gistfile1.txt

from Bio.Seq import Seq
from Bio import Entrez
from Bio import pairwise2
from Bio.Align import substitution_matrices
from Bio.pairwise2 import format_alignment
Entrez.email = "<hidden @ mail>"
blosum62 = substitution_matrices.load("BLOSUM62")


def get_protein_sequence(id: str) -> str:
    fasta = Entrez.efetch(db="protein", id=id,
                          rettype="fasta", retmode="txt")
    fasta_list = fasta.readlines()
    fasta_list.pop(0)
    return "".join(fasta_list).strip().replace("\n", "")


human_id = "CAA35621.1"
fly_id = "NP_476761.3"

human_sequence = get_protein_sequence(human_id)
fly_sequence = get_protein_sequence(fly_id)
alignments = pairwise2.align.localds(
    # Gap costs taken from the defaults on the blast algorithm page
    # for BlOSUM62
    Seq(human_sequence[-10:]), Seq(fly_sequence[-10:]), blosum62, -11, -1)

for a in alignments:
    print(format_alignment(*a))

# output:
TSCAQNWIYE
|..|..||||
TPAAKDWIYE
Score=37