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NC_060137.1__YP_010246724.1__L3Y25_gp065__00065

Bact-Vir

NC_060137.1__YP_010246724.1__L3Y25_gp065__00065

Identity

Accession:
NC_060137 ↗
Kingdom:
phage

Quality

81.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Octobienvirus› Gordonia_phage_Syleon

TaxID: 2653718

Cluster

View cluster (4 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 3-94
PDB
Domain cluster: rep: MH020239.1__AVP42093.1__SEA_NACA_56__00055__D3-80
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2d73A01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.70 49.0 3.45e-01 72.8% 45.1%
1ksiA03 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.66 49.0 3.18e-01 78.3% 39.7%
2o3oA01 2.40.128.690 Mainly Beta › Beta Barrel › Lipocalin › YycH protein, domain 3-like 0.66 52.0 4.72e-01 83.7% 77.7%
1d6uA03 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.65 48.0 3.12e-01 78.3% 38.8%
5e1qB01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.64 47.0 3.34e-01 77.2% 37.5%
3px5A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.62 44.0 4.10e-01 73.9% 80.2%
2chrA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.61 44.0 3.93e-01 73.9% 74.0%
3wa2X01 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 43.0 4.43e-01 75.0% 77.0%
1bqgA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.59 43.0 3.79e-01 76.1% 62.3%
3vfcA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.59 43.0 3.66e-01 75.0% 59.7%
3toyA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.59 43.0 3.89e-01 77.2% 71.7%
5n9bA01 2.60.40.2160 Mainly Beta › Sandwich › Immunoglobulin-like › Interleukin-17 receptor A/B, fibronectin-III-like domain 1 0.59 44.0 3.84e-01 79.3% 70.8%
4e6fA00 3.30.530.80 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.58 40.0 3.30e-01 71.7% 62.0%
6ro0F00 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 37.0 3.65e-01 79.3% 60.2%
4it1B01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.57 41.0 3.46e-01 75.0% 56.2%
4gxbA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 44.0 4.23e-01 90.2% 74.0%
3ugvA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.56 41.0 3.72e-01 77.2% 72.2%
2oz8A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.56 39.0 3.55e-01 73.9% 51.9%
4f3lA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 38.0 3.52e-01 71.7% 95.8%
2k4nA00 3.30.720.70 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.55 42.0 4.00e-01 82.6% 71.2%
2zadA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.55 38.0 3.54e-01 70.7% 57.0%
2pgwA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.55 39.0 3.41e-01 77.2% 60.7%
1fhvA02 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 38.0 3.44e-01 72.8% 62.1%
2oztA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 38.0 3.53e-01 73.9% 66.9%
4uv3E01 3.40.50.10610 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ABC-type transport auxiliary lipoprotein component 0.54 39.0 3.04e-01 77.2% 53.2%
3bxoA02 2.20.130.10 Mainly Beta › Single Sheet › S-adenosyl-L-methionine-dependent methyltransferases › CAC2371-like domains 0.53 30.0 3.57e-01 83.7% 84.7%
3jvaA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 38.0 3.63e-01 76.1% 80.7%
1tkkA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 38.0 3.59e-01 76.1% 81.7%
2wraA00 2.60.120.400 Mainly Beta › Sandwich › Jelly Rolls › Calcium-mediated lectin 0.53 40.0 3.64e-01 79.3% 97.5%
2xefA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.53 37.0 2.56e-01 71.7% 32.5%
3q45A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 38.0 3.47e-01 76.1% 73.8%
2qddA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 38.0 3.42e-01 76.1% 72.3%
1kczA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 37.0 3.14e-01 73.9% 74.8%
1wznA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.52 31.0 3.69e-01 80.4% 94.6%
4gn2A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 43.0 3.23e-01 91.3% 97.9%
5tseA00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.52 44.0 3.89e-01 92.4% 75.0%
1p1jA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.52 36.0 3.38e-01 71.7% 95.7%
3ik4B01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 39.0 3.59e-01 78.3% 77.1%
1ae2A00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 36.0 3.77e-01 75.0% 98.8%
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 35.0 2.57e-01 70.7% 89.5%
1fw3A00 2.40.230.10 Mainly Beta › Beta Barrel › Outer membrane phospholipase (ompla); Chain C › Phospholipase A1 0.51 42.0 3.19e-01 93.5% 86.0%
