MMSYN1 0128

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Author Information

Max Kucera

Basic Information

  • ID: MMSYN1_0128
  • Name: rpoE
  • Organism: JCVI-Syn3.0
  • Description: This protein conducts biological processes as well as the regulation of transcription. It is also a process that modulates the frequency, rate and extent of cellular DNA-templated transcription. Furthermore, it specializes in response to heat shock and other membrane stresses. [1] [2]
  • DNA Length: 429
  • DNA sequence:

ATG TCG AAG GTT CGC AAC CTG GAT TTG GTG TAT TCA TAC CTG CAA AGT ACA AAA ACC CCC TCC AGT TTG AAT GAG ATT TGG AAG TCC ATT TCT AAA GAC ATC ATC TCT CAG AAA AAA GAC GAA ATT AGC GTT ATT GCC GAC TTG TAT GGG GAC ATG GTA CTG GAC AAT CGT TTT GCT TTG ACT ACG GAT AAC TTA TGG GCT CTT TCG TCG AAC TCA TCG GTT GAG AAT ATC AAA AAG CAG TAC GAC GAC TTT ATC AAT ACG GAT CAT AAG CAT CGC TAC TCA GAT TCT GAC GAG GAG CTT ACT ATC GAT GAC GAG ATG TTG TTG GAT GAA GAT TAC GAC AGT GAC TTC ACA CAG GAG TTA GAC GAT TTC GAT GAA GAC TTC GAC GAT ACC GAC CAA ACG TAC ATC GAT GAC GAC GAA TAT AAC CGT TAG

  • Amino Acid length: 142
  • Amino Acid sequence:

MSKVRNLDLVYSYLQSTKTPSSLNEIWKSISKDIISQKKDEISVIADLYGDMVLDNRFALTTDNLWALSSNSSVENIKKQYDDFINTDHKHRYSDSDEELTIDDEMLLDEDYDSDFTQELDDFDEDFDDTDQTYIDDDEYNR

Function and Homologs

  • Product: Uncharacterized protein
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • DNA-directed RNA polymerase subunit delta [Mycoplasma feriruminatoris], 254/100%/2e-85/94, [1]
    • DNA-directed RNA polymerase subunit delta [Mycoplasma capricolum], 212/100%/1e-68/87, [2]
    • DNA-directed RNA polymerase subunit delta [Mycoplasma leachii], 204/100%/3e-65/83, [3]
  • Equivalent E. coli / JCVI functional protein: EG11897

Expression

  • Expression Level: [high]
  • Expression Level Hypothesis: This gene is used in heat shock in cell membranes. Since organisms are commonly being exposed to heat through the use of energy and exposure to outside elements, this protein would have to be produced a lot to resist the heat negatively affecting the cells.
  • Expression Level References and Description: I found out that the protein is produced a lot at 464 proteins/cell through the File:MgenitaliumSimProteinCounts.xlsx database. [3] I learned about the cells function from the ecocyc database. [4]
  • Expression Time: [early]
  • Expression Level Hypothesis: This gene helps regulate the transcription of heat shock proteins. This happens during the growth of the cell and is a crucial part of the central dogma components so it happens early on in the process.
  • Expression Time References and Description: Ecocyc database and a cell cycle guide. [5] [6]

Gene Context

  • Other Components: EG10894
  • Possible Dependencies: This gene initiates the transcription of peptidyl-prolyl cis-trans isomerase FkpA [[4]]. The FkpA also acts as a chaperone to the periplasm, so without this gene, our RNA would not be able to carry out its regulation of the transcription. [7]
  • Process: RNA Polymerase, transcription [8]
    • 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
  • http://www.uniprot.org/uniprot/C7LLZ8
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • http://e80boot.org/index.php?title=File:MgenitaliumSimProteinCounts.xlsx
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • http://www.atdbio.com/content/14/Transcription-Translation-and-Replication
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG11897
  • Retrieved from "http://e80boot.org/index.php?title=MMSYN1_0128&oldid=13320"