodatabase> | *<aureodatabase>gene synonyms</aureodatabase> | ||
* <aureodatabase>product</aureodatabase> | *<aureodatabase>product</aureodatabase> | ||
</protect> | </protect> | ||
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==General== | ==General== | ||
* <aureodatabase>gene type</aureodatabase> | *<aureodatabase>gene type</aureodatabase> | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>gene symbol</aureodatabase> | *<aureodatabase>gene symbol</aureodatabase> | ||
* <aureodatabase>product</aureodatabase> | *<aureodatabase>product</aureodatabase> | ||
* <aureodatabase>gene replicon</aureodatabase> | *<aureodatabase>gene replicon</aureodatabase> | ||
* <aureodatabase>strand</aureodatabase> | *<aureodatabase>strand</aureodatabase> | ||
* <aureodatabase>gene coordinates</aureodatabase> | *<aureodatabase>gene coordinates</aureodatabase> | ||
* <aureodatabase>gene length</aureodatabase> | *<aureodatabase>gene length</aureodatabase> | ||
* <aureodatabase>essential</aureodatabase> | *<aureodatabase>essential</aureodatabase> | ||
*<aureodatabase>gene comment</aureodatabase> | |||
</protect> | </protect> | ||
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==Accession numbers== | ==Accession numbers== | ||
* <aureodatabase>gene GI</aureodatabase> | *<aureodatabase>gene GI</aureodatabase> | ||
* <aureodatabase>gene RefSeq</aureodatabase> | *<aureodatabase>gene RefSeq</aureodatabase> | ||
*<aureodatabase>gene BioCyc</aureodatabase> | |||
*<aureodatabase>gene MicrobesOnline</aureodatabase> | |||
</protect> | </protect> | ||
<protect> | <protect> | ||
==Phenotype== | ==Phenotype== | ||
</protect> | </protect> | ||
Share your knowledge and add information here. [<span class="plainlinks">[//aureowiki.med.uni-greifswald.de/index.php?title={{PAGENAMEE}}&veaction=edit§ion=6 edit]</span>] | |||
<protect> | <protect> | ||
==DNA sequence== | ==DNA sequence== | ||
* <aureodatabase>gene sequence</aureodatabase> | *<aureodatabase>gene sequence</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
<aureodatabase>RNA regulated operons</aureodatabase> | |||
</protect> | |||
<protect> | |||
=Protein= | =Protein= | ||
<aureodatabase>protein 3D view</aureodatabase> | <aureodatabase>protein 3D view</aureodatabase> | ||
==General== | ==General== | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>protein symbol</aureodatabase> | *<aureodatabase>protein symbol</aureodatabase> | ||
* <aureodatabase>protein description</aureodatabase> | *<aureodatabase>protein description</aureodatabase> | ||
* <aureodatabase>protein length</aureodatabase> | *<aureodatabase>protein length</aureodatabase> | ||
* <aureodatabase>theoretical pI</aureodatabase> | *<aureodatabase>theoretical pI</aureodatabase> | ||
* <aureodatabase>theoretical MW</aureodatabase> | *<aureodatabase>theoretical MW</aureodatabase> | ||
* <aureodatabase>GRAVY</aureodatabase> | *<aureodatabase>GRAVY</aureodatabase> | ||
</protect> | </protect> | ||
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==Function== | ==Function== | ||
* <aureodatabase>protein reaction</aureodatabase> | *<aureodatabase>protein reaction</aureodatabase> | ||
* <aureodatabase>protein TIGRFAM</aureodatabase> | *<aureodatabase>protein TIGRFAM</aureodatabase> | ||
* <aureodatabase>protein TheSeed</aureodatabase> | *<aureodatabase>protein TheSeed</aureodatabase> | ||
* <aureodatabase>protein PFAM</aureodatabase> | *<aureodatabase>protein PFAM</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
==Structure, modifications & | ==Structure, modifications & cofactors== | ||
* <aureodatabase>protein domains</aureodatabase> | *<aureodatabase>protein domains</aureodatabase> | ||
