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NC_041861.1__YP_009592507.1__FDG77_gp66__00066

Bact-Vir

NC_041861.1__YP_009592507.1__FDG77_gp66__00066

Identity

Accession:
NC_041861 ↗
Kingdom:
phage

Quality

87.9 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 3-58
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.74 64.0 5.83e-01 100.0% 72.4%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.72 62.0 5.62e-01 100.0% 72.4%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.70 54.0 5.15e-01 100.0% 71.6%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.67 55.0 4.59e-01 98.2% 53.2%
3lqmA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 45.0 3.78e-01 100.0% 40.2%
5kfzA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.64 53.0 4.24e-01 98.2% 49.6%
1d0nA05 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.64 38.0 3.20e-01 98.2% 33.3%
1alo006 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.63 46.0 3.68e-01 82.1% 56.3%
1n26A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 45.0 3.70e-01 100.0% 41.3%
3hvnA01 3.90.840.10 Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain 0.61 50.0 3.69e-01 98.2% 32.6%
4faoC00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.60 40.0 3.70e-01 100.0% 52.0%
2vtfA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.60 51.0 3.64e-01 98.2% 31.1%
4yrdA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.60 40.0 3.25e-01 100.0% 33.6%
5e55B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 44.0 3.82e-01 100.0% 49.5%
1t4aA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.60 49.0 4.50e-01 98.2% 94.9%
3ir9A02 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.60 44.0 3.47e-01 100.0% 37.5%
3lb6C01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 40.0 3.60e-01 100.0% 46.6%
2hj1A00 3.10.20.280 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RnfH-like 0.59 48.0 4.38e-01 100.0% 67.5%
3o2iA00 3.30.70.2710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 41.0 3.51e-01 73.2% 69.9%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.59 43.0 4.13e-01 100.0% 69.7%
5koxA02 3.30.70.2450 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 48.0 4.28e-01 98.2% 93.0%
1f6fB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 40.0 3.52e-01 100.0% 44.3%
1cttA02 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.57 47.0 3.88e-01 100.0% 52.2%
6grqA05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 43.0 3.69e-01 98.2% 49.5%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.56 48.0 3.06e-01 100.0% 95.5%
3b8fB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.55 42.0 3.32e-01 98.2% 35.9%
3loiA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 39.0 2.86e-01 100.0% 27.5%
6le1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 37.0 3.48e-01 71.4% 100.0%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 44.0 3.87e-01 100.0% 97.9%
2o6cA00 2.60.40.2480 Mainly Beta › Sandwich › Immunoglobulin-like › Periplasmic metal-binding protein Tp34-type 0.54 40.0 3.07e-01 100.0% 31.0%
3pbkA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.54 46.0 3.76e-01 98.2% 52.8%
4hfqA02 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.53 44.0 3.45e-01 100.0% 57.6%
1l1lA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.53 46.0 2.69e-01 96.4% 21.7%
4m8rA01 2.60.40.3920 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 44.0 3.73e-01 98.2% 53.4%
2ajgA00 3.90.740.10 Alpha Beta › Alpha-Beta Complex › Isoleucyl-tRNA Synthetase; domain 2 › Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain 0.53 43.0 3.13e-01 98.2% 94.6%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.53 40.0 2.99e-01 98.2% 29.3%
4qpwA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 45.0 3.42e-01 100.0% 51.4%
2z5bA00 3.30.230.100 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.50 43.0 3.35e-01 96.4% 66.1%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5081134 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.79 60.0 5.96e-01 100.0% 78.3%
4939739 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.76 68.0 6.70e-01 100.0% 93.2%
4967222 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.76 67.0 6.61e-01 100.0% 91.7%
2831852 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.76 66.0 5.44e-01 100.0% 54.5%
4013514 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.74 64.0 5.23e-01 100.0% 52.4%
4084879 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.74 66.0 5.72e-01 100.0% 69.4%
5067865 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.73 64.0 5.95e-01 100.0% 78.6%
2106285 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.73 63.0 5.09e-01 100.0% 50.9%
4128974 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.72 64.0 5.71e-01 100.0% 73.8%
4937773 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.72 62.0 6.19e-01 100.0% 94.8%
