In order to support the genotype assignment based on the NS5B region, sequence analysis was performed on the core region for selected isolates, confirming the subtype assignment performed within the NS5B region in 63 of them (Figure 3).
Sequence analysis was based on ≈726 nt in the 3′ variable region of eae, which corresponded to amino acids 33 275 within the C-terminal 280 aa of intimin (Int280).
Based on this information, PCR and sequence analysis was used to recover the complete Epulopiscium gpr - spoIIP operon.
Nipponbare, based on sequence analysis are classified into five categories (column 1).
Since the mass calculated based on sequence analysis is 6172.2, the difference of 6 mass units indicates that all of the six Cys residues are involved in 3 disulfide bonds.
wittichii) strain RW1, had a single LigE homologue that, based on sequence analysis, is more similar to RpHypGST (which had a shorter sequence and did not exhibit β-etherase activity) than to the confirmed β-etherases in the LigE cluster.
This also means that examination of Transcription Factor Binding Sites based on DNA sequence analysis are of little value here.
While no formal guidelines have been established for what constitutes a significant sequence similarity between an introduced protein and familiar proteins normally present in foods, one general recommendation based on evolutionary sequence analysis is that proteins sharing <20% identity over 100 or more amino acids should not be considered homologs (Doolittle, 1990).
Since we obtained soluble proteins for all 14 yBRDs, the domain boundary for yBRD constructs, which was defined based on the SMART/PFAM sequence analysis, is likely correct.
With the increasing number of M protein types being described over the year, a new system based on emm gene sequence analysis is adopted.
