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SR-VP_0-2_scaffold_141_5191495_prodigal-single.1__X__X__00120

Bact-Vir

SR-VP_0-2_scaffold_141_5191495_prodigal-single.1__X__X__00120

Identity

Kingdom:
phage

Quality

71.5 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 5-173
PDB
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2hw2A00 3.20.170.40 Alpha Beta › Alpha-Beta Barrel › ADP-ribosylation fold › Rifampin ADP-ribosyltransferase domain 0.70 41.0 4.55e-01 95.3% 71.7%
2j0wA02 1.20.120.1320 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartokinase, catalytic domain 0.54 25.0 3.21e-01 70.4% 74.2%
1t07A00 1.10.3880.10 Mainly Alpha › Orthogonal Bundle › YggX-like › Fe(II) trafficking protein YggX 0.54 25.0 3.48e-01 85.8% 90.1%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.51 22.0 3.40e-01 92.3% 100.0%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
7449 237.1.1.16 a+b complex topology › ADP-ribosylation › ADP-ribosylation › ADP-ribosylation › DUF2441 0.65 61.0 5.79e-01 98.2% 97.4%
D2 high residues 547-718
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01743.27 best PolyA_pol 70.8 1.90e-19 82.0% 99.2%
D3 high residues 962-1006
PDB
D4 medium residues 180-209_241-281
PDB
D5 medium residues 719-779
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12627.13 best PolyA_pol_RNAbd 41.1 1.70e-10 62.3% 53.1%
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mivA02 1.10.110.30 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › 0.95 90.0 7.53e-01 100.0% 63.5%
4x4wA02 1.10.3090.10 Mainly Alpha › Orthogonal Bundle › cca-adding enzyme, domain 2 › cca-adding enzyme, domain 2 0.95 91.0 6.02e-01 100.0% 31.8%
3h37A02 1.10.110.30 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › 0.94 88.0 7.69e-01 100.0% 73.3%
1lujB01 1.10.10.490 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Beta-catenin-interacting ICAT 0.65 45.0 4.81e-01 80.3% 84.9%
3beeA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.63 44.0 3.86e-01 72.1% 84.6%
5mi7A03 1.20.58.460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hyaluronidase post-catalytic domain-like 0.59 48.0 3.21e-01 91.8% 51.5%
2chnB03 1.20.58.460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hyaluronidase post-catalytic domain-like 0.59 48.0 3.51e-01 91.8% 75.6%
4ks9A01 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.58 47.0 3.88e-01 98.4% 59.5%
1j1vA00 1.10.1750.10 Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain 0.56 42.0 3.78e-01 85.2% 71.3%
4f91B04 1.10.3380.10 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › Sec63 N-terminal domain-like domain 0.56 35.0 2.68e-01 96.7% 27.5%
2z16B01 1.20.91.10 Mainly Alpha › Up-down Bundle › Influenza Virus Matrix Protein; Chain A, domain 1 › Influenza matrix M1, N-terminal subdomain 1 0.55 44.0 4.11e-01 93.4% 69.2%
2vxgA02 1.10.220.100 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › conserved c-terminal region of ge- 1 0.53 42.0 3.97e-01 100.0% 90.6%
3nbiA01 1.10.8.1020 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › RecQ-mediated genome instability protein 1, N-terminal domain 0.53 32.0 3.34e-01 90.2% 63.8%
3qwuA03 3.30.70.2160 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 41.0 3.27e-01 90.2% 45.3%
1anxA04 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.52 42.0 4.05e-01 98.4% 87.5%
3h1nA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 43.0 3.59e-01 100.0% 77.5%
1x9bA00 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.52 37.0 3.90e-01 100.0% 88.7%
3fghA00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.52 38.0 3.77e-01 83.6% 73.1%
6hxpA01 1.10.230.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450-Terp; domain 2 › Cytochrome P450-Terp, domain 2 0.50 36.0 3.17e-01 78.7% 94.9%
6fu1A00 3.40.800.20 Alpha Beta › 3-Layer(aba) Sandwich › Arginase; Chain A › Histone deacetylase domain 0.50 41.0 2.62e-01 100.0% 37.0%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3950512 131.2.1.1 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › HD,PolyA_pol_RNAbd 0.97 92.0 5.57e-01 100.0% 19.4%
