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RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00570

Bact-Vir

RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00570

Identity

Kingdom:
phage

Quality

79.4 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 3-85
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF14243.12 best R2K_3 36.2 9.80e-09 84.3% 32.9%
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3tiiB02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.78 71.0 5.43e-01 100.0% 66.5%
3orqA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.76 69.0 5.07e-01 100.0% 52.6%
3k5iA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.76 69.0 5.15e-01 100.0% 58.6%
1gsoA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.75 66.0 5.62e-01 100.0% 83.5%
3vpbB03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.74 68.0 6.12e-01 100.0% 85.7%
3votB02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.74 67.0 4.56e-01 100.0% 42.0%
4e4tA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.74 67.0 4.98e-01 100.0% 56.4%
1kutA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.74 53.0 4.54e-01 75.9% 85.7%
3wnzA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.74 66.0 5.52e-01 100.0% 72.9%
1iowA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.73 67.0 5.45e-01 100.0% 74.5%
1ehiA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.73 66.0 5.45e-01 100.0% 83.3%
5h80B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.73 65.0 4.62e-01 100.0% 46.6%
1uc8A03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.72 62.0 5.98e-01 100.0% 84.0%
1e4eB01 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.71 64.0 5.21e-01 100.0% 76.3%
2z04B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.71 62.0 4.85e-01 100.0% 58.6%
2i87B02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.70 63.0 5.07e-01 100.0% 66.7%
5dmxB02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.70 63.0 5.11e-01 100.0% 55.8%
3l2pA03 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.68 51.0 4.50e-01 79.5% 78.3%
1auvA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.66 51.0 4.69e-01 80.7% 63.8%
5oomJ01 3.30.1550.10 Alpha Beta › 2-Layer Sandwich › Ribosomal protein L11, N-terminal domain › Ribosomal protein L11/L12, N-terminal domain 0.66 46.0 5.01e-01 73.5% 98.5%
3a58A01 2.30.29.90 Mainly Beta › Roll › PH-domain like › 0.65 46.0 3.69e-01 75.9% 79.9%
2e7zA01 2.20.25.90 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ADC-like domains 0.60 30.0 3.48e-01 79.5% 66.7%
5y6iA02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.60 44.0 3.64e-01 79.5% 87.6%
7jsnA02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.60 44.0 3.32e-01 78.3% 76.2%
3ty2A00 3.40.1210.10 Alpha Beta › 3-Layer(aba) Sandwich › Stationary-phase Survival Protein Sure Homolog; Chain: A, › Survival protein SurE-like phosphatase/nucleotidase 0.58 39.0 2.89e-01 71.1% 59.6%
2qybA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.57 42.0 3.56e-01 80.7% 79.5%
2l55A00 2.40.50.320 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Copper binding periplasmic protein CusF 0.56 42.0 4.30e-01 83.1% 95.1%
2q0oA01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.55 45.0 3.63e-01 90.4% 76.2%
5l09B00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.55 45.0 3.63e-01 89.2% 80.5%
4bwiB01 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.54 42.0 3.25e-01 84.3% 39.1%
1f5mA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.54 36.0 2.86e-01 86.7% 32.4%
6p58A00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.53 40.0 3.36e-01 80.7% 79.3%
6cc0A01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.53 47.0 3.78e-01 98.8% 79.9%
1ujcA00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.53 39.0 3.22e-01 78.3% 98.7%
1rh8A00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.53 40.0 3.36e-01 80.7% 64.1%
1dgsA04 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 37.0 3.90e-01 73.5% 100.0%
4pj2A00 2.40.128.460 Mainly Beta › Beta Barrel › Lipocalin › Periplasmic lysozyme inhibitor of I-type lysozyme 0.53 36.0 3.25e-01 71.1% 96.7%
4pz7A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 41.0 3.57e-01 86.7% 65.7%
3soyA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 37.0 3.16e-01 74.7% 85.9%
3w2zA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.51 38.0 3.09e-01 80.7% 70.8%
2xepB01 3.10.450.280 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 38.0 3.42e-01 78.3% 93.9%
3kstA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.51 43.0 3.06e-01 97.6% 85.6%
4r70B01 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.51 37.0 2.85e-01 78.3% 56.7%
ECOD (62)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3288472 206.1.3.32 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › R2K_3 0.84 76.0 5.57e-01 100.0% 40.0%
3542430 206.1.3.18 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › D123 0.82 75.0 4.99e-01 100.0% 30.0%
3346566 1.1.7.85 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › BRX 0.80 32.0 3.99e-01 78.3% 58.2%
3830939 206.1.3.18 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › D123 0.80 73.0 4.94e-01 100.0% 31.6%
3987360 206.1.3.84 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › R2K_2 0.79 71.0 5.49e-01 100.0% 47.1%
4937607 206.1.3.8 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATP-grasp_3 0.78 71.0 5.26e-01 100.0% 51.7%
4527067 206.1.3.40 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATPgrasp_YheCD 0.78 71.0 4.94e-01 100.0% 47.8%
4205235 206.1.3.12 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL 0.78 70.0 4.70e-01 100.0% 49.7%
