Saved in:
| Main Authors: | , |
|---|---|
| Format: | Recurso digital |
| Language: | |
| Published: |
Zenodo
2025
|
| Online Access: | https://doi.org/10.5281/zenodo.17964500 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Table of Contents:
- <p>PLSDB_conjugative_gp_reps_esmfold.zip</p> <ul> <li>ESMFold predictions for all representative PLSDB proteins from G+ and conjugative origin</li> </ul> <p> </p> <p>PLSDB_AF3_reps_VirB6_pentamers.zip </p> <ul> <li>AlphaFold 3 predictions for pentamers of all 174 representative VirB6-like proteins</li> </ul> <p> </p> <p>PLSDB_AF3_reps_VirB6_VirB2_multimers.zip</p> <ul> <li>AlphaFold 3 predictions for multimer predictions of all 174 representative VirB6-like proteins (pentamer) together with their VirB2-like candidate proteins (decamer), 320 predictions total.</li> </ul> <p> </p> <p>AF3_gram_positive_reference_plasmids.zip</p> <ul> <li>AlphaFold 3 predictions from AlphaFold server for G+ example plasmids with VirB6-like proteins (pentamer) together with their VirB2-like candidate proteins (decamer). Also contains custom PAE plots. Includes the following plasmids: <ul> <li>pAD1</li> <li>pAMB1</li> <li>pCER270</li> <li>pCF10</li> <li>pCLJ</li> <li>pCP13</li> <li>pCW3</li> <li>pGO1</li> <li>pIP501</li> <li>pKAPB2</li> <li>pMG1</li> <li>pSK41</li> <li>pXO1</li> <li>pXO2</li> </ul> </li> </ul> <p>Gram-positive_reference_plasmids.zip</p> <ul> <li>Contains genomic information for each gram-positive reference plasmid <ul> <li>Plasmid nucleotide fasta</li> <li>Plasmid protein fasta (as annotated by Prokka)</li> <li>Plasmid GenBank data (as annotated by Prokka)</li> <li>DeepTMHMM predictions in 3line format</li> </ul> </li> </ul> <p> </p> <p>PLSDB_sequences.zip</p> <ul> <li>PLSDB_2024_05_31_v2_proteins.fasta <ul> <li>PLSDB protein sequences for the PLSDB release used in this study</li> </ul> </li> <li>conjugative_gp_proteins.fasta <ul> <li>Subset of the PLSDB protein sequences with G+ and conjugative origin, as annotated by PLSDB</li> </ul> </li> <li>conjugative_gp_proteins_cluster_cluster.tsv <ul> <li>MMseqs2 clusters (90% identity and 90% coverage) of conjugative G+ proteins</li> </ul> </li> <li>conjugative_gp_proteins_cluster_rep_seq.fasta <ul> <li>Representative protein sequences of the MMseqs2 clusters</li> </ul> </li> <li>conjugative_gp_proteins_cluster_all_seqs.fasta <ul> <li>All protein sequences (all representatives and members)</li> </ul> </li> </ul> <p> </p> <p> </p>