2801534 131.2.1.4 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd,tRNA_NucTran2_2 0.96 92.0 5.85e-01 100.0% 25.5%
4558118 131.2.1.3 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd 0.96 90.0 5.61e-01 100.0% 22.9%
4524098 131.2.1.3 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd 0.96 90.0 5.64e-01 100.0% 23.7%
4044665 131.2.1.4 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd,tRNA_NucTran2_2 0.95 90.0 5.70e-01 100.0% 23.9%
4037315 131.2.1.4 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd,tRNA_NucTran2_2 0.95 89.0 5.66e-01 100.0% 23.9%
4275218 131.2.1.4 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd,tRNA_NucTran2_2 0.95 89.0 5.68e-01 100.0% 24.4%
3839665 131.2.1.3 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd 0.95 89.0 5.68e-01 100.0% 24.9%
3429759 131.2.1.3 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd 0.92 86.0 5.33e-01 100.0% 20.7%
3352880 131.2.1.3 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd 0.92 86.0 5.54e-01 100.0% 24.9%
3447473 131.2.1.3 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd 0.91 85.0 5.24e-01 100.0% 20.3%
2387767 131.2.1.0 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like 0.86 78.0 5.11e-01 100.0% 26.2%
3202189 109.27.1.0 alpha superhelices › Repetitive alpha hairpins › BACK domain › BACK domain 0.60 47.0 4.38e-01 100.0% 67.1%
3226718 109.4.1.2000 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, TPR_7, TPR_8, TPR_10, TPR_12, TPR_MalT 0.59 50.0 3.28e-01 100.0% 23.0%
4027362 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 49.0 3.53e-01 100.0% 54.0%
4141643 4002.1.1.4 alpha bundles › alpha-helical domain in dehydroquinate synthase-like enzymes › alpha-helical domain in dehydroquinate synthase-like enzymes › alpha-helical domain in dehydroquinate synthase-like enzymes › DHQS_C 0.57 49.0 3.47e-01 100.0% 64.0%
3257049 109.3.1.0 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.56 47.0 3.69e-01 100.0% 45.5%
4020513 109.4.1.447 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PI4K_N 0.56 46.0 2.99e-01 100.0% 51.4%
4424233 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 45.0 3.23e-01 100.0% 64.7%
1788098 2.1.1.95 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Lig_C 0.54 41.0 3.38e-01 90.2% 48.5%
4677488 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.53 36.0 2.65e-01 70.5% 64.2%
3186536 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.53 42.0 3.08e-01 90.2% 51.9%
4026671 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.52 41.0 3.47e-01 91.8% 75.7%
3495156 109.58.1.1 alpha superhelices › Repetitive alpha hairpins › DNA repair protein Rev1 C-terminal domain › DNA repair protein Rev1 C-terminal domain › REV1_C 0.51 44.0 3.98e-01 100.0% 87.1%
5036214 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.51 42.0 4.24e-01 91.8% 100.0%
3800338 109.4.1.429 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec7-like_HDS 0.50 44.0 3.05e-01 98.4% 58.5%
3577937 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.50 40.0 3.37e-01 93.4% 79.1%
D6 medium residues 780-884
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01966.29 best HD 31.1 3.60e-07 75.2% 45.7%
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1xx7A00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.67 58.0 4.86e-01 93.3% 64.0%
5fgzA02 1.10.3810.10 Mainly Alpha › Orthogonal Bundle › Penicillin binding protein transpeptidase fold › Biosynthetic peptidoglycan transglycosylase-like 0.61 54.0 4.66e-01 98.1% 90.2%
2oqoA00 1.10.3810.10 Mainly Alpha › Orthogonal Bundle › Penicillin binding protein transpeptidase fold › Biosynthetic peptidoglycan transglycosylase-like 0.60 53.0 4.43e-01 98.1% 94.5%
1t3dA01 1.10.3130.10 Mainly Alpha › Orthogonal Bundle › serine acetyltransferase, domain 1 › serine acetyltransferase, domain 1 0.60 47.0 4.31e-01 85.7% 98.6%
1iduA02 1.10.606.10 Mainly Alpha › Orthogonal Bundle › Vanadium-containing Chloroperoxidase; domain 2 › Vanadium-containing Chloroperoxidase, domain 2 0.56 48.0 3.35e-01 99.0% 67.0%
