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NC_019720.1__YP_007112349.1__F857_gp06__00006
Bact-VirNC_019720.1__YP_007112349.1__F857_gp06__00006
Identity
- Accession:
- NC_019720 ↗
- Kingdom:
- phage
Quality
96.7
mean pLDDT
Taxonomy
TaxID: 1147156
Cluster
View cluster (6 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
high
residues 11-50
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF09956.16 best | Phage_cement_2 | 28.4 | 2.40e-06 | 97.5% | 34.9% |
CATH (25)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3k3sH01 | 2.30.130.110 | Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › | 0.75 | 66.0 | 5.20e-01 | 97.5% | 76.8% |
| 3wx7A02 | 2.10.10.90 | Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › | 0.72 | 58.0 | 4.43e-01 | 87.5% | 44.2% |
| 3prbA02 | 2.40.10.330 | Mainly Beta › Beta Barrel › Thrombin, subunit H › | 0.71 | 59.0 | 5.84e-01 | 100.0% | 95.5% |
| 1wvvB01 | 2.10.10.20 | Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › Carbohydrate-binding module superfamily 5/12 | 0.70 | 56.0 | 5.33e-01 | 90.0% | 79.2% |
| 3c8vA02 | 2.160.10.10 | Mainly Beta › 3 Solenoid › UDP N-Acetylglucosamine Acyltransferase; domain 1 › Hexapeptide repeat proteins | 0.69 | 48.0 | 2.97e-01 | 75.0% | 20.9% |
| 1ed7A00 | 2.10.10.20 | Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › Carbohydrate-binding module superfamily 5/12 | 0.68 | 52.0 | 5.13e-01 | 87.5% | 91.1% |
| 1yueA02 | 2.10.10.40 | Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › | 0.67 | 53.0 | 4.69e-01 | 90.0% | 85.2% |
| 1goiB03 | 2.10.10.20 | Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › Carbohydrate-binding module superfamily 5/12 | 0.67 | 51.0 | 4.83e-01 | 87.5% | 72.5% |
| 4m1xD00 | 3.30.1360.240 | Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › | 0.66 | 47.0 | 4.00e-01 | 82.5% | 44.4% |
| 2i7xA02 | 3.40.50.10890 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.60 | 43.0 | 2.87e-01 | 80.0% | 33.5% |
| 2nqwA00 | 3.30.465.10 | Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › | 0.59 | 48.0 | 3.92e-01 | 100.0% | 81.6% |
| 2ztbA03 | 2.60.40.3040 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.58 | 45.0 | 4.29e-01 | 97.5% | 72.9% |
| 4ncdA02 | 2.60.40.3970 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.58 | 51.0 | 3.97e-01 | 100.0% | 54.5% |
| 4djmA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.58 | 49.0 | 4.01e-01 | 100.0% | 50.0% |
| 2eyqA05 | 2.40.10.170 | Mainly Beta › Beta Barrel › Thrombin, subunit H › | 0.54 | 38.0 | 3.43e-01 | 72.5% | 52.5% |
| 7razA01 | 3.30.70.100 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.54 | 40.0 | 3.34e-01 | 90.0% | 43.5% |
| 6evgA01 | 2.60.40.420 | Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins | 0.53 | 47.0 | 3.29e-01 | 100.0% | 31.8% |
| 1w3fA02 | 2.170.15.10 | Mainly Beta › Beta Complex › Proaerolysin; Chain A, domain 3 › Proaerolysin, chain A, domain 3 | 0.53 | 42.0 | 2.88e-01 | 95.0% | 61.2% |
| 3va7A07 | 2.40.50.100 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain | 0.52 | 38.0 | 3.43e-01 | 100.0% | 90.8% |
| 3ey7A01 | 3.10.180.10 | Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 | 0.52 | 40.0 | 2.98e-01 | 92.5% | 46.3% |
| 1nr6A00 | 1.10.630.10 | Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 | 0.51 | 39.0 | 2.28e-01 | 90.0% | 72.7% |
| 6zj8D01 | 3.30.450.20 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain | 0.51 | 39.0 | 3.04e-01 | 95.0% | 75.4% |
| 1zvfB01 | 2.60.120.10 | Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls | 0.51 | 44.0 | 2.93e-01 | 100.0% | 26.8% |
| 2ve3B00 | 1.10.630.10 | Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 | 0.51 | 39.0 | 2.31e-01 | 90.0% | 71.9% |
| 2d8iA01 | 2.30.42.10 | Mainly Beta › Roll › Pdz3 Domain › PDZ domain | 0.51 | 40.0 | 3.31e-01 | 100.0% | 94.3% |
ECOD (22)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3981632 | 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 | 0.97 | 87.0 | 8.72e-01 | 100.0% | 95.0% |
