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NC_042106.1__YP_009622881.1__FDJ31_gp83__00083

Bact-Vir

NC_042106.1__YP_009622881.1__FDJ31_gp83__00083

Identity

Accession:
NC_042106 ↗
Kingdom:
phage

Quality

95.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bingvirus› Streptomyces_phage_Bing

TaxID: 2079427

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 120-165
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 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 0.87 79.0 6.86e-01 100.0% 70.6%
1y6uA01 3.90.105.50 Alpha Beta › Alpha-Beta Complex › Molybdopterin biosynthesis moea protein, domain 2 › 0.71 48.0 4.76e-01 84.8% 67.3%
5i41B00 1.10.1660.10 Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › 0.68 47.0 4.19e-01 73.9% 94.0%
2i9dA00 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.68 49.0 3.13e-01 78.3% 83.1%
3h5tA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.65 47.0 4.72e-01 78.3% 93.6%
4mf9B01 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.65 45.0 3.14e-01 73.9% 78.2%
2mtzA01 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.64 47.0 4.59e-01 78.3% 92.0%
5c8qB02 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.59 46.0 4.69e-01 87.0% 97.8%
5tjjA01 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 0.59 47.0 4.16e-01 95.7% 58.9%
2isyA01 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 0.58 48.0 3.45e-01 95.7% 35.5%
1j75A00 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 44.0 4.24e-01 95.7% 73.7%
1e0gA00 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.57 41.0 4.09e-01 80.4% 93.8%
2fa5A00 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 46.0 3.37e-01 95.7% 32.4%
2p8tA01 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 41.0 3.66e-01 95.7% 52.0%
3bwgB01 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 45.0 4.04e-01 95.7% 78.3%
3tqnA01 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 0.55 46.0 4.05e-01 97.8% 64.4%
3eetA01 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 43.0 3.97e-01 95.7% 80.0%
1s6lA01 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 4.41e-01 97.8% 88.5%
1wquA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.53 44.0 3.43e-01 100.0% 77.2%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4414927 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.84 75.0 6.52e-01 100.0% 71.0%
3171408 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.82 71.0 6.99e-01 97.8% 96.0%
3587703 101.1.14.0 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases 0.79 69.0 6.79e-01 100.0% 94.0%
4278221 101.1.9.8 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › IF2_N 0.69 50.0 4.43e-01 76.1% 78.5%
2876157 101.1.9.105 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › PF30176 0.68 46.0 4.47e-01 71.7% 100.0%
3698670 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.68 53.0 4.82e-01 84.8% 85.0%
3987930 101.1.4.2 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › LacI 0.66 48.0 4.25e-01 80.4% 67.1%
4468802 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.62 47.0 4.02e-01 84.8% 94.9%
3788382 101.1.15.0 ↗ alpha arrays › HTH › HTH › HAT1, C-terminal domain 0.61 51.0 4.29e-01 95.7% 60.0%
4015134 108.1.1.29 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_7 0.58 43.0 3.54e-01 84.8% 82.1%
3947892 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.58 47.0 4.67e-01 91.3% 96.0%
3084 103.1.1.27 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › UBA_7 0.54 38.0 3.76e-01 76.1% 90.2%
D2 medium residues 1-109
PDB
Domain cluster: rep: OP056089.1__UYD72102.1__X__00002__D5-102
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07463.17 best NUMOD4 26.1 1.10e-05 39.5% 98.0%
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM01 3.90.75.20 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › 0.84 77.0 7.82e-01 98.2% 99.1%
1a73A00 3.90.75.10 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A 0.60 51.0 4.47e-01 93.6% 87.0%
2i2lA01 2.10.70.50 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.52 25.0 3.25e-01 79.8% 88.5%
3le4A00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.51 27.0 3.52e-01 72.5% 98.2%
3a5zD02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 23.0 2.79e-01 75.2% 60.9%
6ruiB04 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.51 37.0 3.11e-01 75.2% 46.2%
5umbA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 42.0 3.59e-01 91.7% 86.7%
7ob9B01 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.50 35.0 2.96e-01 73.4% 42.7%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3586841 378.1.1.7 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › NUMOD4,HNH_3 0.84 76.0 7.49e-01 95.4% 100.0%
3926624 4184.1.1.0 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat 0.67 28.0 4.01e-01 78.9% 84.0%
8233 378.1.1.6 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › zf-His_Me_endon 0.60 51.0 4.47e-01 93.6% 87.0%
4952930 2.21.1.0 ↗ beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) 0.58 32.0 3.56e-01 79.8% 68.2%
959119 4.1.1.75 ↗ beta barrels › SH3 › SH3 › SH3 › NdhS 0.54 24.0 3.16e-01 80.7% 75.9%
3889019 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.52 42.0 3.60e-01 88.1% 82.7%
4677426 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.52 37.0 3.08e-01 73.4% 43.2%
3876697 5.1.5.110 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Beta-prop_FAM234A_B 0.52 39.0 2.52e-01 78.9% 22.5%
3313424 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.51 43.0 3.64e-01 90.8% 85.6%
None — 0.51 42.0 3.34e-01 89.0% 68.2%
3598645 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.51 44.0 2.97e-01 97.2% 73.9%
3733375 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.51 36.0 2.98e-01 73.4% 43.0%
3692769 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.51 41.0 3.28e-01 89.0% 66.1%
3595871 511.1.1.0 ↗ beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.51 44.0 3.21e-01 98.2% 88.7%
4028527 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.50 41.0 3.58e-01 91.7% 86.7%
3348808 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.50 44.0 3.03e-01 99.1% 73.3%
3597261 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 41.0 3.50e-01 90.8% 82.1%
3474499 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.50 44.0 2.97e-01 98.2% 71.4%