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NC_007623.1__YP_418154.1__PPEV_gp121__00121

Bact-Vir

NC_007623.1__YP_418154.1__PPEV_gp121__00121

Identity

Accession:
NC_007623 ↗
Kingdom:
phage

Quality

90.2 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 5-99
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2bcqA03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.68 62.0 5.65e-01 100.0% 85.4%
4p4mA02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.67 61.0 5.71e-01 100.0% 97.4%
2fclA00 3.30.460.40 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.67 60.0 5.03e-01 100.0% 59.6%
4ebjA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.66 49.0 4.46e-01 100.0% 58.6%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.59 44.0 3.29e-01 100.0% 31.4%
6fgjA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.58 51.0 4.48e-01 100.0% 90.7%
7w3rB01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.58 49.0 3.44e-01 93.7% 90.3%
2be3B01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.58 50.0 4.54e-01 98.9% 89.6%
4kc3B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 37.0 3.80e-01 72.6% 92.6%
4mh4A02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.53 46.0 4.70e-01 100.0% 96.8%
3mgxB00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.52 43.0 2.94e-01 93.7% 53.5%
3clvA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 36.0 3.02e-01 100.0% 40.0%
1k25B02 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 46.0 3.24e-01 100.0% 61.8%
2k4nA00 3.30.720.70 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.50 43.0 4.06e-01 93.7% 78.4%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5078572 316.1.1.21 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Aminoglyc_resit 0.71 61.0 5.22e-01 98.9% 59.3%
5079184 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.69 62.0 4.82e-01 100.0% 47.2%
3726440 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.68 62.0 4.89e-01 100.0% 50.3%
3721514 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.68 60.0 4.51e-01 100.0% 40.4%
5069234 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.66 57.0 4.65e-01 98.9% 51.4%
5074217 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.66 59.0 4.71e-01 98.9% 50.3%
4979743 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.64 55.0 4.27e-01 100.0% 43.4%
4953678 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.63 58.0 5.33e-01 100.0% 86.7%
3500833 2004.1.1.54 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Septin 0.63 36.0 2.57e-01 100.0% 20.0%
4998667 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.63 58.0 5.08e-01 100.0% 88.1%
5034346 207.2.1.13 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › NosD 0.56 34.0 2.36e-01 98.9% 16.0%
3612051 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 38.0 2.91e-01 97.9% 28.9%
3217893 11.1.1.97 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.55 47.0 3.95e-01 93.7% 66.1%
3991286 2003.1.3.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › DAO 0.54 47.0 3.25e-01 100.0% 92.9%
3255418 2011.1.1.8 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.54 38.0 2.58e-01 73.7% 63.1%
3795464 11.1.1.1171 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set, PF26428 0.54 48.0 3.81e-01 100.0% 83.6%
4004219 11.1.1.97 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.53 47.0 4.29e-01 97.9% 88.8%
4670754 304.51.1.2 a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › RAMPs 0.51 44.0 3.53e-01 98.9% 90.7%
3581240 2004.1.1.54 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Septin 0.50 41.0 3.65e-01 90.5% 82.9%
3244603 11.1.1.179 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.50 44.0 3.80e-01 97.9% 72.0%
4025719 3156.3.1.0 beta sandwiches › Cupredoxin-like › Surface antigen 1 (SAG1)-related-sequence (SRS) family › Surface antigen 1 (SAG1)-related-sequence (SRS) family 0.50 41.0 3.59e-01 98.9% 58.0%
D2 medium residues 121-160
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.93 77.0 7.19e-01 100.0% 75.0%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.90 82.0 6.36e-01 100.0% 60.5%
2a26B01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.90 79.0 7.65e-01 95.0% 86.4%
2qtfA02 6.10.250.2860 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.90 82.0 7.72e-01 100.0% 85.1%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.89 81.0 5.79e-01 100.0% 37.9%
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.89 81.0 7.76e-01 100.0% 88.9%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.89 75.0 6.59e-01 100.0% 63.8%
2jdiH02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.89 78.0 7.75e-01 97.5% 92.9%
4fppB01 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.89 77.0 6.39e-01 100.0% 56.3%
