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SR-VP_2-4_scaffold_141_5652861_prodigal-single.1__X__X__00222

Bact-Vir

SR-VP_2-4_scaffold_141_5652861_prodigal-single.1__X__X__00222

Identity

Kingdom:
phage

Quality

66.5 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 2-113
PDB
CATH (58)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6jimB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.70 64.0 5.90e-01 100.0% 100.0%
1c4oA03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 53.0 4.55e-01 83.0% 84.0%
3vkwA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.67 59.0 5.47e-01 95.5% 95.1%
3rc3A03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.65 57.0 5.09e-01 96.4% 90.6%
4rkcA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.64 54.0 4.24e-01 92.9% 81.4%
3axsA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.64 53.0 3.89e-01 92.9% 90.1%
3p1tA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.63 52.0 4.38e-01 92.9% 80.0%
2r3sA03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.62 53.0 4.36e-01 94.6% 88.7%
3ffhB02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.62 52.0 4.28e-01 93.8% 81.4%
3eucA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.61 51.0 4.25e-01 92.9% 82.6%
5dj1A02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.61 51.0 4.09e-01 92.9% 72.8%
2z61A02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.61 50.0 4.19e-01 92.0% 79.3%
7cpxA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.61 53.0 3.85e-01 98.2% 99.4%
6qp2A01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.60 50.0 3.99e-01 92.0% 76.1%
3dnfB01 3.40.1010.20 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain 0.60 42.0 4.41e-01 72.3% 90.0%
1vw3D00 3.40.1370.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L4; Chain: A; › Ribosomal protein L4/L1 0.60 43.0 3.39e-01 74.1% 92.5%
1y44A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.59 46.0 3.49e-01 83.0% 97.8%
1i9gA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.59 49.0 4.26e-01 93.8% 88.6%
3futA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 49.0 4.14e-01 94.6% 86.9%
2i7xA02 3.40.50.10890 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 51.0 4.31e-01 97.3% 94.7%
4obvA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.58 50.0 3.95e-01 95.5% 86.6%
2hlzA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.58 51.0 3.83e-01 100.0% 87.8%
3egeA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 49.0 3.84e-01 93.8% 98.4%
1i4wA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 48.0 3.84e-01 94.6% 92.7%
1lwdA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.57 52.0 3.51e-01 100.0% 47.9%
4ritA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.57 48.0 3.88e-01 94.6% 87.7%
5t5dA00 3.40.35.10 Alpha Beta › 3-Layer(aba) Sandwich › Fructose Permease › Phosphotransferase system, sorbose subfamily IIB component 0.57 49.0 4.52e-01 96.4% 93.3%
1bleA00 3.40.35.10 Alpha Beta › 3-Layer(aba) Sandwich › Fructose Permease › Phosphotransferase system, sorbose subfamily IIB component 0.57 50.0 4.43e-01 97.3% 91.3%
3zokA01 3.40.50.1970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 45.0 3.96e-01 86.6% 88.5%
3ry7A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.56 50.0 3.72e-01 100.0% 84.8%
3uwcA01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.56 46.0 3.74e-01 92.9% 73.4%
4tkzA00 3.40.50.510 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component 0.56 40.0 3.85e-01 75.0% 96.9%
1uu1A02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.56 49.0 4.13e-01 100.0% 69.0%
3lfjB00 3.40.35.10 Alpha Beta › 3-Layer(aba) Sandwich › Fructose Permease › Phosphotransferase system, sorbose subfamily IIB component 0.56 49.0 4.32e-01 98.2% 89.2%
6khnA01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.55 46.0 3.59e-01 94.6% 79.2%
5ereA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 43.0 4.06e-01 83.9% 100.0%
2gpyB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 47.0 3.99e-01 94.6% 82.3%
2e7jA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.55 46.0 3.75e-01 94.6% 78.0%
4qq8A01 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.55 45.0 3.93e-01 92.0% 79.1%
2xr1B04 3.40.50.10890 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 47.0 4.09e-01 95.5% 86.9%
4r0mB01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.55 45.0 3.02e-01 87.5% 71.4%
3oidC00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 49.0 3.83e-01 100.0% 92.7%
6gyzA03 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.54 38.0 4.19e-01 93.8% 95.2%
7f8aA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 48.0 4.17e-01 98.2% 98.3%
3u7qB01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.54 46.0 4.22e-01 92.9% 93.8%
4rv9A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 45.0 3.78e-01 92.9% 87.6%
3zwfA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.54 47.0 3.68e-01 100.0% 98.8%
2a3nA02 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.54 43.0 3.82e-01 85.7% 82.6%
3i3wA03 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.53 36.0 4.06e-01 93.8% 95.1%
3bxoA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 44.0 3.88e-01 93.8% 89.3%
