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SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00151

Bact-Vir

SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00151

Identity

Kingdom:
phage

Quality

89.0 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 3-63
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.82 68.0 6.29e-01 100.0% 72.4%
3e0jB00 3.90.1030.20 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain 0.74 52.0 3.93e-01 100.0% 31.5%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.74 59.0 5.72e-01 100.0% 79.1%
1x9tA02 3.90.1620.10 Alpha Beta › Alpha-Beta Complex › adenovirus 2 penton base, domain 2 › adenovirus 2 penton base, domain 2 0.72 62.0 4.06e-01 100.0% 44.3%
4aw7A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.70 43.0 3.43e-01 100.0% 31.4%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.70 59.0 5.53e-01 96.7% 75.0%
1vwxS01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.70 60.0 5.78e-01 100.0% 83.1%
3ddcB00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.69 60.0 4.73e-01 100.0% 72.2%
4a18X01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.69 60.0 5.47e-01 100.0% 73.4%
2hj1A00 3.10.20.280 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RnfH-like 0.69 54.0 5.01e-01 100.0% 67.5%
2zw2A00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.69 60.0 5.38e-01 98.4% 96.5%
6lumB01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.66 58.0 4.82e-01 100.0% 84.5%
1zoyB01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.66 57.0 4.80e-01 100.0% 84.0%
2bs2B01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.65 56.0 4.72e-01 100.0% 83.0%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.64 54.0 4.55e-01 100.0% 55.0%
2il5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.63 49.0 3.67e-01 86.9% 90.7%
1kf6B01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.63 54.0 4.60e-01 100.0% 82.7%
2z13A00 2.30.29.170 Mainly Beta › Roll › PH-domain like › 0.62 55.0 4.46e-01 100.0% 77.8%
1n26A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 42.0 3.91e-01 100.0% 55.1%
1e3hA03 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.61 51.0 3.58e-01 95.1% 60.1%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.61 51.0 3.53e-01 98.4% 43.5%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 50.0 3.50e-01 100.0% 27.9%
2d8bA01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.61 47.0 3.58e-01 83.6% 55.7%
1hq6B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.60 50.0 3.52e-01 100.0% 32.0%
3o2iA00 3.30.70.2710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 43.0 3.74e-01 78.7% 69.9%
3k8aB00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 48.0 4.04e-01 91.8% 68.9%
2nytD00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.57 46.0 3.43e-01 100.0% 32.4%
2kf2A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 42.0 3.19e-01 82.0% 83.2%
2kvkA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.56 44.0 3.36e-01 85.2% 50.0%
2xskA00 2.60.40.2420 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 45.0 3.97e-01 100.0% 58.9%
2n59A00 2.60.40.2420 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 44.0 3.89e-01 100.0% 56.4%
3v6oA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 36.0 3.28e-01 98.4% 46.0%
2g3wA00 3.10.640.10 Alpha Beta › Roll › Restriction endonuclease-like alpha-beta roll fold › Restriction endonuclease-like alpha-beta roll domain 0.55 47.0 3.47e-01 98.4% 91.6%
3waiA02 2.60.40.3390 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 42.0 3.77e-01 98.4% 57.0%
4d10F01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.55 44.0 3.31e-01 93.4% 50.8%
1t3yA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.55 43.0 3.38e-01 85.2% 55.7%
4hsaF02 2.60.40.2150 Mainly Beta › Sandwich › Immunoglobulin-like › Interleukin-17 receptor A/B, fibronectin-III-like domain 2 0.54 44.0 3.77e-01 93.4% 83.8%
1r0uA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 45.0 3.55e-01 100.0% 91.5%
3i3tA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.53 45.0 2.99e-01 100.0% 85.5%
