←Back to structures

NC_029008.1__YP_009218153.1__XO28_0020__00020

Bact-Vir

NC_029008.1__YP_009218153.1__XO28_0020__00020

Identity

Accession:
NC_029008 ↗
Kingdom:
phage

Quality

92.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rockvillevirus› Bacillus_phage_phi4J1

TaxID: 1643326

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 3-155
PDB
Domain cluster: rep: NC_041875.1__YP_009594310.1__FDG92_gp21__00021__D5-180
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01510.31 best Amidase_2 72.0 8.60e-20 79.7% 97.7%
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1yb0B00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.99 97.0 9.61e-01 100.0% 96.2%
3rdrA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.93 89.0 8.98e-01 100.0% 98.7%
4olsA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.89 86.0 7.93e-01 100.0% 95.7%
3latA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.86 83.0 7.31e-01 100.0% 80.2%
4ivvA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.84 81.0 7.68e-01 100.0% 96.6%
2bh7A02 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.81 69.0 6.94e-01 87.6% 98.0%
2y28B00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.80 75.0 7.12e-01 99.3% 95.5%
2rkqA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.79 74.0 7.13e-01 99.3% 95.3%
1ohtA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.79 74.0 7.05e-01 99.3% 93.1%
6su5A01 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.78 73.0 7.35e-01 98.7% 98.7%
2eaxA00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.78 73.0 7.14e-01 99.3% 97.0%
2xz4A00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.78 72.0 7.03e-01 98.7% 97.6%
1aroL00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.78 68.0 6.96e-01 94.8% 94.6%
3ep1A00 3.40.80.10 Alpha Beta › 3-Layer(aba) Sandwich › Lysozyme-like › Peptidoglycan recognition protein-like 0.75 70.0 6.82e-01 99.3% 97.6%
2jfvA01 3.40.50.1860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.65 38.0 3.84e-01 87.6% 55.4%
4jmjA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.63 37.0 3.53e-01 86.9% 47.5%
2zskA01 3.40.50.1860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 38.0 4.31e-01 86.9% 81.9%
1duvG01 3.40.50.1370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase 0.59 32.0 3.31e-01 88.2% 53.3%
3og9A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.58 45.0 4.07e-01 98.0% 60.2%
4wy5A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 45.0 3.57e-01 100.0% 40.0%
1e5tA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 46.0 3.47e-01 100.0% 36.4%
5l2pA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 45.0 3.63e-01 92.8% 43.5%
3lyuA01 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.56 39.0 4.57e-01 86.9% 99.1%
3fk5A02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.55 30.0 3.20e-01 88.2% 57.1%
2g6tA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 30.0 3.67e-01 86.3% 82.7%
4i0wB01 3.40.50.200 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain 0.55 45.0 3.54e-01 88.2% 49.8%
3l6aA01 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.55 42.0 3.93e-01 100.0% 65.3%
3lm3A01 3.20.20.510 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Uncharacterised protein PF12979, DUF3863 0.55 39.0 3.07e-01 72.5% 98.1%
4fo5A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 32.0 3.42e-01 94.1% 64.0%
4i4cB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 45.0 3.33e-01 97.4% 34.2%
3lxuX01 3.40.50.200 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain 0.54 45.0 3.48e-01 88.2% 51.4%
3o38B01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 43.0 3.79e-01 86.3% 73.3%
2hoeA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 37.0 3.76e-01 88.2% 70.2%
2qm1B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 36.0 3.70e-01 87.6% 69.7%
2higB03 3.40.50.460 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphofructokinase domain 0.53 37.0 3.77e-01 79.7% 72.8%
3cqjA00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.51 42.0 3.48e-01 94.1% 48.6%
7esrA01 3.40.800.10 Alpha Beta › 3-Layer(aba) Sandwich › Arginase; Chain A › Ureohydrolase domain 0.51 39.0 2.97e-01 93.5% 34.5%
4lw8A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 42.0 3.77e-01 90.2% 71.6%
