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NC_024379.1__YP_009044291.1__PE3_043__00043

Bact-Vir

NC_024379.1__YP_009044291.1__PE3_043__00043

Identity

Accession:
NC_024379 ↗
Kingdom:
phage

Quality

75.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Autographivirales› Autotranscriptaviridae› Kayfunavirus› Escherichia_phage_PE3-1

TaxID: 1498170

Cluster

View cluster (2 members)

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 4-80_93-126
PDB
Domain cluster: rep: NC_027397.1__YP_009153046.1__ACQ41_gp20__00020__D9-117
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03906.21 best Phage_T7_tail 25.8 1.40e-05 97.3% 78.4%
D2 high residues 572-721
PDB
D3 medium residues 133-229
PDB
Domain cluster: rep: MZ501051.1__QXV76169.1__bas01_0038__00038__D174-271
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF18668.7 best Tail_spike_N 76.1 2.50e-21 70.1% 81.4%
D4 medium residues 345-430_444-480
PDB
Domain cluster: representative
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2y2wC02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.76 70.0 4.94e-01 100.0% 57.5%
3lgdA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.73 67.0 4.44e-01 100.0% 38.6%
1jndA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.73 67.0 4.96e-01 100.0% 67.0%
1fkwA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.70 65.0 4.62e-01 100.0% 53.0%
3chvA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.69 64.0 4.85e-01 100.0% 52.7%
1ea0B03 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.69 63.0 4.37e-01 100.0% 52.6%
6ddtA03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.67 61.0 4.36e-01 100.0% 71.9%
7sf2A03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.67 62.0 4.63e-01 100.0% 45.7%
6bygA03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.66 61.0 4.33e-01 100.0% 46.9%
2chrA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.66 59.0 4.99e-01 100.0% 59.4%
5n6uA03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.66 61.0 4.35e-01 100.0% 44.7%
3i4kA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.66 59.0 4.63e-01 100.0% 47.6%
3lmzA00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.65 59.0 4.68e-01 100.0% 69.7%
1j5sA01 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.65 58.0 4.20e-01 100.0% 61.6%
1tv8B00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.64 58.0 4.29e-01 100.0% 73.0%
4i6vA01 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.64 58.0 4.22e-01 100.0% 68.8%
3qg5C02 3.30.160.210 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › DNA double-strand break repair nuclease 0.64 35.0 4.53e-01 86.2% 93.0%
3qldA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.64 55.0 4.47e-01 100.0% 49.8%
2pgeA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.63 57.0 4.68e-01 100.0% 65.9%
3gg7A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.63 57.0 4.57e-01 100.0% 66.7%
4jgiB02 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.62 44.0 4.37e-01 71.5% 90.5%
2lciA00 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 43.0 4.21e-01 83.7% 67.2%
4gx0B04 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.60 42.0 4.15e-01 72.4% 91.6%
2vyoA00 3.20.20.370 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycoside hydrolase/deacetylase 0.59 54.0 4.51e-01 100.0% 93.2%
3h49B00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.59 53.0 4.00e-01 100.0% 55.9%
1reqA02 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.56 44.0 4.05e-01 84.6% 68.9%
3ajdA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 42.0 3.67e-01 80.5% 90.2%
1xoiA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.55 47.0 3.18e-01 93.5% 85.1%
6cv6D00 3.40.50.9100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dehydroquinase, class II 0.55 43.0 4.13e-01 84.6% 89.6%
3uj9A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 48.0 3.87e-01 100.0% 82.9%
3hv2A00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 43.0 4.20e-01 84.6% 77.9%
3hn7A03 3.90.190.20 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Mur ligase, C-terminal domain 0.54 41.0 3.93e-01 84.6% 68.0%
1j0aA02 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 36.0 3.92e-01 77.2% 82.7%
4fx5A02 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.53 43.0 3.80e-01 87.8% 90.8%
2csuA02 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.53 41.0 3.98e-01 83.7% 77.3%
2jk1A00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 42.0 4.05e-01 84.6% 76.1%
4yacA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 46.0 3.82e-01 100.0% 89.1%
2b8tA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 40.0 3.86e-01 81.3% 77.0%
