←Back to structures
OP056089.1__UYD72115.1__X__00015
Bact-VirOP056089.1__UYD72115.1__X__00015
Identity
- Accession:
- OP056089 ↗
- Kingdom:
- phage
Quality
77.5
mean pLDDT
Taxonomy
Heunggongvirae›
Uroviricota›
Caudoviricetes›
Chaseviridae›
Liaoningvirus›
Vibrio_phage_vB_VpaM_VPs20
TaxID: 2978980
Cluster
View cluster (116 members)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 16-27_95-154
Domain cluster:
representative
CATH (12)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1c5eA00 | 2.40.300.10 | Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D | 0.67 | 54.0 | 4.90e-01 | 87.5% | 93.7% |
| 3gqhA01 | 2.40.300.10 | Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D | 0.62 | 56.0 | 4.64e-01 | 98.6% | 87.0% |
| 1fx0B01 | 2.40.10.170 | Mainly Beta › Beta Barrel › Thrombin, subunit H › | 0.62 | 45.0 | 4.40e-01 | 100.0% | 70.9% |
| 2gk6A02 | 2.40.30.230 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › | 0.58 | 44.0 | 4.23e-01 | 100.0% | 71.1% |
| 3pehA02 | 3.30.70.2140 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.57 | 34.0 | 4.15e-01 | 84.7% | 97.7% |
| 3girA04 | 2.40.30.110 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains | 0.57 | 34.0 | 3.38e-01 | 79.2% | 55.1% |
| 8agcA01 | 3.40.50.12610 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.56 | 48.0 | 3.51e-01 | 97.2% | 89.9% |
| 1pj5A05 | 2.40.30.110 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains | 0.54 | 31.0 | 3.10e-01 | 79.2% | 51.3% |
| 3ihmA02 | 3.30.9.40 | Alpha Beta › 2-Layer Sandwich › D-Amino Acid Oxidase; Chain A, domain 2 › | 0.54 | 35.0 | 2.87e-01 | 86.1% | 34.0% |
| 2l9pA00 | 3.30.530.20 | Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain | 0.52 | 44.0 | 3.50e-01 | 100.0% | 75.6% |
| 2ea3A01 | 2.40.10.10 | Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases | 0.50 | 32.0 | 3.09e-01 | 100.0% | 53.6% |
| 4e9jA02 | 3.30.1370.120 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › | 0.50 | 35.0 | 3.55e-01 | 87.5% | 76.8% |
ECOD (17)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3945288 | 70.4.1.7 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › XM1_gp53_minor_capsid | 0.82 | 69.0 | 5.43e-01 | 90.3% | 100.0% |
| 3986892 | 70.4.1.8 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement | 0.82 | 65.0 | 6.48e-01 | 84.7% | 98.7% |
| 3945811 | 70.4.1.7 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › XM1_gp53_minor_capsid | 0.74 | 55.0 | 5.92e-01 | 77.8% | 96.7% |
| 3981037 | 70.4.1.9 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement_2 | 0.72 | 52.0 | 5.80e-01 | 79.2% | 100.0% |
| 5083816 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.69 | 53.0 | 5.45e-01 | 83.3% | 97.1% |
| 364260 | 70.4.1.3 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Peptidase_G2 | 0.62 | 56.0 | 4.24e-01 | 98.6% | 90.2% |
| 3507639 | 4.1.1.219 ↗ | beta barrels › SH3 › SH3 › SH3 › LSM12_LSM | 0.61 | 38.0 | 3.84e-01 | 72.2% | 64.3% |
| 2526359 | 70.4.1.2 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr | 0.60 | 45.0 | 4.77e-01 | 87.5% | 98.3% |
| 5022524 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.59 | 45.0 | 4.62e-01 | 87.5% | 88.6% |
| 4930420 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.59 | 46.0 | 4.65e-01 | 91.7% | 90.0% |
| 4935036 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.58 | 46.0 | 4.64e-01 | 87.5% | 100.0% |
| 5014572 | 2.21.1.3 ↗ | beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) › HTH_OrfB_IS605 | 0.58 | 43.0 | 3.41e-01 | 83.3% | 100.0% |
