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NC_048686.1__YP_009836121.1__HWB41_gp02__00002

Bact-Vir

NC_048686.1__YP_009836121.1__HWB41_gp02__00002

Identity

Accession:
NC_048686 ↗
Kingdom:
phage

Quality

95.6 mean pLDDT

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 8-163
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01510.31 best Amidase_2 65.8 6.80e-18 82.0% 98.5%
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3latA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.85 82.0 7.30e-01 100.0% 83.1%
2y28B00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.85 80.0 7.57e-01 97.4% 94.9%
4ivvA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.81 76.0 7.28e-01 98.7% 97.1%
5xz3B00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.81 75.0 7.26e-01 96.2% 94.0%
2rkqA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.80 74.0 7.18e-01 96.2% 94.1%
1ohtA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.80 74.0 7.09e-01 96.2% 91.9%
2eaxA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.79 73.0 7.17e-01 96.2% 95.7%
3rdrA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.79 73.0 7.39e-01 98.1% 98.0%
4olsA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.79 75.0 7.00e-01 100.0% 96.8%
1yb0B00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.78 74.0 7.40e-01 100.0% 98.1%
1aroL00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.78 68.0 6.98e-01 92.9% 94.6%
2xz4A00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.78 71.0 7.01e-01 96.2% 96.4%
6su5A01 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.78 71.0 7.28e-01 97.4% 99.3%
3ep1A00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.76 70.0 6.88e-01 96.8% 97.0%
2xz8A00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.71 58.0 6.18e-01 89.1% 97.8%
1toaA02 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.63 36.0 3.91e-01 93.6% 66.4%
4f2gA01 3.40.50.1370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase 0.56 30.0 3.14e-01 89.7% 53.7%
2c2xA02 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.54 31.0 3.21e-01 89.7% 55.8%
2imgA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.52 38.0 3.96e-01 91.0% 79.2%
2xtkA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.52 40.0 3.27e-01 95.5% 41.9%
1g4wR02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.50 42.0 3.76e-01 93.6% 63.8%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4265814 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.92 87.0 8.52e-01 97.4% 98.8%
3278570 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.91 87.0 8.23e-01 100.0% 95.0%
3957313 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.86 82.0 7.37e-01 100.0% 94.1%
2774594 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.86 76.0 7.73e-01 98.1% 94.1%
1902112 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.85 82.0 7.30e-01 100.0% 83.1%
3967132 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.85 79.0 7.49e-01 96.8% 92.8%
3587007 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.84 79.0 7.48e-01 98.7% 93.8%
4088805 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.83 78.0 7.25e-01 97.4% 84.3%
1904118 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.82 76.0 7.35e-01 97.4% 98.3%
4650125 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.82 79.0 7.52e-01 100.0% 96.6%
2845647 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.82 74.0 7.49e-01 98.1% 95.4%
1914461 285.1.1.0 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like 0.81 76.0 7.32e-01 98.7% 97.7%
4291672 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.81 74.0 7.31e-01 96.2% 95.8%
2445367 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.81 70.0 7.05e-01 96.2% 90.4%
3897241 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.80 75.0 7.50e-01 98.1% 100.0%
3767503 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.80 74.0 7.11e-01 96.2% 91.9%
1903375 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.80 74.0 7.18e-01 96.2% 94.1%
3416111 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.80 74.0 7.14e-01 96.2% 93.5%
3910569 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.80 73.0 6.85e-01 96.2% 88.1%
4429159 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.80 73.0 5.25e-01 96.2% 40.6%
3401062 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.80 73.0 7.07e-01 96.2% 95.9%
3389811 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.79 73.0 7.00e-01 96.2% 90.9%
4031908 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.79 75.0 7.00e-01 100.0% 95.2%
2494148 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.79 72.0 6.93e-01 96.2% 90.3%
