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NC_022053.1__YP_008408837.1__N842_gp051__00051

Bact-Vir

NC_022053.1__YP_008408837.1__N842_gp051__00051

Identity

Accession:
NC_022053 ↗
Kingdom:
phage

Quality

93.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Papyrusvirus› Mycobacterium_phage_Papyrus

TaxID: 1383056

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 4-53
PDB
Domain cluster: representative
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vpkA02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.75 64.0 4.81e-01 100.0% 39.1%
3pweA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.70 55.0 4.28e-01 100.0% 38.2%
6ptrB01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.67 54.0 4.30e-01 100.0% 42.5%
6w1kA01 3.10.180.50 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 0.66 53.0 3.37e-01 96.0% 21.9%
3s98A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 55.0 4.49e-01 94.0% 93.5%
2r5vA01 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 48.0 3.55e-01 86.0% 30.7%
4dsdA00 3.40.1420.30 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › 0.64 50.0 3.79e-01 96.0% 34.9%
4agrB00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.64 54.0 3.98e-01 100.0% 57.6%
5utkA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 49.0 4.11e-01 88.0% 97.8%
4ihqA01 3.30.450.370 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.63 47.0 3.41e-01 84.0% 27.7%
3djwA00 3.30.160.300 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 48.0 4.02e-01 88.0% 52.6%
1zswA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.62 49.0 3.42e-01 92.0% 27.0%
4exrA01 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 49.0 4.33e-01 94.0% 69.1%
1y4oA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.62 48.0 3.83e-01 86.0% 83.7%
6iw6A02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.62 47.0 3.77e-01 86.0% 44.4%
1y13A00 3.30.479.10 Alpha Beta › 2-Layer Sandwich › Tetrahydropterin Synthase; Chain A › 6-pyruvoyl tetrahydropterin synthase/QueD 0.61 49.0 3.45e-01 90.0% 55.8%
2e1bA02 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.61 46.0 3.52e-01 86.0% 72.1%
4bjzA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.61 48.0 3.48e-01 94.0% 84.5%
3rheA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.61 47.0 3.75e-01 90.0% 41.2%
4g41A00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.61 44.0 2.88e-01 88.0% 16.9%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.60 40.0 2.98e-01 70.0% 54.3%
5yrzB00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.60 45.0 4.32e-01 84.0% 72.4%
2cw8A03 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.60 40.0 2.90e-01 76.0% 21.3%
1sqiA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.60 44.0 3.23e-01 86.0% 29.9%
2wkkA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.60 50.0 3.69e-01 100.0% 50.0%
1q67A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 47.0 3.58e-01 94.0% 78.6%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 42.0 3.56e-01 84.0% 50.5%
3d4eA01 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.59 43.0 3.79e-01 84.0% 56.0%
1ln1A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 43.0 2.96e-01 82.0% 27.1%
5mmjh01 3.30.1370.30 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.58 39.0 3.54e-01 72.0% 46.7%
4hbrA00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 46.0 3.44e-01 98.0% 32.9%
2r9zA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.58 47.0 3.69e-01 96.0% 88.1%
3ms6A00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.58 42.0 3.55e-01 80.0% 90.0%
2pt7C01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.57 44.0 3.59e-01 92.0% 43.4%
3d1cA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 44.0 3.60e-01 96.0% 90.4%
2cxcA02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.56 41.0 3.73e-01 78.0% 84.1%
4d6wA03 2.30.29.130 Mainly Beta › Roll › PH-domain like › 0.56 42.0 3.59e-01 88.0% 74.7%
4at7A02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.56 44.0 3.36e-01 100.0% 41.4%
1x9yA01 3.10.500.10 Alpha Beta › Roll › prostaphopain b, domain 1 › Staphopain proregion domain 0.56 42.0 3.09e-01 92.0% 47.6%
2e55A00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 41.0 2.78e-01 82.0% 97.1%
4jpdA00 3.30.920.10 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Frataxin/CyaY 0.55 42.0 3.44e-01 90.0% 42.2%
1db3A02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.55 43.0 3.53e-01 98.0% 57.8%
4fr9A00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 42.0 3.25e-01 96.0% 34.0%
6gpkA02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.54 42.0 3.46e-01 94.0% 49.5%
7yh1A01 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.54 41.0 3.23e-01 86.0% 78.1%
2retA00 3.30.1300.30 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › GSPII I/J protein-like 0.54 39.0 3.41e-01 82.0% 88.1%
4exrA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 44.0 4.02e-01 98.0% 77.5%
1skoB00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.53 41.0 3.24e-01 88.0% 100.0%
1skoA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.53 40.0 3.21e-01 90.0% 99.2%
2n3lA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.52 38.0 3.28e-01 84.0% 70.8%
1yfbA00 2.10.260.10 Mainly Beta › Ribbon › Pemi-like Protein 1; Chain: D › 0.51 34.0 3.46e-01 72.0% 86.5%
1fyhB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 40.0 3.45e-01 100.0% 83.5%
2mnjB00 2.60.40.4160 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 42.0 3.61e-01 100.0% 75.0%
2ijzA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.51 34.0 2.77e-01 72.0% 79.4%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4569733 227.1.1.7 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_2 0.73 63.0 4.63e-01 100.0% 35.7%
3281112 227.1.1.7 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_2 0.73 57.0 4.48e-01 100.0% 38.3%
3370663 896.1.1.1 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Ribosomal_L38e 0.71 56.0 5.33e-01 88.0% 76.3%
