←Back to structures
NC_006820.1__YP_195213.1__S-PM2p181__00183
Bact-VirNC_006820.1__YP_195213.1__S-PM2p181__00183
Identity
- Accession:
- NC_006820 ↗
- Kingdom:
- phage
Quality
87.7
mean pLDDT
Taxonomy
Heunggongvirae›
Uroviricota›
Caudoviricetes›
Pantevenvirales›
Kyanoviridae›
Nodensvirus›
Synechococcus_phage_S-PM2
TaxID: 238854
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
medium
residues 1-110
Domain cluster:
representative
CATH (4)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1gccA00 | 3.30.730.10 | Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain | 0.67 | 32.0 | 4.12e-01 | 78.2% | 77.8% |
| 4njcA00 | 3.10.20.730 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like | 0.62 | 34.0 | 4.36e-01 | 82.7% | 98.3% |
| 1pzxA03 | 3.30.1180.10 | Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › | 0.54 | 37.0 | 3.60e-01 | 70.9% | 89.3% |
| 1qxfA00 | 2.20.25.100 | Mainly Beta › Single Sheet › N-terminal domain of TfIIb › Ribosomal protein S27 | 0.53 | 28.0 | 3.67e-01 | 82.7% | 96.6% |
ECOD (13)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4974123 | 821.1.1.14 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › DUF2797 | 0.80 | 48.0 | 5.06e-01 | 72.7% | 67.0% |
| 3666940 | 821.1.1.1 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG | 0.73 | 48.0 | 4.71e-01 | 73.6% | 61.7% |
| 5014684 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.66 | 34.0 | 4.61e-01 | 85.5% | 96.6% |
| 4016088 | 821.1.1.3 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › T5orf172 | 0.65 | 47.0 | 4.81e-01 | 73.6% | 80.0% |
| 3651077 | 252.2.1.0 ↗ | a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like | 0.63 | 31.0 | 3.81e-01 | 78.2% | 72.9% |
| 3478944 | 821.1.1.0 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease | 0.62 | 44.0 | 4.56e-01 | 75.5% | 97.1% |
| 5067865 | 3115.1.1.0 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like | 0.61 | 39.0 | 4.66e-01 | 82.7% | 100.0% |
| 5044314 | 3203.1.1.0 ↗ | a+b two layers › Putative oxidoreductase › Putative oxidoreductase › Putative oxidoreductase | 0.60 | 34.0 | 3.68e-01 | 81.8% | 66.7% |
| 5000510 | 3115.1.1.1 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A | 0.59 | 38.0 | 4.45e-01 | 85.5% | 97.3% |
| 3174499 | 7552.1.1.1 ↗ | a/b three-layered sandwiches › Amidase signature (AS) enzymes › Amidase signature (AS) enzymes › Amidase signature (AS) enzymes › Amidase | 0.53 | 43.0 | 2.87e-01 | 92.7% | 59.4% |
| 3718703 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.52 | 38.0 | 3.97e-01 | 76.4% | 95.0% |
| 4796557 | 4012.3.1.0 ↗ | a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 | 0.51 | 30.0 | 3.62e-01 | 74.5% | 98.4% |
| 3285401 | 3986.2.1.0 ↗ | a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd | 0.51 | 34.0 | 4.05e-01 | 81.8% | 100.0% |
D2
medium
residues 134-208
Domain cluster:
representative
CATH (5)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5dkaA00 | 3.30.40.10 | Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) | 0.54 | 43.0 | 4.00e-01 | 86.7% | 75.0% |
| 1t3aA00 | 3.90.1240.10 | Alpha Beta › Alpha-Beta Complex › Zincin-like › "Metalloproteases (""zincins""), catalytic domain like" | 0.53 | 45.0 | 2.90e-01 | 98.7% | 39.3% |
| 4q0jA03 | 3.30.450.270 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain | 0.51 | 39.0 | 3.17e-01 | 81.3% | 80.3% |
| 3hhmA03 | 3.10.20.90 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 | 0.51 | 35.0 | 2.96e-01 | 74.7% | 44.7% |
| 4mbsA00 | 1.20.1070.10 | Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins | 0.50 | 38.0 | 2.52e-01 | 82.7% | 91.6% |
ECOD (6)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3911109 | 386.1.1.290 ↗ | few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › Zf-C2H2_ZNF451_C | 0.64 | 45.0 | 4.38e-01 | 90.7% | 65.9% |
| 3773803 | 386.1.1.358 ↗ | few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › Zf-C2H2_ZNF451 | 0.59 | 49.0 | 4.20e-01 | 92.0% | 72.5% |
| 3853801 | 386.1.1.398 ↗ | few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2, Zf-C2H2_ZNF451_2nd, Zf-C2H2_ZNF451 | 0.58 | 46.0 | 3.28e-01 | 89.3% | 28.3% |
| 4384880 | 101.1.14.3 ↗ | alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 | 0.55 | 40.0 | 3.90e-01 | 77.3% | 89.4% |
| 4507638 | 101.1.2.31 ↗ | alpha arrays › HTH › HTH › winged helix domain › TFIIE_alpha | 0.51 | 32.0 | 2.51e-01 | 82.7% | 29.1% |
| 5041303 | 2498.1.1.6 ↗ | mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M3 | 0.50 | 41.0 | 2.53e-01 | 96.0% | 62.3% |