MMSYN1 0407

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Author Information

Max Kucera

Basic Information

  • ID: MMSYN1_0407
  • Name: rpoD
  • Organism: JCVI-Syn3.0
  • Description: DNA Binding, sigma factor activity, transcription factor activity, and sequence-specific DNA binding. It has a strong interaction with the RNA polymerase and is key to the growth of the organism. [1] [2]
  • DNA Length: 1521
  • DNA sequence:

ATG GCT AAA TTC AAT AAC AAA TCC GAA TTG AAA AAG ATC GCA TCA TTT AAC GAT TTC CTG GAT TAT ACT GTG TCA TTT GCA AAC AAA AAC AAC AAT GAG ATC AGT TCG GAG GAC GTG CTG GAA GTT TTT GCA AAC ATC TTC CCA AAT GCG TCA GAC AAC GAA AGT GAA AAA ATT TTA GAT GTC CTG CAA CAG AAA GGT ATC GTA TTC AGC GAC TTG ATT GAC GAT GAC ATC GAA CAA GAA GAG CTT GAA GAA GTG GAG GAG GAG ATT GAA GAC GTT AAC TTG GAG GAG CTT GAA GAA CTG GAA AAT TTG GAG GAT CTT GAC GAC CTG GAC TTC GAT TTA GAT TCC ACT TCT AAC AAC TTG GAC GAT TAC GAC GAA AAT GTT AAT GAC GAT CTG GAC GAG TTC AAA GAG GCC AAG AGC GCG GCA ATC AAG GGT CGT AAG TCC GCG AAG TCG AGC AAC CAT ATG AAG TAT CGC GTA GGT GGA ATT TCG AAT GAG ACA AAG ATT CAA GAC ATT ATT AAG ACG TAC TTC TAC AAA ATT GGT CAG GCA CCT ATC TTG ACC AAG GAG CAG GAG ATT ATT TAC GCC AAG ATG GCC GTA TCC GAT GAC CCA GAA GAT GTT CAG GAA GGG CGC AAT AAG CTT ATT GAA AGC AAT CTG AAA TTA GTA ATT TCT GTG GCT CGT AAG CAC TTA AAT CGC GGT TTG GAT TTC GCC GAC TTG ATT GAG GAG GGG AAT ATC GGA CTG ATG AAA GCG GTT GAC AAG TTT GAG TAT GAA AAA GGA TTT AAA TTC TCA ACA TAT GCT ACC TGG TGG ATT CGC CAG GCC ATT ACA CGT GCT ATT GCG GAC CAA GCA CGC ACG ATT CGC ATC CCT GTG CAT ATG GTT GAA ACG ATC AAT AAA CTG GCA CGT GTT GAG CGT CAG CTG ACA CAG GAA CTG GGG CGC GAG CCG AAT GCC GAC GAA ATC GCA AAC CGC GTA GGC GAA GGG ATC ACG GGG GAT AAG GTT ATC GAG ATT AAA AAG CTT TCG ATT GAA CCA GTG TCG CTG GAA AAA CCG TTT GGG GAC GAG GAT GAT ACG CAT TTC GGA GAT TTT GTT GAG GAC AAG GAT ATG GTG AGC CCC AAT GAA TAC ACA GAG AAG GAG ATT TTA AAA GAG GTT ATG GAT AAG GTA TTT GAA GAC ATG CCC CCA CGC GAA GAG AAA GTC ATC CGC ATG CGC TAT GGT ATT GTT CCT ACT CGT CTT CGT ACA CTG CTG CGC TTA GCT CAA GAA TGT AAC GAT TCA AAC GCA AAG GAG CTG AAG CAG GCC ATC GAG GAA TTA GAC ATC CAC TTA GAC ACT CCG ATT GAA AAG GTC CGT AAG TTT AAC AAT CAG ATT ATT AAT AAC AAC TTG GCT AAA TAT GAT TCG GCA CGC ACA CTG GAA GAG GTC GGA AAG GAA TTG AAC GTG ACT CGC GAG CGT ATT CGC CAG ATT GAA GCG AAA ACC ATT CGC AAG CTG AAA CAA CCG TCG CCC AAT AAC AAG TCA GGA AAG ACG TTA AAA GAA TTC TAT AAG GGT TAT TAG

  • Amino Acid length: 506
  • Amino Acid sequence:

MAKFNNKSELKKIASFNDFLDYTVSFANKNNNEISSEDVLEVFANIFPNASDNESEKILDVLQQKGIVFSDLIDDDIEQEELEEVEEEIEDVNLEELEELENLEDLDDLDFDLDSTSNNLDDYDENVNDDLDEFKEAKSAAIKGRKSAKSSNHMKYRVGGISNETKIQDIIKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRGLDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPFGDEDDTHFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPTRLRTLLRLAQECNDSNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSARTLEEVGKELNVTRERIRQIEAKTIRKLKQPSPNNKSGKTLKEFYKGY

Function and Homologs

  • Product: RNA polymerase sigma factor
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • RNA polymerase sigma factor RpoD [Mycoplasma capricolum], 276/100%/3e-88/82%, [1]
    • RNA polymerase subunit sigma [Mycoplasma capricolum], 266/100%/4e-84/82%, [2]
    • DNA-directed RNA polymerase sigma-70 factor [Mycoplasma feriruminatoris], 241/100%r/3e-74/75%, [3]
  • Equivalent E. coli / JCVI functional protein: EG10896.

Expression

  • Expression Level: [medium]
  • Expression Level Hypothesis: This gene is part of the transcription process which is a key component in the cell cycle so it is needed a lot for this. It is probably only medium, though, because the other rpoX family genes are not as abundant and they all work together meaning that a lack of those genes would justify less of this gene.
  • Expression Level References and Description: I found out that the protein is produced at 61 proteins/cell through the File:MgenitaliumSimProteinCounts.xlsx database. [3] I learned about the cell regulating growth through the ecocyc database. [4]
  • 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. [5]

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. [6]
  • Process: RNA Polymerase, transcription [7]
    • 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/C7LMQ6
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG10896
  • http://e80boot.org/index.php?title=File:MgenitaliumSimProteinCounts.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=MMSYN1_0407&oldid=11894"