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NC_024392.1__YP_009045103.1__LP114_049__00048

Bact-Vir

NC_024392.1__YP_009045103.1__LP114_049__00048

Identity

Accession:
NC_024392 ↗
Kingdom:
phage

Quality

86.9 mean pLDDT

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 6-63
PDB
CATH (24)
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 › 0.88 82.0 6.53e-01 100.0% 55.7%
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 0.65 55.0 3.95e-01 100.0% 75.5%
2af5A01 2.40.128.160 Mainly Beta › Beta Barrel › Lipocalin › C1 set domains (antibody constant domain-like) 0.60 40.0 4.14e-01 70.7% 81.5%
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 0.58 49.0 3.63e-01 98.3% 48.8%
4l8jA01 2.40.420.20 Mainly Beta › Beta Barrel › conserved putative lor/sdh protein from methanococcus maripaludis s2 fold › 0.58 45.0 3.77e-01 86.2% 50.0%
3d2fA02 3.30.30.30 Alpha Beta › 2-Layer Sandwich › Defensin A-like › 0.56 43.0 4.02e-01 86.2% 100.0%
4hntA04 3.10.600.10 Alpha Beta › Roll › pyruvate carboxylase f1077a mutant fold › pyruvate carboxylase f1077a mutant domain 0.56 45.0 3.76e-01 87.9% 89.1%
6gfaA02 3.30.30.30 Alpha Beta › 2-Layer Sandwich › Defensin A-like › 0.56 43.0 4.39e-01 86.2% 100.0%
3jtzA00 3.30.160.390 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Integrase, DNA-binding domain 0.56 41.0 3.76e-01 77.6% 71.4%
2ra6C00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 46.0 3.62e-01 100.0% 69.2%
4gniB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 46.0 3.45e-01 94.8% 72.5%
1i3zA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.55 41.0 3.53e-01 84.5% 81.6%
3vwoA02 2.10.70.40 Mainly Beta › Ribbon › Complement Module; domain 1 › peptidoglycan hydrolase 0.55 29.0 3.11e-01 77.6% 56.9%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.54 39.0 3.97e-01 79.3% 94.7%
7rpyA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 43.0 3.66e-01 93.1% 86.4%
3wt0A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 48.0 3.43e-01 100.0% 36.9%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 36.0 3.01e-01 98.3% 39.6%
3weeB03 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.52 46.0 3.69e-01 100.0% 83.5%
1upsA02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.52 40.0 3.19e-01 87.9% 74.4%
2xgtB01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 36.0 3.09e-01 75.9% 74.3%
6j8yC00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.51 38.0 2.59e-01 84.5% 92.9%
1d4tA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.51 38.0 3.34e-01 87.9% 59.6%
1vq8Q00 2.30.30.70 Mainly Beta › Roll › SH3 type barrels. › Ribosomal protein L21 0.51 39.0 3.36e-01 94.8% 51.6%
2lezA00 3.30.2450.10 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › Secreted effector protein pipB2 0.51 42.0 3.48e-01 100.0% 57.5%
ECOD (21)
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 0.90 84.0 6.50e-01 100.0% 61.7%
4998606 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.78 43.0 4.81e-01 75.9% 68.9%
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 0.62 52.0 3.32e-01 100.0% 26.6%
3935332 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.59 38.0 2.96e-01 100.0% 29.2%
5079015 2484.1.1.71 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RACo_C_ter 0.58 49.0 3.30e-01 98.3% 26.1%
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 0.58 49.0 3.63e-01 98.3% 48.8%
89916 378.1.1.0 few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.58 49.0 3.62e-01 98.3% 48.8%
3280401 243.3.1.3 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › PepSY 0.57 42.0 4.13e-01 93.1% 72.3%
2439577 214.1.1.0 a+b two layers › SH2 › SH2 › SH2 0.55 39.0 3.25e-01 79.3% 49.6%
3808578 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.55 37.0 3.49e-01 100.0% 55.4%
4211951 2.1.1.14 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RuvA_N 0.53 47.0 4.22e-01 96.6% 83.7%
3476221 2498.1.1.14 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M8 0.53 46.0 2.69e-01 96.6% 16.3%
4389834 2484.1.1.1 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.53 43.0 3.15e-01 94.8% 87.4%
