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NC_021539.2__YP_008126697.1__LP030nr2_001__00001

Bact-Vir

NC_021539.2__YP_008126697.1__LP030nr2_001__00001

Identity

Accession:
NC_021539 ↗
Kingdom:
phage

Quality

89.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Psavirus› Listeria_phage_LP-030-2

TaxID: 1173743

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 9-108
PDB
Domain cluster: rep: KR816341.1__AKQ06902.1__X__00043__D7-98
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05119.18 best Terminase_4 28.5 2.30e-06 91.0% 83.7%
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 52.0 5.09e-01 70.0% 72.5%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 52.0 5.10e-01 71.0% 75.5%
2wb7A03 1.20.120.870 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › pT26-6p, five-helical bundle domain 0.73 55.0 4.90e-01 90.0% 57.4%
5figA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.68 48.0 4.88e-01 92.0% 74.0%
3jysA01 1.25.40.390 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.68 50.0 3.82e-01 77.0% 70.0%
3kavA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.68 48.0 4.78e-01 92.0% 71.6%
1jmwA00 1.20.120.30 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartate receptor, ligand-binding domain 0.67 49.0 4.34e-01 77.0% 84.9%
4d8mA01 1.20.190.10 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › Pesticidal crystal protein, N-terminal domain 0.67 48.0 3.74e-01 75.0% 45.4%
1fxkC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 45.0 4.16e-01 71.0% 84.2%
2q12A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.66 52.0 3.89e-01 84.0% 65.3%
3thxB04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.64 48.0 4.43e-01 79.0% 82.8%
5fq4A00 1.25.40.390 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.63 46.0 2.95e-01 76.0% 86.2%
3llwD00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.63 55.0 3.99e-01 97.0% 84.1%
1ewqA04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.63 47.0 4.17e-01 77.0% 74.3%
1qgtB00 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.63 46.0 4.07e-01 87.0% 53.1%
3x29A00 1.20.140.150 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.63 53.0 4.47e-01 92.0% 81.3%
4p79A00 1.20.140.150 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.63 54.0 4.46e-01 95.0% 79.6%
2p7vA00 1.20.120.1370 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Regulator of RNA polymerase sigma(70) subunit, domain 4 0.61 49.0 4.35e-01 91.0% 58.3%
5yk4A04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.61 45.0 4.10e-01 78.0% 79.4%
5xnyA02 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.61 54.0 4.05e-01 97.0% 85.2%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.61 52.0 4.91e-01 93.0% 94.1%
3pltA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.60 51.0 3.99e-01 93.0% 70.1%
7d3uC01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 46.0 4.57e-01 93.0% 79.4%
1s12A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.58 43.0 4.42e-01 91.0% 81.9%
3floB00 1.10.3200.20 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › DNA Polymerase alpha, zinc finger 0.58 42.0 3.50e-01 76.0% 77.8%
5lbmA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.58 43.0 4.72e-01 78.0% 96.4%
1rq0A01 6.10.140.160 Special › Helix non-globular › Helix Hairpins › 0.58 45.0 4.84e-01 84.0% 100.0%
3e9lA02 1.20.80.40 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › Prp8 RNase H domain, fingers region 0.58 35.0 3.65e-01 76.0% 64.2%
4nqiD00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.57 47.0 3.65e-01 91.0% 73.7%
6wngA02 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.56 46.0 3.43e-01 91.0% 38.4%
1nu7D02 1.20.120.760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Staphylcoagulase, helix bundle, domain 2 0.55 41.0 3.78e-01 78.0% 74.2%
2bl2A00 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.54 46.0 3.98e-01 93.0% 82.1%
3fedA03 1.20.930.40 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Transferrin receptor-like, dimerisation domain 0.54 44.0 3.84e-01 90.0% 71.6%
1e6vB02 1.20.840.10 Mainly Alpha › Up-down Bundle › Methyl-coenzyme M Reductase; Chain B, domain 2 › Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal 0.53 48.0 3.48e-01 100.0% 92.0%
6okdA03 1.20.930.40 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Transferrin receptor-like, dimerisation domain 0.53 43.0 3.88e-01 88.0% 90.6%
2rd9B01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.52 42.0 3.49e-01 86.0% 76.0%
2pg4A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 30.0 3.17e-01 91.0% 61.5%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4030787 605.1.1.303 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Terminase_4 0.86 69.0 6.98e-01 91.0% 85.0%
4033043 616.1.1.41 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Terminase_4 0.80 67.0 7.04e-01 88.0% 100.0%
5041857 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.76 53.0 4.69e-01 71.0% 84.2%
3931606 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.76 53.0 5.01e-01 71.0% 85.2%
4953135 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.76 53.0 4.64e-01 72.0% 81.4%
4951472 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.76 52.0 4.49e-01 71.0% 87.9%
3506058 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.75 52.0 5.21e-01 70.0% 88.0%
3630462 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.75 52.0 4.57e-01 71.0% 59.3%
5028061 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.75 52.0 5.52e-01 71.0% 86.7%
