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SR-VP_0-2_scaffold_141_6534022_prodigal-single.1__X__X__00133

Bact-Vir

SR-VP_0-2_scaffold_141_6534022_prodigal-single.1__X__X__00133

Identity

Kingdom:
phage

Quality

86.9 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 3-59
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3gb0A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.67 58.0 3.80e-01 100.0% 88.5%
1i1iP02 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.64 54.0 4.09e-01 100.0% 79.5%
2x5gA00 3.30.720.60 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.63 41.0 3.61e-01 73.7% 41.8%
4qbnA00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.63 57.0 4.80e-01 100.0% 95.7%
1hw7A01 3.55.30.10 Alpha Beta › 3-Layer(bab) Sandwich › Hsp33 domain › Hsp33 domain 0.62 51.0 3.81e-01 100.0% 60.1%
1mpyA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.61 52.0 3.86e-01 98.2% 36.2%
3aa0B02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.61 50.0 3.80e-01 100.0% 83.9%
4ic6C01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.59 43.0 3.54e-01 78.9% 76.4%
4owpB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.59 47.0 3.45e-01 89.5% 85.5%
3dv8A02 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 38.0 3.40e-01 100.0% 48.7%
3gkeA01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.58 49.0 3.80e-01 96.5% 79.2%
5gneA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.57 47.0 3.15e-01 100.0% 84.8%
1zswA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.57 47.0 3.43e-01 96.5% 33.1%
4wyqB00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 44.0 4.12e-01 89.5% 85.3%
2zylA01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.57 48.0 3.72e-01 98.2% 77.8%
1azsA00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.56 49.0 3.43e-01 100.0% 58.9%
1k32A01 2.120.10.60 Mainly Beta › 6 Propeller › Neuraminidase › Tricorn protease N-terminal domain 0.56 43.0 2.86e-01 100.0% 18.8%
1kutA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 39.0 3.08e-01 75.4% 42.1%
6d0aA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.56 46.0 3.78e-01 98.2% 78.3%
1f1uA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.56 44.0 3.38e-01 96.5% 35.1%
6b1pA02 3.90.800.10 Alpha Beta › Alpha-Beta Complex › Glutamyl-tRNA Synthetase; domain 3 › Glutamyl-tRNA Synthetase; Domain 3 0.55 43.0 3.78e-01 87.7% 86.5%
3hfqA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 46.0 2.93e-01 100.0% 22.6%
2mdrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 46.0 3.98e-01 96.5% 75.5%
2qmiA01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.55 43.0 2.72e-01 91.2% 97.7%
3dkqA01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.54 39.0 2.79e-01 77.2% 79.7%
3fgqA01 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.54 39.0 2.90e-01 82.5% 58.2%
1vpkA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.54 40.0 3.30e-01 89.5% 41.2%
5eo6B00 3.40.1500.10 Alpha Beta › 3-Layer(aba) Sandwich › oxygen-dependent coproporphyrinogen oxidase › Coproporphyrinogen III oxidase, aerobic 0.53 46.0 2.93e-01 100.0% 83.1%
4fr9A00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 43.0 3.42e-01 100.0% 63.1%
1em2A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 44.0 3.09e-01 100.0% 52.8%
4fzxC00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 36.0 2.68e-01 71.9% 42.4%
1rypA00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.52 38.0 2.63e-01 84.2% 84.8%
4griA02 3.90.800.10 Alpha Beta › Alpha-Beta Complex › Glutamyl-tRNA Synthetase; domain 3 › Glutamyl-tRNA Synthetase; Domain 3 0.52 38.0 3.17e-01 87.7% 84.6%
1qmeA01 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.51 33.0 2.88e-01 87.7% 39.6%
1lomA00 2.30.60.10 Mainly Beta › Roll › HIV-inactivating Protein, Cyanovirin-n › Cyanovirin-N 0.51 33.0 2.87e-01 80.7% 38.6%
1rypC00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.50 41.0 2.82e-01 100.0% 32.0%
3b79A00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.50 40.0 3.28e-01 96.5% 82.4%
6muwK00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.50 41.0 2.98e-01 100.0% 38.5%
1v4pA02 3.30.54.20 Alpha Beta › 2-Layer Sandwich › Replication Terminator Protein; Chain A, domain 2 › 0.50 33.0 3.60e-01 70.2% 97.9%
ECOD (62)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5049517 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.69 62.0 4.32e-01 100.0% 67.8%
3271533 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.68 59.0 4.82e-01 100.0% 67.6%
4966560 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.67 58.0 3.83e-01 100.0% 31.4%
4934833 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.67 58.0 4.42e-01 96.5% 79.2%
5015489 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.66 57.0 3.34e-01 100.0% 16.3%
4928998 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.65 57.0 4.29e-01 100.0% 94.5%
3970165 330.10.1.0 ↗ a+b two layers › dsRBD-like › Heterocyclase TruD C-terminal domain › Heterocyclase TruD C-terminal domain 0.65 57.0 4.34e-01 100.0% 54.8%
5082988 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.65 56.0 4.69e-01 98.2% 93.0%
4538612 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.64 54.0 3.37e-01 100.0% 21.4%
4586844 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.64 55.0 3.24e-01 100.0% 16.2%
3961733 330.10.1.0 ↗ a+b two layers › dsRBD-like › Heterocyclase TruD C-terminal domain › Heterocyclase TruD C-terminal domain 0.63 54.0 4.76e-01 100.0% 81.1%
