Protein Embedding Analysis Pipeline¶

This notebook demonstrates how to fetch protein data, calculate embeddings, and visualize protein relationships using t-SNE.

This notebook demonstrates an end-to-end pipeline for protein embedding analysis. Here, we connect to a Neo4j database to fetch protein sequences from the NCBI protein database, compute high-dimensional embeddings using a pre-trained model, and then project these embeddings into two dimensions using t-SNE. The final visualization provides insights into the relationships among proteins based on their sequence properties.

In [3]:

import sys

from loguru import logger
import pandas as pd
import matplotlib.pyplot as plt
from pyeed import Pyeed
from pyeed.analysis.embedding_analysis import EmbeddingTool

logger.remove()
level = logger.add(sys.stderr, level="INFO")

import sys from loguru import logger import pandas as pd import matplotlib.pyplot as plt from pyeed import Pyeed from pyeed.analysis.embedding_analysis import EmbeddingTool logger.remove() level = logger.add(sys.stderr, level="INFO")

Database Connection and Setup¶

Now we'll connect to our Neo4j database and prepare it for new data by:

1. Establishing a connection
2. Wiping any existing data
3. Removing old constraints

In [4]:

uri = "bolt://129.69.129.130:7687"
user = "neo4j"
password = "12345678"

eedb = Pyeed(uri, user=user, password=password)

uri = "bolt://129.69.129.130:7687" user = "neo4j" password = "12345678" eedb = Pyeed(uri, user=user, password=password)

📡 Connected to database.

In [70]:

et = EmbeddingTool()

et = EmbeddingTool()

Fetching Protein Data¶

We'll now fetch protein sequences from the NCBI protein database using a list of protein IDs.

In [71]:

# these are example ids
df = pd.read_csv("resources/data_example.csv", delimiter=";")
print("The data has the following columns:")
print(df.columns)

# create a dict with protein_id_database as key and phenotype as value
dict_data = dict(zip(df["protein_id_database"], df["phenotype"]))

# these are example ids df = pd.read_csv("resources/data_example.csv", delimiter=";") print("The data has the following columns:") print(df.columns) # create a dict with protein_id_database as key and phenotype as value dict_data = dict(zip(df["protein_id_database"], df["phenotype"]))

The data has the following columns:
Index(['protein_name', 'phenotype', 'protein_id', 'protein_id_database'], dtype='object')

In [72]:

# now fecth all of the proteins from the database
eedb.fetch_from_primary_db(df["protein_id_database"].tolist(), db="ncbi_protein")

# now fecth all of the proteins from the database eedb.fetch_from_primary_db(df["protein_id_database"].tolist(), db="ncbi_protein")

