Source:
Generated By: https://synbiohub.org/public/igem/igem2sbol/1
Created by: Gavin Sutton, Shivani Shah
Date created: 2016-09-26 11:00:00
Date modified: 2016-10-08 02:45:00
Attachment Protein g3p, N-terminal Domain
| Types | DnaRegion |
| Roles | CDS Coding |
| Sequences | BBa_K2022000_sequence (Version 1) |
Description
Expression of this part is suggested to induce hypervesiculation in E. coli (Henry et al, 2004), i.e. direct the bacterium to overproduce outer membrane vesicles (OMVs).References:
Henry, T., Pommier, S., Journet, L., Bernadac, A., Gorvel, J.P. and Lloub??s, R., 2004. Improved methods for producing outer membrane vesicles in Gram-negative bacteria. Research in Microbiology, 155, pp.437-446.
Stothard, P., 2000. The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques, 28, pp.1102-1104.
Notes
As mentioned in the source section, we reverse translated the amino acid sequence using an E. coli codon-optimisation tool (Stothard, 2000). To codon optimise, however, this tool converts each amino acid to its most commonly used codon, rather than distributing across the degenerate codons proportional to their usage by E. coli (e.g. if an amino acid is coded by two codons, typically distributed 3:2 in other E. coli proteins, then all the amino acids in the optimised sequence will use the most abundant codon and never one of lesser abundance). This may not be ideal, hence alternative tools may be used in the futureWe also added a double stop (TAATAA) to terminate translation, for added stringency, something not included in the original sequence.
Further, we opted to include two versions in the registry: one with, and one without a his-tag. The aim here was provide future users with flexibility and choice
Source
The sequence for this part use was taken from Henry et al (2004), which listed it as residues 1-71 of Attachment Protein g3p from the M13 phage. We took those residues from the Uniprot entry on the protein, and reverse translated using the E. coli codon-optimisation tool (Stothard, 2000). It is worth noting that their version also fused a 6-His tag to the C-terminus; we made this construct as a separate part.| Sequence Annotation | Location | Component / Role(s) |
| Start Double Stop | 1,3 217,222 | start_codon feature/start feature/stop stop_codon |