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SR-VP_0-2_scaffold_141_2072294_prodigal-single.1__X__X__00100

Bact-Vir

SR-VP_0-2_scaffold_141_2072294_prodigal-single.1__X__X__00100

Identity

Kingdom:
phage

Quality

92.5 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 3-76
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2o8eA01 3.40.1170.10 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › DNA repair protein MutS, domain I 0.60 41.0 3.50e-01 86.5% 43.0%
1xzpB00 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.56 44.0 3.69e-01 87.8% 69.5%
4f07E00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 46.0 3.71e-01 93.2% 77.2%
1ecxB01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 46.0 4.06e-01 95.9% 70.4%
3g2fA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 45.0 4.32e-01 91.9% 83.9%
7emfR01 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.55 37.0 2.85e-01 70.3% 97.7%
4ixoA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 45.0 3.93e-01 95.9% 69.7%
5zspA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.54 44.0 3.81e-01 95.9% 72.1%
1s2oA02 3.90.1070.10 Alpha Beta › Alpha-Beta Complex › Hypothetical Protein Ta0175; Chain: A, domain 2 › 0.54 41.0 4.18e-01 93.2% 87.3%
4k2mA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 44.0 3.74e-01 95.9% 77.9%
4zasA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 44.0 3.85e-01 95.9% 79.5%
2ogaA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 44.0 3.74e-01 95.9% 77.6%
1w23A02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 44.0 3.99e-01 95.9% 71.8%
3frkA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 42.0 3.72e-01 95.9% 80.0%
4kvxA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 42.0 3.42e-01 95.9% 65.8%
1rz1A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 42.0 3.39e-01 93.2% 76.3%
4c0tA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 41.0 3.93e-01 91.9% 82.6%
1vjoA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 42.0 3.60e-01 95.9% 58.0%
3j7yU00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.51 39.0 3.48e-01 85.1% 70.3%
3islA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 42.0 3.61e-01 95.9% 59.4%
5hl8C00 3.30.1360.100 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › General secretion pathway protein M, EpsM 0.51 42.0 4.18e-01 94.6% 89.9%
2fyfA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.50 41.0 3.78e-01 95.9% 72.4%
3vwaA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.50 39.0 3.79e-01 90.5% 78.9%
3eleC01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.50 41.0 3.22e-01 95.9% 41.5%
2bkwA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.50 41.0 3.63e-01 95.9% 65.8%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4030198 304.107.1.3 ↗ a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain › TrmE_N 0.60 46.0 3.79e-01 85.1% 65.0%
1429395 4056.1.1.5 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein › P22_portal 0.58 49.0 3.65e-01 95.9% 75.3%
3725623 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 0.58 49.0 4.37e-01 95.9% 74.5%
3973073 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 0.57 45.0 2.94e-01 95.9% 18.9%
4188472 3016.1.1.1 ↗ 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 › Aminotran_1_2 0.56 45.0 4.00e-01 95.9% 60.0%
3387578 3016.1.1.3 ↗ 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 › Aminotran_5 0.56 46.0 4.00e-01 95.9% 74.4%
3283649 3696.1.1.0 ↗ a+b two layers › DNA helicase UvsW N-terminal a+b domain-related › DNA helicase UvsW N-terminal a+b domain-related › DNA helicase UvsW N-terminal a+b domain-related 0.56 37.0 3.55e-01 87.8% 58.8%
3509819 3016.1.1.3 ↗ 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 › Aminotran_5 0.56 46.0 4.04e-01 95.9% 77.5%
4298978 3016.1.1.3 ↗ 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 › Aminotran_5 0.55 45.0 3.88e-01 95.9% 69.9%
4329706 3016.1.1.1 ↗ 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 › Aminotran_1_2 0.55 43.0 3.96e-01 95.9% 62.9%
3635270 3016.1.1.1 ↗ 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 › Aminotran_1_2 0.55 46.0 3.97e-01 95.9% 68.3%
4281507 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 0.54 42.0 4.34e-01 93.2% 91.4%
1152522 3016.1.1.3 ↗ 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 › Aminotran_5 0.54 45.0 4.07e-01 95.9% 75.5%
4098149 3016.1.1.1 ↗ 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 › Aminotran_1_2 0.54 42.0 4.32e-01 93.2% 91.4%
1152520 3016.1.1.3 ↗ 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 › Aminotran_5 0.54 44.0 3.97e-01 95.9% 74.8%
3599518 810.1.1.0 ↗ a+b two layers › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) 0.54 46.0 3.53e-01 97.3% 84.4%
4986830 3016.1.1.3 ↗ 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 › Aminotran_5 0.53 44.0 3.60e-01 95.9% 62.7%
5030278 314.1.1.2 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.53 43.0 2.85e-01 97.3% 85.7%
3994997 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 0.53 43.0 3.60e-01 95.9% 65.5%
4874102 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 3.82e-01 95.9% 86.2%