2025-02-07 15:21:19.142 | INFO     | pyeed.main:fetch_from_primary_db:87 - Found 0 sequences in the database.
2025-02-07 15:21:19.143 | INFO     | pyeed.main:fetch_from_primary_db:89 - Fetching 68 sequences from ncbi_protein.
2025-02-07 15:21:19.167 | INFO     | pyeed.adapter.primary_db_adapter:execute_requests:140 - Starting requests for 7 batches.
2025-02-07 15:21:19.168 | DEBUG    | pyeed.adapter.primary_db_adapter:execute_requests:142 - Prepared 7 request payloads.
2025-02-07 15:21:19.170 | DEBUG    | pyeed.adapter.primary_db_adapter:_fetch_response:121 - Sending request to https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi with parameters: {'retmode': 'text', 'rettype': 'genbank', 'db': 'protein', 'id': 'AAP20891.1,CAJ85677.1,SAQ02853.1,CDR98216.1,WP_109963600.1,CAA41038.1,WP_109874025.1,CAA46344.1,APG33178.1,AKC98298.1'}
2025-02-07 15:21:19.671 | DEBUG    | pyeed.adapter.primary_db_adapter:_fetch_response:121 - Sending request to https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi with parameters: {'retmode': 'text', 'rettype': 'genbank', 'db': 'protein', 'id': 'KJO56189.1,KLP91446.1,CAA46346.1,CAA74912.2,AFN21551.1,ACB22021.1,CAA76794.1,CAA76795.1,CCG28759.1,KLG19745.1'}
2025-02-07 15:21:20.171 | DEBUG    | pyeed.adapter.primary_db_adapter:_fetch_response:121 - Sending request to https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi with parameters: {'retmode': 'text', 'rettype': 'genbank', 'db': 'protein', 'id': 'AAC32891.1,CAA76796.1,CAD24670.1,ARF45649.1,CTA52364.1,ADL13944.1,AGQ50511.1,AKA60778.1,APT65830.1,HAH6232254.1'}
2025-02-07 15:21:20.672 | DEBUG    | pyeed.adapter.primary_db_adapter:_fetch_response:121 - Sending request to https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi with parameters: {'retmode': 'text', 'rettype': 'genbank', 'db': 'protein', 'id': 'QDO66746.1,CBX53726.1,AAC32889.2,CAA64682.1,CAA71322.1,CAA71323.1,CAA71324.1,AEC32455.1,AAD22538.1,AAD22539.1'}
2025-02-07 15:21:20.749 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAP20891.1
2025-02-07 15:21:20.750 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAP20891.1: Taxonomy ID: 470
2025-02-07 15:21:20.751 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAP20891.1: Mapped organism 'Acinetobacter baumannii' with taxonomy ID 470.
2025-02-07 15:21:20.787 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAP20891.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:20.788 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAP20891.1: Mapped protein with name 'beta-lactamase TEM-1' to 'Protein' object.
2025-02-07 15:21:20.900 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAP20891.1: Mapped 0 site(s).
2025-02-07 15:21:20.901 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAP20891.1.
2025-02-07 15:21:20.902 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAP20891.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:20.902 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:20.940 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAP20891.1: Mapped 1 region(s).
2025-02-07 15:21:20.999 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAP20891.1.
2025-02-07 15:21:21.000 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAP20891.1 in database
2025-02-07 15:21:21.001 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAJ85677.1
2025-02-07 15:21:21.001 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAJ85677.1: Taxonomy ID: 35419
2025-02-07 15:21:21.002 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAJ85677.1: Mapped organism 'Birmingham IncP-alpha plasmid' with taxonomy ID 35419.
2025-02-07 15:21:21.007 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAJ85677.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.008 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAJ85677.1: Mapped protein with name 'beta lactamase' to 'Protein' object.
2025-02-07 15:21:21.018 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAJ85677.1: Mapped 0 site(s).
2025-02-07 15:21:21.018 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAJ85677.1.
2025-02-07 15:21:21.019 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAJ85677.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.019 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.024 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAJ85677.1: Mapped 1 region(s).
2025-02-07 15:21:21.061 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAJ85677.1.
2025-02-07 15:21:21.061 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAJ85677.1 in database
2025-02-07 15:21:21.062 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record SAQ02853.1
2025-02-07 15:21:21.063 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record SAQ02853.1: Taxonomy ID: 571
2025-02-07 15:21:21.063 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record SAQ02853.1: Mapped organism 'Klebsiella oxytoca' with taxonomy ID 571.
2025-02-07 15:21:21.068 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record SAQ02853.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.069 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record SAQ02853.1: Mapped protein with name 'beta-lactamase' to 'Protein' object.
2025-02-07 15:21:21.078 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record SAQ02853.1: Mapped 0 site(s).
2025-02-07 15:21:21.079 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein SAQ02853.1.
2025-02-07 15:21:21.080 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record SAQ02853.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.080 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.113 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record SAQ02853.1: Mapped 1 region(s).
2025-02-07 15:21:21.123 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein SAQ02853.1.
2025-02-07 15:21:21.124 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein SAQ02853.1 in database
2025-02-07 15:21:21.124 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CDR98216.1
2025-02-07 15:21:21.125 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CDR98216.1: Taxonomy ID: 573
2025-02-07 15:21:21.126 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CDR98216.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:21.131 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CDR98216.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.131 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CDR98216.1: Mapped protein with name 'beta-lactamase TEM-4' to 'Protein' object.
2025-02-07 15:21:21.142 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CDR98216.1: Mapped 0 site(s).
2025-02-07 15:21:21.143 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CDR98216.1.
2025-02-07 15:21:21.144 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CDR98216.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.144 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.149 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CDR98216.1: Mapped 1 region(s).
2025-02-07 15:21:21.159 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CDR98216.1.
2025-02-07 15:21:21.160 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CDR98216.1 in database
2025-02-07 15:21:21.160 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record WP_109963600.1
2025-02-07 15:21:21.161 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record WP_109963600.1: Taxonomy ID: 562
2025-02-07 15:21:21.162 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record WP_109963600.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:21.167 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record WP_109963600.1: Mapped protein with name 'extended-spectrum class A beta-lactamase TEM-5' to 'Protein' object.
2025-02-07 15:21:21.206 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record WP_109963600.1: Mapped 0 site(s).
2025-02-07 15:21:21.207 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein WP_109963600.1.
2025-02-07 15:21:21.207 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:174 - Record WP_109963600.1: No CDS feature found.
2025-02-07 15:21:21.208 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record WP_109963600.1: Mapped 1 region(s).
2025-02-07 15:21:21.218 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein WP_109963600.1.
2025-02-07 15:21:21.219 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein WP_109963600.1 in database
2025-02-07 15:21:21.220 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA41038.1
2025-02-07 15:21:21.220 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA41038.1: Taxonomy ID: 562
2025-02-07 15:21:21.221 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA41038.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:21.265 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA41038.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.265 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA41038.1: Mapped protein with name 'beta lactamase TEM6' to 'Protein' object.
2025-02-07 15:21:21.277 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA41038.1: Mapped 0 site(s).
2025-02-07 15:21:21.278 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA41038.1.
2025-02-07 15:21:21.278 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA41038.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.279 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.284 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA41038.1: Mapped 1 region(s).
2025-02-07 15:21:21.295 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA41038.1.
2025-02-07 15:21:21.296 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA41038.1 in database
2025-02-07 15:21:21.296 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record WP_109874025.1
2025-02-07 15:21:21.297 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record WP_109874025.1: Taxonomy ID: 543
2025-02-07 15:21:21.298 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record WP_109874025.1: Mapped organism 'Enterobacteriaceae' with taxonomy ID 543.
2025-02-07 15:21:21.302 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record WP_109874025.1: Mapped protein with name 'extended-spectrum class A beta-lactamase TEM-7' to 'Protein' object.
2025-02-07 15:21:21.314 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record WP_109874025.1: Mapped 0 site(s).
2025-02-07 15:21:21.314 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein WP_109874025.1.
2025-02-07 15:21:21.315 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:174 - Record WP_109874025.1: No CDS feature found.
2025-02-07 15:21:21.316 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record WP_109874025.1: Mapped 1 region(s).
2025-02-07 15:21:21.327 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein WP_109874025.1.
2025-02-07 15:21:21.328 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein WP_109874025.1 in database
2025-02-07 15:21:21.329 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA46344.1
2025-02-07 15:21:21.329 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA46344.1: Taxonomy ID: 573
2025-02-07 15:21:21.330 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA46344.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:21.336 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA46344.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.337 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA46344.1: Mapped protein with name 'extended spectrum beta-lactamase CAZ-2' to 'Protein' object.
2025-02-07 15:21:21.349 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA46344.1: Mapped 0 site(s).
2025-02-07 15:21:21.350 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA46344.1.
2025-02-07 15:21:21.350 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA46344.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.351 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.356 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA46344.1: Mapped 1 region(s).
2025-02-07 15:21:21.367 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA46344.1.
2025-02-07 15:21:21.368 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA46344.1 in database
2025-02-07 15:21:21.369 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record APG33178.1
2025-02-07 15:21:21.369 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record APG33178.1: Taxonomy ID: 562
2025-02-07 15:21:21.370 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record APG33178.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:21.376 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record APG33178.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.377 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record APG33178.1: Mapped protein with name 'class A extended-spectrum beta-lactamase TEM-9' to 'Protein' object.
2025-02-07 15:21:21.389 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record APG33178.1: Mapped 0 site(s).
2025-02-07 15:21:21.389 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein APG33178.1.
2025-02-07 15:21:21.390 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record APG33178.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.390 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.395 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record APG33178.1: Mapped 1 region(s).
2025-02-07 15:21:21.407 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein APG33178.1.
2025-02-07 15:21:21.408 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein APG33178.1 in database
2025-02-07 15:21:21.408 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AKC98298.1
2025-02-07 15:21:21.409 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AKC98298.1: Taxonomy ID: 562
2025-02-07 15:21:21.410 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AKC98298.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:21.417 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AKC98298.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.418 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AKC98298.1: Mapped protein with name 'TEM-1' to 'Protein' object.
2025-02-07 15:21:21.429 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AKC98298.1: Mapped 0 site(s).
2025-02-07 15:21:21.430 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AKC98298.1.
2025-02-07 15:21:21.430 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AKC98298.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.431 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.482 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AKC98298.1: Mapped 1 region(s).
2025-02-07 15:21:21.494 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AKC98298.1.
2025-02-07 15:21:21.495 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AKC98298.1 in database
2025-02-07 15:21:21.502 | DEBUG    | pyeed.adapter.primary_db_adapter:_fetch_response:121 - Sending request to https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi with parameters: {'retmode': 'text', 'rettype': 'genbank', 'db': 'protein', 'id': 'ABB97007.1,ACJ43254.1,AAC05975.1,BCD58813.1,AAK17194.1,AAD33116.2,CAB92324.1,AAL03985.1,AAF19151.1,AAF05613.1'}
2025-02-07 15:21:21.509 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record KJO56189.1
