Bioinformatics results related to the article "Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29"
Sequence:
>AYJ74695.1 lysozyme [Thermus phage phiKo]
MNWIEFWRSKKPTWRHRPVDPAYIVLHHTAGPVDQAPQAIWDYHVKVRGWPHGGYHFLVYHDGTVVKMLPLSAQPICVGEYNHLAICIALVGNFVGGYPPEWNERAPGWKSLAWLVRELRKHDSGLRLRLVRHKDLRPTKCPGTVTWEEALVRGGVPQEQVETLKVAGVIA
>RAP-29 - phiKo derived potent antimicrobial peptide (105-133 aa)
RAPGWKSLAWLVRELRKHDSGLRLRLVRH
Models are done by:
1) Phyre2 (intensive mode)
./models/phyre2/final.casp.pdb
2) hhsearch+modeller (modelled on all templates) - quite poor model
./models/modeller_2483784.pdb
3) AlphaFold2 (colab over pdb70)
./models/PhiKo_f9d15.result.af2
4) deepfold (https://zhanggroup.org/DeepFold/) - quite poor model
./models/DeepFold/model1_DeepFold.pdb
5) omegafold
./models/omegafold/phiKo.pdb
6) RGN2 - unexpectly, quite poor model
./models/RGN2/phiKo_729bd0_prediction_RGN2.pdb
7) RoseTTAFold (run online)
./models/rosseta
8) ESMFold --> the best model
./models/ESMFold/ptm0.912_r3_default.ESMFold.pdb
Additionally, from one of the templates (Ts2631 PDB:6SU5) Zn i PO4 had been taken to complement the catalytic center
.
├── figure1_alignment.gb
├── models
│ ├── all_models_aligned.pdf
│ ├── all_models_aligned.tif
│ ├── all_models_aligned_Zn_added.py
│ ├── all_models_aligned_Zn_added.pyc
│ ├── DeepFold
│ ├── ESMFold
│ ├── Fig_S1a.png
│ ├── Fig_S1a_ray.png
│ ├── Fig_S1b.png
│ ├── Fig_S1b_ray.png
│ ├── Fig_S1.png
│ ├── Fig_S2a.png
│ ├── Fig_S2.png
│ ├── modeller_2483784.pdb
│ ├── model_with_black105-133.tif
│ ├── model_with_black140.tif
│ ├── omegafold
│ ├── phiKo_all.mp4
│ ├── phiKo_catalitic_center_closeup_T7_Ts2631.py
│ ├── phiKo_catalitic_center_plus_K140.py
│ ├── phiKo_catalitic_center_plus_K140.pyc
│ ├── phiKo_catalitic_center.py
│ ├── phiKo_catalytic_center_all.mp4
│ ├── phiKo_catalytic_center_all.pdf
│ ├── phiKo_catalytic_center_all.tif
│ ├── phiKo_catalytic_center_plus_K140.webm
│ ├── phiKo_catalytic_center.tif
│ ├── PhiKo_f9d15.result.af2
│ ├── phiKo_main_model_with_ligands_all_models.py
│ ├── phiKo_main_model_with_ligands_all_models.pyc
│ ├── phiKo_main_model_with_ligands_all_models_v2.py
│ ├── phiKo_main_model_with_ligands.pdb
│ ├── phiKo_main_model_with_ligands.py
│ ├── phiKo_main_model_with_ligands.tif
│ ├── phiKo.mp4
│ ├── phiKo_vs_T7.mp4
│ ├── phiKo_vs_T7.pdf
│ ├── phiKo_vs_T7.py
│ ├── phiKo_vs_T7.pyc
│ ├── phiKo_vs_T7.tif
│ ├── phiKo_vs_T7_Ts2631_ph2119.png
│ ├── phiKo_vs_T7_Ts2631_ph2119.py
│ ├── phiKo_vs_Ts2631.mp4
│ ├── phiKo_vs_Ts2631.py
│ ├── phiKo_vs_Ts2631.pyc
│ ├── phiKo_vs_Ts2631.tif
│ ├── phyre2
│ ├── RGN2
│ └── rosseta
├── phiKo.fas
├── RAP-29.fas
└── README.txt
Files *.py are UCSF Chimera viewer sessions storing superposition of
multiple models, homolog proteins, catalytic center zoom in, etc.