3201810 285.1.1.0 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like 0.78 74.0 6.91e-01 98.7% 89.2%
1900462 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.78 68.0 6.98e-01 92.9% 94.6%
3873499 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.77 61.0 6.42e-01 81.4% 96.4%
3395991 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.77 70.0 6.74e-01 96.2% 90.3%
1900947 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.76 70.0 6.88e-01 96.8% 97.0%
3400014 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.74 67.0 6.65e-01 96.2% 92.5%
6943 285.1.1.1 a+b three layers › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › N-acetylmuramoyl-L-alanine amidase-like › Amidase_2 0.69 65.0 6.09e-01 100.0% 93.0%
None 0.68 38.0 3.91e-01 90.4% 56.0%
3892998 2007.2.3.2 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › DSPc 0.51 39.0 4.04e-01 92.3% 82.7%
3238716 2007.2.3.12 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Tc-R-P 0.51 39.0 3.95e-01 92.3% 80.0%
3705962 2007.2.3.11 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › PTP-SAK 0.50 41.0 3.66e-01 91.7% 62.3%
D2 high residues 179-248
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01471.24 best PG_binding_1 26.4 9.00e-06 88.6% 96.5%
CATH (12)
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 0.89 75.0 7.50e-01 100.0% 87.5%
3bkhA01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.87 73.0 6.78e-01 100.0% 73.3%
4c2dA02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.84 74.0 6.90e-01 100.0% 77.6%
1lbuA01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.83 73.0 6.80e-01 98.6% 78.6%
4f92B10 1.10.3380.10 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › Sec63 N-terminal domain-like domain 0.61 45.0 3.66e-01 88.6% 39.9%
4arvA02 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.57 45.0 3.80e-01 90.0% 85.7%
2rijA01 3.30.70.2010 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 44.0 3.38e-01 90.0% 58.4%
3aleA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.54 36.0 2.97e-01 70.0% 90.9%
3bqyA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.54 43.0 3.37e-01 87.1% 98.0%
4c0kA01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.54 39.0 3.57e-01 81.4% 74.3%
3qaoA00 1.10.1660.10 Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › 0.53 36.0 2.98e-01 72.9% 62.9%
2ghaB02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 36.0 2.70e-01 75.7% 66.7%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3201809 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.95 91.0 8.64e-01 100.0% 87.5%
1934000 144.1.1.2 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1,PG_binding_5 0.88 73.0 5.45e-01 100.0% 39.2%
4032027 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 75.0 6.96e-01 100.0% 76.5%
4173379 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 76.0 7.26e-01 100.0% 83.7%
3590520 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 76.0 7.30e-01 100.0% 85.0%
1165079 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 74.0 6.59e-01 100.0% 67.7%
5019285 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.84 78.0 6.96e-01 100.0% 74.7%
3589440 144.1.1.7 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PF30262 0.84 74.0 5.78e-01 100.0% 47.9%
3302194 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.83 75.0 6.69e-01 100.0% 71.6%
3395 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.83 73.0 6.83e-01 98.6% 79.5%
4096813 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.82 76.0 6.67e-01 100.0% 78.0%
3319740 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.82 71.0 6.66e-01 100.0% 77.6%
3356981 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.81 72.0 6.90e-01 100.0% 85.0%
4011396 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.79 72.0 6.06e-01 100.0% 61.9%
3957237 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.79 71.0 6.95e-01 97.1% 96.0%
3299934 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.78 70.0 6.08e-01 100.0% 65.7%
3332533 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.78 71.0 6.29e-01 100.0% 79.0%
4038380 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.78 68.0 6.64e-01 97.1% 88.0%
3060287 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.75 60.0 5.87e-01 100.0% 81.3%
1904136 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.73 59.0 5.78e-01 95.7% 81.3%
3806393 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.51 34.0 3.58e-01 77.1% 75.4%
3661763 5051.1.1.6 alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Aa_trans 0.51 39.0 2.46e-01 84.3% 80.0%