2025-02-07 15:21:21.509 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record KJO56189.1: Taxonomy ID: 299766
2025-02-07 15:21:21.510 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record KJO56189.1: Mapped organism 'Enterobacter hormaechei subsp. steigerwaltii' with taxonomy ID 299766.
2025-02-07 15:21:21.519 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record KJO56189.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.519 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record KJO56189.1: Mapped protein with name 'beta-lactamase TEM' to 'Protein' object.
2025-02-07 15:21:21.541 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record KJO56189.1: Mapped 0 site(s).
2025-02-07 15:21:21.542 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein KJO56189.1.
2025-02-07 15:21:21.542 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record KJO56189.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.543 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.547 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record KJO56189.1: Mapped 1 region(s).
2025-02-07 15:21:21.567 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein KJO56189.1.
2025-02-07 15:21:21.568 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein KJO56189.1 in database
2025-02-07 15:21:21.568 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record KLP91446.1
2025-02-07 15:21:21.569 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record KLP91446.1: Taxonomy ID: 1812934
2025-02-07 15:21:21.569 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record KLP91446.1: Mapped organism 'Enterobacter hormaechei subsp. hoffmannii' with taxonomy ID 1812934.
2025-02-07 15:21:21.574 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record KLP91446.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.575 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record KLP91446.1: Mapped protein with name 'class A beta-lactamase' to 'Protein' object.
2025-02-07 15:21:21.586 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record KLP91446.1: Mapped 0 site(s).
2025-02-07 15:21:21.587 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein KLP91446.1.
2025-02-07 15:21:21.587 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record KLP91446.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.588 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.592 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record KLP91446.1: Mapped 1 region(s).
2025-02-07 15:21:21.608 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein KLP91446.1.
2025-02-07 15:21:21.609 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein KLP91446.1 in database
2025-02-07 15:21:21.609 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA46346.1
2025-02-07 15:21:21.610 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA46346.1: Taxonomy ID: 573
2025-02-07 15:21:21.610 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA46346.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:21.616 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA46346.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.617 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA46346.1: Mapped protein with name 'extended spectrum beta-lactamase CAZ-7' to 'Protein' object.
2025-02-07 15:21:21.631 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA46346.1: Mapped 0 site(s).
2025-02-07 15:21:21.632 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA46346.1.
2025-02-07 15:21:21.633 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA46346.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.633 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.638 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA46346.1: Mapped 1 region(s).
2025-02-07 15:21:21.648 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA46346.1.
2025-02-07 15:21:21.649 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA46346.1 in database
2025-02-07 15:21:21.649 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA74912.2
2025-02-07 15:21:21.650 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA74912.2: Taxonomy ID: 1018
2025-02-07 15:21:21.650 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA74912.2: Mapped organism 'Capnocytophaga ochracea' with taxonomy ID 1018.
2025-02-07 15:21:21.655 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA74912.2: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.656 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA74912.2: Mapped protein with name 'beta-lactamase class A' to 'Protein' object.
2025-02-07 15:21:21.666 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA74912.2: Mapped 0 site(s).
2025-02-07 15:21:21.667 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA74912.2.
2025-02-07 15:21:21.668 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA74912.2: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.668 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.673 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA74912.2: Mapped 1 region(s).
2025-02-07 15:21:21.683 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA74912.2.
2025-02-07 15:21:21.684 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA74912.2 in database
2025-02-07 15:21:21.686 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AFN21551.1
2025-02-07 15:21:21.686 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AFN21551.1: Taxonomy ID: 470
2025-02-07 15:21:21.687 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AFN21551.1: Mapped organism 'Acinetobacter baumannii' with taxonomy ID 470.
2025-02-07 15:21:21.692 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AFN21551.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.693 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AFN21551.1: Mapped protein with name 'beta-lactamase TEM-19' to 'Protein' object.
2025-02-07 15:21:21.703 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AFN21551.1: Mapped 0 site(s).
2025-02-07 15:21:21.704 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AFN21551.1.
2025-02-07 15:21:21.705 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AFN21551.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.705 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.710 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AFN21551.1: Mapped 1 region(s).
2025-02-07 15:21:21.720 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AFN21551.1.
2025-02-07 15:21:21.721 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AFN21551.1 in database
2025-02-07 15:21:21.721 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record ACB22021.1
2025-02-07 15:21:21.722 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record ACB22021.1: Taxonomy ID: 562
2025-02-07 15:21:21.722 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record ACB22021.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:21.728 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record ACB22021.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.729 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record ACB22021.1: Mapped protein with name 'extended spectrum beta-lactamase blaTEM-20' to 'Protein' object.
2025-02-07 15:21:21.741 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record ACB22021.1: Mapped 0 site(s).
2025-02-07 15:21:21.742 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein ACB22021.1.
2025-02-07 15:21:21.742 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record ACB22021.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.743 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.747 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record ACB22021.1: Mapped 1 region(s).
2025-02-07 15:21:21.757 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein ACB22021.1.
2025-02-07 15:21:21.758 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein ACB22021.1 in database
2025-02-07 15:21:21.758 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA76794.1
2025-02-07 15:21:21.759 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA76794.1: Taxonomy ID: 573
2025-02-07 15:21:21.759 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA76794.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:21.766 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA76794.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.766 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA76794.1: Mapped protein with name 'beta-lactamase class A' to 'Protein' object.
2025-02-07 15:21:21.777 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA76794.1: Mapped 0 site(s).
2025-02-07 15:21:21.778 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA76794.1.
2025-02-07 15:21:21.778 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA76794.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.779 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.790 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA76794.1: Mapped 1 region(s).
2025-02-07 15:21:21.804 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA76794.1.
2025-02-07 15:21:21.805 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA76794.1 in database
2025-02-07 15:21:21.805 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA76795.1
2025-02-07 15:21:21.806 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA76795.1: Taxonomy ID: 573
2025-02-07 15:21:21.807 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA76795.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:21.813 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA76795.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.814 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA76795.1: Mapped protein with name 'beta-lactamase class A' to 'Protein' object.
2025-02-07 15:21:21.825 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA76795.1: Mapped 0 site(s).
2025-02-07 15:21:21.826 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA76795.1.
2025-02-07 15:21:21.826 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA76795.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.827 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.832 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA76795.1: Mapped 1 region(s).
2025-02-07 15:21:21.843 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA76795.1.
2025-02-07 15:21:21.843 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA76795.1 in database
2025-02-07 15:21:21.844 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CCG28759.1
2025-02-07 15:21:21.844 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CCG28759.1: Taxonomy ID: 935296
2025-02-07 15:21:21.845 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CCG28759.1: Mapped organism 'Klebsiella aerogenes EA1509E' with taxonomy ID 935296.
2025-02-07 15:21:21.849 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CCG28759.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.850 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CCG28759.1: Mapped protein with name 'Beta-lactamase (EC 3.5.2.6)' to 'Protein' object.
2025-02-07 15:21:21.862 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CCG28759.1: Mapped 0 site(s).
2025-02-07 15:21:21.862 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CCG28759.1.
2025-02-07 15:21:21.863 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CCG28759.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.864 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.914 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CCG28759.1: Mapped 1 region(s).
2025-02-07 15:21:21.925 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CCG28759.1.
2025-02-07 15:21:21.926 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CCG28759.1 in database
2025-02-07 15:21:21.926 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record KLG19745.1
2025-02-07 15:21:21.927 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record KLG19745.1: Taxonomy ID: 208224
2025-02-07 15:21:21.927 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record KLG19745.1: Mapped organism 'Enterobacter kobei' with taxonomy ID 208224.
2025-02-07 15:21:21.932 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record KLG19745.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.933 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record KLG19745.1: Mapped protein with name 'beta-lactamase TEM' to 'Protein' object.
2025-02-07 15:21:21.944 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record KLG19745.1: Mapped 0 site(s).
2025-02-07 15:21:21.945 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein KLG19745.1.
2025-02-07 15:21:21.945 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record KLG19745.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.946 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.951 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record KLG19745.1: Mapped 1 region(s).
2025-02-07 15:21:21.962 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein KLG19745.1.
2025-02-07 15:21:21.963 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein KLG19745.1 in database
2025-02-07 15:21:21.970 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAC32891.1
2025-02-07 15:21:21.971 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAC32891.1: Taxonomy ID: 562
2025-02-07 15:21:21.971 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAC32891.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:21.977 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAC32891.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:21.978 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAC32891.1: Mapped protein with name 'beta-lactamase TEM-28' to 'Protein' object.
2025-02-07 15:21:21.990 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAC32891.1: Mapped 0 site(s).
2025-02-07 15:21:21.991 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAC32891.1.
2025-02-07 15:21:21.991 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAC32891.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:21.992 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:21.997 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAC32891.1: Mapped 1 region(s).
2025-02-07 15:21:22.007 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAC32891.1.
2025-02-07 15:21:22.008 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAC32891.1 in database
2025-02-07 15:21:22.008 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA76796.1
2025-02-07 15:21:22.009 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA76796.1: Taxonomy ID: 562
2025-02-07 15:21:22.010 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA76796.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.021 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA76796.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.022 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA76796.1: Mapped protein with name 'beta-lactamase class A' to 'Protein' object.
2025-02-07 15:21:22.033 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA76796.1: Mapped 0 site(s).
2025-02-07 15:21:22.034 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA76796.1.