3912111 214.1.1.1 a+b two layers › SH2 › SH2 › SH2 › SH2 0.52 43.0 3.57e-01 100.0% 72.2%
3422058 5.1.3.144 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › b-prop_At3g26010-like 0.52 42.0 2.79e-01 93.1% 22.3%
3965157 2003.1.2.58 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox, Pyr_redox_2 0.52 44.0 3.04e-01 94.8% 45.3%
5037381 375.1.1.19 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RNA_POL_M_15KD 0.51 36.0 3.78e-01 77.6% 88.0%
4602126 214.1.1.1 a+b two layers › SH2 › SH2 › SH2 › SH2 0.51 38.0 3.26e-01 87.9% 56.4%
3702424 10.1.1.56 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › TS_C 0.51 44.0 3.49e-01 100.0% 80.8%
3499649 220.4.1.0 beta barrels › PH domain-like › second barrel domain in viral glycoproteins › second barrel domain in viral glycoproteins 0.50 43.0 3.81e-01 100.0% 87.8%
3932020 59.1.1.2 beta complex topology › triple barrel › triple barrel › Rap30/74 interaction domains-like › RNA_pol_Rpc4 0.50 43.0 3.49e-01 98.3% 78.3%
D2 medium residues 70-105
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13392.13 best HNH_3 33.2 4.30e-08 88.9% 56.5%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1jmuB01 3.90.1370.10 Alpha Beta › Alpha-Beta Complex › Protein mu-1, chain B, domain 1 › Protein mu-1, chain B, domain 1 0.63 42.0 3.07e-01 75.0% 21.7%
5oomK00 3.90.1180.10 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L13p; Chain: A; › Ribosomal protein L13 0.62 42.0 2.81e-01 91.7% 15.3%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4949181 378.1.1.2 few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.80 69.0 5.47e-01 100.0% 48.0%
4303143 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.80 63.0 4.85e-01 97.2% 38.8%
3266965 378.1.2.2 few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › Inactive Tox-GHH domain of teneurin › HNH_3 0.79 62.0 5.17e-01 88.9% 49.2%
5053631 378.1.1.19 few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH_3 0.65 58.0 4.14e-01 100.0% 42.7%
3637118 4294.1.1.0 few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like 0.59 42.0 3.94e-01 75.0% 60.0%
4950847 7592.1.1.0 a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains 0.55 37.0 2.54e-01 75.0% 77.6%
1508939 4063.1.1.0 a+b complex topology › a+b domain in membrane penetration protein mu1 › a+b domain in membrane penetration protein mu1 › a+b domain in membrane penetration protein mu1 0.52 35.0 3.12e-01 75.0% 41.9%
3268189 904.1.1.0 few secondary structure elements › B-box zinc-binding domain-like › B-box zinc-binding domain › B-box zinc-binding domain 0.51 35.0 2.49e-01 80.6% 19.4%
D3 medium residues 117-158
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3vfzB00 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 0.84 67.0 5.84e-01 100.0% 58.7%
5fgmA00 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 0.83 66.0 5.72e-01 100.0% 56.9%
3t0yA02 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 0.81 61.0 5.43e-01 100.0% 58.3%
4nqwA02 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 0.81 62.0 5.51e-01 100.0% 57.8%
2cobA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.80 63.0 6.26e-01 100.0% 84.1%
3hugA00 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 0.80 62.0 5.08e-01 100.0% 46.3%
1k6yA01 1.10.10.200 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Integrase, N-terminal zinc-binding domain 0.69 53.0 5.26e-01 100.0% 82.6%
5cz2G00 1.10.10.200 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Integrase, N-terminal zinc-binding domain 0.65 48.0 4.82e-01 95.2% 87.8%
1w98B02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.63 52.0 3.94e-01 100.0% 51.8%
2raaA00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.63 51.0 3.50e-01 100.0% 26.4%
4eqqA02 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 0.63 53.0 5.18e-01 100.0% 91.7%
2a6cA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.63 49.0 4.16e-01 100.0% 50.0%
1a1vA03 1.10.820.10 Mainly Alpha › Orthogonal Bundle › RNA Helicase; Chain A, domain 3 › RNA Helicase Chain A , domain 3 0.62 51.0 3.54e-01 100.0% 31.7%