4h3wA02 2.60.120.1260 Mainly Beta › Sandwich › Jelly Rolls › 0.53 43.0 3.31e-01 100.0% 38.2%
2nlkA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.52 45.0 2.99e-01 98.4% 65.0%
4h5bA00 3.30.1460.70 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.52 44.0 3.39e-01 100.0% 79.6%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.52 40.0 3.56e-01 88.5% 91.5%
3qtdA01 3.30.2290.10 Alpha Beta › 2-Layer Sandwich › PmbA/TldD fold › PmbA/TldD superfamily 0.52 39.0 2.73e-01 83.6% 21.9%
5chtB00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 43.0 2.87e-01 98.4% 85.3%
3gtyX02 3.10.50.30 Alpha Beta › Roll › Chitinase A; domain 3 › Transcription elongation factor, GreA/GreB, C-terminal domain 0.51 43.0 3.95e-01 98.4% 83.3%
3d0jA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 35.0 2.83e-01 96.7% 33.3%
3bzwF00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.50 43.0 2.87e-01 95.1% 71.2%
2czrA02 3.90.79.30 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › TBP-interacting protein, C-terminal domain 0.50 35.0 2.95e-01 77.0% 69.2%
ECOD (67)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3227513 3115.1.1.3 a+b two layers › GP2-like › RplX-like › RplX-like › NRF 0.86 72.0 5.92e-01 100.0% 52.4%
4084879 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.85 76.0 6.72e-01 100.0% 69.4%
4939739 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.84 71.0 7.23e-01 100.0% 93.2%
4951473 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.83 69.0 6.89e-01 100.0% 87.3%
3345090 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.82 68.0 5.56e-01 100.0% 50.9%
3396683 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.81 61.0 5.60e-01 100.0% 62.0%
4128974 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.81 72.0 6.50e-01 100.0% 73.8%
4983090 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.81 67.0 6.14e-01 100.0% 69.6%
5065436 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.80 66.0 6.52e-01 100.0% 85.9%
5030993 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 65.0 5.91e-01 100.0% 68.8%
4937773 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.78 65.0 6.71e-01 100.0% 96.6%
4942818 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.75 67.0 5.10e-01 100.0% 44.3%
3280008 3115.1.1.2 a+b two layers › GP2-like › RplX-like › RplX-like › DUF4288 0.75 66.0 5.81e-01 100.0% 80.0%
3413240 3115.1.1.3 a+b two layers › GP2-like › RplX-like › RplX-like › NRF 0.74 65.0 4.77e-01 100.0% 43.8%
4967222 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.73 63.0 6.35e-01 96.7% 95.0%
5000510 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.73 63.0 5.86e-01 100.0% 77.3%
2106285 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.71 62.0 5.07e-01 100.0% 54.6%
3892842 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.70 60.0 5.88e-01 100.0% 89.2%
4013514 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.70 61.0 5.05e-01 100.0% 56.2%
3994984 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.70 58.0 5.71e-01 100.0% 89.2%
2527501 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.69 60.0 5.03e-01 100.0% 56.7%
4332626 3532.1.1.0 alpha arrays › RNA-binding domain of telomerase › RNA-binding domain of telomerase › RNA-binding domain of telomerase 0.69 60.0 3.47e-01 100.0% 10.4%
5074648 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.69 59.0 5.53e-01 98.4% 77.3%
4943401 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.68 61.0 5.45e-01 100.0% 71.8%
3411558 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 0.68 59.0 4.56e-01 98.4% 46.4%
4996552 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.68 61.0 5.47e-01 100.0% 72.9%
3375176 1.1.7.15 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Peptidase_M18 0.68 60.0 4.66e-01 100.0% 74.1%
3358839 1.1.7.15 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Peptidase_M18 0.67 60.0 4.35e-01 100.0% 73.5%
2512518 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.67 58.0 4.94e-01 100.0% 58.4%
2831852 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.67 57.0 4.88e-01 100.0% 58.4%