2025-02-07 15:21:22.035 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA76796.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.035 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.041 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA76796.1: Mapped 1 region(s).
2025-02-07 15:21:22.051 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA76796.1.
2025-02-07 15:21:22.052 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA76796.1 in database
2025-02-07 15:21:22.053 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAD24670.1
2025-02-07 15:21:22.053 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAD24670.1: Taxonomy ID: 562
2025-02-07 15:21:22.054 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAD24670.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.060 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAD24670.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.061 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAD24670.1: Mapped protein with name 'beta-lactamase' to 'Protein' object.
2025-02-07 15:21:22.073 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAD24670.1: Mapped 0 site(s).
2025-02-07 15:21:22.074 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAD24670.1.
2025-02-07 15:21:22.074 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAD24670.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.075 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.080 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAD24670.1: Mapped 1 region(s).
2025-02-07 15:21:22.091 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAD24670.1.
2025-02-07 15:21:22.091 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAD24670.1 in database
2025-02-07 15:21:22.092 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record ARF45649.1
2025-02-07 15:21:22.092 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record ARF45649.1: Taxonomy ID: 32630
2025-02-07 15:21:22.093 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record ARF45649.1: Mapped organism 'synthetic construct' with taxonomy ID 32630.
2025-02-07 15:21:22.098 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record ARF45649.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.098 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record ARF45649.1: Mapped protein with name 'beta-lactamase TEM-1 variant' to 'Protein' object.
2025-02-07 15:21:22.109 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record ARF45649.1: Mapped 0 site(s).
2025-02-07 15:21:22.110 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein ARF45649.1.
2025-02-07 15:21:22.110 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record ARF45649.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.111 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.116 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record ARF45649.1: Mapped 1 region(s).
2025-02-07 15:21:22.127 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein ARF45649.1.
2025-02-07 15:21:22.128 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein ARF45649.1 in database
2025-02-07 15:21:22.129 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CTA52364.1
2025-02-07 15:21:22.129 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CTA52364.1: Taxonomy ID: 624
2025-02-07 15:21:22.130 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CTA52364.1: Mapped organism 'Shigella sonnei' with taxonomy ID 624.
2025-02-07 15:21:22.135 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CTA52364.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.136 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CTA52364.1: Mapped protein with name 'Beta-lactamase TEM precursor' to 'Protein' object.
2025-02-07 15:21:22.147 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CTA52364.1: Mapped 0 site(s).
2025-02-07 15:21:22.148 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CTA52364.1.
2025-02-07 15:21:22.148 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CTA52364.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.149 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.154 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CTA52364.1: Mapped 1 region(s).
2025-02-07 15:21:22.165 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CTA52364.1.
2025-02-07 15:21:22.166 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CTA52364.1 in database
2025-02-07 15:21:22.166 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record ADL13944.1
2025-02-07 15:21:22.167 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record ADL13944.1: Taxonomy ID: 562
2025-02-07 15:21:22.168 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record ADL13944.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.174 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record ADL13944.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.175 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record ADL13944.1: Mapped protein with name 'TEM-33' to 'Protein' object.
2025-02-07 15:21:22.187 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record ADL13944.1: Mapped 0 site(s).
2025-02-07 15:21:22.188 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein ADL13944.1.
2025-02-07 15:21:22.188 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record ADL13944.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.189 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.193 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record ADL13944.1: Mapped 1 region(s).
2025-02-07 15:21:22.205 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein ADL13944.1.
2025-02-07 15:21:22.206 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein ADL13944.1 in database
2025-02-07 15:21:22.206 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AGQ50511.1
2025-02-07 15:21:22.207 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AGQ50511.1: Taxonomy ID: 562
2025-02-07 15:21:22.207 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AGQ50511.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.213 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AGQ50511.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.214 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AGQ50511.1: Mapped protein with name 'beta lactamase blaTEM-34' to 'Protein' object.
2025-02-07 15:21:22.225 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AGQ50511.1: Mapped 0 site(s).
2025-02-07 15:21:22.225 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AGQ50511.1.
2025-02-07 15:21:22.226 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AGQ50511.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.226 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.231 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AGQ50511.1: Mapped 1 region(s).
2025-02-07 15:21:22.242 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AGQ50511.1.
2025-02-07 15:21:22.243 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AGQ50511.1 in database
2025-02-07 15:21:22.244 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AKA60778.1
2025-02-07 15:21:22.244 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AKA60778.1: Taxonomy ID: 562
2025-02-07 15:21:22.245 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AKA60778.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.252 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AKA60778.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.253 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AKA60778.1: Mapped protein with name 'beta-lactamase' to 'Protein' object.
2025-02-07 15:21:22.263 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AKA60778.1: Mapped 0 site(s).
2025-02-07 15:21:22.264 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AKA60778.1.
2025-02-07 15:21:22.265 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AKA60778.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.266 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.270 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AKA60778.1: Mapped 1 region(s).
2025-02-07 15:21:22.281 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AKA60778.1.
2025-02-07 15:21:22.282 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AKA60778.1 in database
2025-02-07 15:21:22.282 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record APT65830.1
2025-02-07 15:21:22.283 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record APT65830.1: Taxonomy ID: 562
2025-02-07 15:21:22.284 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record APT65830.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.290 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record APT65830.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.291 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record APT65830.1: Mapped protein with name 'inhibitor-resistant class A broad-spectrum beta-lactamase TEM-36' to 'Protein' object.
2025-02-07 15:21:22.303 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record APT65830.1: Mapped 0 site(s).
2025-02-07 15:21:22.303 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein APT65830.1.
2025-02-07 15:21:22.304 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record APT65830.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.304 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.309 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record APT65830.1: Mapped 1 region(s).
2025-02-07 15:21:22.320 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein APT65830.1.
2025-02-07 15:21:22.321 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein APT65830.1 in database
2025-02-07 15:21:22.321 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record HAH6232254.1
2025-02-07 15:21:22.322 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record HAH6232254.1: Taxonomy ID: 562
2025-02-07 15:21:22.322 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record HAH6232254.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.328 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record HAH6232254.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.329 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record HAH6232254.1: Mapped protein with name 'TEM family class A beta-lactamase' to 'Protein' object.
2025-02-07 15:21:22.340 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record HAH6232254.1: Mapped 0 site(s).
2025-02-07 15:21:22.341 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein HAH6232254.1.
2025-02-07 15:21:22.341 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record HAH6232254.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.342 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.391 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record HAH6232254.1: Mapped 0 region(s).
2025-02-07 15:21:22.392 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 0 region(s) to protein HAH6232254.1.
2025-02-07 15:21:22.392 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein HAH6232254.1 in database
2025-02-07 15:21:22.398 | DEBUG    | pyeed.adapter.primary_db_adapter:_fetch_response:121 - Sending request to https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi with parameters: {'retmode': 'text', 'rettype': 'genbank', 'db': 'protein', 'id': 'AAF05614.1,AAF05612.1,AAF05611.1,AAM15527.1,AAL29433.1,AAL29434.1,AAL29435.1,AAL29436.1,CAC43229.1,CAC43230.1'}
2025-02-07 15:21:22.495 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record ABB97007.1
2025-02-07 15:21:22.495 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record ABB97007.1: Taxonomy ID: 562
2025-02-07 15:21:22.496 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record ABB97007.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.503 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record ABB97007.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.504 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record ABB97007.1: Mapped protein with name 'beta-lactamase TEM-55' to 'Protein' object.
2025-02-07 15:21:22.516 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record ABB97007.1: Mapped 0 site(s).
2025-02-07 15:21:22.517 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein ABB97007.1.
2025-02-07 15:21:22.517 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record ABB97007.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.518 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.522 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record ABB97007.1: Mapped 1 region(s).
2025-02-07 15:21:22.532 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein ABB97007.1.
2025-02-07 15:21:22.533 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein ABB97007.1 in database
2025-02-07 15:21:22.534 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record ACJ43254.1
2025-02-07 15:21:22.534 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record ACJ43254.1: Taxonomy ID: 562
2025-02-07 15:21:22.535 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record ACJ43254.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.542 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record ACJ43254.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.542 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record ACJ43254.1: Mapped protein with name 'TEM-57 beta-lactamase' to 'Protein' object.
2025-02-07 15:21:22.555 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record ACJ43254.1: Mapped 0 site(s).
2025-02-07 15:21:22.555 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein ACJ43254.1.
2025-02-07 15:21:22.556 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record ACJ43254.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.557 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.561 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record ACJ43254.1: Mapped 1 region(s).
2025-02-07 15:21:22.572 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein ACJ43254.1.
2025-02-07 15:21:22.573 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein ACJ43254.1 in database
2025-02-07 15:21:22.573 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAC05975.1
2025-02-07 15:21:22.574 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAC05975.1: Taxonomy ID: 588
2025-02-07 15:21:22.574 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAC05975.1: Mapped organism 'Providencia stuartii' with taxonomy ID 588.
2025-02-07 15:21:22.579 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAC05975.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.580 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAC05975.1: Mapped protein with name 'beta-lactamase TEM-60' to 'Protein' object.
2025-02-07 15:21:22.591 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAC05975.1: Mapped 0 site(s).
2025-02-07 15:21:22.592 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAC05975.1.
2025-02-07 15:21:22.593 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAC05975.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.593 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.598 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAC05975.1: Mapped 1 region(s).
2025-02-07 15:21:22.609 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAC05975.1.
2025-02-07 15:21:22.609 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAC05975.1 in database
