EG11657

From BioE80 Boot
Jump to: navigation, search

Author Information

Danny Pantuso

Basic Information

  • ID: EG11657
  • Name: ybbA
  • Organism: E. coli
  • UniProt ID: [1]
  • Description: ybbA is an efflux ABC transporter, permease protein. The permeases are membrane transport proteins, a class of multipass transmembrane proteins that facilitate the diffusion of a specific molecule in or out of the cell by using proton motive force, an active transport. [2] ABC transporters often consist of multiple subunits, one or two of which are transmembrane proteins and one or two of which are membrane-associated ATPases. The ATPase subunits utilize the energy of adenosine triphosphate (ATP) binding and hydrolysis to energize the translocation of various substrates across membranes, either for uptake or for export of the substrate.[3] Efflux means to throw out of, particularly a cell. Thus, the efflux ABC transporter is the disposal system protein for the cell.
  • DNA Length: 687 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 222 amino acids.
  • Amino Acid sequence:

MPAENIVEVHHLKKSVGQGEHELSILTGVELVVKRGETIALVGESGSGKSTLLAILAGLD DGSSGEVSLVGQPLHNMDEEARAKLRAKHVGFVFQSFMLIPTLNALENVELPALLRGESS AESRNGAKALLEQLGLGKRLDHLPAQLSGGEQQRVALARAFNGRPDVLFADEPTGNLDRQ TGDKIADLLFSLNREHGTTLIMVTHDLQLAARCDRCLRLVNGQLQEEA

Function and Homologs

  • Product: efflux ABC transporter, permease protein
  • Module: putative transport complex
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • MULTISPECIES: ABC transporter ATP-binding protein [Proteobacteria] 454 100% 2e-161 100% WP_001110573.1
    • ABC transporter ATP-binding protein [Escherichia coli] 454 100% 2e-161 99% WP_048224656.1
    • ABC transporter ATP-binding protein [Escherichia coli] 454 100% 2e-161 99% WP_053883298.1
  • Equivalent E. coli / JCVI functional protein:MMSYN1_0399.

Expression

  • Expression Level: medium
  • Expression Level Hypothesis: Cells must regularly discard waste products as the cell grows and consumes resources. Although the exact function of this gene is unknown, we can guess that an ABC transporter must be produced at a medium amount so that the "trash" is taken out, but not so much that resources are thrown out unnecessarily.
  • Expression Level References and Description: I was unable to determine which exact ABC transporter this gene encodes, but as a whole, ABC transporters generally have a medium expression rate according to the Ecoli Data Set.
  • Expression Time: Late
  • Expression Level Hypothesis: The cell does not need to immediately start disposing of toxins. Waste accumulation and disposal process is a result time and decay, so it follows that this protein should be expressed later on in the cell's lifecycle.
  • Expression Time References and Description: Gene description.

Gene Context

  • Other Components: Unknown
  • Possible Dependencies: Protein Salvage
  • Process: metabolite uptake transport
    • Inputs: ATP, molecule being transported
    • Outputs: ADP, phosphate, molecule being transported
    • Reference: [[2]]

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