MMSYN1 0422

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Author Information

Luis Fernando Varela

Basic Information

  • ID: MMSYN1_0422
  • Name: rpmB
  • Organism: JCVI-Syn3.0
  • Description: The L28 protein is a component of the 50S subunit of the ribosome and is required for ribosome assembly. L28 interacts with 23S rRNA and crosslinks to L9. L28 is labeled by the macrolides carbomycin A, niddamycin and tylosin, which inhibit ribosomal activity. As a note, 50S is the larger subunit of the 70S ribosome of prokaryotes. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. Also, for its functions, 50S includes the activity that catalyzes peptide bond formation (peptidyl transfer reaction), prevents premature polypeptide hydrolysis, provides a binding site for the G-protein factors (assists initiation, elongation, and termination), and helps protein folding after synthesis.
  • DNA Length: 195 base pairs.
  • DNA sequence:

ATG GCA CGC CGC GAC GCA TTA ACA GGT AAA AGT GCC TTG TCT GGA CAA TCA CGC TCA CAT GCC CTG AAT GCA ACA AAG CGT AAG TGG AAT TTA AAT TTA CAA AAG GTG CGT GTG ATG GAT GAA AAC GGC AGT GTT TTC AAT ATC AAG GTA TCC GCT CGC ACG CTG CGT ACA TTA AAA AAG CAA GAG AAA ATC GTA

  • Amino Acid length: 65 amino acids.
  • Amino Acid sequence:

MARRDALTGKSALSGQSRSHALNATKRKWNLNLQKVRVMDENGSVFNIKVSARTLRTLKKQEKIV

Function and Homologs

  • Product: 50S ribosomal protein L28
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • 50S ribosomal protein L28 [Mycoplasma leachii], Max score: 128 / Query Cover: 100% / E-Value: 7e-38 / Ident: 98%, WP_013447791.1
    • 50S ribosomal protein L28 [Entomoplasma lucivorax], Max score: 95.9 / Query Cover: 98% / E-Value: 7e-25 / Ident: 72%, WP_028127065.1
    • 50S ribosomal protein L28 [Mycoplasma imitans], Max score: 77.8 / Query Cover: 95% / E-Value: 1e-17 / Ident: 63%, WP_027121847.1
  • Equivalent E. coli functional protein: EG10886

Expression

  • Expression Level: high
  • Expression Level Hypothesis: is a part of a functioning ribosomes, which the cell needs in order to build all proteins; a large number of ribosomes facilitates fast cell growth.
  • Expression Level References and Description: M. genitalium model data
  • Expression Time: right at the beginning
  • Expression Level Hypothesis: This protein is a subunit of the ribosome and is critical in the ribosome assembly, which is critical for protein synthesis, so my theory is that it should function right at the beginning
  • Expression Time References and Description: Found information about ribosomes and their functionality in [1]

Gene Context

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file