2025-02-07 15:21:22.610 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record BCD58813.1
2025-02-07 15:21:22.610 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record BCD58813.1: Taxonomy ID: 615
2025-02-07 15:21:22.611 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record BCD58813.1: Mapped organism 'Serratia marcescens' with taxonomy ID 615.
2025-02-07 15:21:22.616 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record BCD58813.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.616 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record BCD58813.1: Mapped protein with name 'class A extended-spectrum beta-lactamase' to 'Protein' object.
2025-02-07 15:21:22.627 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record BCD58813.1: Mapped 0 site(s).
2025-02-07 15:21:22.628 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein BCD58813.1.
2025-02-07 15:21:22.629 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record BCD58813.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.629 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.634 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record BCD58813.1: Mapped 1 region(s).
2025-02-07 15:21:22.645 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein BCD58813.1.
2025-02-07 15:21:22.646 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein BCD58813.1 in database
2025-02-07 15:21:22.646 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAK17194.1
2025-02-07 15:21:22.647 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAK17194.1: Taxonomy ID: 562
2025-02-07 15:21:22.647 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAK17194.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.654 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAK17194.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.654 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAK17194.1: Mapped protein with name 'extended spectrum beta-lactamase TEM-63' to 'Protein' object.
2025-02-07 15:21:22.666 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAK17194.1: Mapped 0 site(s).
2025-02-07 15:21:22.666 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAK17194.1.
2025-02-07 15:21:22.667 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAK17194.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.667 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.672 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAK17194.1: Mapped 1 region(s).
2025-02-07 15:21:22.683 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAK17194.1.
2025-02-07 15:21:22.684 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAK17194.1 in database
2025-02-07 15:21:22.684 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAD33116.2
2025-02-07 15:21:22.685 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAD33116.2: Taxonomy ID: 584
2025-02-07 15:21:22.685 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAD33116.2: Mapped organism 'Proteus mirabilis' with taxonomy ID 584.
2025-02-07 15:21:22.690 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAD33116.2: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.691 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAD33116.2: Mapped protein with name 'beta-lactamase' to 'Protein' object.
2025-02-07 15:21:22.702 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAD33116.2: Mapped 0 site(s).
2025-02-07 15:21:22.702 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAD33116.2.
2025-02-07 15:21:22.703 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAD33116.2: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.703 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.709 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAD33116.2: Mapped 1 region(s).
2025-02-07 15:21:22.719 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAD33116.2.
2025-02-07 15:21:22.720 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAD33116.2 in database
2025-02-07 15:21:22.720 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAB92324.1
2025-02-07 15:21:22.721 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAB92324.1: Taxonomy ID: 72407
2025-02-07 15:21:22.721 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAB92324.1: Mapped organism 'Klebsiella pneumoniae subsp. pneumoniae' with taxonomy ID 72407.
2025-02-07 15:21:22.727 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAB92324.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.727 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAB92324.1: Mapped protein with name 'TEM-68 ES-beta-lactamase' to 'Protein' object.
2025-02-07 15:21:22.739 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAB92324.1: Mapped 0 site(s).
2025-02-07 15:21:22.740 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAB92324.1.
2025-02-07 15:21:22.740 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAB92324.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.741 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.746 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAB92324.1: Mapped 1 region(s).
2025-02-07 15:21:22.756 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAB92324.1.
2025-02-07 15:21:22.757 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAB92324.1 in database
2025-02-07 15:21:22.758 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAL03985.1
2025-02-07 15:21:22.758 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAL03985.1: Taxonomy ID: 573
2025-02-07 15:21:22.759 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAL03985.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:22.765 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAL03985.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.766 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAL03985.1: Mapped protein with name 'extended-spectrum beta-lactamase TEM-71' to 'Protein' object.
2025-02-07 15:21:22.779 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAL03985.1: Mapped 0 site(s).
2025-02-07 15:21:22.780 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAL03985.1.
2025-02-07 15:21:22.781 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAL03985.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.782 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.786 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAL03985.1: Mapped 1 region(s).
2025-02-07 15:21:22.798 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAL03985.1.
2025-02-07 15:21:22.798 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAL03985.1 in database
2025-02-07 15:21:22.799 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAF19151.1
2025-02-07 15:21:22.800 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAF19151.1: Taxonomy ID: 582
2025-02-07 15:21:22.800 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAF19151.1: Mapped organism 'Morganella morganii' with taxonomy ID 582.
2025-02-07 15:21:22.805 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAF19151.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.806 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAF19151.1: Mapped protein with name 'beta-lactamase TEM-72' to 'Protein' object.
2025-02-07 15:21:22.817 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAF19151.1: Mapped 0 site(s).
2025-02-07 15:21:22.819 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAF19151.1.
2025-02-07 15:21:22.819 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAF19151.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.820 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.825 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAF19151.1: Mapped 1 region(s).
2025-02-07 15:21:22.837 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAF19151.1.
2025-02-07 15:21:22.838 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAF19151.1 in database
2025-02-07 15:21:22.838 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAF05613.1
2025-02-07 15:21:22.838 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAF05613.1: Taxonomy ID: 562
2025-02-07 15:21:22.839 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAF05613.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.846 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAF05613.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.847 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAF05613.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-76' to 'Protein' object.
2025-02-07 15:21:22.858 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAF05613.1: Mapped 0 site(s).
2025-02-07 15:21:22.859 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAF05613.1.
2025-02-07 15:21:22.859 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAF05613.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.860 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.865 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAF05613.1: Mapped 1 region(s).
2025-02-07 15:21:22.878 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAF05613.1.
2025-02-07 15:21:22.879 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAF05613.1 in database
2025-02-07 15:21:22.891 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record QDO66746.1
2025-02-07 15:21:22.892 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record QDO66746.1: Taxonomy ID: 562
2025-02-07 15:21:22.893 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record QDO66746.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.899 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record QDO66746.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.900 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record QDO66746.1: Mapped protein with name 'beta-lactamase TEM-39' to 'Protein' object.
2025-02-07 15:21:22.913 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record QDO66746.1: Mapped 0 site(s).
2025-02-07 15:21:22.914 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein QDO66746.1.
2025-02-07 15:21:22.915 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record QDO66746.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.915 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.921 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record QDO66746.1: Mapped 1 region(s).
2025-02-07 15:21:22.932 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein QDO66746.1.
2025-02-07 15:21:22.933 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein QDO66746.1 in database
2025-02-07 15:21:22.933 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CBX53726.1
2025-02-07 15:21:22.934 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CBX53726.1: Taxonomy ID: 562
2025-02-07 15:21:22.934 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CBX53726.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:22.941 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CBX53726.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.942 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CBX53726.1: Mapped protein with name 'beta-lactamase TEM-40' to 'Protein' object.
2025-02-07 15:21:22.954 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CBX53726.1: Mapped 0 site(s).
2025-02-07 15:21:22.955 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CBX53726.1.
2025-02-07 15:21:22.955 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CBX53726.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.956 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:22.961 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CBX53726.1: Mapped 1 region(s).
2025-02-07 15:21:22.972 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CBX53726.1.
2025-02-07 15:21:22.973 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CBX53726.1 in database
2025-02-07 15:21:22.974 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAC32889.2
2025-02-07 15:21:22.974 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAC32889.2: Taxonomy ID: 573
2025-02-07 15:21:22.974 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAC32889.2: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:22.981 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAC32889.2: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:22.982 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAC32889.2: Mapped protein with name 'beta-lactamase TEM-43' to 'Protein' object.
2025-02-07 15:21:22.995 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAC32889.2: Mapped 0 site(s).
2025-02-07 15:21:22.995 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAC32889.2.
2025-02-07 15:21:22.997 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAC32889.2: Processing CDS feature with qualifiers.
2025-02-07 15:21:22.997 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.002 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAC32889.2: Mapped 1 region(s).
2025-02-07 15:21:23.013 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAC32889.2.
2025-02-07 15:21:23.014 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAC32889.2 in database
2025-02-07 15:21:23.015 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA64682.1
2025-02-07 15:21:23.015 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA64682.1: Taxonomy ID: 562
2025-02-07 15:21:23.016 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA64682.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.022 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA64682.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.023 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA64682.1: Mapped protein with name 'beta-lactamase' to 'Protein' object.
2025-02-07 15:21:23.035 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA64682.1: Mapped 0 site(s).
2025-02-07 15:21:23.036 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA64682.1.
2025-02-07 15:21:23.037 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA64682.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.037 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.042 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA64682.1: Mapped 1 region(s).
2025-02-07 15:21:23.054 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA64682.1.
2025-02-07 15:21:23.055 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA64682.1 in database
2025-02-07 15:21:23.055 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA71322.1
2025-02-07 15:21:23.056 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA71322.1: Taxonomy ID: 573
2025-02-07 15:21:23.056 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA71322.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:23.063 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA71322.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.063 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA71322.1: Mapped protein with name 'ES-beta-lactamase' to 'Protein' object.
2025-02-07 15:21:23.076 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA71322.1: Mapped 0 site(s).
2025-02-07 15:21:23.076 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA71322.1.
2025-02-07 15:21:23.077 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA71322.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.077 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.082 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA71322.1: Mapped 1 region(s).
