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SR-VP_0-2_scaffold_141_4939684_prodigal-single.1__X__X__00166

Bact-Vir

SR-VP_0-2_scaffold_141_4939684_prodigal-single.1__X__X__00166

Identity

Kingdom:
phage

Quality

74.7 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 57-105
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1wg1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.68 51.0 4.62e-01 100.0% 59.2%
5tkwA01 3.30.420.380 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.66 56.0 3.94e-01 100.0% 31.8%
4nb5B01 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 0.66 49.0 4.11e-01 81.6% 76.5%
1qupA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 52.0 4.66e-01 100.0% 62.9%
2xzmP00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 54.0 3.95e-01 100.0% 34.5%
1qy9A02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.65 46.0 3.22e-01 77.6% 24.5%
2o8mB01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.63 46.0 4.24e-01 100.0% 59.1%
2e5gA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.63 49.0 4.42e-01 100.0% 61.1%
3su0A01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.63 46.0 3.55e-01 100.0% 34.8%
1oeyA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.62 51.0 4.45e-01 98.0% 87.8%
4z1xA02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.61 44.0 3.26e-01 100.0% 27.3%
3nlcA01 3.30.70.2700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 51.0 4.54e-01 100.0% 71.1%
1g87A02 2.60.40.710 Mainly Beta › Sandwich › Immunoglobulin-like › Endoglucanase-like 0.61 54.0 3.75e-01 100.0% 31.4%
3pfiA03 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 0.61 45.0 4.05e-01 79.6% 86.3%
1g8aA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 50.0 3.51e-01 100.0% 29.0%
5xyiY00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 47.0 3.91e-01 100.0% 49.5%
3zssA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 48.0 3.81e-01 100.0% 42.5%
1z2mA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.58 46.0 4.19e-01 98.0% 85.7%
2mkxA00 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.58 45.0 4.55e-01 100.0% 88.2%
3gtzA00 3.30.1330.40 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › RutC-like 0.58 47.0 3.75e-01 100.0% 79.1%
2qlzA03 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 41.0 3.85e-01 77.6% 90.5%
2ylmA03 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.57 47.0 3.88e-01 98.0% 83.5%
1ft9A02 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 47.0 4.05e-01 93.9% 98.7%
1ku3A00 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 39.0 3.69e-01 73.5% 72.1%
6cc0A02 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 3.67e-01 79.6% 85.7%
2mtzA01 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.56 45.0 4.49e-01 100.0% 92.0%
2aymA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 41.0 3.67e-01 100.0% 53.0%
6qssB02 3.90.110.10 Alpha Beta › Alpha-Beta Complex › L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 › Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal 0.55 39.0 2.69e-01 75.5% 23.5%
6ahuH01 3.30.70.3250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribonuclease P, Pop5 subunit 0.55 42.0 3.69e-01 100.0% 61.1%
5c8qB02 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.55 43.0 4.47e-01 100.0% 100.0%
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 38.0 3.44e-01 75.5% 71.2%
4idiB00 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.54 41.0 3.45e-01 100.0% 92.2%
1ekrA00 3.30.70.640 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Molybdopterin cofactor biosynthesis C (MoaC) domain 0.54 45.0 3.33e-01 100.0% 62.9%
5hb5B00 3.30.1610.10 Alpha Beta › 2-Layer Sandwich › c-terminal autoproteolytic domain of nucleoporin nup98 › Peptidase S59, nucleoporin 0.54 43.0 3.20e-01 100.0% 32.9%
3zn6A02 2.60.40.3410 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 44.0 3.78e-01 100.0% 96.6%
1z2zA02 3.30.70.3160 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 43.0 3.67e-01 100.0% 53.3%
4e9jA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.53 44.0 4.01e-01 100.0% 78.3%
6eg0A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 43.0 3.66e-01 100.0% 53.8%
3en9A03 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 44.0 3.97e-01 100.0% 82.2%
7pzaA02 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 0.52 42.0 3.60e-01 91.8% 86.0%
3rq4A02 2.170.270.10 Mainly Beta › Beta Complex › Beta-clip-like › SET domain 0.52 43.0 3.21e-01 100.0% 76.1%
2npiA03 2.40.30.330 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Pre-mRNA cleavage complex subunit Clp1, C-terminal domain 0.51 43.0 3.49e-01 100.0% 79.6%
4je0B01 2.60.40.1280 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 41.0 3.06e-01 100.0% 34.2%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5034699 286.1.1.2 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › PhzC-PhzF 0.69 51.0 3.58e-01 79.6% 25.2%
3589586 101.1.2.266 ↗ alpha arrays › HTH › HTH › winged helix domain › Phage_rep_org_N 0.68 50.0 3.73e-01 79.6% 55.2%
5078837 304.109.1.4 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e 0.67 55.0 4.62e-01 100.0% 55.8%
4651626 11.1.1.171 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Big_5 0.66 58.0 4.61e-01 100.0% 49.0%
3999277 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.65 53.0 4.28e-01 100.0% 54.5%