| 3216225 | 304.9.1.0 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD | 0.56 | 41.0 | 3.81e-01 | 97.2% | 60.0% |
| 3332789 | 1.1.8.18 ↗ | beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › POP1_C | 0.52 | 43.0 | 3.73e-01 | 93.1% | 61.7% |
| 3986112 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.51 | 40.0 | 2.91e-01 | 88.9% | 38.2% |
| 4485646 | 4186.1.1.1 ↗ | beta barrels › Ribosomal protein L21p › Ribosomal protein L21p › Ribosomal protein L21p › Ribosomal_L21p | 0.50 | 44.0 | 4.18e-01 | 100.0% | 82.4% |
| 3172569 | 220.1.1.245 ↗ | beta barrels › PH domain-like › PH domain-like › PH domain-like › PF29445 | 0.50 | 33.0 | 2.75e-01 | 95.8% | 35.6% |
D2
medium
residues 28-94
Domain cluster:
rep: MZ375300.1__QZB86124.1__seszw30S_13__00015__D21-83
CATH (5)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6xgqb01 | 2.40.300.10 | Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D | 0.74 | 62.0 | 5.43e-01 | 100.0% | 63.4% |
| 1c5eA00 | 2.40.300.10 | Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D | 0.72 | 55.0 | 4.94e-01 | 100.0% | 58.9% |
| 8bveA03 | 2.40.340.10 | Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV | 0.68 | 62.0 | 6.09e-01 | 100.0% | 100.0% |
| 1wu2A04 | 2.40.340.10 | Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV | 0.66 | 60.0 | 5.78e-01 | 100.0% | 89.6% |
| 6ethA04 | 2.40.340.10 | Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV | 0.66 | 59.0 | 5.40e-01 | 100.0% | 88.8% |
ECOD (18)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2559744 | 70.4.1.2 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr | 0.85 | 62.0 | 6.56e-01 | 100.0% | 86.4% |
| 3602933 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.78 | 66.0 | 6.69e-01 | 100.0% | 92.3% |
| 5022524 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.76 | 59.0 | 5.80e-01 | 100.0% | 77.1% |
| 5039270 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.76 | 57.0 | 6.21e-01 | 98.5% | 94.5% |
| 5016125 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.76 | 57.0 | 6.30e-01 | 100.0% | 96.4% |
| 2526359 | 70.4.1.2 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr | 0.75 | 57.0 | 5.95e-01 | 100.0% | 90.0% |
| 2640772 | 70.4.1.1 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › HDPD | 0.74 | 62.0 | 5.29e-01 | 100.0% | 59.0% |
| 5002645 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.73 | 57.0 | 6.07e-01 | 100.0% | 96.6% |
| 3227803 | 70.1.1.0 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like | 0.68 | 61.0 | 6.20e-01 | 100.0% | 100.0% |
| 3513462 | 70.4.1.8 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement | 0.67 | 53.0 | 5.60e-01 | 100.0% | 95.0% |
| 5025019 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.67 | 61.0 | 5.68e-01 | 100.0% | 86.9% |
| 4956897 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.67 | 62.0 | 5.81e-01 | 100.0% | 91.3% |
| 4991571 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.67 | 61.0 | 5.73e-01 | 100.0% | 91.3% |
| 4975116 | 70.1.1.0 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like | 0.67 | 60.0 | 5.70e-01 | 100.0% | 90.0% |
| 4983299 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.67 | 60.0 | 5.58e-01 | 100.0% | 84.7% |
| 4988093 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.66 | 61.0 | 5.17e-01 | 100.0% | 66.3% |
| 5083817 | 70.4.1.0 ↗ | beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) | 0.64 | 56.0 | 5.67e-01 | 98.5% | 98.5% |
| 3737549 | 3008.1.1.0 ↗ | a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.50 | 40.0 | 2.76e-01 | 89.6% | 89.4% |