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MT897908.1__QNO12851.1__SEA_SHAKENBAKE_34__00034

Bact-Vir

MT897908.1__QNO12851.1__SEA_SHAKENBAKE_34__00034

Identity

Accession:
MT897908 ↗
Kingdom:
phage

Quality

73.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Streptomyces_phage_ShakeNBake

TaxID: 2768142

Cluster

Singleton — not in a non-trivial cluster

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 8-75
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6p10B02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.65 42.0 3.89e-01 76.5% 50.5%
1vq8P03 1.10.1200.60 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.62 43.0 4.62e-01 76.5% 89.1%
2hoqA02 1.10.150.520 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.61 46.0 4.45e-01 83.8% 87.3%
4xpwA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.60 43.0 3.48e-01 76.5% 57.3%
1bgcA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.56 49.0 3.78e-01 100.0% 66.5%
7b7tA01 1.20.1270.30 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.55 42.0 3.16e-01 80.9% 88.2%
2p6vA00 1.20.120.1110 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › TAFH/NHR1 domain 0.55 46.0 4.23e-01 100.0% 70.1%
3pw3D00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.55 49.0 3.10e-01 100.0% 36.0%
2zueA01 3.30.1360.70 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Arginyl tRNA synthetase N-terminal domain 0.55 48.0 4.09e-01 100.0% 84.3%
3zgyA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.53 45.0 3.76e-01 100.0% 86.8%
4bqnB01 3.40.50.12080 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 40.0 3.09e-01 89.7% 95.1%
3q5dA02 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.52 41.0 3.62e-01 100.0% 59.8%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3393066 103.1.1.85 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › PF28528 0.65 44.0 4.54e-01 76.5% 73.8%
3554055 3567.1.1.12 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › CD47 0.61 44.0 3.32e-01 76.5% 84.1%
4978938 2002.1.1.134 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_2 0.60 43.0 2.82e-01 76.5% 82.4%
3637195 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.60 42.0 3.81e-01 76.5% 80.0%
3402740 102.1.3.8 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain › Mab-21_C 0.59 45.0 3.62e-01 83.8% 76.4%
4037941 4966.1.1.1 ↗ alpha arrays › inserted helical bundle subdomain in T7 RNA polymerase › inserted helical bundle subdomain in T7 RNA polymerase › inserted helical bundle subdomain in T7 RNA polymerase › RNA_pol 0.58 49.0 4.74e-01 100.0% 91.3%
3661711 592.1.1.1 ↗ alpha arrays › PWI domain-like › PWI domain › PWI domain › PWI 0.55 49.0 4.65e-01 100.0% 96.2%
4484002 4966.1.1.0 ↗ alpha arrays › inserted helical bundle subdomain in T7 RNA polymerase › inserted helical bundle subdomain in T7 RNA polymerase › inserted helical bundle subdomain in T7 RNA polymerase 0.54 45.0 4.40e-01 100.0% 96.2%
3260092 101.1.1.123 ↗ alpha arrays › HTH › HTH › Three-helical HTH › MCRS_N 0.54 36.0 3.66e-01 100.0% 68.6%
4972168 7073.1.1.1 ↗ alpha arrays › C-terminal domain of Malic enzyme › C-terminal domain of Malic enzyme › C-terminal domain of Malic enzyme › Malic_M 0.54 40.0 3.36e-01 95.6% 46.1%
5000893 7073.1.1.0 ↗ alpha arrays › C-terminal domain of Malic enzyme › C-terminal domain of Malic enzyme › C-terminal domain of Malic enzyme 0.53 40.0 3.41e-01 95.6% 48.7%
D2 high residues 83-172
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3l50A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.63 57.0 4.98e-01 100.0% 77.2%
6x5vA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 41.0 4.07e-01 77.8% 64.6%
1x67A01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.61 55.0 4.82e-01 100.0% 75.9%
5ynrA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.60 54.0 4.67e-01 100.0% 79.7%
2mp4A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.59 51.0 4.28e-01 100.0% 79.4%
6tdxG01 3.40.1380.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › ATP synthase, F1 complex, gamma subunit 0.58 52.0 3.95e-01 100.0% 74.8%
1ry6A00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.57 48.0 3.26e-01 90.0% 48.9%
2ee3A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 38.0 3.66e-01 81.1% 57.4%
2xf1A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.57 51.0 4.64e-01 100.0% 79.5%
5dn6G02 3.40.1380.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › ATP synthase, F1 complex, gamma subunit 0.56 50.0 3.91e-01 98.9% 68.0%
1vq8B03 3.30.1430.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L3; Chain: B; domain 2, › 0.55 48.0 4.56e-01 100.0% 94.6%
2r76A00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.54 43.0 3.84e-01 100.0% 59.8%
2jxpA01 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.53 44.0 3.78e-01 100.0% 57.4%
4kwyA00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.51 39.0 3.45e-01 82.2% 81.8%
1ilvA00 3.40.1210.10 Alpha Beta › 3-Layer(aba) Sandwich › Stationary-phase Survival Protein Sure Homolog; Chain: A, › Survival protein SurE-like phosphatase/nucleotidase 0.51 41.0 3.07e-01 90.0% 87.8%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3194506 220.1.1.201 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF7493 0.71 36.0 3.37e-01 84.4% 39.1%
3200646 220.1.1.201 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF7493 0.65 35.0 3.30e-01 96.7% 44.8%
4012363 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.63 57.0 4.89e-01 100.0% 75.0%
4976645 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.63 57.0 5.07e-01 100.0% 82.0%
3742638 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.62 56.0 4.90e-01 100.0% 80.0%
4975793 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.61 55.0 4.88e-01 100.0% 80.0%
3594967 206.1.3.70 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DUF7920 0.61 43.0 2.99e-01 74.4% 65.6%
3443030 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 40.0 4.27e-01 100.0% 78.8%
3679783 7519.1.1.1 ↗ a/b three-layered sandwiches › ATP synthase (F1-ATPase), gamma subunit › ATP synthase (F1-ATPase), gamma subunit › ATP synthase (F1-ATPase), gamma subunit › ATP-synt 0.59 54.0 3.78e-01 100.0% 55.4%
5053278 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.59 41.0 2.74e-01 73.3% 20.0%
4309637 1036.1.1.1 ↗ a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.58 41.0 4.22e-01 73.3% 100.0%
3283168 210.1.3.3 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_4 0.57 46.0 3.33e-01 90.0% 30.7%
5049975 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.56 45.0 3.33e-01 92.2% 72.7%
1281053 230.1.1.6 ↗ a+b two layers › T-fold › Tetrahydrobiopterin biosynthesis enzymes-like › Tetrahydrobiopterin biosynthesis enzymes-like › QueF 0.56 39.0 3.44e-01 73.3% 55.2%
None — 0.55 45.0 3.02e-01 90.0% 48.7%
3722378 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.54 26.0 2.68e-01 78.9% 44.3%
1197 10.2.1.28 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Denso_VP4 0.53 43.0 2.84e-01 91.1% 77.1%
5027780 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.53 34.0 3.85e-01 96.7% 96.7%
5079898 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.52 47.0 4.16e-01 100.0% 94.6%
3839558 7503.1.1.5 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › NLBH 0.52 38.0 3.05e-01 81.1% 78.9%
3355880 2004.1.1.250 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin,Microtub_bd 0.52 43.0 2.91e-01 92.2% 57.1%