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NC_020835.1__YP_007672691.1__PROG_00041__00038

Bact-Vir

NC_020835.1__YP_007672691.1__PROG_00041__00038

Identity

Accession:
NC_020835 ↗
Kingdom:
phage

Quality

59.7 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 1-70
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ednA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.61 53.0 4.31e-01 97.1% 71.6%
2r2dA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.59 45.0 3.10e-01 84.3% 98.9%
1nrjA00 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.56 38.0 3.05e-01 71.4% 100.0%
4gw9A02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 39.0 3.61e-01 77.1% 75.0%
1vpkA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.53 38.0 3.27e-01 77.1% 83.2%
3r7wB02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 37.0 3.17e-01 77.1% 45.8%
3bxwA03 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.51 29.0 3.16e-01 97.1% 67.3%
4ffgA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.50 43.0 2.81e-01 97.1% 95.4%
1q8iA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.50 42.0 3.21e-01 98.6% 40.0%
1cruA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.50 39.0 2.50e-01 92.9% 46.9%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4508406 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.63 42.0 3.74e-01 81.4% 46.7%
4977215 304.117.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC 0.59 38.0 4.12e-01 98.6% 78.3%
3737473 223.2.1.8 a+b three layers › Profilin-like › profilin-like › profilin-like › Sybindin 0.57 43.0 3.37e-01 81.4% 83.9%
3884500 6129.1.1.1 beta barrels › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › VWD 0.56 41.0 3.06e-01 82.9% 57.7%
1680485 4963.1.2.1 alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal domain in vesicular stomatitis virus RNA polymerase L › Mononeg_RNA_pol 0.56 42.0 2.73e-01 82.9% 50.7%
3319006 101.1.2.497 alpha arrays › HTH › HTH › winged helix domain › PF25874 0.55 47.0 4.08e-01 95.7% 73.6%
3395491 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.55 46.0 3.58e-01 97.1% 52.4%
3404837 7585.1.1.0 a/b three-layered sandwiches › Rossmann-like domains in Sec1/munc18-like proteins › Rossmann-like domains in Sec1/munc18-like proteins › Rossmann-like domains in Sec1/munc18-like proteins 0.55 45.0 3.61e-01 95.7% 52.9%
3230503 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.55 43.0 3.28e-01 91.4% 37.9%
3405581 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.54 47.0 3.61e-01 97.1% 51.5%
4944777 2011.1.1.0 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases 0.52 44.0 3.04e-01 100.0% 85.8%
3989230 2011.1.1.11 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M42 0.51 41.0 3.00e-01 98.6% 83.1%
3957726 222.1.1.12 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › PS-DH 0.51 39.0 3.02e-01 87.1% 81.1%
3585719 2484.1.1.1 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.51 40.0 2.95e-01 87.1% 55.6%
3535572 239.3.1.1 beta barrels › Ribosomal protein L25-like › FAS1 domain › FAS1 domain › Fasciclin 0.51 41.0 3.37e-01 92.9% 72.9%
5046158 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.50 38.0 2.88e-01 87.1% 47.5%
D2 high residues 105-244
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2hc5A01 3.30.160.170 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › FlaG-like 0.68 34.0 4.03e-01 75.0% 68.4%
4mtnA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.58 30.0 3.58e-01 74.3% 72.6%
3o8eD02 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.54 24.0 3.53e-01 79.3% 95.0%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3388135 4292.2.1.1 a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain › FlaG 0.70 35.0 4.61e-01 72.9% 89.3%
5028555 4292.2.1.0 a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.65 32.0 4.49e-01 70.0% 100.0%
4313114 378.1.1.30 few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › PF30178 0.63 39.0 4.22e-01 81.4% 72.5%
4618205 604.1.1.150 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF28954 0.59 23.0 2.53e-01 75.7% 42.5%
D3 medium residues 256-411
PDB
Domain cluster: representative
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1y9wA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.67 44.0 5.25e-01 95.5% 100.0%
2fl4A02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.66 44.0 5.18e-01 94.9% 100.0%
2bkyX00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.64 36.0 4.66e-01 75.6% 100.0%
1vm0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.62 36.0 4.46e-01 76.3% 94.6%
3g6sA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.60 51.0 4.28e-01 91.0% 70.5%
1akoA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.60 51.0 4.27e-01 91.7% 74.3%
1tigA00 3.30.110.10 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Translation initiation factor 3 (IF-3), C-terminal domain 0.59 35.0 4.37e-01 98.1% 100.0%
3iabB01 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.59 36.0 4.42e-01 84.0% 96.0%
3dnsA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 46.0 4.99e-01 100.0% 100.0%
3ngqA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.57 49.0 3.87e-01 93.6% 78.8%
