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SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00436
Bact-VirSR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00436
Identity
- Kingdom:
- phage
Quality
78.4
mean pLDDT
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
high
residues 6-205
Domain cluster:
representative
CATH (17)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2e52B01 | 3.40.91.70 | Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Type II restriction endonuclease, HindIII | 0.71 | 55.0 | 5.27e-01 | 92.5% | 71.0% |
| 2fokA03 | 3.40.91.30 | Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › | 0.68 | 50.0 | 5.36e-01 | 86.0% | 86.9% |
| 1knvB00 | 3.40.91.10 | Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › | 0.67 | 57.0 | 5.00e-01 | 90.5% | 89.3% |
| 8a57D01 | 3.40.50.11060 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › GTPase HflX, N-terminal domain | 0.61 | 31.0 | 4.19e-01 | 74.5% | 93.1% |
| 1z9bA01 | 3.40.50.10050 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Translation initiation factor IF- 2, domain 3 | 0.60 | 25.0 | 3.73e-01 | 78.0% | 89.3% |
| 2gb7D00 | 3.40.91.80 | Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › | 0.59 | 56.0 | 4.85e-01 | 100.0% | 89.7% |
| 2kyrA00 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.56 | 26.0 | 3.39e-01 | 71.5% | 76.9% |
| 6pexA01 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.55 | 30.0 | 3.64e-01 | 70.0% | 79.7% |
| 2j3rB00 | 3.30.1380.20 | Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 | 0.55 | 29.0 | 3.30e-01 | 82.0% | 64.3% |
| 2o5hA00 | 1.10.3510.10 | Mainly Alpha › Orthogonal Bundle › NMB0513-like › NMB0513-like | 0.55 | 31.0 | 3.85e-01 | 94.5% | 87.5% |
| 1j8yF01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.54 | 24.0 | 3.63e-01 | 80.0% | 97.7% |
| 1d02B00 | 3.40.580.10 | Alpha Beta › 3-Layer(aba) Sandwich › ECO RI Endonuclease; Chain A › Eco RI Endonuclease, subunit A | 0.53 | 43.0 | 4.37e-01 | 84.5% | 84.0% |
| 2l3fA00 | 3.40.470.10 | Alpha Beta › 3-Layer(aba) Sandwich › Uracil-DNA Glycosylase, subunit E › Uracil-DNA glycosylase-like domain | 0.52 | 33.0 | 3.63e-01 | 82.5% | 77.6% |
| 4esjA01 | 3.40.210.30 | Alpha Beta › 3-Layer(aba) Sandwich › PvuII Endonuclease; Chain A › Dam replacing family, catalytic PD-(D/E)XK domain | 0.51 | 39.0 | 4.30e-01 | 83.5% | 100.0% |
| 7tocA01 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.51 | 33.0 | 3.33e-01 | 75.0% | 61.2% |
| 1vwxQ00 | 3.100.10.10 | Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › | 0.51 | 29.0 | 2.99e-01 | 90.5% | 54.5% |
| 3phhA02 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.50 | 33.0 | 3.93e-01 | 86.0% | 100.0% |
ECOD (28)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3955210 | 2008.1.1.60 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat_2 | 0.80 | 63.0 | 6.93e-01 | 91.0% | 97.6% |
| 5037144 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.76 | 40.0 | 5.03e-01 | 90.5% | 82.3% |
| 5081250 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.75 | 40.0 | 5.05e-01 | 80.5% | 83.2% |
| 4977513 | 2008.1.1.16 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat | 0.74 | 53.0 | 6.03e-01 | 89.0% | 94.8% |
| 5014475 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.71 | 47.0 | 5.50e-01 | 87.0% | 93.1% |
| 149562 | 2008.1.1.26 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Bse634I | 0.70 | 60.0 | 5.26e-01 | 90.5% | 89.7% |
| 4948814 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.65 | 49.0 | 5.42e-01 | 77.0% | 98.8% |
| 3603146 | 2008.1.1.95 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DpnII | 0.65 | 51.0 | 4.55e-01 | 82.0% | 95.8% |
