MMSYN1 0042 lilzhu8

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Author Information

Lillian Zhu

Basic Information

  • ID: MMSYN1_0042
  • Name: rpiR
  • Organism: JCVI-Syn3.0
  • Description: This protein's putative function is transcription regulation (rpiR family). It is not well characterized, but aligns fairly well with an E. coli gene that is involved in repressing transcription by binding directly to DNA. RpiR genes tend to be involved in sugar processing and the synthesis of phosphosugars. It controls a family of genes likely involved in the pentose phosphate pathway, where 5-carbon sugars are interconverted. [1] Ribose can be converted to a number of other isomeric sugars. The sugar will bind to the rpiR protein, inactivating it and allowing the genes it controls to be expressed. Like many rpiR family transcription regulator proteins, this gene contains a helix-turn-helix motif, which is crucial for DNA binding. [2] [3]
  • DNA Length: 828 base pairs.
  • DNA sequence:


  • Amino Acid length: 275 amino acids.
  • Amino Acid sequence:


Function and Homologs

  • Product: A MurR/RpiR family transcription regulator protein (putative) [4]
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • MurR/RpiR family transcriptional regulator [Mycoplasma yeatsii], 316/99%/2e-105/57%, WP_004428675.1
    • MurR/RpiR family transcriptional regulator [Mycoplasma putrefaciens], 246/99%/6e-78/47%, WP_015587146.1
    • MurR/RpiR family transcriptional regulator [Mesoplasma syrphidae], 209/100%/4e-63/38%, WP_027048288.1
  • Equivalent E. coli / JCVI functional protein: EG12459.


  • Expression Level: high.
  • Expression Level Hypothesis: The ribulose-ribose interconversion may be more important in M. mycoides than E. coli, so it is under greater control and needs more of the regulatory element.
  • Expression Level References and Description: M. genitalium Simulation
  • Expression Time: early
  • Expression Time Hypothesis: Since ribose is a component of many other molecules, and sugar processing is important, this gene should probably come online early to help regulate the mechanism.
  • Expression Time References and Description: Inference based on function and product, somewhat hypothetical since this is based on homology

Gene Context

  • Other Components in the functional module: rpiB, catalyzes the interconversion of ribulose-5-P and ribose-5-P
  • Possible Dependencies: gap, an enzyme important in glycolysis, from which the pentoses are derived
  • Reactions: pentose phosphate pathway [1]
    • Input: ribulose-5-phosphate
    • Output: ribose-5-phosphate

Pentose phosphate pathway.png


  • 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


  1. 1.0 1.1 [1] JB article
  2. [2] NCBI
  3. [3] UniProt
  4. [4] NCBI result