3599208 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.77 70.0 4.58e-01 100.0% 51.3%
3841807 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.77 70.0 4.69e-01 100.0% 45.6%
5033884 206.1.3.40 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATPgrasp_YheCD 0.77 70.0 5.06e-01 100.0% 46.2%
3716760 206.1.3.12 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL 0.77 69.0 4.34e-01 100.0% 40.5%
4028466 206.1.3.55 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL, ATPgrasp_YheCD 0.76 69.0 4.55e-01 100.0% 51.3%
4673494 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.76 69.0 4.75e-01 100.0% 40.5%
3400913 206.1.3.12 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL 0.76 69.0 4.56e-01 100.0% 52.0%
5063412 206.1.3.19 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C 0.75 68.0 4.50e-01 100.0% 37.5%
4588934 206.1.3.25 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATP-grasp_4 0.74 67.0 4.58e-01 100.0% 41.4%
5046855 206.1.3.21 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.74 67.0 5.00e-01 100.0% 47.3%
1837665 206.1.3.25 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATP-grasp_4 0.74 67.0 5.00e-01 100.0% 60.3%
5036063 206.1.3.21 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.74 67.0 5.17e-01 100.0% 56.1%
None 0.73 67.0 4.86e-01 100.0% 43.6%
4060053 206.1.3.21 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.73 67.0 4.79e-01 100.0% 41.7%
4966381 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.73 65.0 4.29e-01 100.0% 43.1%
4880373 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.73 65.0 5.08e-01 100.0% 53.4%
4062153 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.73 66.0 4.47e-01 100.0% 37.6%
None 0.73 66.0 4.71e-01 100.0% 47.7%
None 0.72 65.0 4.95e-01 100.0% 57.9%
4973439 206.1.3.8 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATP-grasp_3 0.72 65.0 4.94e-01 100.0% 51.3%
4233261 206.1.3.21 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.72 65.0 4.49e-01 100.0% 34.6%
980877 206.1.3.21 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.72 66.0 5.04e-01 100.0% 48.9%
4947584 206.1.3.19 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C 0.72 65.0 4.69e-01 100.0% 55.2%
2756576 206.1.3.21 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.72 65.0 4.76e-01 100.0% 47.0%
5020794 206.1.3.19 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C 0.71 64.0 4.53e-01 100.0% 49.8%
5058364 206.1.3.19 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C 0.71 64.0 4.72e-01 100.0% 56.3%
4568153 206.1.3.19 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C 0.70 63.0 4.51e-01 100.0% 48.6%
3640064 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.70 51.0 4.19e-01 75.9% 71.3%
5050960 206.1.3.16 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Ins134_P3_kin 0.70 64.0 4.69e-01 100.0% 42.9%
3510399 206.1.3.9 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Synapsin_C 0.68 60.0 4.49e-01 100.0% 45.1%
4411405 206.1.3.9 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Synapsin_C 0.67 60.0 4.99e-01 100.0% 64.1%
5027371 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.67 49.0 3.85e-01 78.3% 49.4%
4986756 206.1.3.9 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Synapsin_C 0.65 58.0 4.02e-01 100.0% 31.6%
5050420 324.1.1.0 a+b two layers › OsmC-like › OsmC-like › OsmC-like 0.63 47.0 4.13e-01 78.3% 72.5%
3740272 5.1.4.32 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Nucleoporin_N 0.61 46.0 2.92e-01 80.7% 33.6%
5082348 223.1.1.3 a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.59 44.0 3.67e-01 79.5% 72.7%
4009068 223.1.1.23 a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.58 37.0 2.93e-01 84.3% 31.2%
5078695 7525.1.1.1 a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_1 0.57 42.0 3.42e-01 78.3% 98.7%
3399234 395.1.1.0 few secondary structure elements › Midkine-related › Midkine-related › Midkine-related 0.57 33.0 3.91e-01 78.3% 94.0%
3844573 5.1.3.170 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Beta-prop_IFT140_2nd 0.56 43.0 2.84e-01 80.7% 45.7%
4972571 7525.1.1.1 a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_1 0.56 42.0 3.42e-01 79.5% 98.7%
3688782 206.1.3.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.56 44.0 2.89e-01 86.7% 25.7%
3789793 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 42.0 2.46e-01 80.7% 17.3%
3197689 2.1.1.28 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › mRNA_cap_C 0.55 42.0 3.56e-01 86.7% 65.8%
4455320 223.1.1.3 a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.54 42.0 2.69e-01 84.3% 19.3%
1271913 223.1.1.3 a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.54 42.0 3.30e-01 84.3% 41.2%
4014123 5.1.2.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.54 44.0 3.07e-01 92.8% 83.3%
3980189 7525.1.1.1 a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_1 0.52 39.0 3.21e-01 79.5% 99.4%
4958964 223.1.1.23 a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.52 44.0 3.50e-01 94.0% 73.7%
3358578 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.52 35.0 3.55e-01 83.1% 68.2%
4360971 2.1.1.293 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF27162 0.52 37.0 4.08e-01 74.7% 100.0%
4989233 223.1.1.23 a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.52 43.0 3.68e-01 94.0% 87.1%
4958416 2.1.1.73 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RsgA_N 0.52 35.0 3.63e-01 74.7% 75.0%
4263787 2.1.1.293 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF27162 0.51 36.0 4.02e-01 74.7% 100.0%