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SRR1747046_scaffold_4_prodigal-single.1__X__X__00156

Bact-Vir

SRR1747046_scaffold_4_prodigal-single.1__X__X__00156

Identity

Kingdom:
phage

Quality

82.8 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 medium residues 1-21_154-212
PDB
Domain cluster: representative
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5optY00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 52.0 4.57e-01 85.0% 67.5%
3bp6B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 42.0 4.06e-01 78.8% 59.1%
2y3uA02 3.30.980.50 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › 0.64 44.0 3.92e-01 70.0% 67.3%
1cqkA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 43.0 3.96e-01 78.8% 55.4%
1kzfA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.63 38.0 2.85e-01 70.0% 24.2%
3qwuA03 3.30.70.2160 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 49.0 4.03e-01 82.5% 48.9%
2lqjA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.62 42.0 3.97e-01 70.0% 62.8%
4q9cA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 44.0 4.06e-01 80.0% 58.1%
5wy8B03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 46.0 4.14e-01 81.2% 60.7%
1a6aB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 42.0 3.95e-01 80.0% 59.2%
2k31A00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.60 44.0 3.61e-01 77.5% 78.5%
1o0vA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 43.0 3.92e-01 78.8% 55.5%
4q97A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 44.0 3.98e-01 78.8% 57.4%
8ediA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 42.0 3.86e-01 82.5% 55.8%
1es0A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 42.0 3.90e-01 80.0% 58.6%
2nn5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 44.0 3.41e-01 77.5% 59.6%
3c19A01 3.30.70.1380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transcriptional regulatory protein pf0864 domain like 0.59 42.0 3.93e-01 73.8% 59.6%
2c42A03 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.59 43.0 3.18e-01 77.5% 30.2%
5h5zA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 39.0 3.82e-01 77.5% 62.5%
7zqiA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 40.0 3.93e-01 78.8% 66.3%
2fbjH02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 41.0 4.24e-01 81.2% 80.8%
4jvuA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 43.0 3.86e-01 80.0% 57.3%
2jzxA02 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.57 40.0 4.06e-01 73.8% 77.2%
3of6E00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 41.0 3.81e-01 78.8% 59.6%
1c16A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 39.0 3.70e-01 78.8% 59.8%
1tz0B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 40.0 3.82e-01 76.2% 99.0%
3f8uD03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 42.0 3.85e-01 81.2% 60.4%
6efyA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 38.0 3.58e-01 81.2% 59.2%
2ld4A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 39.0 3.19e-01 80.0% 90.1%
5u1xA02 2.60.490.10 Mainly Beta › Sandwich › atp-gated p2x4 ion channel fold › atp-gated p2x4 ion channel domain 0.54 39.0 2.72e-01 76.2% 91.6%
3luyA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 36.0 3.58e-01 72.5% 98.9%
1ug8A00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.53 38.0 3.71e-01 87.5% 69.0%
3d2uA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.61e-01 78.8% 65.2%
4dn9B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 37.0 3.56e-01 77.5% 100.0%
5lf5A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 35.0 3.38e-01 80.0% 61.3%
2rf4C01 3.30.1490.120 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RNA polymerase Rpb7-like, N-terminal domain 0.51 38.0 3.68e-01 80.0% 91.2%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
168067 2.1.1.95 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Lig_C 0.64 49.0 4.04e-01 81.2% 46.4%
3377143 304.166.1.3 a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › DUF7036 0.62 43.0 3.82e-01 71.2% 57.4%
3454041 304.151.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain of receptor-type protein tyrosine phosphatase › Ferredoxin-like domain of receptor-type protein tyrosine phosphatase 0.62 42.0 3.62e-01 71.2% 60.0%
3992861 389.4.1.0 few secondary structure elements › EGF-like › Fibulin-4 EGF-like 1 domain › Fibulin-4 EGF-like 1 domain 0.62 38.0 4.08e-01 72.5% 71.4%
3307398 304.8.1.45 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant 0.62 44.0 4.00e-01 78.8% 54.5%
3995832 2003.1.5.73 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.62 46.0 3.50e-01 78.8% 84.3%
3268698 309.1.2.0 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain 0.62 44.0 3.45e-01 73.8% 79.4%
3994103 389.2.1.3 few secondary structure elements › EGF-like › Serine protease inhibitors › Serine protease inhibitors › TIL_2 0.62 38.0 4.16e-01 70.0% 75.4%
4353523 11.1.1.96 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.62 44.0 4.10e-01 78.8% 60.0%
4001196 389.4.1.7 few secondary structure elements › EGF-like › Fibulin-4 EGF-like 1 domain › Fibulin-4 EGF-like 1 domain › TIL_2 0.61 37.0 3.99e-01 70.0% 70.0%
4954977 304.6.1.1 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › FAD-oxidase_C 0.61 44.0 3.10e-01 75.0% 28.1%
1240941 872.5.1.1 a+b two layers › Dodecin subunit-like › D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain › D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain › OAM_dimer 0.61 45.0 4.40e-01 80.0% 74.4%
4004124 389.4.1.0 few secondary structure elements › EGF-like › Fibulin-4 EGF-like 1 domain › Fibulin-4 EGF-like 1 domain 0.61 39.0 3.85e-01 71.2% 61.2%
4189854 2004.1.3.2 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR,EKR 0.60 45.0 3.09e-01 78.8% 24.8%