3d5lA02 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 51.0 5.02e-01 100.0% 93.3%
3e3vA01 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 0.60 51.0 4.80e-01 100.0% 84.9%
3g2eB00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.60 47.0 3.22e-01 100.0% 85.9%
5jxxA02 1.20.1180.10 Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain 0.59 48.0 4.25e-01 100.0% 62.1%
4ragA02 1.10.10.430 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Phosphatase 2C, C-terminal domain suprefamily 0.57 45.0 4.05e-01 100.0% 72.1%
3hruB01 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 49.0 3.49e-01 100.0% 41.6%
2jmsA01 1.20.50.40 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › 0.55 41.0 4.07e-01 97.6% 89.4%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.54 45.0 3.86e-01 100.0% 81.3%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 42.0 3.52e-01 95.2% 87.7%
4xzjA01 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.51 41.0 2.76e-01 100.0% 23.2%
3p42A02 6.10.250.2280 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.50 37.0 3.15e-01 81.0% 100.0%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3969325 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.91 74.0 6.13e-01 100.0% 52.9%
3953011 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.90 73.0 6.64e-01 100.0% 67.3%
3834548 101.1.3.12 alpha arrays › HTH › HTH › tetra-helical, LuxR-like › PF26138 0.90 73.0 6.21e-01 100.0% 56.9%
4683276 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.89 71.0 5.38e-01 100.0% 38.9%
4393383 101.1.1.62 alpha arrays › HTH › HTH › Three-helical HTH › HTH_24 0.87 70.0 7.15e-01 100.0% 92.5%
3967026 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.87 70.0 5.72e-01 100.0% 49.3%
3968008 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.87 70.0 6.57e-01 100.0% 74.0%
3971860 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.85 68.0 6.44e-01 100.0% 74.0%
3973360 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.85 68.0 5.71e-01 100.0% 52.9%
4280807 101.1.1.13 alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_1 0.85 67.0 6.18e-01 100.0% 67.3%
3967748 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.84 66.0 5.27e-01 100.0% 43.5%
4303963 101.1.1.42 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4_2 0.83 65.0 5.37e-01 100.0% 49.3%
3965313 101.1.1.63 alpha arrays › HTH › HTH › Three-helical HTH › HTH_28 0.82 66.0 6.06e-01 100.0% 69.1%
4583223 101.1.1.63 alpha arrays › HTH › HTH › Three-helical HTH › HTH_28 0.81 65.0 5.99e-01 100.0% 69.1%
4945040 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.75 66.0 5.90e-01 100.0% 70.0%
4017824 101.1.3.0 alpha arrays › HTH › HTH › tetra-helical, LuxR-like 0.74 65.0 5.35e-01 100.0% 61.3%
3946360 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.73 63.0 5.51e-01 100.0% 64.6%
3636036 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.72 61.0 5.49e-01 100.0% 71.7%
3252439 198.1.1.10 alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2, SapB_1, Saposin 0.69 56.0 4.74e-01 100.0% 66.3%
4167193 101.35.1.1 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH2 0.68 58.0 5.72e-01 100.0% 95.6%
4971151 2004.1.3.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.67 56.0 3.69e-01 100.0% 24.5%
3244407 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.66 56.0 5.08e-01 100.0% 73.3%
3319321 101.35.1.1 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH2 0.65 52.0 5.15e-01 95.2% 91.1%
5049790 2004.1.3.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.64 52.0 3.53e-01 100.0% 24.9%
4945578 2004.1.3.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.62 51.0 3.42e-01 100.0% 25.6%
5071263 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.62 49.0 3.99e-01 100.0% 44.4%
4500830 101.35.1.1 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH2 0.61 50.0 4.81e-01 100.0% 86.0%
3324409 7000.1.1.0 alpha arrays › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS 0.61 49.0 4.65e-01 100.0% 80.0%
2581460 2004.1.3.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.60 49.0 3.28e-01 100.0% 24.5%