4046558 3016.1.1.3 ↗ 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 › Aminotran_5 0.52 42.0 3.75e-01 95.9% 76.7%
3290128 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 0.52 42.0 3.76e-01 95.9% 75.4%
4017191 7579.1.1.6 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.52 41.0 2.70e-01 89.2% 87.1%
3975784 310.3.1.10 ↗ 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 › HofO 0.52 40.0 3.91e-01 91.9% 77.6%
4500961 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.52 44.0 4.23e-01 98.6% 92.9%
3738339 242.1.1.1 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.51 43.0 3.76e-01 100.0% 62.4%
4968784 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 0.51 44.0 4.01e-01 97.3% 78.0%
224326 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 0.51 42.0 3.90e-01 95.9% 75.2%
4341252 3016.1.1.1 ↗ 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 › Aminotran_1_2 0.51 41.0 2.68e-01 95.9% 18.9%
1192643 3016.1.1.3 ↗ 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 › Aminotran_5 0.51 42.0 3.83e-01 95.9% 72.9%
5027605 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.51 44.0 4.22e-01 100.0% 84.7%
3291654 206.1.1.11 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › APH 0.51 39.0 2.81e-01 85.1% 74.6%
3510621 7577.1.1.3 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Aminotran_5 0.51 42.0 2.75e-01 97.3% 24.4%
4998291 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 42.0 3.89e-01 95.9% 74.5%
1192604 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 42.0 3.85e-01 95.9% 72.0%
4992525 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 42.0 3.34e-01 95.9% 46.9%
224346 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 41.0 3.78e-01 95.9% 75.2%
D2 medium residues 77-164
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.66 40.0 4.46e-01 72.7% 78.8%
3qvnA02 3.55.40.20 Alpha Beta › 3-Layer(bab) Sandwich › minor pseudopilin epsh fold › Iron/manganese superoxide dismutase, C-terminal domain 0.61 48.0 4.38e-01 89.8% 64.1%
3glkA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.59 31.0 3.61e-01 72.7% 72.9%
8d8lF01 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.58 41.0 3.66e-01 72.7% 83.7%
2op5B01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 40.0 3.88e-01 75.0% 100.0%
3rgzA02 3.30.1490.310 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.56 36.0 4.12e-01 84.1% 95.1%
1zpwX00 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 39.0 4.07e-01 75.0% 86.6%
4lvnP00 3.30.70.2380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 43.0 4.51e-01 85.2% 100.0%
7o4xA01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 37.0 3.61e-01 70.5% 85.9%
1pnjA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.54 37.0 3.79e-01 70.5% 98.8%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.54 41.0 4.20e-01 80.7% 98.8%
2a74A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.54 35.0 3.37e-01 76.1% 56.2%
3bzcA02 1.10.3500.10 Mainly Alpha › Orthogonal Bundle › Tex N-terminal region-like › Tex N-terminal region-like 0.53 41.0 3.07e-01 86.4% 34.2%
3nrbB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 37.0 3.86e-01 73.9% 100.0%
2ww4A02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.53 42.0 3.85e-01 86.4% 100.0%
7c51A01 3.30.70.2970 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Protein of unknown function (DUF541), domain 2 0.53 37.0 3.51e-01 72.7% 100.0%
2byeA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 33.0 3.23e-01 73.9% 55.4%
1svdM00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.52 35.0 3.33e-01 76.1% 57.4%
3kalB05 3.30.1490.50 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Glutathione synthase lid domain 0.51 27.0 3.10e-01 73.9% 71.2%
1wr2A02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.50 35.0 3.68e-01 72.7% 96.2%
5mz2I00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.50 34.0 3.01e-01 73.9% 45.3%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1291966 304.7.1.5 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › SUB1_ProdP9 0.55 43.0 4.51e-01 85.2% 100.0%
3988500 4342.1.1.1 ↗ alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like › Tex_central_region 0.55 42.0 3.42e-01 86.4% 42.6%
4031329 4342.1.1.1 ↗ alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like › Tex_central_region 0.54 42.0 3.29e-01 86.4% 40.5%
3580832 11.2.1.4 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › Spond_N 0.54 36.0 2.88e-01 77.3% 33.5%
4902 4342.1.1.1 ↗ alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like › Tex_central_region 0.54 42.0 3.27e-01 86.4% 43.8%
4928856 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.53 41.0 3.94e-01 84.1% 100.0%
4883629 302.2.1.1 ↗ a+b two layers › Reverse ferredoxin › RuBisCO, small subunit › RuBisCO, small subunit › RuBisCO_small 0.51 35.0 3.26e-01 75.0% 54.9%
4932798 304.8.1.81 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › REP_ORF2-G2P 0.51 41.0 3.33e-01 88.6% 66.9%
5083040 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.51 38.0 3.68e-01 79.5% 97.0%
4659490 302.2.1.1 ↗ a+b two layers › Reverse ferredoxin › RuBisCO, small subunit › RuBisCO, small subunit › RuBisCO_small 0.50 35.0 3.22e-01 76.1% 55.7%