3rd4B00 2.40.50.660 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 38.0 4.03e-01 81.5% 98.8%
3njtA01 2.40.160.50 Mainly Beta › Beta Barrel › Porin › membrane protein fhac: a member of the omp85/tpsb transporter family 0.51 31.0 2.20e-01 79.3% 18.1%
5cflA02 3.40.50.12100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Stimulator of interferon genes protein 0.51 32.0 2.78e-01 75.0% 38.8%
3pqvA02 3.30.360.20 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › RNA 3'-terminal phosphate cyclase, insert domain 0.51 35.0 3.50e-01 71.7% 100.0%
1jkgA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 39.0 3.46e-01 84.8% 78.4%
2gdqA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.50 34.0 3.34e-01 73.9% 61.7%
6kghA02 3.30.450.330 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.50 41.0 3.50e-01 90.2% 73.4%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2163580 12.3.1.22 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › GH97_N 0.71 51.0 3.60e-01 73.9% 39.6%
4284296 12.3.1.22 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › GH97_N 0.70 51.0 3.74e-01 77.2% 45.3%
4254206 12.3.1.22 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › GH97_N 0.64 46.0 3.26e-01 73.9% 36.7%
1942596 12.3.1.22 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › GH97_N 0.64 46.0 3.41e-01 76.1% 42.2%
3621025 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.64 44.0 5.06e-01 75.0% 100.0%
3564421 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 44.0 4.13e-01 85.9% 57.4%
3646843 5.1.4.16 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A 0.62 47.0 3.10e-01 78.3% 41.5%
4305490 218.1.1.0 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.61 44.0 3.84e-01 73.9% 62.2%
1174509 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.61 44.0 4.02e-01 75.0% 70.2%
5000178 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.61 43.0 3.84e-01 73.9% 71.5%
3458732 243.3.1.19 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF3615 0.61 37.0 4.30e-01 80.4% 93.3%
5027407 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.59 42.0 3.97e-01 75.0% 82.3%
4444614 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 44.0 4.68e-01 98.9% 90.0%
3913071 220.1.1.52 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SNX17_FERM_C 0.59 48.0 4.20e-01 89.1% 74.3%
4514345 274.1.1.50 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits › Spore_YunB 0.58 43.0 3.68e-01 77.2% 71.0%
4948942 3425.2.1.0 ↗ a+b three layers › Two-component system yycF/yycG regulatory protein yycH-like › YycH C-terminal domain › YycH C-terminal domain 0.58 41.0 3.03e-01 75.0% 99.6%
3821015 218.1.1.0 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.57 41.0 3.47e-01 75.0% 67.1%
3535752 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 40.0 3.55e-01 98.9% 48.6%
3606640 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 51.0 4.82e-01 98.9% 86.4%
2141160 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 40.0 3.92e-01 73.9% 70.3%
4445572 4099.1.1.22 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › CENP-P 0.56 34.0 3.07e-01 79.3% 43.8%
1174516 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.55 39.0 3.67e-01 77.2% 76.5%
5026704 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 38.0 2.75e-01 72.8% 47.6%
3609908 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 43.0 4.03e-01 98.9% 70.9%
3466381 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 38.0 3.60e-01 73.9% 63.6%
3254982 295.1.1.4 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › COMM_domain 0.53 38.0 4.17e-01 76.1% 98.6%
3508672 2003.1.5.4 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › PCMT 0.53 42.0 3.14e-01 83.7% 90.2%
3927095 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.52 40.0 3.81e-01 80.4% 90.5%
4929294 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.52 45.0 3.70e-01 100.0% 74.4%
3288634 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.51 37.0 3.63e-01 77.2% 91.0%
5059744 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.51 36.0 3.64e-01 88.0% 74.4%
3371527 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 39.0 3.54e-01 81.5% 60.5%
5001274 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.51 38.0 3.40e-01 79.3% 80.8%
5076770 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.51 36.0 3.57e-01 89.1% 69.0%
3718960 4051.1.1.2 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F-actin_cap_A 0.51 45.0 3.49e-01 100.0% 70.5%
3892517 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.50 39.0 3.52e-01 85.9% 77.8%