geneviewer
0.3.11GitHub

Erythromycin protein alignment results ​

This dataset contains detailed information on genes involved in the biosynthesis of Erythromycin, an antibiotic produced by the bacterium Saccharopolyspora erythraea and several homologous gene clusters identified by antiSMASH. It includes gene identifiers, chromosomal positions, orientations, and annotations regarding their products and functions, as well as identity and similarity scores from protein_blast(), which uses global pairwise protein alignments.

Usage ​

python
from geneviewer import datasets

erythromycin_BlastP = datasets.load("erythromycin_BlastP")

Format ​

A pandas DataFrame with 148 observations and 16 variables:

  • protein_id: Unique protein identifiers. A character vector.
  • region: The chromosomal region of the gene, indicating start and end positions and strand. A character vector.
  • translation: Amino acid sequence of the protein encoded by the gene. A character vector.
  • cluster: Identifier of the gene cluster to which the gene belongs. A character vector.
  • strand: The strand orientation ("forward" or "complement") of the gene. A character vector.
  • start: The start position of the gene on the chromosome. A numeric vector.
  • end: The end position of the gene on the chromosome. A numeric vector.
  • rowID: A unique identifier for each row in the dataset. An integer vector.
  • identity: The percentage of identical positions in the global alignment with the best hit. A numeric vector.
  • similarity: The percentage of identical or similar amino acids in the global alignment with the best hit. A numeric vector.
  • BlastP: The protein_id of the best hit in the query cluster, or NA if there is none. A character vector.
  • score: Synteny score of the cluster with the query cluster, based on the hits. A numeric vector.
  • Gene: Gene name or identifier if available, otherwise NA. A character vector.
  • Position: Formatted string indicating the gene's position and orientation on the chromosome. A character vector.
  • Product: Description of the gene product. A character vector.
  • Functions: Functional categorization of the gene. A character vector.

Source ​

Derived from protein_blast() alignments of Saccharopolyspora erythraea genes involved in Erythromycin production.