EG10896

From BioE80 Boot
Jump to: navigation, search

Author Information

Max Kucera

Basic Information

  • ID: EG10896
  • Name: rpoD
  • Organism: E. coli
  • Description: This gene is the primary sigma factor during exponential growth by targeting RNA polymerase sigma 70 with promoters that are essential for normal growth. Additionally, it transcribes with higher efficiency genes encoding ribosomal proteins and other protein synthesis-related genes, such as rRNA- and tRNA-encoding genes and prfB. [1]
  • DNA Length: 1842
  • DNA sequence:

atgGAGCAAA ACCCGCAGTC ACAGCTGAAA CTTCTTGTCA CCCGTGGTAA GGAGCAAGGC TATCTGACCT ATGCCGAGGT CAATGACCAT CTGCCGGAAG ATATCGTCGA TTCAGATCAG ATCGAAGACA TCATCCAAAT GATCAACGAC ATGGGCATTC AGGTGATGGA AGAAGCACCG GATGCCGATG ATCTGATGCT GGCTGAAAAC ACCGCGGACG AAGATGCTGC CGAAGCCGCC GCGCAGGTGC TTTCCAGCGT GGAATCTGAA ATCGGGCGCA CGACTGACCC GGTACGCATG TACATGCGTG AAATGGGCAC CGTTGAACTG TTGACCCGCG AAGGCGAAAT TGACATCGCT AAGCGTATTG AAGACGGGAT CAACCAGGTT CAATGCTCCG TTGCTGAATA TCCGGAAGCG ATCACCTATC TGCTGGAACA GTACGATCGT GTTGAAGCAG AAGAAGCGCG TCTGTCCGAT CTGATCACCG GCTTTGTTGA CCCGAACGCA GAAGAAGATC TGGCACCTAC CGCCACTCAC GTCGGTTCTG AGCTTTCCCA GGAAGATCTG GACGATGACG AAGATGAAGA CGAAGAAGAT GGCGATGACG ACAGCGCCGA TGATGACAAC AGCATCGACC CGGAACTGGC TCGCGAAAAA TTTGCGGAAC TACGCGCTCA GTACGTTGTA ACGCGTGACA CCATCAAAGC GAAAGGTCGC AGTCACGCTA CCGCTCAGGA AGAGATCCTG AAACTGTCTG AAGTATTCAA ACAGTTCCGC CTGGTGCCGA AGCAGTTTGA CTACCTGGTC AACAGCATGC GCGTCATGAT GGACCGCGTT CGTACGCAAG AACGTCTGAT CATGAAGCTC TGCGTTGAGC AGTGCAAAAT GCCGAAGAAA AACTTCATTA CCCTGTTTAC CGGCAACGAA ACCAGCGATA CCTGGTTCAA CGCGGCAATT GCGATGAACA AGCCGTGGTC GGAAAAACTG CACGATGTCT CTGAAGAAGT GCATCGCGCC CTGCAAAAAC TGCAGCAGAT TGAAGAAGAA ACCGGCCTGA CCATCGAGCA GGTTAAAGAT ATCAACCGTC GTATGTCCAT CGGTGAAGCG AAAGCCCGCC GTGCGAAGAA AGAGATGGTT GAAGCGAACT TACGTCTGGT TATTTCTATC GCTAAGAAAT ACACCAACCG TGGCTTGCAG TTCCTTGACC TGATTCAGGA AGGCAACATC GGTCTGATGA AAGCGGTTGA TAAATTCGAA TACCGCCGTG GTTACAAGTT CTCCACCTAC GCAACCTGGT GGATCCGTCA GGCGATCACC CGCTCTATCG CGGATCAGGC GCGCACCATC CGTATTCCGG TGCATATGAT TGAGACCATC AACAAGCTCA ACCGTATTTC TCGCCAGATG CTGCAAGAGA TGGGCCGTGA ACCGACGCCG GAAGAACTGG CTGAACGTAT GCTGATGCCG GAAGACAAGA TCCGCAAAGT GCTGAAGATC GCCAAAGAGC CAATCTCCAT GGAAACGCCG ATCGGTGATG ATGAAGATTC GCATCTGGGG GATTTCATCG AGGATACCAC CCTCGAGCTG CCGCTGGATT CTGCGACCAC CGAAAGCCTG CGTGCGGCAA CGCACGACGT GCTGGCTGGC CTGACCGCGC GTGAAGCAAA AGTTCTGCGT ATGCGTTTCG GTATCGATAT GAACACCGAC TACACGCTGG AAGAAGTGGG TAAACAGTTC GACGTTACCC GCGAACGTAT CCGTCAGATC GAAGCGAAGG CGCTGCGCAA ACTGCGTCAC CCGAGCCGTT CTGAAGTGCT GCGTAGCTTC CTGGACGATt aa

