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NC_054965.1__YP_010078886.1__KMC53_gp71__00071

Bact-Vir

NC_054965.1__YP_010078886.1__KMC53_gp71__00071

Identity

Accession:
NC_054965 ↗
Kingdom:
phage

Quality

85.6 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 37-88
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3jtzA00 3.30.160.390 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Integrase, DNA-binding domain 0.91 82.0 7.01e-01 100.0% 64.9%
4oxwA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.67 58.0 4.67e-01 100.0% 73.6%
1xteA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.66 56.0 4.43e-01 100.0% 68.1%
2o95B00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.64 46.0 3.27e-01 80.8% 33.0%
5zc1D00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 48.0 3.97e-01 92.3% 44.9%
2obdA01 3.15.20.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 2 › Bactericidal permeability-increasing protein; domain 2 0.62 47.0 2.93e-01 80.8% 39.9%
4gnxC03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 49.0 3.57e-01 100.0% 50.8%
1okjB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.61 44.0 3.46e-01 100.0% 33.9%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 48.0 3.67e-01 100.0% 35.6%
6v04A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.60 41.0 3.24e-01 75.0% 94.5%
2el8A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.59 47.0 4.11e-01 100.0% 70.3%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.58 48.0 3.79e-01 100.0% 42.4%
4aghA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.58 38.0 3.46e-01 71.2% 52.5%
6nhsA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.57 46.0 3.12e-01 98.1% 81.6%
1d5aA01 3.30.342.10 Alpha Beta › 2-Layer Sandwich › DNA Polymerase; Chain A, domain 1 › DNA Polymerase, chain B, domain 1 0.57 47.0 3.51e-01 100.0% 82.8%
4oddA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 40.0 3.00e-01 76.9% 83.2%
1mhxA00 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 39.0 3.78e-01 76.9% 61.5%
1mpgA01 3.30.310.20 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › DNA-3-methyladenine glycosylase AlkA, N-terminal domain 0.56 39.0 3.15e-01 75.0% 74.1%
1te5A00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.56 45.0 2.90e-01 90.4% 48.2%
2k75A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 40.0 3.27e-01 92.3% 38.8%
6baoA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 45.0 3.38e-01 92.3% 45.5%
2vf9A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.56 46.0 3.62e-01 100.0% 51.9%
1h0hB01 3.30.70.20 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 40.0 2.93e-01 76.9% 76.7%
1ah5A03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.56 45.0 3.99e-01 100.0% 61.6%
2veaA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 45.0 3.43e-01 92.3% 46.2%
7xinA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.56 41.0 3.36e-01 82.7% 93.6%
2hj1A00 3.10.20.280 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RnfH-like 0.55 38.0 3.47e-01 76.9% 50.6%
1f2uB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 36.0 2.68e-01 80.8% 24.1%
2d8bA01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.54 42.0 3.31e-01 98.1% 54.3%
1ln1A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 43.0 3.04e-01 100.0% 78.8%
4ebrA00 3.30.1460.50 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.54 41.0 3.14e-01 96.2% 85.4%
1aq3A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.54 43.0 3.44e-01 100.0% 51.9%
4ckbD03 2.40.50.830 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 45.0 3.45e-01 100.0% 86.6%
3md7A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.52 42.0 2.68e-01 98.1% 17.4%
2cy5A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 41.0 3.28e-01 96.2% 39.5%
4e1oA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 42.0 3.59e-01 100.0% 88.8%
3zugB02 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.52 35.0 2.68e-01 71.2% 64.8%
4c23B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 39.0 2.72e-01 92.3% 59.0%
1e5pA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 36.0 2.80e-01 78.8% 83.2%
1khiA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.52 39.0 3.54e-01 100.0% 58.7%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 40.0 3.79e-01 100.0% 76.1%
2l33A00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 35.0 2.97e-01 94.2% 41.8%
5c94A00 2.40.10.250 Mainly Beta › Beta Barrel › Thrombin, subunit H › Replicase NSP9 0.50 41.0 3.30e-01 98.1% 81.0%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.50 40.0 3.71e-01 100.0% 74.3%
2qm4A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.50 38.0 2.78e-01 82.7% 87.4%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3984933 252.2.1.5 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_3 0.87 77.0 6.32e-01 100.0% 55.6%
4009814 252.2.1.5 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_3 0.87 76.0 7.06e-01 100.0% 76.9%
136649 252.2.1.5 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_3 0.87 77.0 6.17e-01 100.0% 52.6%
3942150 252.2.1.5 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_3 0.85 75.0 6.14e-01 100.0% 55.6%
4007983 252.2.1.5 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_3 0.83 70.0 5.74e-01 100.0% 51.6%
3793090 2004.1.1.87 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.75 56.0 3.27e-01 80.8% 10.8%
3580295 2004.1.1.198 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.74 56.0 3.87e-01 82.7% 24.0%