2336722 221.1.1.47 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Fer2_3 0.66 57.0 4.85e-01 100.0% 82.9%
3926687 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 0.66 56.0 4.56e-01 98.4% 50.0%
3874464 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.65 57.0 3.55e-01 100.0% 17.5%
4031853 221.1.1.47 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Fer2_3 0.63 54.0 4.53e-01 98.4% 82.7%
3619496 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.63 56.0 3.41e-01 100.0% 18.4%
5032784 11.1.4.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.63 44.0 3.90e-01 100.0% 48.4%
3616146 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.62 41.0 3.53e-01 100.0% 41.0%
3507557 4081.1.1.11 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › CreD 0.61 55.0 3.62e-01 100.0% 34.0%
3999001 10.7.1.0 beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.60 53.0 4.44e-01 100.0% 59.0%
3382614 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.59 51.0 3.00e-01 100.0% 19.3%
4796845 284.1.3.1 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.58 45.0 4.32e-01 100.0% 73.3%
3867539 633.23.1.0 alpha bundles › Bromodomain-like › Claudin › Claudin 0.58 46.0 3.23e-01 91.8% 69.6%
3180837 1.1.5.30 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyridox_oxase_2 0.58 51.0 3.40e-01 100.0% 32.8%
3204836 2492.1.1.32 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › OTT_1508_deam 0.58 47.0 3.67e-01 98.4% 39.4%
3863714 633.23.1.0 alpha bundles › Bromodomain-like › Claudin › Claudin 0.58 46.0 3.24e-01 95.1% 65.4%
5044379 2004.1.1.19 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.57 43.0 3.15e-01 83.6% 73.9%
3265334 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.57 39.0 3.31e-01 73.8% 50.0%
3813872 5.1.4.550 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_FKB95 0.57 49.0 3.16e-01 100.0% 99.3%
3483062 221.1.1.116 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Ubiquitin_6 0.57 48.0 3.97e-01 100.0% 55.8%
5031862 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.56 41.0 3.07e-01 98.4% 29.4%
3787702 2487.1.1.0 a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" 0.56 46.0 3.60e-01 100.0% 97.4%
3533633 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.56 48.0 3.91e-01 100.0% 87.5%
3676790 2484.1.1.157 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4371 0.55 44.0 3.57e-01 100.0% 41.6%
3930805 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.55 45.0 4.08e-01 95.1% 68.2%
3220022 382.1.1.27 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › DUF7773 0.55 46.0 3.81e-01 100.0% 63.6%
3580898 2007.2.3.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.54 44.0 3.26e-01 90.2% 45.6%
4954522 878.1.1.1 a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.54 41.0 3.62e-01 83.6% 55.3%
3490255 11.1.4.114 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › DUF7062 0.53 38.0 3.35e-01 100.0% 49.0%
3489525 219.1.1.3 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.53 44.0 3.01e-01 95.1% 50.8%
5045252 878.1.1.1 a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.52 38.0 3.36e-01 82.0% 96.0%
3260887 5090.1.1.7 beta complex topology › Viral glycoprotein, central and dimerisation domains-like › Viral glycoprotein, central and dimerisation domains › Viral glycoprotein, central and dimerisation domains › HAP2-GCS1 0.52 41.0 2.95e-01 90.2% 89.5%
5010561 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 44.0 3.59e-01 100.0% 80.0%
3351981 3792.1.1.2 beta sandwiches › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain › 26S proteasome subunit Rpn2 C-terminal domain › APC1_3rd 0.51 39.0 3.29e-01 100.0% 48.6%
3391461 3308.2.1.1 beta duplicates or obligate multimers › periplasmic lysozyme inhibitor of I-type lysozyme-like › XAC2610 protein › XAC2610 protein › 4_1_CTD 0.51 44.0 4.14e-01 98.4% 82.7%
5070432 314.1.1.11 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.51 45.0 3.21e-01 100.0% 42.2%
10062 2007.5.1.8 a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.50 42.0 2.86e-01 95.1% 69.8%
5047498 3662.1.1.4 a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC_bac 0.50 37.0 3.16e-01 85.2% 72.2%