* <aureodatabase>protein modifications</aureodatabase> | *<aureodatabase>protein modifications</aureodatabase> | ||
* <aureodatabase>protein cofactors</aureodatabase> | *<aureodatabase>protein cofactors</aureodatabase> | ||
* <aureodatabase>protein effectors</aureodatabase> | *<aureodatabase>protein effectors</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein regulated operons</aureodatabase> | ||
</protect> | </protect> | ||
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==Localization== | ==Localization== | ||
* <aureodatabase>protein Psortb</aureodatabase> | *<aureodatabase>protein Psortb</aureodatabase> | ||
* <aureodatabase>protein LocateP</aureodatabase> | *<aureodatabase>protein LocateP</aureodatabase> | ||
* <aureodatabase>protein SignalP</aureodatabase> | *<aureodatabase>protein SignalP</aureodatabase> | ||
* <aureodatabase>protein TMHMM</aureodatabase> | *<aureodatabase>protein TMHMM</aureodatabase> | ||
</protect> | </protect> | ||
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==Accession numbers== | ==Accession numbers== | ||
* <aureodatabase>protein GI</aureodatabase> | *<aureodatabase>protein GI</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein RefSeq</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein UniProt</aureodatabase> | ||
</protect> | </protect> | ||
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==Protein sequence== | ==Protein sequence== | ||
* <aureodatabase>protein sequence</aureodatabase> | *<aureodatabase>protein sequence</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
== | ==Experimental data== | ||
* <aureodatabase>protein validated peptides</aureodatabase> | *<aureodatabase>protein validated peptides</aureodatabase> | ||
*<aureodatabase>protein validated localization</aureodatabase> | |||
*<aureodatabase>protein validated quantitative data</aureodatabase> | |||
*<aureodatabase>protein partners</aureodatabase> | |||
</protect> | </protect> | ||
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==Operon== | ==Operon== | ||
* <aureodatabase>operons</aureodatabase> | *<aureodatabase>operons</aureodatabase> | ||
</protect> | </protect> | ||
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==Regulation== | ==Regulation== | ||
*<aureodatabase>regulators</aureodatabase> | |||
* <aureodatabase>regulators</aureodatabase> | |||
</protect> | </protect> | ||
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==Transcription pattern== | ==Transcription pattern== | ||
* <aureodatabase>expression browser</aureodatabase> | *<aureodatabase>expression browser</aureodatabase> | ||
</protect> | </protect> | ||
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==Protein synthesis (provided by Aureolib)== | ==Protein synthesis (provided by Aureolib)== | ||
* <aureodatabase>protein synthesis Aureolib</aureodatabase> | *<aureodatabase>protein synthesis Aureolib</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
== | ==Protein stability== | ||
* <aureodatabase>protein half-life</aureodatabase> | *<aureodatabase>protein half-life</aureodatabase> | ||
</protect> | </protect> | ||
Latest revision as of 22:25, 10 March 2016
NCBI: 26-AUG-2013
⊟Summary[edit | edit source]
- organism: Staphylococcus aureus N315
- locus tag: SA1869 [new locus tag: SA_RS10750 ]
- pan locus tag?: SAUPAN005333000
- symbol: sigB
- 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: SA1869 [new locus tag: SA_RS10750 ]
- symbol: sigB
- product: RNA polymerase sigma factor SigB
- replicon: chromosome
- strand: -
- coordinates: 2118150..2118920
- length: 771
- essential: no DEG other strains
⊟Accession numbers[edit | edit source]
- Gene ID: 1124768 NCBI
- RefSeq: NP_375172 NCBI
- BioCyc: see SA_RS10750
