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NC_025431.1__YP_009100103.1__Lo5R7ANS_56__00056

Bact-Vir

NC_025431.1__YP_009100103.1__Lo5R7ANS_56__00056

Identity

Accession:
NC_025431 ↗
Kingdom:
phage

Quality

71.0 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 1-141
PDB
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2dqaA00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.73 59.0 6.30e-01 91.5% 96.7%
3bkhA02 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.72 66.0 6.01e-01 97.9% 97.8%
4qdnA00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.70 54.0 5.86e-01 97.9% 97.5%
4dq5B00 1.10.530.50 Mainly Alpha › Orthogonal Bundle › Lysozyme › Peptidase U40 0.69 59.0 5.63e-01 90.1% 91.3%
4hjzA00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.69 63.0 5.71e-01 97.9% 92.3%
1qsaA03 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.68 63.0 5.87e-01 99.3% 89.0%
4c5fA02 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.68 62.0 5.81e-01 97.2% 98.8%
1hfxA00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.68 56.0 5.92e-01 100.0% 98.4%
4yibA01 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.67 62.0 5.95e-01 99.3% 91.8%
4kt3A00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.67 57.0 5.78e-01 100.0% 91.5%
7k5cB01 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.66 55.0 5.26e-01 87.9% 98.7%
153lA00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.66 60.0 5.51e-01 100.0% 76.8%
3fi7A01 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.65 54.0 5.61e-01 100.0% 94.6%
3w6bB00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.65 59.0 5.73e-01 98.6% 92.2%
1k87A02 1.10.2060.10 Mainly Alpha › Orthogonal Bundle › PutA proline dehydrogenase (PRODH), domain 2 › PutA proline dehydrogenase (PRODH), domain 2 0.60 32.0 3.60e-01 100.0% 64.2%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.59 28.0 3.65e-01 70.9% 79.7%
1ichA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.57 35.0 4.20e-01 90.1% 97.7%
2dbdA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.53 32.0 3.63e-01 91.5% 77.6%
2dbhA01 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.53 30.0 3.88e-01 92.2% 98.7%
1dgnA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.53 32.0 3.83e-01 79.4% 93.3%
3fyaB00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.53 30.0 3.78e-01 90.8% 100.0%
3ungC04 1.20.120.1260 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-Cas system, Cmr2 subunit, D4 domain, six-helix bundle 0.53 26.0 3.00e-01 70.2% 62.9%
1wxpA01 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.52 31.0 3.85e-01 91.5% 98.8%
4dwnA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.52 32.0 3.77e-01 83.7% 89.7%
2ahoB02 1.10.150.190 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Translation initiation factor 2; subunit 1; domain 2 0.50 30.0 3.61e-01 85.8% 91.2%
3cymA03 1.10.150.80 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › HRDC domain 0.50 31.0 3.68e-01 90.1% 95.5%
1cy5A00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.50 30.0 3.54e-01 89.4% 88.0%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3964630 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.77 62.0 5.86e-01 100.0% 72.0%
3945171 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.75 64.0 6.35e-01 97.9% 87.6%
3587750 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.72 52.0 6.00e-01 89.4% 100.0%
3947473 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.71 62.0 6.14e-01 97.9% 88.0%
4431057 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.70 65.0 6.48e-01 99.3% 96.6%
3985073 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.70 62.0 6.32e-01 98.6% 98.5%
3205219 235.1.1.0 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.69 62.0 5.77e-01 95.0% 78.2%
3970721 235.1.1.0 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.69 64.0 5.96e-01 100.0% 89.1%
3692876 235.1.1.0 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.69 63.0 5.76e-01 97.2% 82.2%
2393514 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.69 64.0 5.76e-01 100.0% 91.1%
3385979 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.69 63.0 5.70e-01 98.6% 76.3%
3978377 235.1.1.0 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.69 64.0 5.68e-01 100.0% 87.2%
3720940 235.1.1.0 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.69 61.0 5.69e-01 96.5% 77.1%
4321901 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.69 63.0 5.76e-01 100.0% 91.4%
4164050 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.69 63.0 5.55e-01 100.0% 82.9%
4515466 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.68 63.0 5.81e-01 100.0% 96.1%
3944103 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.68 63.0 5.81e-01 100.0% 88.9%
3941811 235.1.1.32 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT, PF27553 0.68 63.0 5.89e-01 99.3% 90.0%
4258903 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.68 58.0 5.49e-01 90.1% 94.5%
3166094 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.68 63.0 5.82e-01 100.0% 97.7%
3691757 235.1.1.0 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.68 61.0 5.15e-01 97.2% 67.4%
3971115 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.68 62.0 5.86e-01 100.0% 94.1%