7u35A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 33.0 3.76e-01 84.6% 85.9%
6r8gA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 40.0 3.83e-01 82.1% 98.6%
3ldhA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 40.0 3.65e-01 82.1% 86.4%
3cfyA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 40.0 3.99e-01 84.6% 80.0%
3lyuA01 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.50 34.0 3.59e-01 83.7% 76.8%
6mh4A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 42.0 3.99e-01 91.1% 89.6%
3k1zA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.50 38.0 3.56e-01 81.3% 96.2%
5uzxA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 44.0 3.65e-01 100.0% 87.4%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3946611 2002.1.1.254 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › GH5_mannosidase 0.74 68.0 4.77e-01 100.0% 52.7%
4664323 284.2.1.1 ↗ a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain › Glyco_hydro_18 0.69 63.0 4.32e-01 100.0% 68.7%
4201813 2002.1.1.116 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PdxJ 0.69 63.0 4.97e-01 100.0% 58.8%
3972136 2002.5.1.1 ↗ a/b barrels › TIM beta/alpha-barrel › EAL domain › EAL domain › EAL 0.69 62.0 4.93e-01 100.0% 66.1%
5030758 2002.1.1.236 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DHQS 0.68 56.0 5.00e-01 100.0% 62.9%
3287822 2002.1.1.16 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Bac_luciferase 0.63 56.0 4.13e-01 100.0% 58.2%
5071139 2007.1.3.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › B12-binding 0.62 45.0 4.49e-01 75.6% 92.3%
4973115 2002.1.1.2 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Enolase_C 0.59 53.0 4.13e-01 100.0% 47.9%
3494545 2002.1.1.2 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Enolase_C 0.59 53.0 3.98e-01 100.0% 41.2%
3779300 2002.1.1.20 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PI-PLC-Y,PI-PLC-X 0.58 52.0 3.81e-01 100.0% 67.2%
3593873 7573.1.1.0 ↗ a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like 0.58 47.0 4.29e-01 90.2% 82.4%
3694855 2003.1.1.93 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › DUF1776 0.57 51.0 3.81e-01 100.0% 85.5%
3208583 2002.1.1.20 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PI-PLC-Y,PI-PLC-X 0.57 51.0 3.77e-01 100.0% 63.7%
None — 0.56 51.0 3.73e-01 100.0% 53.5%
4175926 2007.1.3.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › B12-binding 0.56 44.0 4.28e-01 84.6% 80.0%
3984466 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.56 49.0 4.20e-01 100.0% 83.8%
3503192 7512.1.1.2 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Phosphorylase 0.55 46.0 3.20e-01 93.5% 87.2%
3843781 2002.1.1.20 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PI-PLC-Y,PI-PLC-X 0.55 49.0 3.51e-01 100.0% 69.5%
3702955 2004.1.1.427 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › RHSP, RHS_N 0.55 41.0 3.38e-01 99.2% 42.7%
3483270 7512.1.1.0 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.55 46.0 3.17e-01 92.7% 89.6%
4820748 304.11.1.0 ↗ a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase 0.55 34.0 4.01e-01 83.7% 92.6%
3686130 2003.1.1.3 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.55 33.0 3.54e-01 82.9% 67.3%
3515561 2007.1.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like 0.54 35.0 3.84e-01 75.6% 82.1%
5051164 7512.1.1.0 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.53 41.0 3.70e-01 83.7% 99.4%
4930751 2007.1.3.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › B12-binding 0.52 42.0 4.19e-01 85.4% 85.9%
3986077 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.52 38.0 2.99e-01 76.4% 48.4%
5011585 2006.1.2.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases 0.52 43.0 3.76e-01 89.4% 76.8%
5051289 2007.1.3.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › B12-binding 0.52 45.0 3.94e-01 96.7% 91.3%
3246973 2003.1.1.80 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › FAS_pseudo-KR 0.52 39.0 3.93e-01 78.9% 87.2%
4019440 2003.1.1.3 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.52 37.0 3.42e-01 74.8% 81.2%
4291296 2007.1.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › Response_reg 0.52 44.0 4.23e-01 100.0% 81.4%
4981231 2003.1.7.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NagB/RpiA/CoA transferase-like 0.51 38.0 3.10e-01 78.9% 43.3%
5032690 7512.1.1.107 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › DUF354 0.51 44.0 3.85e-01 100.0% 99.0%
4365581 2007.1.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › Response_reg 0.50 40.0 3.78e-01 86.2% 70.0%
3457175 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 44.0 3.55e-01 100.0% 95.4%