2025-02-07 15:21:23.095 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA71322.1.
2025-02-07 15:21:23.095 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA71322.1 in database
2025-02-07 15:21:23.096 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA71323.1
2025-02-07 15:21:23.096 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA71323.1: Taxonomy ID: 573
2025-02-07 15:21:23.097 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA71323.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:23.103 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA71323.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.104 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA71323.1: Mapped protein with name 'ES-beta-lactamase' to 'Protein' object.
2025-02-07 15:21:23.116 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA71323.1: Mapped 0 site(s).
2025-02-07 15:21:23.116 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA71323.1.
2025-02-07 15:21:23.117 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA71323.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.117 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.122 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA71323.1: Mapped 1 region(s).
2025-02-07 15:21:23.135 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA71323.1.
2025-02-07 15:21:23.136 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA71323.1 in database
2025-02-07 15:21:23.137 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAA71324.1
2025-02-07 15:21:23.138 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAA71324.1: Taxonomy ID: 562
2025-02-07 15:21:23.139 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAA71324.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.146 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAA71324.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.147 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAA71324.1: Mapped protein with name 'ES-beta-lactamase' to 'Protein' object.
2025-02-07 15:21:23.159 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAA71324.1: Mapped 0 site(s).
2025-02-07 15:21:23.160 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAA71324.1.
2025-02-07 15:21:23.161 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAA71324.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.161 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.167 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAA71324.1: Mapped 1 region(s).
2025-02-07 15:21:23.179 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAA71324.1.
2025-02-07 15:21:23.180 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAA71324.1 in database
2025-02-07 15:21:23.180 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AEC32455.1
2025-02-07 15:21:23.181 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AEC32455.1: Taxonomy ID: 562
2025-02-07 15:21:23.182 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AEC32455.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.189 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AEC32455.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.190 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AEC32455.1: Mapped protein with name 'beta-lactamase' to 'Protein' object.
2025-02-07 15:21:23.202 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AEC32455.1: Mapped 0 site(s).
2025-02-07 15:21:23.203 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AEC32455.1.
2025-02-07 15:21:23.204 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AEC32455.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.205 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.211 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AEC32455.1: Mapped 1 region(s).
2025-02-07 15:21:23.223 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AEC32455.1.
2025-02-07 15:21:23.224 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AEC32455.1 in database
2025-02-07 15:21:23.224 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAD22538.1
2025-02-07 15:21:23.225 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAD22538.1: Taxonomy ID: 573
2025-02-07 15:21:23.226 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAD22538.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:23.233 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAD22538.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.234 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAD22538.1: Mapped protein with name 'extended spectrum beta-lactamase TEM-53' to 'Protein' object.
2025-02-07 15:21:23.246 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAD22538.1: Mapped 0 site(s).
2025-02-07 15:21:23.247 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAD22538.1.
2025-02-07 15:21:23.247 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAD22538.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.248 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.253 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAD22538.1: Mapped 1 region(s).
2025-02-07 15:21:23.263 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAD22538.1.
2025-02-07 15:21:23.264 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAD22538.1 in database
2025-02-07 15:21:23.265 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAD22539.1
2025-02-07 15:21:23.266 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAD22539.1: Taxonomy ID: 562
2025-02-07 15:21:23.266 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAD22539.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.273 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAD22539.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.273 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAD22539.1: Mapped protein with name 'inhibitor resistant beta lactamase TEM-54' to 'Protein' object.
2025-02-07 15:21:23.286 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAD22539.1: Mapped 0 site(s).
2025-02-07 15:21:23.287 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAD22539.1.
2025-02-07 15:21:23.288 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAD22539.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.288 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.293 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAD22539.1: Mapped 1 region(s).
2025-02-07 15:21:23.304 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAD22539.1.
2025-02-07 15:21:23.305 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAD22539.1 in database
2025-02-07 15:21:23.309 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAF05614.1
2025-02-07 15:21:23.310 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAF05614.1: Taxonomy ID: 562
2025-02-07 15:21:23.310 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAF05614.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.317 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAF05614.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.318 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAF05614.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-77' to 'Protein' object.
2025-02-07 15:21:23.329 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAF05614.1: Mapped 0 site(s).
2025-02-07 15:21:23.330 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAF05614.1.
2025-02-07 15:21:23.330 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAF05614.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.331 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.335 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAF05614.1: Mapped 1 region(s).
2025-02-07 15:21:23.346 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAF05614.1.
2025-02-07 15:21:23.347 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAF05614.1 in database
2025-02-07 15:21:23.348 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAF05612.1
2025-02-07 15:21:23.348 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAF05612.1: Taxonomy ID: 562
2025-02-07 15:21:23.349 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAF05612.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.356 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAF05612.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.356 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAF05612.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-78' to 'Protein' object.
2025-02-07 15:21:23.368 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAF05612.1: Mapped 0 site(s).
2025-02-07 15:21:23.369 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAF05612.1.
2025-02-07 15:21:23.370 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAF05612.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.370 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.375 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAF05612.1: Mapped 1 region(s).
2025-02-07 15:21:23.388 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAF05612.1.
2025-02-07 15:21:23.388 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAF05612.1 in database
2025-02-07 15:21:23.389 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAF05611.1
2025-02-07 15:21:23.389 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAF05611.1: Taxonomy ID: 562
2025-02-07 15:21:23.390 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAF05611.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.396 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAF05611.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.397 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAF05611.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-79' to 'Protein' object.
2025-02-07 15:21:23.408 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAF05611.1: Mapped 0 site(s).
2025-02-07 15:21:23.409 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAF05611.1.
2025-02-07 15:21:23.410 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAF05611.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.410 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.415 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAF05611.1: Mapped 1 region(s).
2025-02-07 15:21:23.426 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAF05611.1.
2025-02-07 15:21:23.427 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAF05611.1 in database
2025-02-07 15:21:23.428 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAM15527.1
2025-02-07 15:21:23.428 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAM15527.1: Taxonomy ID: 550
2025-02-07 15:21:23.429 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAM15527.1: Mapped organism 'Enterobacter cloacae' with taxonomy ID 550.
2025-02-07 15:21:23.434 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAM15527.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.435 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAM15527.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-80' to 'Protein' object.
2025-02-07 15:21:23.449 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAM15527.1: Mapped 0 site(s).
2025-02-07 15:21:23.449 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAM15527.1.
2025-02-07 15:21:23.450 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAM15527.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.451 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.456 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAM15527.1: Mapped 1 region(s).
2025-02-07 15:21:23.467 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAM15527.1.
2025-02-07 15:21:23.468 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAM15527.1 in database
2025-02-07 15:21:23.469 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAL29433.1
2025-02-07 15:21:23.470 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAL29433.1: Taxonomy ID: 562
2025-02-07 15:21:23.471 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAL29433.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.477 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAL29433.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.478 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAL29433.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-81' to 'Protein' object.
2025-02-07 15:21:23.490 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAL29433.1: Mapped 0 site(s).
2025-02-07 15:21:23.491 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAL29433.1.
2025-02-07 15:21:23.491 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAL29433.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.492 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.496 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAL29433.1: Mapped 1 region(s).
2025-02-07 15:21:23.507 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAL29433.1.
2025-02-07 15:21:23.508 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAL29433.1 in database
2025-02-07 15:21:23.509 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAL29434.1
2025-02-07 15:21:23.509 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAL29434.1: Taxonomy ID: 562
2025-02-07 15:21:23.510 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAL29434.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.516 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAL29434.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.517 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAL29434.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-82' to 'Protein' object.
2025-02-07 15:21:23.529 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAL29434.1: Mapped 0 site(s).
2025-02-07 15:21:23.530 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAL29434.1.
2025-02-07 15:21:23.531 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAL29434.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.531 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.536 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAL29434.1: Mapped 1 region(s).
2025-02-07 15:21:23.547 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAL29434.1.
2025-02-07 15:21:23.547 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAL29434.1 in database
2025-02-07 15:21:23.548 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAL29435.1
2025-02-07 15:21:23.549 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAL29435.1: Taxonomy ID: 562
2025-02-07 15:21:23.549 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAL29435.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.556 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAL29435.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.556 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAL29435.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-83' to 'Protein' object.
2025-02-07 15:21:23.567 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAL29435.1: Mapped 0 site(s).
2025-02-07 15:21:23.568 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAL29435.1.
2025-02-07 15:21:23.569 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAL29435.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.569 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.574 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAL29435.1: Mapped 1 region(s).