3969917 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.68 63.0 5.53e-01 100.0% 80.0%
3965879 235.1.1.32 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT, PF27553 0.67 62.0 5.85e-01 99.3% 88.5%
1086527 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.67 57.0 5.78e-01 100.0% 91.5%
3989161 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.67 54.0 5.10e-01 99.3% 70.6%
3582448 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.67 54.0 5.62e-01 92.2% 92.3%
3838879 235.1.1.9 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT 0.66 61.0 6.01e-01 100.0% 94.0%
4821783 235.1.1.2 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glyco_hydro_19 0.66 59.0 5.37e-01 95.0% 98.3%
3222819 235.1.1.12 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Destabilase 0.64 54.0 5.67e-01 89.4% 98.4%
3731869 235.1.1.0 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.64 59.0 5.26e-01 100.0% 85.1%
3245104 235.1.1.12 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Destabilase 0.63 52.0 5.52e-01 97.2% 99.2%
3728943 235.1.1.0 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like 0.63 51.0 4.83e-01 95.7% 71.8%
4007762 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.62 58.0 5.36e-01 100.0% 86.1%
4680920 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.62 57.0 5.56e-01 99.3% 96.1%
1693577 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.62 56.0 4.73e-01 98.6% 60.4%
3285050 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.60 56.0 5.28e-01 100.0% 95.2%
3590542 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.60 56.0 5.37e-01 100.0% 92.5%
4520768 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.60 56.0 5.23e-01 100.0% 87.6%
4443068 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.58 53.0 4.53e-01 100.0% 62.2%
3508049 235.1.1.10 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.58 53.0 5.17e-01 100.0% 92.3%
3877052 235.1.1.31 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › PF31087 0.53 46.0 4.33e-01 100.0% 77.6%
D2 high residues 582-727
PDB
D3 medium residues 219-289
PDB
D4 medium residues 364-388_407-463_749-802
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.67 34.0 4.37e-01 73.5% 83.5%
6dv2G02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.67 33.0 3.01e-01 81.6% 34.8%
2kobA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.60 31.0 3.72e-01 77.9% 73.1%
5cwhA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.59 33.0 3.21e-01 81.6% 47.4%
2i2xB01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.56 32.0 3.61e-01 79.4% 74.0%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4945453 2003.1.1.36 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › 3HCDH_N 0.69 34.0 3.03e-01 81.6% 34.6%
3364093 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.67 29.0 3.99e-01 74.3% 81.5%
4883934 2003.1.1.155 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › 3HCDH_N, F420_oxidored 0.66 33.0 2.98e-01 81.6% 35.7%
3841169 186.2.1.1 alpha arrays › lambda integrase-N-like › VEFS domain › VEFS domain › VEFS-Box 0.61 37.0 3.53e-01 77.9% 51.0%
3598051 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 34.0 3.60e-01 81.6% 60.0%
3475614 186.2.1.1 alpha arrays › lambda integrase-N-like › VEFS domain › VEFS domain › VEFS-Box 0.60 37.0 3.85e-01 77.9% 64.6%
3959087 106.1.1.0 alpha arrays › Globin-like › Globin-like › Globin-like 0.54 37.0 3.65e-01 81.6% 63.3%
4959096 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.52 36.0 3.63e-01 81.6% 70.4%
3452753 109.4.1.70 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CID 0.52 33.0 3.07e-01 81.6% 49.7%
5075503 633.21.1.0 alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.51 32.0 3.43e-01 99.3% 70.8%
D5 medium residues 1062-1143
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7dswA01 1.20.1530.20 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › 0.67 50.0 3.19e-01 79.3% 18.3%
1aepA00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.66 58.0 4.77e-01 98.8% 91.5%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.63 47.0 4.88e-01 97.6% 83.3%
2fiwA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.60 40.0 3.19e-01 92.7% 35.0%
1wn0A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.60 50.0 4.24e-01 89.0% 84.7%
3bg2A01 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.58 45.0 3.49e-01 84.1% 38.1%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.57 51.0 4.43e-01 98.8% 93.7%
5gl7A01 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.56 47.0 3.86e-01 98.8% 94.6%
1ny9A00 1.10.490.50 Mainly Alpha › Orthogonal Bundle › Globin-like › Antibiotic binding domain of TipA-like multidrug resistance regulators 0.54 36.0 3.47e-01 92.7% 59.6%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4664276 589.1.2.1 alpha arrays › Triger factor/SurA peptide-binding domain-like › Triger factor/SurA peptide-binding domain-like › TF C-terminus (Pfam 05698) › Trigger_C 0.62 45.0 3.42e-01 97.6% 32.3%
4950461 1079.1.1.5 alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › DsbD_2 0.61 54.0 3.99e-01 97.6% 73.3%
3982352 4207.1.2.90 alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region › FxsA 0.61 49.0 4.52e-01 89.0% 73.6%
3991181 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.59 48.0 3.54e-01 92.7% 60.0%