4177976 2487.1.1.3 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › Aconitase_C 0.70 55.0 4.30e-01 100.0% 39.1%
5045102 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.68 51.0 4.23e-01 84.0% 54.7%
3268750 316.1.1.56 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PF26128 0.68 54.0 3.77e-01 92.0% 26.3%
5001319 2004.1.1.16 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Arf 0.67 53.0 3.75e-01 90.0% 30.4%
2325499 7579.1.1.32 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › FrsA-like 0.67 49.0 3.02e-01 84.0% 25.2%
3938315 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.64 55.0 3.70e-01 100.0% 32.7%
3195886 316.1.1.56 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PF26128 0.63 51.0 3.11e-01 96.0% 41.7%
4977899 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.62 48.0 3.95e-01 94.0% 100.0%
4419552 2003.1.2.16 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3,NAD_binding_8 0.62 47.0 2.87e-01 88.0% 86.6%
5045566 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.61 47.0 3.84e-01 88.0% 100.0%
4985746 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.61 45.0 3.53e-01 78.0% 70.5%
3967106 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.61 45.0 3.06e-01 92.0% 18.7%
3414531 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.61 48.0 3.91e-01 86.0% 92.6%
5014636 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.61 47.0 3.56e-01 88.0% 71.5%
3641285 109.4.1.1254 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.59 41.0 2.31e-01 94.0% 6.3%
5045707 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.59 50.0 4.49e-01 100.0% 81.3%
3237008 2484.1.1.233 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF1280 0.59 45.0 3.24e-01 96.0% 41.5%
4944343 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.59 43.0 3.57e-01 80.0% 91.5%
5051250 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.59 47.0 3.55e-01 92.0% 97.7%
3945997 309.1.2.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain 0.59 45.0 3.48e-01 88.0% 72.6%
3390111 223.2.1.16 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › LAMTOR5 0.59 45.0 3.77e-01 84.0% 92.2%
4792845 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.58 44.0 3.00e-01 88.0% 73.0%
1171964 809.2.1.0 ↗ a+b two layers › BLIP-like › BT0923-like › BT0923-like 0.58 47.0 4.53e-01 98.0% 81.0%
3936376 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 42.0 3.29e-01 82.0% 92.5%
3924796 223.2.1.12 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › MAPKK1_Int 0.57 44.0 3.50e-01 88.0% 100.0%
4002901 223.2.1.12 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › MAPKK1_Int 0.57 46.0 3.54e-01 98.0% 93.6%
3777109 109.3.1.166 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank, Ank_2, Ank_3 0.56 45.0 2.72e-01 96.0% 15.6%
5044629 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 39.0 3.03e-01 92.0% 32.2%
5079496 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 40.0 3.24e-01 80.0% 100.0%
3384014 109.4.1.1269 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, E_motif 0.56 37.0 3.01e-01 94.0% 35.8%
3311403 2003.1.5.31 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GRAS 0.56 42.0 2.53e-01 90.0% 10.7%
4003738 59.1.1.8 ↗ beta complex topology › triple barrel › triple barrel › Rap30/74 interaction domains-like › TFIIF_beta_N 0.56 44.0 3.71e-01 100.0% 85.7%
5012120 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.56 42.0 3.21e-01 82.0% 64.2%
4962423 211.1.1.1 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase 0.55 40.0 3.79e-01 84.0% 76.9%
4263405 4263.2.1.0 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain 0.55 40.0 4.00e-01 88.0% 81.8%
3682274 109.4.1.1331 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_long, E_motif 0.54 37.0 2.26e-01 94.0% 10.3%
3654164 109.4.1.1156 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › E_motif 0.54 35.0 2.51e-01 92.0% 20.7%
5073130 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.54 40.0 3.16e-01 82.0% 79.8%
4943458 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 41.0 3.31e-01 98.0% 100.0%
3215570 223.2.1.12 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › MAPKK1_Int 0.54 41.0 3.30e-01 90.0% 100.0%
5074161 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.53 42.0 3.35e-01 98.0% 98.4%
4991922 3926.1.1.1 ↗ alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.53 42.0 2.94e-01 94.0% 42.6%
4945992 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 40.0 3.09e-01 86.0% 71.3%
2075065 223.1.1.20 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › DUF3365 0.52 40.0 2.98e-01 92.0% 57.1%
4998444 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.52 37.0 2.84e-01 78.0% 93.3%
3164224 874.1.1.2 ↗ a+b duplicates or obligate multimers › Smc hinge domain › Smc hinge domain › Smc hinge domain › MukB_hinge 0.52 43.0 3.41e-01 100.0% 69.6%
5044431 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.52 39.0 2.83e-01 86.0% 57.4%
4950433 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 38.0 3.02e-01 84.0% 72.6%
4243492 243.3.1.3 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › PepSY 0.51 39.0 3.80e-01 92.0% 85.0%
4031258 4317.1.1.0 ↗ a+b duplicates or obligate multimers › YdfO-like › YdfO-like › YdfO-like 0.51 38.0 3.70e-01 86.0% 88.3%
3453217 109.4.1.1272 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, E_motif 0.51 34.0 2.10e-01 90.0% 9.9%
4537639 874.1.1.0 ↗ a+b duplicates or obligate multimers › Smc hinge domain › Smc hinge domain › Smc hinge domain 0.51 42.0 2.47e-01 96.0% 47.8%
4929561 223.2.1.62 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › DUF6659 0.51 42.0 3.24e-01 98.0% 72.0%
3338289 109.4.1.1254 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.51 39.0 2.20e-01 84.0% 48.0%
3242274 145.1.1.0 ↗ alpha arrays › F-box domain › F-box domain › F-box domain 0.51 42.0 3.74e-01 96.0% 64.0%
4976809 223.2.1.5 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.50 37.0 2.94e-01 86.0% 70.0%