2025-02-07 15:21:23.586 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAL29435.1.
2025-02-07 15:21:23.586 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAL29435.1 in database
2025-02-07 15:21:23.587 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAL29436.1
2025-02-07 15:21:23.588 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAL29436.1: Taxonomy ID: 562
2025-02-07 15:21:23.588 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAL29436.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:23.594 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAL29436.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.595 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAL29436.1: Mapped protein with name 'inhibitor-resistant beta-lactamase TEM-84' to 'Protein' object.
2025-02-07 15:21:23.606 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAL29436.1: Mapped 0 site(s).
2025-02-07 15:21:23.607 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAL29436.1.
2025-02-07 15:21:23.607 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAL29436.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.608 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.613 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAL29436.1: Mapped 1 region(s).
2025-02-07 15:21:23.623 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAL29436.1.
2025-02-07 15:21:23.624 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAL29436.1 in database
2025-02-07 15:21:23.625 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAC43229.1
2025-02-07 15:21:23.625 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAC43229.1: Taxonomy ID: 573
2025-02-07 15:21:23.626 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAC43229.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:23.632 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAC43229.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.633 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAC43229.1: Mapped protein with name 'TEM-85 ES-beta-lactamase' to 'Protein' object.
2025-02-07 15:21:23.644 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAC43229.1: Mapped 0 site(s).
2025-02-07 15:21:23.645 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAC43229.1.
2025-02-07 15:21:23.645 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAC43229.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.646 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.651 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAC43229.1: Mapped 1 region(s).
2025-02-07 15:21:23.663 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAC43229.1.
2025-02-07 15:21:23.663 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAC43229.1 in database
2025-02-07 15:21:23.664 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAC43230.1
2025-02-07 15:21:23.664 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAC43230.1: Taxonomy ID: 573
2025-02-07 15:21:23.665 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAC43230.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:23.671 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAC43230.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:23.672 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAC43230.1: Mapped protein with name 'TEM-86 ES-beta-lactamase' to 'Protein' object.
2025-02-07 15:21:23.683 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAC43230.1: Mapped 0 site(s).
2025-02-07 15:21:23.684 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAC43230.1.
2025-02-07 15:21:23.684 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAC43230.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:23.685 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:23.689 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAC43230.1: Mapped 1 region(s).
2025-02-07 15:21:23.699 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAC43230.1.
2025-02-07 15:21:23.700 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAC43230.1 in database
2025-02-07 15:21:23.701 | DEBUG    | pyeed.adapter.primary_db_adapter:_fetch_response:121 - Sending request to https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi with parameters: {'retmode': 'text', 'rettype': 'genbank', 'db': 'protein', 'id': 'AAG44570.1,AAK14792.1,AAK30619.1,BAB16308.1,AAF66653.1,CAC85660.1,CAC85661.1,CAC67290.1'}
2025-02-07 15:21:24.377 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAG44570.1
2025-02-07 15:21:24.377 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAG44570.1: Taxonomy ID: 584
2025-02-07 15:21:24.378 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAG44570.1: Mapped organism 'Proteus mirabilis' with taxonomy ID 584.
2025-02-07 15:21:24.385 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAG44570.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:24.386 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAG44570.1: Mapped protein with name 'class A beta-lactamase TEM-87' to 'Protein' object.
2025-02-07 15:21:24.398 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAG44570.1: Mapped 0 site(s).
2025-02-07 15:21:24.399 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAG44570.1.
2025-02-07 15:21:24.399 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAG44570.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:24.400 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:24.405 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAG44570.1: Mapped 1 region(s).
2025-02-07 15:21:24.416 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAG44570.1.
2025-02-07 15:21:24.417 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAG44570.1 in database
2025-02-07 15:21:24.417 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAK14792.1
2025-02-07 15:21:24.418 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAK14792.1: Taxonomy ID: 573
2025-02-07 15:21:24.418 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAK14792.1: Mapped organism 'Klebsiella pneumoniae' with taxonomy ID 573.
2025-02-07 15:21:24.425 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAK14792.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:24.425 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAK14792.1: Mapped protein with name 'extended-spectrum beta-lactamase TEM-88' to 'Protein' object.
2025-02-07 15:21:24.437 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAK14792.1: Mapped 0 site(s).
2025-02-07 15:21:24.437 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAK14792.1.
2025-02-07 15:21:24.438 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAK14792.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:24.439 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:24.443 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAK14792.1: Mapped 1 region(s).
2025-02-07 15:21:24.455 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAK14792.1.
2025-02-07 15:21:24.456 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAK14792.1 in database
2025-02-07 15:21:24.456 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAK30619.1
2025-02-07 15:21:24.457 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAK30619.1: Taxonomy ID: 562
2025-02-07 15:21:24.457 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAK30619.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:24.464 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAK30619.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:24.464 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAK30619.1: Mapped protein with name 'TEM-90 beta-lactamase' to 'Protein' object.
2025-02-07 15:21:24.477 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAK30619.1: Mapped 0 site(s).
2025-02-07 15:21:24.479 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAK30619.1.
2025-02-07 15:21:24.479 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAK30619.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:24.480 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:24.486 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAK30619.1: Mapped 1 region(s).
2025-02-07 15:21:24.497 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAK30619.1.
2025-02-07 15:21:24.498 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAK30619.1 in database
2025-02-07 15:21:24.499 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record BAB16308.1
2025-02-07 15:21:24.499 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record BAB16308.1: Taxonomy ID: 562
2025-02-07 15:21:24.500 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record BAB16308.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:24.507 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record BAB16308.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:24.507 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record BAB16308.1: Mapped protein with name 'TEM-derived extended-spectrum beta-lactamase' to 'Protein' object.
2025-02-07 15:21:24.519 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record BAB16308.1: Mapped 0 site(s).
2025-02-07 15:21:24.520 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein BAB16308.1.
2025-02-07 15:21:24.521 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record BAB16308.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:24.522 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:24.527 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record BAB16308.1: Mapped 1 region(s).
2025-02-07 15:21:24.540 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein BAB16308.1.
2025-02-07 15:21:24.541 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein BAB16308.1 in database
2025-02-07 15:21:24.542 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record AAF66653.1
2025-02-07 15:21:24.543 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record AAF66653.1: Taxonomy ID: 584
2025-02-07 15:21:24.543 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record AAF66653.1: Mapped organism 'Proteus mirabilis' with taxonomy ID 584.
2025-02-07 15:21:24.550 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record AAF66653.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:24.551 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record AAF66653.1: Mapped protein with name 'class A beta-lactamase' to 'Protein' object.
2025-02-07 15:21:24.564 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record AAF66653.1: Mapped 0 site(s).
2025-02-07 15:21:24.565 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein AAF66653.1.
2025-02-07 15:21:24.566 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record AAF66653.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:24.566 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:24.571 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record AAF66653.1: Mapped 1 region(s).
2025-02-07 15:21:24.583 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein AAF66653.1.
2025-02-07 15:21:24.584 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein AAF66653.1 in database
2025-02-07 15:21:24.584 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAC85660.1
2025-02-07 15:21:24.585 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAC85660.1: Taxonomy ID: 562
2025-02-07 15:21:24.585 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAC85660.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:24.592 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAC85660.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:24.593 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAC85660.1: Mapped protein with name 'TEM-93 ES-beta-lactamase' to 'Protein' object.
2025-02-07 15:21:24.606 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAC85660.1: Mapped 0 site(s).
2025-02-07 15:21:24.606 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAC85660.1.
2025-02-07 15:21:24.607 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAC85660.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:24.608 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:24.613 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAC85660.1: Mapped 1 region(s).
2025-02-07 15:21:24.625 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAC85660.1.
2025-02-07 15:21:24.626 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAC85660.1 in database
2025-02-07 15:21:24.626 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAC85661.1
2025-02-07 15:21:24.627 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAC85661.1: Taxonomy ID: 562
2025-02-07 15:21:24.627 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAC85661.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:24.634 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAC85661.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:24.634 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAC85661.1: Mapped protein with name 'TEM-94 ES-beta-lactamase' to 'Protein' object.
2025-02-07 15:21:24.646 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAC85661.1: Mapped 0 site(s).
2025-02-07 15:21:24.647 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAC85661.1.
2025-02-07 15:21:24.647 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAC85661.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:24.648 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:24.653 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAC85661.1: Mapped 1 region(s).
2025-02-07 15:21:24.663 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAC85661.1.
2025-02-07 15:21:24.664 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAC85661.1 in database
2025-02-07 15:21:24.664 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_to_db:259 - Processing NCBI protein record CAC67290.1
2025-02-07 15:21:24.665 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:49 - Record CAC67290.1: Taxonomy ID: 562
2025-02-07 15:21:24.665 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_organism:77 - Record CAC67290.1: Mapped organism 'Escherichia coli' with taxonomy ID 562.
2025-02-07 15:21:24.671 | WARNING  | pyeed.adapter.ncbi_protein_mapper:map_protein:115 - Record CAC67290.1: Molecular weight missing or invalid; setting to None.
2025-02-07 15:21:24.672 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_protein:128 - Record CAC67290.1: Mapped protein with name 'beta lactamase TEM-95' to 'Protein' object.
2025-02-07 15:21:24.684 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_sites:149 - Record CAC67290.1: Mapped 0 site(s).
2025-02-07 15:21:24.684 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_sites:160 - Connected 0 site(s) to protein CAC67290.1.
2025-02-07 15:21:24.685 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_cds:183 - Record CAC67290.1: Processing CDS feature with qualifiers.
2025-02-07 15:21:24.685 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:get_cds_regions:211 - Extracted 1 CDS region(s).
2025-02-07 15:21:24.690 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:map_regions:234 - Record CAC67290.1: Mapped 1 region(s).
2025-02-07 15:21:24.701 | DEBUG    | pyeed.adapter.ncbi_protein_mapper:add_regions:247 - Connected 1 region(s) to protein CAC67290.1.
2025-02-07 15:21:24.702 | INFO     | pyeed.adapter.ncbi_protein_mapper:add_to_db:301 - Added/updated NCBI protein CAC67290.1 in database

