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MZ422438.1__QXN67958.1__FPHOBKDP_00208__00204

Bact-Vir

MZ422438.1__QXN67958.1__FPHOBKDP_00208__00204

Identity

Accession:
MZ422438 ↗
Kingdom:
phage

Quality

54.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Listeria_phage_LPJP1

TaxID: 2852115

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 230-390_409-421
PDB
D2 high residues 448-600
PDB
D3 high residues 782-852
PDB
Domain cluster: rep: LC680885.1__BDE75681.1__X__00143__D376-440
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01471.24 best PG_binding_1 30.8 3.70e-07 85.9% 94.7%
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4c2dA02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.93 80.0 7.45e-01 100.0% 75.3%
3bkhA01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.90 77.0 7.17e-01 100.0% 74.4%
4g54A02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.89 76.0 7.61e-01 100.0% 88.9%
1lbuA01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.86 77.0 7.20e-01 100.0% 79.8%
4bolA02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.86 65.0 6.27e-01 85.9% 71.2%
1ck7A01 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.82 60.0 4.05e-01 84.5% 23.0%
1eakA01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.81 60.0 6.36e-01 85.9% 87.3%
7aj9A01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.80 63.0 6.51e-01 87.3% 89.6%
4bthA00 1.10.439.10 Mainly Alpha › Orthogonal Bundle › Penicillin Amidohydrolase; domain 1 › Penicillin Amidohydrolase, domain 1 0.66 46.0 3.54e-01 73.2% 73.8%
2m4eA00 1.20.120.1930 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein PF16691 family 0.63 49.0 4.69e-01 88.7% 82.6%
2ef8A00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.59 45.0 4.28e-01 83.1% 88.1%
2jifA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.57 40.0 3.17e-01 74.6% 92.2%
1vw4801 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.54 38.0 3.82e-01 74.6% 80.8%
3fnrA02 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.54 40.0 2.67e-01 81.7% 83.9%
8f2lE01 1.10.1740.110 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.52 37.0 3.33e-01 74.6% 92.9%
2l0rA00 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.51 41.0 3.66e-01 90.1% 74.5%
3s5wA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 43.0 2.79e-01 100.0% 86.6%
2wzvA01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.51 40.0 2.89e-01 87.3% 62.8%
2vwaA00 1.20.58.1330 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Plasmodium falciparum UIS3 membrane protein 0.50 36.0 3.18e-01 73.2% 54.5%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1934000 144.1.1.2 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1,PG_binding_5 0.96 82.0 6.03e-01 100.0% 39.9%
1498420 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.94 80.0 7.83e-01 100.0% 82.9%
1165079 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.93 80.0 7.08e-01 100.0% 66.7%
3959835 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.92 83.0 8.43e-01 98.6% 95.7%
3263339 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.92 85.0 8.38e-01 100.0% 92.0%
4032027 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.92 79.0 7.37e-01 100.0% 75.3%
3291401 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.92 84.0 7.79e-01 100.0% 80.0%
5019285 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.91 81.0 7.20e-01 100.0% 69.5%
224034 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.89 76.0 7.24e-01 100.0% 79.0%
4117418 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.89 67.0 7.24e-01 84.5% 93.3%
2859574 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.88 72.0 7.25e-01 100.0% 85.9%
4312892 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.87 66.0 7.13e-01 87.3% 93.3%
4055540 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.87 71.0 7.27e-01 90.1% 88.4%
3299326 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.87 69.0 7.22e-01 87.3% 90.8%
4473649 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.87 81.0 7.60e-01 100.0% 85.9%
3356981 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 77.0 7.37e-01 100.0% 83.7%
3275963 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 77.0 7.02e-01 100.0% 74.4%
3395 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 77.0 7.23e-01 100.0% 80.7%
4173379 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 75.0 7.20e-01 100.0% 82.5%
4380775 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.85 66.0 4.66e-01 88.7% 29.0%
3319740 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.85 74.0 6.91e-01 100.0% 77.6%
3299934 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.85 77.0 6.59e-01 100.0% 64.8%
1877329 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.84 67.0 6.58e-01 90.1% 78.9%
4010440 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.83 70.0 6.91e-01 100.0% 85.3%
3957237 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.83 79.0 7.72e-01 100.0% 98.7%
3955223 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.83 79.0 7.50e-01 100.0% 92.5%
3302194 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.81 76.0 6.79e-01 100.0% 74.7%
2819638 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.81 70.0 5.91e-01 100.0% 57.8%
3539881 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.81 65.0 6.39e-01 88.7% 80.0%
3060287 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.81 66.0 6.50e-01 100.0% 82.7%
4321110 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.81 62.0 6.14e-01 87.3% 77.3%
1904136 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.80 67.0 6.58e-01 97.2% 85.3%
3930763 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.80 68.0 6.65e-01 88.7% 85.3%
3772398 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.80 67.0 6.45e-01 100.0% 78.8%
3221065 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.80 65.0 6.40e-01 85.9% 90.7%
4600634 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.79 62.0 6.72e-01 83.1% 98.3%
3994858 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.79 65.0 6.18e-01 87.3% 76.2%
3332533 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.79 73.0 6.43e-01 100.0% 81.0%
3537259 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.78 64.0 6.14e-01 87.3% 77.5%
4945529 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.78 66.0 6.84e-01 100.0% 100.0%
3933825 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.78 63.0 6.18e-01 85.9% 84.0%
3772718 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.77 64.0 5.98e-01 87.3% 74.1%
3201809 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.77 70.0 6.78e-01 100.0% 90.0%
3893524 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.77 62.0 6.27e-01 84.5% 85.7%
3621525 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.76 62.0 6.14e-01 85.9% 93.3%
4857662 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.76 59.0 5.97e-01 87.3% 81.7%
3765966 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.76 62.0 5.77e-01 88.7% 71.8%
4160453 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.76 60.0 6.07e-01 85.9% 84.3%
3247155 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.74 56.0 5.88e-01 100.0% 89.2%
3764906 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.74 62.0 5.98e-01 90.1% 82.5%
3222017 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.70 65.0 5.92e-01 100.0% 80.0%
D4 medium residues 601-693
PDB
D5 medium residues 694-747
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01471.24 best PG_binding_1 23.7 6.40e-05 61.1% 54.4%
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4g54A02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.83 63.0 5.72e-01 85.2% 61.1%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4038380 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.96 68.0 5.95e-01 79.6% 53.3%
3263339 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.95 72.0 6.31e-01 79.6% 60.0%
3959835 144.1.1.0 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.93 72.0 6.54e-01 81.5% 65.7%
3291401 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.90 74.0 6.22e-01 87.0% 57.6%
4473649 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.84 74.0 6.26e-01 94.4% 68.2%
4962391 144.1.1.11 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_2 0.79 54.0 4.47e-01 79.6% 42.2%
3717787 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.60 43.0 2.54e-01 75.9% 16.0%
3390570 213.1.1.19 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › FR47 0.59 42.0 3.05e-01 77.8% 62.7%