  • Amino Acid length: 614
  • Amino Acid sequence:

MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND MGIQVMEEAP DADDLMLAEN TADEDAAEAA AQVLSSVESE IGRTTDPVRM YMREMGTVEL LTREGEIDIA KRIEDGINQV QCSVAEYPEA ITYLLEQYDR VEAEEARLSD LITGFVDPNA EEDLAPTATH VGSELSQEDL DDDEDEDEED GDDDSADDDN SIDPELAREK FAELRAQYVV TRDTIKAKGR SHATAQEEIL KLSEVFKQFR LVPKQFDYLV NSMRVMMDRV RTQERLIMKL CVEQCKMPKK NFITLFTGNE TSDTWFNAAI AMNKPWSEKL HDVSEEVHRA LQKLQQIEEE TGLTIEQVKD INRRMSIGEA KARRAKKEMV EANLRLVISI AKKYTNRGLQ FLDLIQEGNI GLMKAVDKFE YRRGYKFSTY ATWWIRQAIT RSIADQARTI RIPVHMIETI NKLNRISRQM LQEMGREPTP EELAERMLMP EDKIRKVLKI AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL RAATHDVLAG LTAREAKVLR MRFGIDMNTD YTLEEVGKQF DVTRERIRQI EAKALRKLRH PSRSEVLRSF LDD

Function and Homologs

  • Product: RNA polymerase, sigma 70 (sigma D) factor
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Chain F, Crystal Structure Of E. Coli Rna Polymerase In Complex With Ppgpp, 1254/100%/0.0/100%, [1]
    • MULTISPECIES: RNA polymerase sigma factor RpoD [Proteobacteria], 1253/100%/0.0/99%, [2]
    • Chain F, Three-dimensional Em Structure Of An Intact Activator-dependent Transcription Initiation Complex, 1251/100%/0.0/99%, [3]
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0407

Expression

  • Expression Level: [high]
  • Expression Level Hypothesis: This gene is part of the transcription process which is a key component in the cell cycle. Furthermore, it is a key component in cell growth which justifies needing a lot of this gene since it is one of the most crucial processes in the system.
  • Expression Level References and Description: I found out that the protein is produced a lot at 1657 proteins/cell through the File:EcoliProteomicExpressionData.xlsx database. [2] I learned about the cell regulating growth through the ecocyc database. [3]
  • Expression Time: [early]
  • Expression Level Hypothesis: Since this gene is part of the transcription process, it must occur during the early stages of the process. Also, as a key component of cell growth, it is needed early on to drive activity.
  • Expression Time References and Description: I used the ecocyc page to look at the processes that this gene is part of and determined at what stage these processes occur in the overall cycle. [4]

Gene Context

  • Other Components: EG10894 rpoB
  • Possible Dependencies: rsd, regulator of σ70 (σD), stationary phase protein is used to control the amount of this gene used. [5]
  • Process: RNA Polymerase, transcription [6]
    • Inputs: DNA
    • Outputs: mRNA

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10896
  • http://e80boot.org/index.php?title=File:EcoliProteomicExpressionData.xlsx
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10896
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10896
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10896
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10896
  • Retrieved from "http://e80boot.org/index.php?title=EG10896&oldid=11882"