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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00503

Bact-Vir

SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00503

Identity

Kingdom:
phage

Quality

86.3 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 4-63
PDB
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4pwuC00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.75 67.0 6.08e-01 96.7% 100.0%
2hfsA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.74 65.0 4.90e-01 100.0% 97.9%
4gxbA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.69 53.0 4.53e-01 100.0% 51.5%
3hxiA01 3.30.760.10 Alpha Beta › 2-Layer Sandwich › RNA Cap, Translation Initiation Factor Eif4e › RNA Cap, Translation Initiation Factor Eif4e 0.67 56.0 4.10e-01 95.0% 33.9%
1svdM00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.67 57.0 4.80e-01 100.0% 55.6%
5d4nC00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 57.0 4.94e-01 100.0% 90.8%
1a7gE00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.66 56.0 5.10e-01 96.7% 100.0%
5abxA00 3.30.760.10 Alpha Beta › 2-Layer Sandwich › RNA Cap, Translation Initiation Factor Eif4e › RNA Cap, Translation Initiation Factor Eif4e 0.66 55.0 4.06e-01 96.7% 33.5%
4iyqA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 57.0 4.73e-01 98.3% 86.0%
2zw2A00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.65 53.0 4.81e-01 95.0% 96.5%
2cuwA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.64 53.0 4.88e-01 96.7% 97.6%
2qv6A01 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.64 54.0 4.31e-01 98.3% 72.7%
2bopA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.64 52.0 4.76e-01 95.0% 100.0%
1o51A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 54.0 4.79e-01 98.3% 98.9%
1cqmA00 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.63 54.0 4.67e-01 98.3% 100.0%
2byeA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.63 52.0 4.48e-01 100.0% 56.4%
3ce8A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 53.0 4.71e-01 96.7% 95.5%
4e98C00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 53.0 4.51e-01 98.3% 86.7%
1wxaA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.63 52.0 4.31e-01 100.0% 50.0%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.62 50.0 4.63e-01 95.0% 96.4%
4liqE05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 53.0 4.55e-01 98.3% 66.0%
3nrnA02 3.90.660.50 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.62 48.0 3.60e-01 91.7% 47.7%
1s7hA02 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 52.0 4.75e-01 96.7% 97.6%
2rilA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 50.0 4.42e-01 96.7% 96.8%
2cyyA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.61 51.0 4.47e-01 98.3% 86.3%
5tf0B03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 51.0 4.19e-01 95.0% 64.0%
4qu7A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.60 48.0 4.43e-01 90.0% 95.1%
3nd1A02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.60 47.0 3.89e-01 100.0% 47.3%
1u8sA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.59 50.0 4.52e-01 98.3% 97.7%
5z9sA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 50.0 3.99e-01 95.0% 57.7%
1l3kA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 49.0 4.40e-01 93.3% 98.8%
1lxjA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 50.0 4.26e-01 98.3% 87.4%
2rrnA01 3.30.70.2040 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 49.0 4.48e-01 98.3% 100.0%
1h7sA02 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.58 37.0 2.88e-01 76.7% 30.7%
2nzcB00 3.30.70.1150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 0.58 48.0 4.45e-01 95.0% 97.5%
2iboA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 46.0 4.22e-01 98.3% 96.6%
1rlhA02 3.40.1520.10 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1634 › Ta1353-like 0.57 46.0 3.94e-01 91.7% 100.0%
3znuA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.57 47.0 4.13e-01 96.7% 92.6%
5jp0A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 47.0 3.75e-01 93.3% 56.5%
1darA05 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 46.0 4.20e-01 98.3% 85.1%
3luyA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.55 46.0 4.17e-01 98.3% 96.6%
3r5dA01 3.30.70.2010 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 46.0 3.72e-01 100.0% 93.8%
4njcA00 3.10.20.730 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like 0.55 41.0 4.18e-01 98.3% 88.3%
2fauA01 2.60.40.640 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 45.0 3.52e-01 100.0% 48.3%
3hluA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 44.0 4.17e-01 93.3% 98.6%
4pg4B03 3.30.70.3100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 44.0 4.20e-01 98.3% 100.0%
2hdeA01 3.10.20.550 Alpha Beta › Roll › Ubiquitin-like (UB roll) › ASAP complex, SAP18 subunit 0.53 45.0 3.65e-01 98.3% 49.6%
4geiA00 2.60.40.640 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 44.0 3.47e-01 100.0% 66.0%
3rgzA02 3.30.1490.310 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.52 44.0 4.43e-01 98.3% 96.7%
3bzcA02 1.10.3500.10 Mainly Alpha › Orthogonal Bundle › Tex N-terminal region-like › Tex N-terminal region-like 0.52 39.0 2.70e-01 86.7% 60.8%
2j58A03 3.30.1950.10 Alpha Beta › 2-Layer Sandwich › wza like fold › wza like domain 0.52 41.0 3.86e-01 95.0% 97.5%
4c47A01 2.60.40.1620 Mainly Beta › Sandwich › Immunoglobulin-like › Lipoprotein YajI-like 0.51 42.0 3.48e-01 98.3% 56.6%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3721982 304.14.1.0 a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.75 65.0 5.55e-01 95.0% 100.0%
4951859 3110.1.1.3 a/b three-layered sandwiches › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › AglB_core-like 0.73 63.0 4.05e-01 95.0% 22.9%
3929041 221.1.1.69 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › SNX17-27-31_F1_FERM 0.71 61.0 5.14e-01 98.3% 59.0%
