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SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00070

Bact-Vir

SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00070

Identity

Kingdom:
phage

Quality

82.7 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 60-273_338-348
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r2cB00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 29.0 4.01e-01 96.0% 87.2%
2fauA01 2.60.40.640 Mainly Beta › Sandwich › Immunoglobulin-like › 0.62 31.0 3.75e-01 95.1% 70.2%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 21.0 3.37e-01 93.8% 87.5%
3qt2A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 26.0 3.78e-01 84.4% 94.8%
3cu7A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.57 28.0 3.96e-01 84.4% 99.1%
3klqA01 2.60.40.3050 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 30.0 3.92e-01 100.0% 95.8%
1cd9B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 26.0 3.66e-01 88.9% 95.9%
1x5iA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 26.0 3.70e-01 86.2% 97.9%
6x5vA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 25.0 3.71e-01 88.4% 100.0%
3bgaA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 28.0 3.84e-01 85.3% 100.0%
5irbA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 26.0 3.66e-01 85.3% 98.1%
4gs3A00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 21.0 3.15e-01 70.7% 86.7%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4944597 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 29.0 4.02e-01 94.7% 80.0%
5040204 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 27.0 3.93e-01 85.8% 93.7%
5069215 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 25.0 3.77e-01 93.8% 94.1%
3258564 11.1.1.801 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF7035 0.60 32.0 3.95e-01 95.6% 80.0%
3525969 11.1.1.239 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › MG3 0.59 29.0 3.87e-01 94.7% 87.0%
5054967 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 31.0 3.70e-01 95.1% 73.3%
3446392 11.1.4.65 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › DUF6598 0.59 26.0 3.90e-01 95.1% 98.9%
5022723 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 23.0 3.51e-01 95.6% 89.4%
3939010 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 24.0 3.45e-01 95.1% 82.1%
3248103 11.1.1.1040 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF28849 0.58 27.0 3.59e-01 95.1% 80.0%
3213808 11.1.1.9 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_N 0.57 32.0 3.88e-01 95.1% 82.0%
3583164 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 25.0 3.61e-01 88.9% 91.6%
4003701 10.10.1.0 ↗ beta sandwiches › jelly-roll › Lipase/lipooxygenase domain (PLAT/LH2 domain) › Lipase/lipooxygenase domain (PLAT/LH2 domain) 0.56 27.0 3.81e-01 99.1% 97.0%
1393539 11.1.4.20 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › FctA 0.55 30.0 3.69e-01 100.0% 83.2%
3239942 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 28.0 3.86e-01 91.6% 100.0%
1069348 11.1.1.102 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › A2M_BRD 0.55 29.0 3.88e-01 90.2% 98.2%
3880104 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.55 25.0 3.62e-01 84.4% 96.8%
3768529 11.1.1.15 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PKD 0.54 29.0 3.79e-01 90.7% 94.8%
3461283 77.1.1.8 ↗ beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › PF28611 0.54 21.0 2.98e-01 76.9% 73.5%
3707901 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.54 22.0 3.11e-01 80.9% 76.2%
3882099 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.54 28.0 3.77e-01 95.6% 95.7%
3543052 11.1.1.284 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PKD_4 0.53 28.0 3.74e-01 90.7% 98.2%
3565481 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.53 26.0 3.57e-01 89.3% 95.2%
3282439 11.1.1.461 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF6299 0.53 28.0 3.73e-01 80.4% 99.1%
5043841 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.53 32.0 3.92e-01 93.8% 100.0%
5022779 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 27.0 3.60e-01 89.3% 100.0%
3415488 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 26.0 3.55e-01 85.3% 95.5%
5047571 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 27.0 3.61e-01 82.2% 99.1%
3991816 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.51 31.0 3.79e-01 96.0% 95.7%
3895929 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.51 24.0 3.39e-01 86.2% 96.0%
4980567 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 29.0 3.66e-01 87.6% 98.4%
D2 medium residues 275-326
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ab7H02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.62 43.0 3.12e-01 73.1% 44.7%
6bs6A04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 46.0 3.59e-01 78.8% 58.6%