3254236 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.75 51.0 5.06e-01 70.0% 80.0%
3538408 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.75 51.0 5.28e-01 70.0% 86.3%
3771989 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.75 52.0 4.65e-01 71.0% 71.9%
3785619 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.75 52.0 4.94e-01 71.0% 84.3%
5073682 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.75 52.0 4.60e-01 71.0% 84.8%
4940192 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.75 52.0 4.97e-01 71.0% 81.6%
3783976 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.74 52.0 5.45e-01 71.0% 93.3%
3710532 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.74 51.0 5.01e-01 70.0% 86.7%
3229643 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.74 52.0 4.82e-01 71.0% 90.8%
5000789 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.74 51.0 5.04e-01 71.0% 80.0%
5036014 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.73 50.0 5.17e-01 70.0% 81.1%
4463557 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.73 51.0 5.22e-01 71.0% 87.4%
4410759 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.72 50.0 4.77e-01 71.0% 94.8%
3718200 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.72 50.0 4.58e-01 71.0% 70.4%
5018039 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.71 59.0 5.60e-01 87.0% 85.2%
3608199 1189.1.1.0 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor 0.71 57.0 4.54e-01 83.0% 76.8%
4988447 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.69 57.0 5.47e-01 87.0% 79.1%
4986986 3633.1.1.0 ↗ alpha duplicates or obligate multimers › Haptoglobin-hemoglobin receptor › Haptoglobin-hemoglobin receptor › Haptoglobin-hemoglobin receptor 0.68 47.0 3.67e-01 71.0% 42.0%
3577241 5054.1.1.2 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans 0.67 51.0 4.80e-01 80.0% 85.0%
5047150 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.67 46.0 3.63e-01 70.0% 43.5%
4458171 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.66 45.0 4.16e-01 70.0% 94.6%
5024938 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.66 45.0 4.15e-01 70.0% 94.6%
4396994 3755.3.1.305 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Rad50_zn_hook 0.66 47.0 2.73e-01 74.0% 64.9%
3790375 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.65 45.0 4.19e-01 71.0% 84.8%
3225544 4006.1.1.0 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain 0.65 52.0 5.28e-01 84.0% 89.0%
3651030 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.65 57.0 4.69e-01 95.0% 54.3%
3451948 601.1.1.91 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › DUF1218 0.65 51.0 4.35e-01 84.0% 54.4%
4950970 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.64 44.0 3.00e-01 71.0% 22.9%
4012325 5001.1.1.85 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Fung_rhodopsin 0.64 58.0 4.24e-01 98.0% 85.1%
4018812 5001.1.1.85 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Fung_rhodopsin 0.64 58.0 4.10e-01 98.0% 81.7%
4083451 192.2.1.20 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › ASNSD1-SEP 0.64 47.0 5.31e-01 78.0% 96.2%
4018571 5001.1.1.85 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Fung_rhodopsin 0.64 58.0 4.22e-01 97.0% 95.7%
3423731 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.64 52.0 4.70e-01 87.0% 67.4%
4019035 5001.1.1.85 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Fung_rhodopsin 0.64 58.0 4.25e-01 99.0% 86.5%
3628456 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.64 47.0 4.41e-01 79.0% 98.4%
3323279 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.63 49.0 4.41e-01 80.0% 99.2%
4013657 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.63 54.0 4.86e-01 95.0% 68.6%
3229806 6157.1.1.1 ↗ alpha bundles › GKAP homology domain 1 › GKAP homology domain 1 › GKAP homology domain 1 › GKAP 0.62 51.0 4.87e-01 88.0% 79.1%
3743247 601.23.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.62 51.0 3.43e-01 87.0% 32.5%
3391109 3684.1.1.21 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › TMEM138 0.61 51.0 4.59e-01 91.0% 70.7%
4448441 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.61 52.0 4.57e-01 90.0% 77.1%
3665807 611.9.1.4 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.61 50.0 4.56e-01 89.0% 96.3%
3229069 633.23.1.5 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Clc-like 0.61 53.0 4.14e-01 95.0% 76.2%
3274541 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.61 43.0 3.98e-01 74.0% 62.3%
3189292 5001.1.1.85 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Fung_rhodopsin 0.61 55.0 4.04e-01 100.0% 92.2%
3295267 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.60 52.0 4.35e-01 95.0% 63.6%
3258488 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.60 47.0 4.79e-01 84.0% 87.0%
3530209 633.23.1.4 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Claudin_2 0.59 52.0 3.87e-01 95.0% 77.8%
3230335 3922.1.1.195 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Pinin_SDK_memA 0.58 47.0 4.04e-01 89.0% 95.2%
3223678 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.57 40.0 3.25e-01 73.0% 72.0%
3427456 611.2.1.2 ↗ alpha bundles › N-cbl like › N-terminal domain of cbl (N-cbl) › N-terminal domain of cbl (N-cbl) › Rx_N 0.57 46.0 4.08e-01 89.0% 88.7%
3440522 5069.1.3.12 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DUF6490 0.56 46.0 4.74e-01 92.0% 95.8%
3595767 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 40.0 2.72e-01 78.0% 30.3%
5028980 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.51 44.0 3.51e-01 95.0% 47.0%