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NC_025440.1__YP_010843640.1__PI27_gp073__00073

Bact-Vir

NC_025440.1__YP_010843640.1__PI27_gp073__00073

Identity

Accession:
NC_025440 ↗
Kingdom:
phage

Quality

96.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Pecentumvirus› Listeria_phage_WIL-1

TaxID: 1541821

Cluster

View cluster (10 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 medium residues 1-147
PDB
Domain cluster: rep: MW344767__QRG24214.1__HarHp1-090__00017__D153-278
Pfam (5)
AccessionNameScoreE-valueQ covHMM cov
PF13599.14 best Pentapeptide_4 43.5 3.80e-11 55.1% 87.2%
PF13576.13 Pentapeptide_3 27.4 4.30e-06 54.4% 95.8%
PF00805.29 Pentapeptide 51.3 9.20e-14 27.2% 100.0%
PF00805.29 Pentapeptide 53.9 1.30e-14 27.2% 100.0%
PF00805.29 Pentapeptide 49.2 4.20e-13 25.2% 92.5%
D2 medium residues 148-216
PDB
Domain cluster: rep: NC_007021.1__YP_238649.1__TwortORF044__00115__D191-248
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2dk6A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.70 36.0 3.28e-01 92.8% 37.2%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.64 52.0 4.43e-01 94.2% 83.2%
2pfuA01 3.30.420.270 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.64 44.0 4.42e-01 87.0% 71.4%
1kaeA03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.64 38.0 4.12e-01 75.4% 72.7%
2hqrA02 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 0.59 41.0 3.57e-01 72.5% 62.3%
2xp1A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.59 41.0 3.75e-01 72.5% 98.9%
2yviA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.59 41.0 3.79e-01 72.5% 74.2%
1yw5A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.59 43.0 4.49e-01 91.3% 87.3%
2kd2A01 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.58 50.0 4.74e-01 98.6% 82.1%
4g09A03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 34.0 3.69e-01 73.9% 72.7%
4nswA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 49.0 4.24e-01 97.1% 92.7%
2zwrB00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 44.0 3.23e-01 94.2% 29.5%
4iw9B01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.56 43.0 3.86e-01 87.0% 98.0%
3q9vA00 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 0.56 44.0 4.00e-01 100.0% 63.3%
2mlkA00 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 0.55 44.0 3.80e-01 100.0% 55.5%
3zq7A00 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 0.55 38.0 3.38e-01 72.5% 64.4%
1kgsA02 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 0.54 41.0 3.73e-01 100.0% 59.2%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.54 45.0 4.34e-01 92.8% 92.3%
2pmuC00 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 0.54 43.0 3.88e-01 85.5% 97.8%
5u8kA02 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 0.54 39.0 3.46e-01 79.7% 83.2%
2ci9B00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.53 40.0 3.59e-01 82.6% 63.0%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.51 34.0 3.55e-01 71.0% 86.4%
3us4A00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.50 37.0 3.45e-01 84.1% 62.9%
6l4lA02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.50 43.0 3.51e-01 98.6% 74.3%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5030187 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.68 53.0 5.17e-01 87.0% 100.0%
3768377 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.66 50.0 4.17e-01 81.2% 54.2%
3387219 2484.6.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Periplasmic domain of ExbD/TolR › Periplasmic domain of ExbD/TolR › ExbD 0.61 47.0 4.32e-01 88.4% 64.4%
3781161 4099.1.1.1 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › MAD 0.61 41.0 3.40e-01 71.0% 57.8%
4508883 2484.6.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Periplasmic domain of ExbD/TolR › Periplasmic domain of ExbD/TolR › ExbD 0.60 43.0 3.97e-01 88.4% 56.8%
3603325 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.59 41.0 2.82e-01 73.9% 28.0%
3480379 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.59 42.0 3.69e-01 75.4% 65.7%
1277880 64.1.1.1 ↗ beta meanders › WW domain-like › WW domain › WW domain › WW 0.59 43.0 4.51e-01 91.3% 88.7%
4334851 3820.1.1.1 ↗ a+b complex topology › CRISPR-associated endonuclease Cas9 C-terminal domain › CRISPR-associated endonuclease Cas9 C-terminal domain › CRISPR-associated endonuclease Cas9 C-terminal domain › Cas9_PI 0.58 40.0 3.11e-01 72.5% 36.8%
4464727 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.58 41.0 3.61e-01 75.4% 65.4%
3990213 220.1.1.7 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › IRS 0.57 47.0 4.21e-01 91.3% 97.0%
5025277 284.1.1.13 ↗ a+b two layers › FKBP-like › FKBP-like › FKBP-like › FKBP-like_N 0.57 41.0 4.45e-01 92.8% 94.5%
3400447 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 44.0 3.07e-01 84.1% 30.0%
3386347 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.56 40.0 3.64e-01 79.7% 54.7%
4096365 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.55 45.0 3.51e-01 89.9% 54.0%
3974177 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 46.0 3.96e-01 89.9% 95.2%
4680240 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.55 40.0 3.45e-01 79.7% 51.3%
5068028 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.55 43.0 3.07e-01 88.4% 68.0%
5018431 109.4.1.210 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_19 0.54 42.0 2.67e-01 85.5% 23.1%
4987925 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 36.0 3.54e-01 94.2% 62.5%
3287693 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.53 43.0 3.73e-01 91.3% 92.6%
3567461 260.1.1.1 ↗ a+b duplicates or obligate multimers › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › Plectin 0.52 44.0 2.92e-01 97.1% 40.3%
3264049 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.52 44.0 3.98e-01 94.2% 88.4%
3988383 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.52 41.0 3.69e-01 100.0% 62.0%
3507017 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.52 42.0 3.75e-01 89.9% 100.0%
4232905 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.51 45.0 3.90e-01 100.0% 66.1%
4427723 375.1.1.145 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › FdhE_C 0.51 39.0 3.79e-01 98.6% 73.8%
4834236 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.51 37.0 3.16e-01 81.2% 48.8%
319515 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.51 41.0 3.57e-01 100.0% 57.8%
3845218 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.50 37.0 3.77e-01 78.3% 87.7%
4887993 139.3.1.1 ↗ few secondary structure elements › Multiheme cytochromes › Photosynthetic reaction centre (cytochrome subunit) › Photosynthetic reaction centre (cytochrome subunit) › CytoC_RC 0.50 45.0 2.93e-01 100.0% 27.1%
4600226 5.1.4.307 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PF29630 0.50 45.0 2.71e-01 100.0% 30.6%