| 5083719 | 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) | 0.89 | 80.0 | 5.50e-01 | 100.0% | 54.4% |
| 4996605 | 70.3.1.12 ↗ | beta barrels › beta-clip › SET domain-like › SET domain-like › PF30644 | 0.79 | 70.0 | 5.48e-01 | 97.5% | 78.8% |
| 4009007 | 64.3.1.0 ↗ | beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain | 0.77 | 62.0 | 5.78e-01 | 90.0% | 82.0% |
| 5041151 | 239.1.1.15 ↗ | beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf | 0.75 | 65.0 | 5.47e-01 | 100.0% | 85.7% |
| 3972100 | 64.3.1.0 ↗ | beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain | 0.75 | 58.0 | 4.99e-01 | 87.5% | 60.0% |
| 3664930 | 1.1.7.50 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › EF-G_D2 | 0.74 | 57.0 | 4.03e-01 | 92.5% | 34.1% |
| 5047208 | 284.4.1.0 ↗ | a+b two layers › FKBP-like › Archaeal FKBP insertion domain › Archaeal FKBP insertion domain | 0.74 | 62.0 | 5.71e-01 | 100.0% | 76.4% |
| 5022325 | 239.1.1.15 ↗ | beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › CPxCG_zf | 0.73 | 63.0 | 4.76e-01 | 100.0% | 64.0% |
| 1322862 | 64.3.1.1 ↗ | beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain › CBM_5_12 | 0.73 | 58.0 | 5.47e-01 | 87.5% | 87.5% |
| 3971347 | 64.3.1.1 ↗ | beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain › CBM_5_12 | 0.72 | 57.0 | 5.11e-01 | 87.5% | 72.4% |
| 4110715 | 64.3.1.1 ↗ | beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain › CBM_5_12 | 0.71 | 58.0 | 5.15e-01 | 90.0% | 71.2% |
| 4307941 | 64.3.1.1 ↗ | beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain › CBM_5_12 | 0.71 | 54.0 | 4.86e-01 | 87.5% | 89.8% |
| 4948029 | 284.4.1.3 ↗ | a+b two layers › FKBP-like › Archaeal FKBP insertion domain › Archaeal FKBP insertion domain › FKBP26_C | 0.68 | 59.0 | 5.52e-01 | 100.0% | 84.0% |
| 5026481 | 64.3.1.3 ↗ | beta meanders › WW domain-like › Carbohydrate binding domain › Carbohydrate binding domain › CBM_5_12_2 | 0.66 | 51.0 | 4.83e-01 | 87.5% | 76.0% |
| 3700965 | 229.1.1.0 ↗ | a+b two layers › Cdc48 domain 2-like › Cdc48 domain 2-like › Cdc48 domain 2-like | 0.64 | 52.0 | 4.42e-01 | 100.0% | 82.7% |
| 3857417 | 1.1.2.42 ↗ | beta barrels › cradle loop barrel › RIFT-related › double psi › PF29595 | 0.63 | 51.0 | 4.36e-01 | 100.0% | 84.0% |
| 3964293 | 207.2.1.0 ↗ | beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like | 0.62 | 44.0 | 2.89e-01 | 82.5% | 18.6% |
| 4941183 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.60 | 52.0 | 3.73e-01 | 100.0% | 39.0% |
| 5027088 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.58 | 50.0 | 3.50e-01 | 100.0% | 63.0% |
| 4301634 | 11.1.1.42 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PapD_C | 0.56 | 49.0 | 3.93e-01 | 100.0% | 58.7% |
| 4385734 | 5.1.4.567 ↗ | beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Helveticin_J | 0.53 | 40.0 | 2.41e-01 | 90.0% | 12.9% |
D2
high
residues 54-106
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF09956.16 best | Phage_cement_2 | 36.4 | 8.10e-09 | 100.0% | 53.4% |
CATH (16)
| 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 | 0.81 | 73.0 | 6.01e-01 | 100.0% | 63.4% |
| 1c5eA00 | 2.40.300.10 | Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D | 0.81 | 73.0 | 5.96e-01 | 100.0% | 60.0% |
| 3gqhA01 | 2.40.300.10 | Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D | 0.73 | 66.0 | 4.95e-01 | 100.0% | 54.5% |
| 8bveA03 | 2.40.340.10 | Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV | 0.63 | 51.0 | 4.76e-01 | 100.0% | 100.0% |
| 1ameA00 | 3.90.1210.10 | Alpha Beta › Alpha-Beta Complex › Type Iii Antifreeze Protein Isoform Hplc 12 › Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain | 0.62 | 50.0 | 4.74e-01 | 92.5% | 89.4% |
| 3girA04 | 2.40.30.110 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains | 0.61 | 47.0 | 4.25e-01 | 100.0% | 60.3% |