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.88 78.0 7.33e-01 97.5% 81.2%
4hb1A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.88 78.0 7.58e-01 97.5% 88.6%
3vkgA02 1.20.140.100 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Dynein motor heavy chain, linker domain, N-terminal subdomain 0.87 77.0 5.14e-01 100.0% 27.2%
1wrdA00 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.87 78.0 5.75e-01 100.0% 40.8%
1kz7A01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.87 77.0 4.85e-01 100.0% 20.7%
2qvaA02 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.86 75.0 6.87e-01 100.0% 81.1%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.86 74.0 6.16e-01 100.0% 63.4%
3q1pA01 6.10.250.1120 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.85 64.0 6.51e-01 82.5% 84.6%
1n1cA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.84 73.0 5.80e-01 100.0% 54.9%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.84 72.0 6.19e-01 95.0% 61.3%
7bi4A01 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.83 67.0 4.26e-01 100.0% 19.4%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.83 73.0 6.05e-01 100.0% 56.3%
1e52A00 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.83 72.0 6.48e-01 100.0% 76.8%
3k6tB00 1.20.5.4010 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.83 73.0 6.85e-01 100.0% 91.8%
3m1cB01 3.30.390.170 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.82 62.0 4.54e-01 95.0% 31.2%
1oxjA02 1.25.40.170 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Smaug, PHAT domain 0.81 62.0 4.60e-01 87.5% 32.1%
1ni3A03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.81 70.0 5.38e-01 100.0% 44.0%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.80 67.0 5.57e-01 100.0% 56.6%
2lf0A01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.80 68.0 6.04e-01 100.0% 71.7%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.78 65.0 5.49e-01 100.0% 90.1%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.71 58.0 5.62e-01 97.5% 97.9%
2mpkA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.70 54.0 4.71e-01 100.0% 52.7%
4k35A03 1.10.287.1170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › glycoside hydrolase family 81 endo-[beta] glucanase 0.69 56.0 4.83e-01 100.0% 62.9%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.69 54.0 4.81e-01 100.0% 61.2%
8fnyA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.67 55.0 3.56e-01 100.0% 20.4%
4cc9B00 1.20.5.4730 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.67 50.0 3.82e-01 82.5% 34.7%
1iipA02 1.10.150.160 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.65 50.0 4.15e-01 100.0% 43.5%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 48.0 4.51e-01 100.0% 95.2%
5wp3B00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.63 51.0 3.89e-01 95.0% 72.5%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3619435 192.8.1.36 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › M_domain 0.98 77.0 5.54e-01 100.0% 34.7%
4014112 192.6.1.0 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.94 87.0 8.32e-01 100.0% 88.9%
3725906 192.6.1.2 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › ATPD_C_fung 0.94 85.0 8.20e-01 100.0% 88.9%
3503933 192.14.1.1 alpha bundles › Long alpha-hairpin › Siah interacting protein N terminal domain-like › Siah interacting protein N terminal domain-like › Siah-Interact_N 0.92 85.0 8.14e-01 100.0% 88.9%
4177393 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.91 82.0 5.44e-01 100.0% 37.2%
4112797 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.90 83.0 5.14e-01 100.0% 20.5%
3594817 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.90 82.0 5.05e-01 100.0% 19.1%
3385229 2003.1.9.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.89 79.0 4.52e-01 100.0% 11.0%
3163939 192.6.1.0 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.88 79.0 7.35e-01 100.0% 80.0%
4552883 192.6.1.0 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.88 81.0 7.50e-01 100.0% 81.6%
5077884 622.4.1.0 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.86 76.0 6.02e-01 100.0% 50.0%
3923922 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.84 74.0 6.00e-01 100.0% 53.3%
4155408 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.83 74.0 4.52e-01 100.0% 18.2%
3603265 2004.1.1.712 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87, HerA_C, TrwB_AAD_bind 0.79 64.0 3.71e-01 97.5% 10.5%
3578909 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.74 61.0 4.67e-01 100.0% 38.1%
3927737 632.8.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 0.69 58.0 4.54e-01 100.0% 43.2%
3360337 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.68 54.0 5.50e-01 95.0% 97.5%