- MicrobesOnline: 104198 MicrobesOnline
⊟Phenotype[edit | edit source]
Share your knowledge and add information here. [edit]
⊟DNA sequence[edit | edit source]
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721ATGGCGAAAGAGTCGAAATCAGCTAATGAAGTTTCACCTGAGCAAATTAACCAATGGATT
AAAGAACACCAAGAAAATAAGAATACAGATGCACAGGATAAGTTAGTTAAACATTACCAA
AAACTAATTGAGTCATTGGCATATAAATATTCTAAAGGACAATCACATCACGAAGATTTA
GTTCAAGTTGGTATGGTTGGTTTAATAGGTGCCATAAATAGATTCGATATGTCCTTTGAA
CGGAAGTTTGAAGCCTTTTTAGTACCTACTGTAATCGGTGAAATCAAAAGATATCTACGA
GATAAAACTTGGAGTGTACATGTTCCGAGACGTATTAAAGAAATTGGGCCAAGAATCAAA
AAAGTGAGCGATGAACTAACCGCTGAATTAGAGCGTTCACCTTCTATCAGTGAAATAGCT
AATCGATTAGAAGTCTCAGAAGAAGAAGTGTTAGAAGCAATGGAAATGGGACAAAGTTAT
AATGCGTTAAGTGTTGATCATTCCATTGAAGCTGATAAAGATGGTTCAACTGTTACGCTA
TTAGATATTATGGGGCAACAAGATGACCATTATGACTTAACTGAAAAACGTATGATTTTA
GAAAAAATATTACCTATATTATCTGATCGCGAACGAGAAATCATACAATGTACGTTTATT
GAAGGATTGAGTCAAAAAGAGACAGGTGAGCGTATCGGTTTAAGTCAAATGCATGTATCA
CGACTTCAGAGAACGGCAATTAAGAAATTACAAGAAGCAGCACATAAATAG60
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⊟Protein[edit | edit source]
⊟General[edit | edit source]
- locus tag: SA1869 [new locus tag: SA_RS10750 ]
- symbol: SigB
- description: RNA polymerase sigma factor SigB
- length: 256
- theoretical pI: 6.06399
- theoretical MW: 29428.3
- GRAVY: -0.61875
⊟Function[edit | edit source]
- TIGRFAM: RNA polymerase sigma-B factor (TIGR02941; HMM-score: 486.4)and 30 moreRNA polymerase sigma-70 factor, sigma-B/F/G subfamily (TIGR02980; HMM-score: 303.1)Cellular processes Sporulation and germination RNA polymerase sigma-F factor (TIGR02885; HMM-score: 179.7)Transcription Transcription factors RNA polymerase sigma-F factor (TIGR02885; HMM-score: 179.7)Cellular processes Sporulation and germination RNA polymerase sigma-G factor (TIGR02850; HMM-score: 144.9)Transcription Transcription factors RNA polymerase sigma-G factor (TIGR02850; HMM-score: 144.9)RNA polymerase sigma factor, sigma-70 family (TIGR02937; HMM-score: 137.5)RNA polymerase sigma factor, FliA/WhiG family (TIGR02479; HMM-score: 120)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)Cellular processes Sporulation and germination RNA polymerase sigma-K factor (TIGR02846; HMM-score: 69.7)Transcription Transcription factors RNA polymerase sigma-K factor (TIGR02846; HMM-score: 69.7)Cellular processes Adaptations to atypical conditions alternative sigma factor RpoH (TIGR02392; HMM-score: 67.3)Transcription Transcription factors alternative sigma factor RpoH (TIGR02392; HMM-score: 67.3)Cellular processes Adaptations to atypical conditions RNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 65.7)Transcription Transcription factors RNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 65.7)Cellular processes Sporulation and germination RNA polymerase sigma-E factor (TIGR02835; HMM-score: 63.1)Transcription Transcription factors RNA polymerase sigma-E factor (TIGR02835; HMM-score: 63.1)RNA polymerase sigma-70 factor, Bacteroides expansion family 1 (TIGR02985; HMM-score: 46.1)RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1 (TIGR02984; HMM-score: 36.2)Cellular processes Sporulation and germination RNA polymerase sigma-H factor (TIGR02859; HMM-score: 35)Transcription Transcription factors RNA polymerase sigma-H factor (TIGR02859; HMM-score: 35)RNA polymerase sigma-70 factor, TIGR02952 family (TIGR02952; HMM-score: 34.2)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)Cellular processes Sporulation and germination RNA polymerase sigma-I factor (TIGR02895; HMM-score: 19.8)Transcription Transcription factors RNA polymerase sigma-I factor (TIGR02895; HMM-score: 19.8)RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family (TIGR02989; HMM-score: 18.8)RNA polymerase sigma-70 factor, Myxococcales family 1 (TIGR03001; HMM-score: 16.3)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: 64.8)Sigma70_r4; Sigma-70, region 4 (PF04545; HMM-score: 62.1)Sigma70_r2; Sigma-70 region 2 (PF04542; HMM-score: 61.7)and 17 moreSigma70_r4_2; Sigma-70, region 4 (PF08281; HMM-score: 24.6)Sigma70_ECF; ECF sigma factor (PF07638; HMM-score: 23)HTH_16; Helix-turn-helix domain (PF12645; HMM-score: 21.7)GerE; Bacterial regulatory proteins, luxR family (PF00196; HMM-score: 20.1)HTH_Tnp_1; Transposase (PF01527; HMM-score: 17.5)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_23; Homeodomain-like domain (PF13384; HMM-score: 16.7)HTH_38; Helix-turn-helix domain (PF13936; HMM-score: 15.9)KORA; TrfB plasmid transcriptional repressor (PF16509; HMM-score: 15.9)HTH_31; Helix-turn-helix domain (PF13560; HMM-score: 14.4)HTH_37; Helix-turn-helix domain (PF13744; HMM-score: 14.4)HTH_AsnC-type; AsnC-type helix-turn-helix domain (PF13404; HMM-score: 13.5)no clan defined ThylakoidFormat; Thylakoid formation protein (PF11264; HMM-score: 13.3)HTH (CL0123) HTH_28; Helix-turn-helix domain (PF13518; HMM-score: 13.2)no clan defined DUF1108; Protein of unknown function (DUF1108) (PF06531; HMM-score: 12.5)HTH (CL0123) HTH_24; Winged helix-turn-helix DNA-binding (PF13412; HMM-score: 12.5)
⊟Structure, modifications & cofactors[edit | edit source]
- domains:
- modifications:
- cofactors:
- effectors:
- genes regulated by
⊟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): 0.007805
- TAT(Tat/SPI): 0.00056
- LIPO(Sec/SPII): 0.000709
- predicted transmembrane helices (TMHMM): 0
⊟Accession numbers[edit | edit source]
⊟Protein sequence[edit | edit source]
- MAKESKSANEVSPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQEAAHK
⊟Experimental data[edit | edit source]
- experimentally validated: data available for COL, NCTC8325
- protein localization: data available for COL
- quantitative data / protein copy number per cell: data available for COL
- interaction partners:
SA1305 (hu) DNA-binding protein II [1] (data from MRSA252) SA0943-1 (pdhA) pyruvate dehydrogenase E1 component subunit alpha [1] (data from MRSA252) SA0944 (pdhB) pyruvate dehydrogenase E1 component subunit beta [1] (data from MRSA252) SA0945 (pdhC) branched-chain alpha-keto acid dehydrogenase E2 subunit [1] (data from MRSA252) SA0946 (pdhD) dihydrolipoamide dehydrogenase [1] (data from MRSA252) SA0496 (rplA) 50S ribosomal protein L1 [1] (data from MRSA252) SA1084 (rplS) 50S ribosomal protein L19 [1] (data from MRSA252) SA1473 (rplU) 50S ribosomal protein L21 [1] (data from MRSA252) SA2023 (rpoA) DNA-directed RNA polymerase subunit alpha [1] (data from MRSA252) SA0500 (rpoB) DNA-directed RNA polymerase subunit beta [1] (data from MRSA252) SA0501 (rpoC) DNA-directed RNA polymerase subunit beta' [1] (data from MRSA252) SA1930 (rpoE) DNA-directed RNA polymerase subunit delta [1] (data from MRSA252) SA1870 (rsbW) serine-protein kinase RsbW [1] (data from MRSA252) SA0323 hypothetical protein [1] (data from MRSA252) SA0941 hypothetical protein [1] (data from MRSA252)
⊟Expression & Regulation[edit | edit source]
⊟Operon[edit | edit source]
- MicrobesOnline: sigB < rsbW < rsbV < rsbU
⊟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]
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 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]
Hong Zhang, Kazuya Morikawa, Toshiko Ohta, Yusuke Kato
In vitro resistance to the CSalphabeta-type antimicrobial peptide ASABF-alpha is conferred by overexpression of sigma factor sigB in Staphylococcus aureus.
J Antimicrob Chemother: 2005, 55(5);686-91
[PubMed:15761069] [WorldCat.org] [DOI] (P p)