3olqA00 3.40.50.12370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 40.0 3.17e-01 98.7% 41.8%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1902111 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 0.97 95.0 9.23e-01 100.0% 92.7%
4140249 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 0.93 90.0 8.72e-01 100.0% 92.1%
4837356 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 73.0 7.23e-01 81.7% 93.0%
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 0.91 88.0 8.32e-01 100.0% 95.4%
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 0.89 86.0 7.91e-01 100.0% 92.6%
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 0.86 83.0 7.31e-01 100.0% 80.2%
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 0.85 82.0 7.69e-01 100.0% 92.7%
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 0.84 80.0 7.65e-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 0.84 76.0 7.63e-01 100.0% 94.1%
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 0.84 80.0 7.66e-01 100.0% 97.7%
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 0.82 78.0 7.34e-01 100.0% 93.9%
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 0.81 77.0 7.50e-01 99.3% 99.4%
1891396 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 69.0 6.53e-01 88.2% 85.7%
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 0.81 76.0 7.12e-01 98.7% 95.0%
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 0.80 74.0 6.89e-01 97.4% 84.3%
3953294 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 76.0 7.08e-01 100.0% 88.1%
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 0.80 75.0 7.00e-01 100.0% 89.2%
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 6.99e-01 98.7% 92.0%
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 0.79 74.0 7.13e-01 99.3% 95.3%
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 0.79 74.0 7.28e-01 99.3% 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 0.79 74.0 7.04e-01 99.3% 93.1%
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 0.78 73.0 7.04e-01 99.3% 97.1%
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 0.78 73.0 7.13e-01 99.3% 97.0%
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 0.78 73.0 7.04e-01 99.3% 94.7%
4034532 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 0.77 73.0 7.24e-01 100.0% 97.5%
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 0.76 71.0 6.80e-01 99.3% 91.4%
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 0.76 63.0 6.57e-01 86.3% 97.1%
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 0.76 68.0 6.78e-01 95.4% 92.3%
4958168 7512.1.1.107 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › DUF354 0.71 35.0 3.22e-01 86.9% 36.4%
3188493 7579.1.1.18 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_2 0.65 47.0 4.21e-01 98.7% 53.0%
5037153 7592.1.1.1 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › Cas_NE0113 0.65 41.0 3.51e-01 86.9% 39.2%
4000139 2007.2.3.2 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › DSPc 0.62 35.0 3.79e-01 86.9% 63.8%
3630015 7579.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.61 40.0 3.28e-01 86.9% 36.4%
141727 7579.1.1.13 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › DLH 0.58 45.0 4.07e-01 98.0% 60.2%
4154245 2484.1.1.29 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ppx-GppA 0.57 39.0 4.22e-01 87.6% 83.1%
4505863 7514.1.1.1 ↗ a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › NAD_binding_1 0.56 38.0 3.81e-01 93.5% 65.8%
3184021 7579.1.1.36 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_3 0.55 47.0 3.43e-01 97.4% 33.5%
1187934 2484.1.1.8 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.55 37.0 4.06e-01 88.2% 82.8%
3685714 7579.1.1.36 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_3 0.54 47.0 3.59e-01 94.1% 46.1%
None — 0.53 44.0 3.43e-01 92.2% 40.3%
4394293 7581.1.1.12 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › ACP_syn_III_C 0.52 31.0 3.10e-01 88.2% 56.5%
4627252 7589.1.1.2 ↗ a/b three-layered sandwiches › YgbK-like › YgbK-like › YgbK-like › NBD_C 0.52 38.0 3.73e-01 87.6% 68.2%
5081226 2499.1.1.1 ↗ a/b three-layered sandwiches › Subtilisin-like › Subtilisin-like › Subtilisin-like › Peptidase_S8 0.51 42.0 3.33e-01 88.2% 43.1%
D2 high residues 178-238
PDB
Domain cluster: rep: MZ983385.1__UAW07777.1__PVJ1_00043__00043__D36-106
D3 high residues 250-317
PDB
Domain cluster: rep: OM293948.2__UKM63008.1__X__00150__D483-544