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NC_025470.1__YP_009104076.1__S140_75__00075

Bact-Vir

NC_025470.1__YP_009104076.1__S140_75__00075

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

60.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shewanella_sp._phage_1/40

TaxID: 1458860

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 169-233
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04545.23 best Sigma70_r4 24.5 2.20e-05 58.5% 66.0%
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r0qC02 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.87 58.0 6.27e-01 70.8% 81.8%
1gdtB03 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.80 52.0 6.18e-01 75.4% 97.8%
1jhgA00 1.10.1270.10 Mainly Alpha › Orthogonal Bundle › Trp Operon Repressor; Chain A › TrpR-like 0.77 56.0 4.83e-01 78.5% 49.5%
3zh9B03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.76 61.0 4.86e-01 86.2% 44.4%
3frwB00 1.10.1270.10 Mainly Alpha › Orthogonal Bundle › Trp Operon Repressor; Chain A › TrpR-like 0.75 53.0 4.64e-01 75.4% 50.0%
4ijaA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.73 46.0 4.70e-01 70.8% 66.7%
8amzO01 1.25.40.570 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.72 54.0 3.38e-01 80.0% 16.8%
3bddD00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.72 52.0 4.12e-01 76.9% 42.4%
3bj6B00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.71 50.0 3.75e-01 73.8% 36.4%
5eriA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.69 49.0 3.68e-01 73.8% 35.9%
2oi8A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.69 52.0 3.67e-01 81.5% 31.5%
5dukB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.69 47.0 4.68e-01 70.8% 73.1%
2m8gX00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.68 48.0 4.69e-01 73.8% 68.6%
2o38A01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.68 46.0 4.62e-01 76.9% 70.8%
4rgxB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.67 46.0 3.69e-01 72.3% 36.6%
2qwwC00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.67 47.0 3.65e-01 72.3% 37.7%
3cuoD00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.66 47.0 4.24e-01 76.9% 96.8%
4b8xA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.66 48.0 3.72e-01 76.9% 41.4%
4nvsA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.64 54.0 4.10e-01 93.8% 81.3%
3ecoB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 47.0 3.79e-01 78.5% 44.2%
1etkA00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.64 46.0 4.49e-01 80.0% 68.0%
4gvpA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.64 48.0 3.45e-01 83.1% 38.8%
3keoA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 44.0 4.25e-01 70.8% 66.7%
3gwzA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 51.0 4.68e-01 90.8% 96.6%
1l0oC00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.62 45.0 4.74e-01 76.9% 96.5%
5zyrA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.57 39.0 2.97e-01 73.8% 30.5%
2ip2A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.57 45.0 4.18e-01 89.2% 90.5%
2zkzC00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 42.0 3.84e-01 80.0% 83.9%
1r1uB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 40.0 3.62e-01 75.4% 92.5%
4e70A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 48.0 4.25e-01 100.0% 79.2%
1u2wD00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 43.0 3.93e-01 87.7% 93.6%
3lstA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 45.0 4.15e-01 96.9% 89.5%
4a6dA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 43.0 3.88e-01 92.3% 85.1%
3f2gA00 3.30.450.410 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 42.0 3.06e-01 93.8% 69.8%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4054648 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.95 73.0 7.87e-01 80.0% 94.5%
4952807 101.1.1.60 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_23 0.88 64.0 6.05e-01 78.5% 65.3%
5063318 101.1.6.12 ↗ alpha arrays › HTH › HTH › TrpR › HTH_23 0.88 62.0 6.73e-01 76.9% 87.3%
3587644 101.1.1.17 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_7 0.87 57.0 5.96e-01 70.8% 73.3%
1159643 101.1.1.17 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_7 0.87 58.0 5.63e-01 70.8% 63.4%
3283589 101.1.1.368 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_58 0.85 55.0 6.18e-01 70.8% 86.0%
5002651 101.1.2.141 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.85 59.0 5.16e-01 72.3% 50.5%
3953111 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.84 61.0 5.94e-01 81.5% 70.0%
4970998 101.1.6.0 ↗ alpha arrays › HTH › HTH › TrpR 0.84 63.0 5.34e-01 80.0% 51.0%
4162857 101.1.1.17 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_7 0.83 57.0 6.44e-01 81.5% 92.0%
4008959 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.81 62.0 6.59e-01 84.6% 98.2%
3287232 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.80 69.0 6.65e-01 100.0% 85.3%
4978102 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.79 60.0 5.50e-01 81.5% 63.5%
4952294 101.1.2.870 ↗ alpha arrays › HTH › HTH › winged helix domain › GerE 0.78 54.0 5.83e-01 81.5% 85.5%
4391758 101.1.6.1 ↗ alpha arrays › HTH › HTH › TrpR › Trp_repressor 0.77 55.0 4.87e-01 75.4% 52.6%
3589184 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.77 54.0 5.15e-01 73.8% 85.3%
5013438 101.1.2.881 ↗ alpha arrays › HTH › HTH › winged helix domain › UPF0175 0.76 51.0 5.32e-01 70.8% 78.3%
4952035 101.1.1.17 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_7 0.75 60.0 6.21e-01 92.3% 91.7%
5053505 101.1.6.0 ↗ alpha arrays › HTH › HTH › TrpR 0.74 51.0 5.59e-01 72.3% 94.0%
5064868 101.1.11.203 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix › UPF0175 0.73 54.0 4.87e-01 80.0% 62.2%
3603739 101.1.1.498 ↗ alpha arrays › HTH › HTH › Three-helical HTH › LAGLIDADG_3 0.72 65.0 4.09e-01 100.0% 33.8%
5050966 101.1.11.2 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix › RHH_1 0.71 55.0 4.96e-01 87.7% 63.2%
5071227 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.71 54.0 3.44e-01 81.5% 57.0%
4008322 101.1.1.17 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_7 0.71 53.0 5.72e-01 86.2% 94.5%
5072014 101.1.11.0 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix 0.70 53.0 5.04e-01 81.5% 74.7%
5051680 101.1.11.0 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix 0.70 54.0 5.15e-01 87.7% 76.2%
4339699 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.69 47.0 5.10e-01 70.8% 89.1%
3933366 101.1.6.12 ↗ alpha arrays › HTH › HTH › TrpR › HTH_23 0.68 53.0 5.20e-01 83.1% 87.1%
3288236 101.1.3.4 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › HTH_30 0.58 39.0 3.56e-01 70.8% 54.4%
4012714 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 41.0 3.25e-01 83.1% 53.3%
D2 medium residues 55-157
PDB