4g1tA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.56 28.0 3.51e-01 92.4% 80.3%
3p9dD02 3.30.260.10 Alpha Beta › 2-Layer Sandwich › GROEL; domain 2 › TCP-1-like chaperonin intermediate domain 0.55 40.0 4.00e-01 77.1% 87.6%
1x42A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.54 39.0 4.26e-01 85.7% 97.6%
3deeA01 1.10.150.690 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DUF2063 0.53 37.0 4.05e-01 86.7% 89.5%
3fbzA01 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 39.0 3.94e-01 80.0% 83.3%
1j3eA00 1.20.1380.10 Mainly Alpha › Up-down Bundle › Replication modulator SeqA, C-terminal DNA-binding domain › Replication modulator SeqA, C-terminal DNA-binding domain 0.51 38.0 3.68e-01 93.3% 69.6%
1t6jA03 1.10.274.20 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Phenylalanine ammonia-lyase 1; domain 3 0.51 41.0 4.14e-01 86.7% 87.4%
6bmeA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 44.0 4.13e-01 93.3% 78.0%
4nufA02 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.51 39.0 3.35e-01 82.9% 69.3%
3mvcB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 45.0 4.00e-01 100.0% 77.3%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.50 31.0 3.57e-01 94.3% 86.7%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4511032 131.2.1.1 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › HD,PolyA_pol_RNAbd 0.98 95.0 6.49e-01 100.0% 37.3%
3985471 131.2.1.0 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like 0.95 77.0 6.20e-01 83.8% 56.7%
4156349 131.2.1.1 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › HD,PolyA_pol_RNAbd 0.94 91.0 6.09e-01 100.0% 40.6%
3950512 131.2.1.1 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › HD,PolyA_pol_RNAbd 0.92 89.0 6.03e-01 100.0% 35.6%
3285930 131.2.1.7 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › HD 0.85 80.0 5.76e-01 100.0% 39.6%
1143835 131.2.1.1 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › HD,PolyA_pol_RNAbd 0.83 80.0 5.65e-01 100.0% 45.0%
4558118 131.2.1.3 alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd 0.83 78.0 5.55e-01 100.0% 37.5%
4984123 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.82 67.0 5.45e-01 99.0% 49.4%
5004208 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.78 68.0 5.23e-01 93.3% 45.2%
4399123 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.77 69.0 5.71e-01 94.3% 60.6%
4951316 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.76 71.0 5.62e-01 100.0% 69.0%
5077860 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.74 65.0 5.12e-01 99.0% 49.2%
5052430 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.72 55.0 5.17e-01 80.0% 74.4%
4929078 131.1.1.10 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD_3 0.69 59.0 4.87e-01 92.4% 61.1%
5024025 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.69 65.0 5.47e-01 100.0% 67.3%
4985358 131.1.1.10 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD_3 0.69 59.0 4.99e-01 92.4% 65.3%
4995646 131.1.1.10 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD_3 0.66 57.0 4.71e-01 92.4% 62.2%
4165534 235.1.1.5 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Transgly 0.61 55.0 4.27e-01 100.0% 82.2%
4234965 2498.5.1.1 mixed a+b and a/b › Zincin-like › GroEL-intermediate domain like › GroEL-intermediate domain like › Cpn60_TCP1 0.58 42.0 4.09e-01 76.2% 85.2%
4937223 604.39.1.0 alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters 0.57 42.0 3.69e-01 78.1% 87.4%
3712740 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 40.0 3.04e-01 79.0% 68.9%
4928310 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.52 39.0 4.14e-01 100.0% 89.2%
3238747 5081.1.1.1 alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.52 44.0 3.81e-01 100.0% 88.3%
3988861 5081.1.1.1 alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.51 44.0 3.59e-01 100.0% 79.5%
4288099 106.1.1.3 alpha arrays › Globin-like › Globin-like › Globin-like › Bac_globin 0.51 43.0 4.00e-01 93.3% 75.2%