5080802 252.2.1.0 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.73 63.0 6.11e-01 100.0% 98.3%
5029914 252.2.1.0 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.69 56.0 5.57e-01 94.2% 96.4%
3587376 386.1.1.344 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › Arm-DNA-bind_4 0.66 53.0 5.26e-01 98.1% 98.2%
3787176 4099.1.1.4 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › CENP-O 0.65 53.0 4.13e-01 100.0% 85.4%
3554073 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.64 54.0 4.16e-01 100.0% 60.0%
3705431 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.63 52.0 4.21e-01 100.0% 49.6%
3701914 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.61 49.0 4.21e-01 98.1% 54.7%
3608102 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.61 52.0 4.75e-01 98.1% 74.3%
4949986 220.1.1.219 beta barrels › PH domain-like › PH domain-like › PH domain-like › CheF-arch 0.60 48.0 3.98e-01 100.0% 46.4%
5001733 881.1.1.0 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.60 46.0 3.48e-01 98.1% 32.4%
4988451 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.59 48.0 3.94e-01 100.0% 47.0%
4025734 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.59 49.0 3.30e-01 100.0% 23.6%
5019514 881.2.1.0 a+b three layers › Mog1p/PsbP-like › TM1622-like › TM1622-like 0.59 45.0 3.42e-01 92.3% 31.7%
3225194 11.10.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like 0.59 49.0 3.79e-01 100.0% 75.4%
3737620 5.1.5.4 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › DPPIV_N 0.59 46.0 2.75e-01 96.2% 20.8%
3289254 220.1.1.82 beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_6 0.58 47.0 3.99e-01 98.1% 53.7%
4018864 5084.5.3.0 beta barrels › Outer membrane meander beta-barrels › Porins › Ligand-gated protein channel 0.57 46.0 2.68e-01 100.0% 8.7%
5007104 220.1.1.219 beta barrels › PH domain-like › PH domain-like › PH domain-like › CheF-arch 0.57 45.0 3.74e-01 96.2% 45.7%
5073525 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.57 48.0 3.75e-01 100.0% 41.6%
4965501 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.57 45.0 3.97e-01 100.0% 56.7%
3237889 7504.1.1.0 a/b three-layered sandwiches › ITPase-like › ITPase-like › ITPase-like 0.57 44.0 3.24e-01 100.0% 55.7%
4999755 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 47.0 3.56e-01 100.0% 45.1%
3825621 3459.1.1.3 beta sandwiches › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › DUF868 0.56 48.0 4.01e-01 100.0% 78.9%
3796107 227.1.1.1 a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.56 35.0 3.01e-01 71.2% 35.6%
5000550 5.1.4.43 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › FG-GAP_3 0.56 46.0 2.85e-01 94.2% 21.2%
4365325 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.56 45.0 3.98e-01 100.0% 60.0%
4182376 323.1.1.25 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › SIDD_N 0.56 45.0 3.33e-01 100.0% 35.3%
4976046 2004.1.1.73 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.56 47.0 3.39e-01 100.0% 76.2%
4068344 7579.1.1.6 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.56 43.0 2.79e-01 100.0% 16.1%
5016315 220.1.1.219 beta barrels › PH domain-like › PH domain-like › PH domain-like › CheF-arch 0.55 42.0 3.45e-01 98.1% 40.0%
3722420 2008.1.1.143 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF7924 0.55 47.0 3.39e-01 100.0% 34.4%
5012583 11.1.4.106 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › PEGA 0.55 38.0 2.83e-01 73.1% 26.1%
3179468 330.1.1.18 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DSRM_DHX29 0.55 43.0 3.27e-01 100.0% 66.9%
3508049 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.54 40.0 3.02e-01 86.5% 67.7%
3259407 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 43.0 3.89e-01 100.0% 65.9%
4120507 292.2.1.1 a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › POLO_box 0.54 38.0 3.30e-01 82.7% 42.1%
4965393 802.1.1.1 a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 › BFN_dom 0.54 41.0 3.52e-01 98.1% 48.9%
4651639 2484.1.1.36 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.53 41.0 2.47e-01 84.6% 65.0%
4639471 2004.1.1.73 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.53 45.0 3.20e-01 100.0% 53.7%
4490186 5001.1.1.1 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.52 41.0 2.60e-01 96.2% 33.0%
4940586 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 42.0 3.40e-01 100.0% 66.7%
4505972 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.52 44.0 2.77e-01 98.1% 53.4%
5037301 2.1.1.111 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ssb-like_OB 0.52 39.0 3.32e-01 92.3% 46.8%
4609498 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.52 42.0 3.80e-01 98.1% 72.5%
3231216 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 33.0 3.41e-01 92.3% 68.0%
3970479 809.1.1.0 a+b two layers › BLIP-like › beta-lactamase-inhibitor protein, BLIP › beta-lactamase-inhibitor protein, BLIP 0.51 36.0 3.33e-01 78.8% 54.7%
3603247 2.1.1.15 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.51 40.0 3.32e-01 100.0% 70.8%
4990980 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.51 34.0 2.92e-01 73.1% 51.6%
3850966 3346.1.1.1 a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › UfSP2_N 0.51 38.0 2.57e-01 90.4% 88.8%
3334359 221.4.1.1 a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.51 36.0 2.64e-01 82.7% 25.0%
3247700 209.1.1.0 a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like 0.50 36.0 2.73e-01 76.9% 31.7%
3650158 221.4.1.0 a+b two layers › beta-Grasp › Nudix › Nudix 0.50 36.0 2.96e-01 78.8% 48.6%