3629781 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.70 53.0 4.45e-01 100.0% 47.6%
3300115 221.1.1.76 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.70 61.0 5.10e-01 100.0% 61.0%
3857592 382.1.1.1 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › UPAR_LY6 0.69 60.0 5.29e-01 100.0% 92.2%
3540023 382.1.1.1 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › UPAR_LY6 0.69 59.0 5.25e-01 100.0% 93.3%
3622519 221.1.1.69 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › SNX17-27-31_F1_FERM 0.67 59.0 4.80e-01 100.0% 61.7%
5028999 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.67 58.0 4.93e-01 100.0% 87.0%
3932136 317.1.1.1 a+b two layers › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › IF4E 0.66 54.0 3.85e-01 95.0% 29.0%
3237087 317.1.1.1 a+b two layers › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › IF4E 0.66 55.0 3.90e-01 96.7% 29.0%
5025693 304.3.1.23 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › TiaS_FLD 0.66 57.0 4.94e-01 100.0% 98.9%
5006368 304.4.1.20 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg2 0.65 56.0 5.05e-01 98.3% 94.1%
5015637 304.5.1.0 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.65 56.0 5.15e-01 98.3% 98.8%
4944755 304.130.1.1 a+b two layers › Alpha-beta plaits › Uncharacterized protein MK0293 N-terminal domain › Uncharacterized protein MK0293 N-terminal domain › Ni_insertion 0.65 57.0 5.03e-01 100.0% 92.2%
3660216 304.44.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 0.65 53.0 4.73e-01 93.3% 85.4%
4930274 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.64 55.0 4.85e-01 98.3% 86.7%
3210164 304.44.1.1 a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 › Ribosomal_S10 0.64 53.0 4.02e-01 95.0% 56.1%
3741311 304.44.1.1 a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 › Ribosomal_S10 0.64 53.0 4.35e-01 96.7% 73.3%
5050897 304.130.1.1 a+b two layers › Alpha-beta plaits › Uncharacterized protein MK0293 N-terminal domain › Uncharacterized protein MK0293 N-terminal domain › Ni_insertion 0.64 55.0 4.97e-01 100.0% 97.6%
4182592 304.44.1.1 a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 › Ribosomal_S10 0.63 53.0 4.23e-01 96.7% 83.1%
162529 317.1.1.1 a+b two layers › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › IF4E 0.63 52.0 3.65e-01 96.7% 27.2%
3538311 11.1.1.469 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3_4 0.63 53.0 4.37e-01 100.0% 50.0%
3477897 304.44.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 0.63 52.0 4.63e-01 96.7% 92.2%
3412857 11.1.1.469 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3_4 0.63 53.0 4.47e-01 100.0% 54.5%
3898606 11.1.1.217 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Izumo-Ig 0.63 50.0 4.35e-01 100.0% 56.8%
3223690 150.3.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine 0.62 49.0 3.70e-01 86.7% 35.2%
5046778 304.130.1.1 a+b two layers › Alpha-beta plaits › Uncharacterized protein MK0293 N-terminal domain › Uncharacterized protein MK0293 N-terminal domain › Ni_insertion 0.62 54.0 4.60e-01 100.0% 84.0%
3553176 11.1.1.805 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_PDGFR_d4 0.62 54.0 4.07e-01 98.3% 45.5%
1758438 11.1.1.179 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.62 53.0 4.48e-01 98.3% 62.9%
5028017 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.62 50.0 4.43e-01 95.0% 89.5%
5043890 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.62 52.0 4.75e-01 100.0% 95.3%
3701279 304.107.1.10 a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain › BBS7_pf 0.61 52.0 4.50e-01 96.7% 98.9%
3789057 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.60 49.0 3.90e-01 93.3% 62.2%
3460588 207.1.1.35 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1,LRR_8,Island 0.60 49.0 3.17e-01 96.7% 19.0%
3929887 221.1.1.87 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_N_2 0.60 50.0 4.22e-01 100.0% 52.7%
3174017 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.60 49.0 4.51e-01 91.7% 98.8%
3593981 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.58 48.0 4.17e-01 100.0% 61.9%
3492718 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.58 48.0 4.17e-01 98.3% 93.0%
3987406 3115.6.1.1 a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › RpoY 0.57 46.0 4.36e-01 95.0% 81.3%
3828980 10.32.1.241 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › SAC9_GBDL_2nd 0.57 46.0 3.31e-01 95.0% 51.2%
4642338 807.1.1.1 a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.56 45.0 4.70e-01 95.0% 100.0%
3995117 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.56 45.0 3.99e-01 93.3% 84.2%
3232486 11.2.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.56 47.0 4.03e-01 98.3% 56.2%
4015453 212.1.1.12 a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › UPF0029 0.56 43.0 3.46e-01 88.3% 69.2%
5049192 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.56 46.0 4.22e-01 100.0% 92.9%
5040537 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 46.0 3.91e-01 100.0% 56.4%
4977520 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.54 44.0 3.81e-01 100.0% 94.5%
None 0.54 44.0 2.83e-01 96.7% 17.6%
3712786 3346.1.1.0 a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 0.53 43.0 3.29e-01 100.0% 35.4%
318718 221.1.1.30 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › SAP18 0.53 45.0 3.46e-01 98.3% 41.2%
4031279 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.53 43.0 3.46e-01 100.0% 45.7%
3670198 221.1.1.4 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.53 40.0 3.46e-01 96.7% 49.5%
3354676 10.9.1.1 beta sandwiches › jelly-roll › C-terminal domain of mullusc hemocyanin › C-terminal domain of mullusc hemocyanin › PPO1_KFDV 0.52 43.0 3.98e-01 100.0% 84.7%
4648475 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.51 40.0 4.06e-01 93.3% 95.0%
None 0.51 40.0 3.97e-01 90.0% 100.0%