1vluB02 3.40.309.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 2 › Aldehyde Dehydrogenase; Chain A, domain 2 0.53 47.0 4.34e-01 100.0% 97.3%
3i9fB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 46.0 4.05e-01 98.2% 90.5%
2bkaA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 46.0 3.71e-01 100.0% 87.4%
1ujnA01 3.40.50.1970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 41.0 3.70e-01 87.5% 87.6%
3fxaA00 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.51 41.0 3.53e-01 87.5% 75.4%
3szuA03 3.40.1010.20 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain 0.51 41.0 4.27e-01 92.9% 96.0%
3hl0A01 3.40.50.1970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 41.0 3.75e-01 91.1% 89.9%
2zvbA01 3.40.1010.10 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › Tetrapyrrole methylase, N-terminal domain 0.50 43.0 4.17e-01 96.4% 96.2%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5006954 2004.1.1.1217 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF7125 0.74 69.0 5.35e-01 100.0% 78.7%
3944293 2004.1.1.200 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_25 0.72 66.0 5.09e-01 100.0% 67.9%
5067247 2004.1.1.120 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ResIII 0.72 63.0 5.00e-01 94.6% 82.3%
2512657 2004.1.1.62 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Viral_helicase1 0.70 61.0 5.39e-01 93.8% 95.6%
3346704 2004.1.1.23 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SNF2-rel_dom 0.70 63.0 4.89e-01 96.4% 81.3%
4928150 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.69 62.0 5.14e-01 100.0% 90.5%
3655562 7510.1.1.1 a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Iso_dh 0.66 49.0 4.13e-01 76.8% 95.7%
3990336 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.66 57.0 4.25e-01 94.6% 51.4%
4950792 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.63 55.0 4.15e-01 94.6% 97.0%
3721871 2003.1.5.73 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.61 51.0 4.18e-01 93.8% 86.7%
4987739 2003.1.5.13 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Spermine_synth 0.61 53.0 4.14e-01 94.6% 72.3%
4257987 7577.1.1.1 a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Aminotran_1_2 0.61 51.0 3.94e-01 93.8% 64.1%
3892980 7510.1.1.1 a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Iso_dh 0.60 50.0 4.99e-01 90.2% 100.0%
5002824 2004.1.1.1204 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF1638 0.59 52.0 4.31e-01 100.0% 96.2%
4970611 2003.1.5.5 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0020 0.59 51.0 4.33e-01 94.6% 93.0%
3277896 2003.1.5.5 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0020 0.59 49.0 4.32e-01 93.8% 92.6%
3638649 2004.1.1.23 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SNF2-rel_dom 0.59 55.0 4.51e-01 100.0% 70.5%
3681692 2003.1.5.73 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.58 51.0 3.87e-01 96.4% 88.9%
5009911 2003.1.5.8 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Ubie_methyltran 0.57 48.0 3.95e-01 93.8% 90.2%
5069821 2003.1.5.79 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_23 0.56 47.0 4.29e-01 93.8% 93.5%
4575490 2003.1.5.42 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_21 0.56 48.0 3.78e-01 93.8% 87.5%
4267884 2004.1.1.231 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › RNase_J_b_CASP 0.56 49.0 4.45e-01 98.2% 96.1%
5011327 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 46.0 4.45e-01 89.3% 86.4%
4077067 2003.1.5.2 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD 0.56 48.0 4.08e-01 94.6% 88.6%
3645180 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.56 38.0 3.29e-01 70.5% 56.3%
141634 7537.1.1.1 a/b three-layered sandwiches › PTS IIb component › PTS IIb component › PTS IIb component › PTSIIB_sorb 0.56 49.0 4.33e-01 98.2% 89.7%
5042627 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.55 45.0 4.31e-01 91.1% 94.6%
4013275 2006.1.1.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.54 45.0 4.25e-01 90.2% 100.0%
5071195 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 46.0 4.45e-01 95.5% 90.8%
4947512 2003.1.10.10 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain › DUF1246 0.54 40.0 4.10e-01 79.5% 90.0%
3993359 2003.1.5.5 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0020 0.54 44.0 3.92e-01 90.2% 90.3%
5065356 2003.1.5.2 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD 0.53 45.0 3.84e-01 96.4% 88.7%
5032479 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 46.0 4.27e-01 96.4% 85.0%
5077025 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 45.0 4.32e-01 98.2% 88.1%
5032033 2006.1.3.9 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › OLD-like_TOPRIM 0.52 39.0 3.69e-01 77.7% 84.1%
3165504 7588.1.1.1 a/b three-layered sandwiches › NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase › NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase › NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase › LYTB 0.52 42.0 4.41e-01 92.0% 97.0%
None 0.52 43.0 3.02e-01 92.9% 56.0%
3326329 2003.1.5.3 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_2 0.52 44.0 3.92e-01 98.2% 99.4%
3967963 2007.6.1.4 a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain › SIS 0.51 41.0 3.38e-01 87.5% 68.3%