4001979 389.4.1.7 few secondary structure elements › EGF-like › Fibulin-4 EGF-like 1 domain › Fibulin-4 EGF-like 1 domain › TIL_2 0.60 38.0 4.10e-01 70.0% 74.3%
3993066 387.1.1.39 few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related › TIL_2 0.60 38.0 3.86e-01 70.0% 65.0%
3310467 304.166.1.3 a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › DUF7036 0.59 41.0 3.56e-01 71.2% 52.0%
3330441 304.8.1.45 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant 0.59 38.0 3.96e-01 78.8% 70.7%
5017032 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.59 40.0 3.05e-01 70.0% 50.0%
3718671 304.55.2.0 a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like 0.59 40.0 2.88e-01 71.2% 48.2%
5022932 304.130.1.1 a+b two layers › Alpha-beta plaits › Uncharacterized protein MK0293 N-terminal domain › Uncharacterized protein MK0293 N-terminal domain › Ni_insertion 0.58 41.0 4.04e-01 73.8% 100.0%
4570129 2003.1.5.73 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.58 43.0 3.24e-01 77.5% 47.0%
3541719 11.1.1.96 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.58 40.0 3.47e-01 77.5% 46.4%
3330430 2003.1.5.19 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › TRM 0.57 47.0 3.28e-01 91.3% 84.0%
3555079 11.1.1.96 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.57 43.0 3.57e-01 81.2% 46.9%
5015738 304.8.1.82 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › PF27325 0.57 39.0 3.37e-01 78.8% 45.6%
4172598 304.8.1.5 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › NIL 0.57 40.0 3.61e-01 78.8% 52.6%
5041991 3501.1.1.0 a+b two layers › protein PCC1 › protein PCC1 › protein PCC1 0.56 37.0 3.59e-01 70.0% 60.0%
3554056 11.1.1.134 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › IL12p40_C 0.55 41.0 3.52e-01 78.8% 50.4%
4384958 2003.1.5.25 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GidB 0.55 42.0 2.98e-01 81.2% 33.3%
3274167 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.54 45.0 3.39e-01 95.0% 80.5%
3422204 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.54 42.0 3.46e-01 82.5% 59.3%
1933637 11.1.1.108 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.54 37.0 3.42e-01 80.0% 55.9%
3346014 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.54 40.0 2.78e-01 81.2% 56.6%
4419286 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.53 37.0 3.59e-01 77.5% 62.4%
4927268 3501.1.1.0 a+b two layers › protein PCC1 › protein PCC1 › protein PCC1 0.53 34.0 3.45e-01 71.2% 65.0%
3580185 3501.1.1.1 a+b two layers › protein PCC1 › protein PCC1 › protein PCC1 › Pcc1 0.53 36.0 3.48e-01 70.0% 61.1%
5038167 256.1.1.1 a+b two layers › MTH1598-like › MTH1598-like › MTH1598-like › Archease 0.53 41.0 3.62e-01 86.3% 75.0%
4328342 2003.1.5.3 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_2 0.52 35.0 2.49e-01 71.2% 28.8%
5036913 11.1.5.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.52 37.0 3.66e-01 77.5% 86.7%
4028975 2003.1.5.69 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GCD14 0.52 40.0 3.02e-01 82.5% 42.1%
3902949 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 43.0 3.15e-01 97.5% 73.4%
D2 medium residues 22-153
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.66 25.0 3.43e-01 96.2% 66.2%
5oj2B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 32.0 3.67e-01 90.2% 67.7%
6gp1A00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.59 25.0 3.31e-01 98.5% 73.8%
6m9yA00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.58 25.0 3.53e-01 97.7% 87.7%
1dq3A03 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.58 32.0 3.83e-01 95.5% 81.6%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 26.0 3.48e-01 96.2% 78.4%
2dchX02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.55 31.0 3.31e-01 94.7% 63.1%
4gs5A02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.54 31.0 3.39e-01 95.5% 68.6%
3ko2A00 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.54 32.0 3.02e-01 94.7% 46.6%
2g2sA00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.53 24.0 3.16e-01 98.5% 79.7%
4z1xA02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.53 31.0 3.06e-01 96.2% 51.7%
1rm6A03 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.53 30.0 3.07e-01 89.4% 53.8%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.53 20.0 2.64e-01 99.2% 56.3%
3c19A02 3.10.20.300 Alpha Beta › Roll › Ubiquitin-like (UB roll) › mk0293 like domain 0.53 28.0 3.47e-01 90.2% 84.6%
3i1iB01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 37.0 2.74e-01 74.2% 95.7%
3o2iA00 3.30.70.2710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 27.0 3.21e-01 90.2% 73.1%
5nqdA01 3.30.200.200 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › 0.50 31.0 2.82e-01 95.5% 45.3%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3218749 295.1.1.4 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › COMM_domain 0.63 21.0 3.09e-01 90.2% 65.0%
5014006 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.62 37.0 4.50e-01 100.0% 91.8%
4679545 242.1.1.1 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.59 33.0 3.35e-01 96.2% 53.3%
5011932 330.2.1.5 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.58 30.0 3.33e-01 100.0% 62.9%
5066423 242.1.1.1 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.58 31.0 3.41e-01 93.9% 61.8%
3596304 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 29.0 3.63e-01 100.0% 80.0%
4355163 242.1.1.1 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.57 32.0 3.28e-01 95.5% 53.4%
2411782 242.1.1.1 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_1 0.56 32.0 3.16e-01 94.7% 50.0%
1159602 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.55 31.0 3.30e-01 94.7% 62.5%
3989498 211.1.1.0 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.55 24.0 3.02e-01 98.5% 66.2%
4020440 7579.1.1.13 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › DLH 0.51 36.0 2.91e-01 74.2% 94.9%