| 1v0fB03 | 2.40.30.20 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › | 0.60 | 47.0 | 4.12e-01 | 100.0% | 55.3% |
| 2w5eA02 | 2.40.10.10 | Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases | 0.58 | 42.0 | 3.89e-01 | 100.0% | 58.1% |
| 2m9uA00 | 2.30.30.850 | Mainly Beta › Roll › SH3 type barrels. › | 0.58 | 41.0 | 3.46e-01 | 79.2% | 44.9% |
| 1vloA04 | 2.40.30.110 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains | 0.57 | 46.0 | 3.97e-01 | 100.0% | 54.9% |
| 1wczA01 | 2.40.10.10 | Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases | 0.57 | 41.0 | 3.37e-01 | 100.0% | 38.3% |
| 3fppA02 | 2.40.50.100 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain | 0.56 | 48.0 | 4.36e-01 | 100.0% | 95.9% |
| 3p26A03 | 2.40.30.10 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors | 0.56 | 45.0 | 3.76e-01 | 100.0% | 59.1% |
| 1vw3C01 | 2.40.30.10 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors | 0.55 | 45.0 | 3.52e-01 | 100.0% | 41.2% |
| 7syvx01 | 2.40.30.10 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors | 0.53 | 44.0 | 3.39e-01 | 100.0% | 50.4% |
| 1bcoA02 | 2.30.30.130 | Mainly Beta › Roll › SH3 type barrels. › Transposase, Mu, C-terminal | 0.51 | 35.0 | 3.35e-01 | 73.6% | 83.8% |
ECOD (24)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 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 | 0.96 | 91.0 | 8.99e-01 | 100.0% | 98.2% |
| 5083172 | 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 | 0.92 | 78.0 | 7.90e-01 | 92.5% | 100.0% |
| 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) | 0.85 | 76.0 | 7.09e-01 | 98.1% | 98.5% |
| 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) | 0.84 | 77.0 | 7.45e-01 | 100.0% | 96.6% |
| 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) | 0.82 | 73.0 | 5.80e-01 | 100.0% | 66.3% |
| 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 | 0.77 | 66.0 | 6.42e-01 | 100.0% | 86.4% |
| 4963571 | 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 | 68.0 | 6.36e-01 | 100.0% | 83.1% |
| 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 | 0.76 | 66.0 | 6.38e-01 | 100.0% | 95.0% |
| 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) | 0.75 | 66.0 | 6.03e-01 | 100.0% | 91.4% |
| 5002644 | 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) | 0.74 | 64.0 | 5.77e-01 | 100.0% | 94.7% |
| 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) | 0.73 | 63.0 | 6.28e-01 | 98.1% | 94.5% |
| 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) | 0.71 | 61.0 | 5.80e-01 | 100.0% | 92.3% |
| 5049149 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.69 | 61.0 | 5.50e-01 | 100.0% | 98.6% |
| 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 | 0.67 | 58.0 | 5.62e-01 | 100.0% | 95.0% |
| 3603211 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.65 | 55.0 | 4.88e-01 | 100.0% | 88.7% |
| 4983299 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.62 | 51.0 | 4.55e-01 | 100.0% | 84.7% |
| 1030933 | 1.1.7.29 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › End_beta_barrel | 0.60 | 47.0 | 4.05e-01 | 100.0% | 52.8% |
| 4956897 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.60 | 49.0 | 4.45e-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 | 0.59 | 48.0 | 4.34e-01 | 100.0% | 93.8% |
| 3907690 | 1.1.17.1 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin | 0.58 | 48.0 | 3.31e-01 | 100.0% | 24.8% |
| 5005052 | 1.1.9.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › PUA domain | 0.57 | 46.0 | 4.57e-01 | 98.1% | 96.4% |
| 4315579 | 1.1.8.20 ↗ | beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › Beta-barrel_CAF17_C | 0.57 | 50.0 | 3.89e-01 | 100.0% | 59.2% |
| 4930449 | 70.1.1.1 ↗ | beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C | 0.57 | 46.0 | 4.29e-01 | 100.0% | 94.7% |
| 3180074 | 1.1.8.11 ↗ | beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GTP-eEF1A_C | 0.57 | 47.0 | 4.01e-01 | 100.0% | 67.4% |