4990637 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.72 58.0 5.16e-01 100.0% 61.4%
5065436 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.72 62.0 5.98e-01 100.0% 85.9%
5039449 302.4.1.0 a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.72 56.0 4.61e-01 100.0% 46.7%
4199730 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.70 61.0 5.03e-01 100.0% 54.3%
4969863 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.70 60.0 5.49e-01 100.0% 73.3%
3184769 302.4.1.0 a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.69 56.0 4.47e-01 100.0% 44.3%
4005437 304.3.1.17 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › Sec_GG 0.68 58.0 4.99e-01 98.2% 86.7%
4952416 304.51.1.1 a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas_Cas6_C 0.67 48.0 3.66e-01 75.0% 49.6%
4945976 302.4.1.1 a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › Hydant_A_C 0.67 56.0 4.49e-01 100.0% 45.0%
3935630 3346.1.1.0 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 0.66 49.0 3.43e-01 83.9% 68.8%
3565481 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.66 49.0 4.10e-01 100.0% 44.8%
4983643 302.4.1.1 a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › Hydant_A_C 0.65 54.0 4.53e-01 100.0% 51.4%
3647799 302.4.1.0 a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.65 52.0 4.18e-01 100.0% 44.3%
5053865 821.1.1.0 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.65 56.0 4.77e-01 100.0% 60.0%
3943893 304.28.1.2 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Sec_GG 0.64 53.0 4.62e-01 98.2% 82.1%
3242873 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 46.0 3.74e-01 98.2% 39.1%
3885081 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.64 46.0 4.01e-01 98.2% 47.4%
3933380 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.64 53.0 4.31e-01 98.2% 47.8%
4634055 219.1.1.76 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF553 0.62 54.0 3.78e-01 100.0% 70.5%
3397739 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 45.0 3.98e-01 100.0% 52.9%
3505737 230.5.1.0 a+b two layers › T-fold › Band 7/SPFH domain › Band 7/SPFH domain 0.60 48.0 4.07e-01 91.1% 65.3%
4031235 3986.2.1.2 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd › DUF2922 0.59 50.0 4.70e-01 98.2% 81.4%
3608234 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.59 47.0 3.75e-01 96.4% 40.7%
3640841 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.59 48.0 3.00e-01 100.0% 13.9%
3600513 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.59 48.0 3.93e-01 100.0% 46.7%
2132899 2492.1.1.20 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › APOBEC3 0.58 46.0 3.34e-01 100.0% 28.4%
4152762 2492.1.1.20 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › APOBEC3 0.58 45.0 3.26e-01 98.2% 26.8%
3905094 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.58 48.0 3.77e-01 100.0% 45.2%
3339933 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 0.57 49.0 3.22e-01 100.0% 22.3%
3891099 11.1.1.99 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set 0.57 47.0 3.60e-01 98.2% 38.6%
3514371 2492.1.1.0 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.57 46.0 3.18e-01 94.6% 24.7%
4956457 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.56 41.0 4.32e-01 98.2% 90.0%
3270012 10.32.1.18 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Endotoxin_C 0.56 46.0 3.55e-01 98.2% 55.9%
3970070 221.4.1.0 a+b two layers › beta-Grasp › Nudix › Nudix 0.55 45.0 3.54e-01 98.2% 60.0%
4927303 525.1.1.1 a+b two layers › Urease, gamma-subunit › Urease, gamma-subunit › Urease, gamma-subunit › Urease_gamma 0.55 45.0 3.72e-01 100.0% 84.2%
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 0.55 47.0 3.14e-01 100.0% 22.8%
4945274 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 40.0 3.17e-01 82.1% 78.4%
4960572 10.1.2.0 beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.54 45.0 3.33e-01 100.0% 48.5%
4344712 284.1.3.1 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.53 42.0 3.72e-01 100.0% 58.0%
3830169 109.4.1.1383 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.52 39.0 2.22e-01 85.7% 15.3%
3480076 11.1.1.179 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.52 43.0 3.32e-01 98.2% 56.2%
3385387 109.4.1.1521 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase, Eplus_motif, E_motif 0.52 40.0 2.31e-01 85.7% 17.4%
3808573 109.4.1.3485 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, DYW_deaminase, Eplus_motif, E_motif 0.52 39.0 2.39e-01 85.7% 24.1%
3285401 3986.2.1.0 a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.52 37.0 3.53e-01 100.0% 62.7%
3273274 10.2.1.0 beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.51 42.0 2.98e-01 100.0% 68.2%
3601299 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 38.0 3.06e-01 85.7% 84.0%
3788129 284.1.3.1 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.50 41.0 3.82e-01 98.2% 73.3%