4253448 304.52.1.1 ↗ a+b two layers › Alpha-beta plaits › YbeD/HP0495-like › YbeD/HP0495-like › DUF493 0.65 55.0 4.63e-01 100.0% 56.8%
5058995 304.109.1.4 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e 0.65 54.0 4.49e-01 100.0% 57.9%
3226412 304.18.1.0 ↗ a+b two layers › Alpha-beta plaits › Anticodon-binding domain of PheRS › Anticodon-binding domain of PheRS 0.64 54.0 4.83e-01 100.0% 68.0%
3715810 304.47.1.2 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › FAZ1_cons 0.64 54.0 4.33e-01 100.0% 59.0%
4296415 304.109.1.4 ↗ a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e 0.64 53.0 4.34e-01 100.0% 55.0%
3806483 387.1.5.7 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like › SCRL 0.62 51.0 5.02e-01 100.0% 92.7%
3784835 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.61 51.0 4.24e-01 100.0% 52.6%
4981665 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.61 50.0 4.43e-01 100.0% 61.3%
3421938 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.61 42.0 3.99e-01 100.0% 60.0%
4024381 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.61 49.0 4.36e-01 100.0% 61.3%
3592555 304.166.1.0 ↗ a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain 0.59 49.0 4.09e-01 100.0% 52.6%
3261110 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.59 50.0 4.91e-01 100.0% 100.0%
3426002 387.1.5.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like 0.59 48.0 4.80e-01 100.0% 98.0%
5062146 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.59 49.0 4.23e-01 100.0% 59.5%
3838040 221.1.2.5 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Alpha-L RNA-binding motif › S4 0.59 47.0 4.44e-01 100.0% 95.4%
3964648 299.1.1.1 ↗ a+b complex topology › YbaK/ProRS associated domain › YbaK/ProRS associated domain › YbaK/ProRS associated domain › tRNA_edit 0.58 49.0 3.58e-01 100.0% 78.6%
3349612 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.58 46.0 4.58e-01 100.0% 88.0%
3252416 304.57.1.1 ↗ a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.58 47.0 3.71e-01 100.0% 52.5%
3903953 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.57 45.0 4.49e-01 100.0% 88.0%
3784007 304.57.1.1 ↗ a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.57 47.0 3.32e-01 100.0% 51.4%
5081005 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.56 47.0 4.10e-01 100.0% 60.2%
2074716 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.56 45.0 4.47e-01 100.0% 90.2%
3338947 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.56 46.0 4.28e-01 100.0% 72.3%
3413357 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.56 46.0 4.12e-01 100.0% 65.7%
3691758 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.55 46.0 4.52e-01 98.0% 87.3%
3408148 304.57.1.1 ↗ a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.55 44.0 3.37e-01 100.0% 48.6%
5049011 221.1.1.14 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › ThiS 0.55 43.0 4.22e-01 100.0% 88.3%
3821115 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.55 44.0 3.83e-01 100.0% 55.3%
3655335 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.55 44.0 3.13e-01 100.0% 27.3%
3165071 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.55 45.0 4.39e-01 100.0% 85.5%
3452845 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.55 44.0 4.27e-01 100.0% 81.8%
3448128 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.54 45.0 3.41e-01 100.0% 41.5%
4026236 304.57.1.0 ↗ a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like 0.54 46.0 3.41e-01 100.0% 56.4%
3172875 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.54 44.0 3.56e-01 100.0% 52.7%
3517460 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.54 45.0 4.34e-01 100.0% 83.6%
4492966 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.54 45.0 4.40e-01 100.0% 83.6%
3175627 11.1.5.133 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › PF29916 0.54 43.0 3.17e-01 100.0% 32.1%
3727183 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.54 42.0 2.70e-01 100.0% 17.2%
4360897 304.102.1.2 ↗ a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › TruD 0.54 42.0 2.99e-01 100.0% 25.3%
3303205 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.53 45.0 4.31e-01 100.0% 95.0%
3611431 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.53 46.0 4.33e-01 100.0% 88.3%
3173902 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.53 46.0 3.54e-01 100.0% 47.0%
3898121 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.53 45.0 4.36e-01 100.0% 87.3%
3716764 101.15.1.12 ↗ alpha arrays › HTH › LysM domain › LysM domain › PF30403 0.53 43.0 4.12e-01 95.9% 86.7%
4015259 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.53 43.0 3.03e-01 100.0% 52.6%
3846469 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.53 44.0 3.70e-01 100.0% 53.3%
3324708 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.53 44.0 4.14e-01 100.0% 78.3%
3232962 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.52 44.0 4.15e-01 100.0% 80.0%
3925474 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.52 43.0 4.37e-01 100.0% 98.0%
3367888 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.52 43.0 3.95e-01 100.0% 91.4%
3337080 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.51 43.0 4.11e-01 100.0% 80.0%
3349597 101.15.1.13 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM1_NFP_LYK 0.51 43.0 4.13e-01 100.0% 85.0%
4969054 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.51 41.0 3.71e-01 100.0% 66.7%