None — 0.63 54.0 3.39e-01 100.0% 23.5%
4446492 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.63 54.0 3.30e-01 100.0% 20.6%
None — 0.63 54.0 3.36e-01 100.0% 21.9%
1349405 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.63 57.0 4.80e-01 100.0% 95.7%
4679871 331.1.1.6 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › DUF3378 0.63 47.0 4.27e-01 100.0% 58.7%
4031212 2008.1.1.31 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › VRR_NUC 0.62 56.0 4.80e-01 100.0% 96.7%
4237612 3006.1.1.6 ↗ a+b two layers › Sm-Like archaeal protein Smap3, C-terminal domain › Sm-Like archaeal protein Smap3, C-terminal domain › Sm-Like archaeal protein Smap3, C-terminal domain › CPSF73-100_C 0.62 52.0 4.70e-01 100.0% 68.2%
4977973 2011.1.1.6 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M20 0.62 54.0 3.48e-01 100.0% 83.9%
3710207 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.61 51.0 3.56e-01 100.0% 67.7%
None — 0.61 52.0 3.20e-01 100.0% 21.1%
4955243 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.60 52.0 3.68e-01 100.0% 60.0%
3952333 243.3.1.3 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › PepSY 0.60 48.0 4.65e-01 93.0% 90.8%
4967744 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 49.0 4.07e-01 96.5% 61.8%
4670546 216.1.1.29 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › PF26204 0.59 49.0 3.51e-01 100.0% 43.0%
5081827 206.1.1.9 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › RIO1 0.59 48.0 3.17e-01 98.2% 48.0%
5048236 314.1.1.3 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2d 0.59 48.0 3.01e-01 100.0% 20.5%
3963015 211.1.1.1 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase 0.58 43.0 3.27e-01 91.2% 32.9%
3744781 109.4.1.69 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IKI3 0.58 44.0 2.88e-01 100.0% 17.0%
2323803 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.57 47.0 3.13e-01 100.0% 82.7%
4937744 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 47.0 3.86e-01 98.2% 90.0%
3904743 2008.1.1.86 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.57 48.0 3.92e-01 98.2% 96.5%
4950522 284.4.1.0 ↗ a+b two layers › FKBP-like › Archaeal FKBP insertion domain › Archaeal FKBP insertion domain 0.57 42.0 4.33e-01 89.5% 83.6%
4022912 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.57 48.0 2.92e-01 96.5% 23.5%
3244845 5.1.4.137 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Nbas_N 0.57 48.0 2.78e-01 100.0% 15.7%
3748189 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.57 48.0 4.32e-01 96.5% 86.3%
3017675 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 48.0 4.45e-01 98.2% 94.7%
3752886 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.56 47.0 3.92e-01 96.5% 65.7%
4324611 2008.1.1.166 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_XcyI 0.56 47.0 3.02e-01 98.2% 44.4%
3910954 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 46.0 3.99e-01 100.0% 79.0%
3823735 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.56 48.0 4.29e-01 100.0% 82.4%
4972351 3016.1.1.6 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › DegT_DnrJ_EryC1 0.55 44.0 3.62e-01 94.7% 91.7%
3543887 330.1.1.6 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Staufen_C 0.55 47.0 3.95e-01 98.2% 71.0%
4106397 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 45.0 4.18e-01 94.7% 88.0%
3999390 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.54 41.0 2.85e-01 87.7% 87.6%
3669719 3422.1.1.0 ↗ a+b two layers › TEN domain of telomerase reverse transcriptase › TEN domain of telomerase reverse transcriptase › TEN domain of telomerase reverse transcriptase 0.53 38.0 2.88e-01 78.9% 82.5%
3637319 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 38.0 2.52e-01 78.9% 16.7%
4290772 825.1.1.2 ↗ beta complex topology › Aerolysin family of pore-forming toxins › Aerolysin family of pore-forming toxins › Aerolysin family of pore-forming toxins › ETX_MTX2 0.52 39.0 2.59e-01 84.2% 47.8%
1587044 3016.1.1.6 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › DegT_DnrJ_EryC1 0.52 43.0 3.57e-01 98.2% 92.1%
5014142 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 43.0 2.70e-01 100.0% 23.0%
4858761 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.52 43.0 3.02e-01 100.0% 35.4%
3599053 210.1.1.0 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits 0.51 42.0 2.98e-01 100.0% 34.4%
3708226 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.51 43.0 2.92e-01 100.0% 30.8%
3201324 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.51 42.0 2.83e-01 100.0% 29.1%
5051502 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.51 36.0 2.67e-01 77.2% 30.9%
4863223 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.51 42.0 3.18e-01 100.0% 45.4%
4483150 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.51 44.0 3.16e-01 94.7% 63.1%
3719304 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.51 39.0 3.11e-01 91.2% 40.3%
3934966 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.51 42.0 2.89e-01 100.0% 31.8%
4023682 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.50 41.0 2.96e-01 100.0% 37.6%
3821839 192.8.1.59 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › ATG14 0.50 43.0 2.78e-01 98.2% 33.2%
1171960 809.2.1.0 ↗ a+b two layers › BLIP-like › BT0923-like › BT0923-like 0.50 41.0 3.82e-01 100.0% 73.1%