Calculate Sequence Embeddings¶

Now we'll convert our protein sequences into numerical representations (embeddings) using a pre-trained model.

In [73]:

eedb.calculate_sequence_embeddings(model_name="esmc_300m")

eedb.calculate_sequence_embeddings(model_name="esmc_300m")

2025-02-07 15:21:25.789 | DEBUG    | pyeed.main:calculate_sequence_embeddings:222 - Calculating embeddings for 68 sequences.
2025-02-07 15:21:25.789 | DEBUG    | pyeed.main:calculate_sequence_embeddings:229 - Processing batch 1/6
2025-02-07 15:21:26.421 | DEBUG    | pyeed.main:calculate_sequence_embeddings:229 - Processing batch 2/6
2025-02-07 15:21:27.004 | DEBUG    | pyeed.main:calculate_sequence_embeddings:229 - Processing batch 3/6
2025-02-07 15:21:27.575 | DEBUG    | pyeed.main:calculate_sequence_embeddings:229 - Processing batch 4/6
2025-02-07 15:21:28.145 | DEBUG    | pyeed.main:calculate_sequence_embeddings:229 - Processing batch 5/6

Visualization with t-SNE¶

Finally, we'll project our high-dimensional embeddings into 2D space using t-SNE and create a visualization. The resulting plot will show how proteins relate to each other in terms of their sequence properties.

In [78]:

# get all of the data from embedding
embedding_tool = EmbeddingTool()
protein_ids, embeddings_2d, labels, colors = (
    embedding_tool.calculate_2d_projection_tsne(
        db=eedb.db,
        ids_list=df["protein_id_database"].tolist(),
        perplexity=1,
        n_iter=3000,
        ids_list_labels=dict_data,
    )
)
print(len(protein_ids))

labels_already_plotted = []

# create a scatter plot for each unique label
for i in range(len(protein_ids)):
    if labels[i] not in labels_already_plotted:
        plt.scatter(
            embeddings_2d[i, 0],
            embeddings_2d[i, 1],
            alpha=0.7,
            s=50,
            edgecolor="k",
            color=colors[i],
            label=labels[i],
        )
        labels_already_plotted.append(labels[i])
    else:
        plt.scatter(
            embeddings_2d[i, 0],
            embeddings_2d[i, 1],
            alpha=0.7,
            s=50,
            edgecolor="k",
            color=colors[i],
        )
plt.title("2D t-SNE Visualization of Protein Embeddings")
plt.xlabel("t-SNE Dimension 1")
plt.ylabel("t-SNE Dimension 2")
plt.legend()
plt.tight_layout()
plt.show()

# get all of the data from embedding embedding_tool = EmbeddingTool() protein_ids, embeddings_2d, labels, colors = ( embedding_tool.calculate_2d_projection_tsne( db=eedb.db, ids_list=df["protein_id_database"].tolist(), perplexity=1, n_iter=3000, ids_list_labels=dict_data, ) ) print(len(protein_ids)) labels_already_plotted = [] # create a scatter plot for each unique label for i in range(len(protein_ids)): if labels[i] not in labels_already_plotted: plt.scatter( embeddings_2d[i, 0], embeddings_2d[i, 1], alpha=0.7, s=50, edgecolor="k", color=colors[i], label=labels[i], ) labels_already_plotted.append(labels[i]) else: plt.scatter( embeddings_2d[i, 0], embeddings_2d[i, 1], alpha=0.7, s=50, edgecolor="k", color=colors[i], ) plt.title("2D t-SNE Visualization of Protein Embeddings") plt.xlabel("t-SNE Dimension 1") plt.ylabel("t-SNE Dimension 2") plt.legend() plt.tight_layout() plt.show()

68

Protein Embedding Search Methods¶

There are two main approaches implemented for searching similar proteins using embeddings:

1. Simple Search Method¶

The simple method (find_closest_matches_simple) loads all embeddings into memory to calculate distances. While straightforward, it's best suited for smaller datasets:

In [75]:

# this is the simple way to find the closest matches it loads all proteins into memory
# so this is not the best way to do this for large datasets
# on very small datasets it is still fine though, and works easily

results = et.find_closest_matches_simple(
    start_sequence_id=df["protein_id_database"].tolist()[0],
    db=eedb.db,
    metric="cosine",
    n=10,
)

print(f"Resulst for index {df['protein_id_database'].tolist()[0]} are:")
print(results)

# this is the simple way to find the closest matches it loads all proteins into memory # so this is not the best way to do this for large datasets # on very small datasets it is still fine though, and works easily results = et.find_closest_matches_simple( start_sequence_id=df["protein_id_database"].tolist()[0], db=eedb.db, metric="cosine", n=10, ) print(f"Resulst for index {df['protein_id_database'].tolist()[0]} are:") print(results)

Resulst for index AAP20891.1 are:
[('AAP20891.1', 0.0), ('AGQ50511.1', 0.00016200621801287785), ('ABB97007.1', 0.0001810048295400879), ('AFN21551.1', 0.00018909362988450695), ('CAC67290.1', 0.00021654775310264718), ('ADL13944.1', 0.0002567003210336427), ('AAK30619.1', 0.0002616398020808264), ('AAL29433.1', 0.0002646931927183793), ('ACJ43254.1', 0.0002669990760338914), ('ACB22021.1', 0.0002755243601859636)]

Advantages:¶

• Simple implementation
• Works well for small datasets
• Flexible distance metrics

Limitations:¶

• Memory intensive for large datasets
• Slower for large-scale searches
• Not scalable for production use with big databases

2. Vector Index Search¶

The vector index method uses Neo4j's native vector indexing capabilities (HNSW algorithm) for efficient similarity search. This is the recommended approach for larger datasets and production use.

Setting up the Vector Index:¶

In [76]:

# the more complex was involes creating a vector index of the embeddings
# the vector index math and implementation is provied by neo4j

# here we drop the vector index
et.drop_vector_index(
    db=eedb.db,
    index_name="vector_index_Protein_embedding",
)
# here we create the vector index
et.create_embedding_vector_index_neo4j(
    db=eedb.db,
    index_name="vector_index_Protein_embedding",
    similarity_function="cosine",
    dimensions=960,
    m=16,
    ef_construction=512,
)

# the more complex was involes creating a vector index of the embeddings # the vector index math and implementation is provied by neo4j # here we drop the vector index et.drop_vector_index( db=eedb.db, index_name="vector_index_Protein_embedding", ) # here we create the vector index et.create_embedding_vector_index_neo4j( db=eedb.db, index_name="vector_index_Protein_embedding", similarity_function="cosine", dimensions=960, m=16, ef_construction=512, )

Parameters Explained:¶

• dimensions: The size of your embedding vectors

  • Use 960 for ESM-C model
  • Use 1280 for ESM-2 model

• m (default=16): Maximum number of connections per node in the HNSW graph

  • Higher values = better accuracy but slower indexing
  • Lower values = faster indexing but potentially less accurate
  • Recommended range: 5-100

• ef_construction (default=512): Controls index quality during construction

  • Higher values = better quality but slower indexing
  • Lower values = faster indexing but potentially lower quality
  • Recommended range: 100-1000

Searching with the Vector Index:¶

In [77]:

# here we use the vector index to find the closest matches
results = et.find_nearest_neighbors_based_on_vector_index(
    db=eedb.db,
    query_protein_id=df["protein_id_database"].tolist()[0],
    index_name="vector_index_Protein_embedding",
    number_of_neighbors=10,
)

print(results)

# here we use the vector index to find the closest matches results = et.find_nearest_neighbors_based_on_vector_index( db=eedb.db, query_protein_id=df["protein_id_database"].tolist()[0], index_name="vector_index_Protein_embedding", number_of_neighbors=10, ) print(results)

[('AAP20891.1', 1.0), ('AGQ50511.1', 0.9999189376831055), ('ABB97007.1', 0.999909520149231), ('AFN21551.1', 0.9999054670333862), ('CAC67290.1', 0.9998918771743774), ('ADL13944.1', 0.9998717904090881), ('AAK30619.1', 0.9998692274093628), ('AAL29433.1', 0.9998676776885986), ('ACJ43254.1', 0.9998666048049927), ('CBX53726.1', 0.9998624920845032)]

Advantages of Vector Index:¶

• Highly efficient for large datasets
• Optimized for high-dimensional data
• Scales well with database size
• Maintains good performance with growing data

Important Notes:¶

1. The vector index needs time to populate after creation. The code automatically waits and shows a progress bar during population.

2. The similarity scores returned by the vector index search are:

   • For cosine similarity: Range [-1 to 1], where 1 is most similar
   • For euclidean similarity: Lower values indicate more similarity

3. The index is persistent in the database and only needs to be created once, unless you want to change its parameters.

4. Memory usage is optimized as the index handles the heavy lifting instead of loading all embeddings into memory.

For most production use cases, the vector index method is recommended as it provides the best balance of performance and scalability.