3tebB00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.56 49.0 4.15e-01 96.8% 75.8%
2ob0C01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 47.0 4.74e-01 94.9% 90.7%
4kvxA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 47.0 4.81e-01 92.9% 97.4%
4rcnB03 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.54 44.0 3.80e-01 87.2% 85.4%
4fvaC00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 47.0 4.04e-01 94.9% 61.8%
2qmlA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 49.0 4.60e-01 100.0% 94.8%
3hrzB01 2.20.130.20 Mainly Beta › Single Sheet › S-adenosyl-L-methionine-dependent methyltransferases › 0.54 24.0 3.28e-01 98.1% 82.9%
2x7bA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 46.0 4.64e-01 92.3% 95.5%
3prbA03 3.30.70.2210 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 28.0 3.68e-01 87.8% 100.0%
3vg8A00 3.30.200.270 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › 0.54 33.0 3.97e-01 78.8% 92.4%
4gt4B01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 26.0 3.36e-01 85.9% 83.3%
1ufhA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 42.0 4.29e-01 86.5% 96.1%
2fe7B00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 40.0 3.95e-01 81.4% 83.7%
3i9sA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 39.0 3.89e-01 81.4% 86.3%
3evzA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 43.0 4.30e-01 100.0% 88.6%
3if8B03 6.20.270.10 Special › Other non-globular › Carboxypeptidase Inhibitor; Chain A › 0.50 18.0 2.74e-01 78.8% 78.3%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3659884 328.5.1.0 a+b two layers › IF3-like › SirA-like › SirA-like 0.63 35.0 4.18e-01 97.4% 80.0%
5041736 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.62 28.0 3.93e-01 79.5% 88.0%
3514938 213.1.1.6 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › ODC_AZ 0.62 45.0 5.08e-01 96.8% 98.3%
3689000 246.3.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos 0.61 52.0 4.07e-01 91.7% 71.0%
3596783 328.1.1.0 a+b two layers › IF3-like › AlbA-like › AlbA-like 0.61 37.0 4.16e-01 98.1% 80.0%
3725989 246.3.1.0 a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like 0.60 51.0 4.09e-01 91.7% 68.6%
3901049 328.3.1.0 a+b two layers › IF3-like › Translation initiation factor IF3, C-terminal domain › Translation initiation factor IF3, C-terminal domain 0.59 35.0 4.04e-01 99.4% 80.9%
3580425 328.3.1.0 a+b two layers › IF3-like › Translation initiation factor IF3, C-terminal domain › Translation initiation factor IF3, C-terminal domain 0.58 35.0 3.99e-01 100.0% 80.9%
3642653 12.1.1.36 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › GHD 0.58 24.0 3.36e-01 84.6% 77.3%
3630902 213.1.1.6 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › ODC_AZ 0.57 46.0 4.87e-01 96.8% 95.7%
4018340 246.3.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos 0.57 49.0 4.49e-01 95.5% 80.0%
3784681 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.56 49.0 4.31e-01 94.9% 96.2%
4020677 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.56 46.0 4.90e-01 92.9% 100.0%
4022277 328.1.1.3 a+b two layers › IF3-like › AlbA-like › AlbA-like › Rpp20 0.55 37.0 4.27e-01 90.4% 94.7%
None 0.54 47.0 4.54e-01 92.9% 96.6%
3735546 213.1.1.25 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.54 50.0 4.30e-01 100.0% 89.8%
4243267 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.54 27.0 2.33e-01 93.6% 28.0%
4011724 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.54 44.0 4.13e-01 87.2% 79.5%
3673212 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.53 44.0 3.77e-01 99.4% 55.2%
5064883 328.1.1.0 a+b two layers › IF3-like › AlbA-like › AlbA-like 0.53 43.0 3.86e-01 87.2% 69.3%
4252267 213.1.1.7 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › FemAB 0.53 46.0 4.42e-01 93.6% 81.7%
4083421 2003.1.5.23 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_4 0.53 47.0 4.24e-01 96.8% 84.2%
4026790 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.53 47.0 3.88e-01 96.8% 62.1%
3948917 213.1.1.25 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.53 47.0 4.61e-01 100.0% 98.9%
3398633 224.1.1.2 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.53 36.0 3.88e-01 85.3% 80.7%
None 0.52 47.0 4.20e-01 100.0% 72.3%
3605286 2008.2.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.52 32.0 3.84e-01 92.3% 96.0%
3833803 2003.1.5.115 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_29 0.51 45.0 3.42e-01 98.1% 55.2%
3449915 2003.1.5.46 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › MTS 0.51 46.0 3.70e-01 100.0% 63.8%
4478130 2003.1.5.17 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_5 0.51 45.0 4.23e-01 96.2% 89.4%
3387423 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.51 43.0 4.23e-01 95.5% 85.5%
4063958 2003.1.5.17 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_5 0.51 44.0 4.13e-01 96.2% 83.5%
3635611 328.1.1.3 a+b two layers › IF3-like › AlbA-like › AlbA-like › Rpp20 0.51 39.0 4.05e-01 86.5% 87.4%
4309637 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.51 27.0 3.35e-01 96.2% 89.3%
4029063 2003.1.5.5 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0020 0.51 45.0 3.93e-01 97.4% 87.2%