3s6gA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.62 41.0 3.06e-01 75.0% 25.3%
4k30A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.61 41.0 2.98e-01 75.0% 24.2%
4dcmA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 43.0 3.06e-01 78.8% 28.7%
3mggB01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.59 40.0 2.90e-01 73.1% 29.3%
1i7qA00 3.60.120.10 Alpha Beta › 4-Layer Sandwich › Anthranilate synthase › Anthranilate synthase 0.58 45.0 2.68e-01 92.3% 19.1%
4kh9B02 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.58 45.0 3.54e-01 86.5% 81.4%
5yuyA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.56 40.0 3.11e-01 76.9% 49.2%
3mnfA00 3.40.50.10900 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › PAC-like subunit 0.56 40.0 2.79e-01 84.6% 33.6%
2j0wA04 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.55 41.0 3.74e-01 84.6% 72.0%
1r89A04 3.30.70.1550 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Archaeal tRNA CCA-adding enzyme catalytic domain 0.55 40.0 4.14e-01 98.1% 100.0%
6k2eA01 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 41.0 3.78e-01 78.8% 63.2%
2bhuA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 39.0 3.26e-01 76.9% 42.7%
2i8eA01 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 37.0 3.40e-01 76.9% 58.1%
5wm1A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.52 41.0 3.42e-01 94.2% 51.4%
1avaA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 35.0 3.45e-01 71.2% 63.8%
8dhaA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 39.0 3.41e-01 86.5% 62.1%
4e1oA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 38.0 3.30e-01 88.5% 78.6%
4nmlA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.51 40.0 3.50e-01 94.2% 81.1%
4xvoA01 2.60.40.3710 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 40.0 3.44e-01 88.5% 80.9%
1js3A03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 37.0 3.27e-01 88.5% 80.4%
2yvsA02 3.30.70.2560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 36.0 3.51e-01 78.8% 71.2%
3ezjA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.50 36.0 3.39e-01 76.9% 73.5%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4942240 205.1.1.20 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_15 0.66 51.0 4.33e-01 84.6% 68.2%
3569385 226.1.1.0 ↗ a+b two layers › POZ domain › POZ domain › POZ domain 0.59 40.0 3.54e-01 73.1% 44.7%
None — 0.59 39.0 2.79e-01 71.2% 23.4%
3810606 376.1.2.16 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1-like_CT 0.59 42.0 3.88e-01 88.5% 58.6%
3183588 12.1.1.116 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Tfb2 0.58 41.0 3.49e-01 80.8% 93.0%
3258106 304.33.1.0 ↗ a+b two layers › Alpha-beta plaits › CheY-binding domain of CheA › CheY-binding domain of CheA 0.58 45.0 4.04e-01 88.5% 68.0%
5034671 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.56 40.0 2.90e-01 76.9% 47.5%
3400673 165.1.1.4 ↗ alpha duplicates or obligate multimers › Dimerisation interlock › SinR repressor dimerisation domain-like › SinR repressor dimerisation domain-like › Tfb2 0.56 40.0 3.42e-01 80.8% 94.0%
4068317 3016.1.1.0 ↗ 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 0.56 39.0 3.86e-01 73.1% 69.1%
4075892 304.20.1.4 ↗ a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.56 41.0 3.38e-01 92.3% 38.3%
3473669 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.56 46.0 2.76e-01 100.0% 18.5%
3623939 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.55 41.0 3.47e-01 80.8% 54.4%
5020256 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.54 37.0 3.49e-01 75.0% 58.5%
4002329 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 42.0 3.29e-01 88.5% 70.0%
4937444 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 42.0 3.96e-01 92.3% 72.3%
4940555 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.53 40.0 2.70e-01 90.4% 20.4%
3391300 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 40.0 2.60e-01 92.3% 24.1%
4643746 12.1.1.5 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Alpha-amyl_C2 0.52 40.0 3.71e-01 88.5% 70.0%
3520927 4081.1.1.5 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Peptidase_M1_N 0.52 41.0 2.76e-01 90.4% 22.7%
3421421 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.51 35.0 2.13e-01 73.1% 14.8%
4971696 5104.1.1.0 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.51 39.0 3.04e-01 88.5% 34.6%
3872986 4001.1.1.4 ↗ a+b duplicates or obligate multimers › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › Cullin_AB 0.51 36.0 2.81e-01 84.6% 32.5%
3208500 109.21.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nup96 0.50 40.0 2.33e-01 98.1% 59.5%
4089840 11.1.1.577 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PFF1_C 0.50 39.0 2.78e-01 92.3% 56.5%
3927598 3016.1.1.0 ↗ 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 0.50 36.0 3.23e-01 86.5% 64.4%