| 4942551 | 2008.1.1.59 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 | 0.63 | 44.0 | 4.27e-01 | 71.0% | 75.0% |
| 5047291 | 2007.1.3.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › Response_reg | 0.63 | 34.0 | 4.13e-01 | 71.0% | 80.0% |
| 4944956 | 2007.1.3.0 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like | 0.63 | 34.0 | 4.14e-01 | 71.0% | 80.0% |
| 4957206 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.62 | 41.0 | 4.90e-01 | 71.0% | 97.0% |
| 4944368 | 2008.1.1.11 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › SfsA | 0.61 | 44.0 | 4.93e-01 | 83.5% | 94.8% |
| 5016968 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.61 | 38.0 | 4.56e-01 | 71.0% | 92.6% |
| 4324611 | 2008.1.1.166 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_XcyI | 0.60 | 48.0 | 4.06e-01 | 82.0% | 95.2% |
| 2817077 | 7590.1.1.2 ↗ | a/b three-layered sandwiches › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Piwi | 0.60 | 32.0 | 3.49e-01 | 74.5% | 59.9% |
| 4999713 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.60 | 47.0 | 5.07e-01 | 97.5% | 94.3% |
| 4946143 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.58 | 38.0 | 4.55e-01 | 76.5% | 96.3% |
| 5004848 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.58 | 40.0 | 4.76e-01 | 74.0% | 100.0% |
| 3929562 | 864.1.1.1 ↗ | a+b two layers › DLC › DLC › DLC › Dynein_light | 0.57 | 22.0 | 3.53e-01 | 78.5% | 88.1% |
| 3497368 | 864.1.1.1 ↗ | a+b two layers › DLC › DLC › DLC › Dynein_light | 0.57 | 23.0 | 3.58e-01 | 79.0% | 89.4% |
| 5022505 | 2007.1.16.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Iron-sulphur enzyme Dph2 › Diphthamide_syn | 0.56 | 28.0 | 3.97e-01 | 80.0% | 100.0% |
| 5019662 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.56 | 40.0 | 4.48e-01 | 75.5% | 94.2% |
| 3962163 | 2007.1.3.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › Response_reg | 0.54 | 33.0 | 3.88e-01 | 87.5% | 85.7% |
| 4943385 | 2490.3.1.0 ↗ | a/b three-layered sandwiches › Ribosomal protein L13/L15p/L18e/L32e › Ribosomal proteins L15p and L18e › Ribosomal proteins L15p and L18e | 0.53 | 27.0 | 3.47e-01 | 90.5% | 83.5% |
| 3969806 | 7512.1.1.0 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase | 0.52 | 36.0 | 4.00e-01 | 90.5% | 89.0% |
| 3380288 | 2003.1.11.1 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Formate/glycerate dehydrogenase catalytic domain-like › 2-Hacid_dh | 0.52 | 29.0 | 3.43e-01 | 71.0% | 77.1% |
| 2595136 | 2002.1.1.89 ↗ | a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_26 | 0.50 | 35.0 | 2.95e-01 | 70.0% | 81.3% |
D2
high
residues 218-262
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF04851.22 best | ResIII | 35.9 | 9.70e-09 | 100.0% | 26.8% |
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1br0A00 | 1.20.58.70 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.59 | 45.0 | 3.38e-01 | 86.7% | 76.7% |
| 2jh3A02 | 3.40.50.1400 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.58 | 45.0 | 3.44e-01 | 88.9% | 40.7% |
| 1tjlA00 | 1.20.120.910 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain | 0.57 | 46.0 | 3.17e-01 | 86.7% | 30.3% |
| 3i2fA02 | 1.10.3020.10 | Mainly Alpha › Orthogonal Bundle › alpha-amino acid ester hydrolase ( Helical cap domain) › alpha-amino acid ester hydrolase ( Helical cap domain) | 0.56 | 41.0 | 3.24e-01 | 80.0% | 36.8% |
| 4am6A03 | 3.30.420.580 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › | 0.54 | 45.0 | 2.88e-01 | 97.8% | 23.3% |
| 4ev6A03 | 1.20.58.340 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region | 0.54 | 39.0 | 3.64e-01 | 80.0% | 69.0% |