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NC_009813.1__YP_001468711.1__LiPB054_gp07__00007

Bact-Vir

NC_009813.1__YP_001468711.1__LiPB054_gp07__00007

Identity

Accession:
NC_009813 ↗
Kingdom:
phage

Quality

70.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Listeria_phage_B054

TaxID: 330397

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 21-87
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22758.3 best Phage_cement 37.0 5.10e-09 100.0% 47.3%
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6xgqb01 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.76 63.0 5.57e-01 92.5% 63.4%
8bveA03 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.71 59.0 5.81e-01 91.0% 98.6%
1g8lA04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.70 59.0 5.74e-01 92.5% 100.0%
1wu2A04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.68 60.0 5.73e-01 97.0% 94.8%
1c5eA00 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.68 56.0 5.01e-01 100.0% 64.2%
6ethA04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.68 56.0 5.10e-01 91.0% 87.6%
3gqhA01 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.63 55.0 4.41e-01 94.0% 55.3%
3girA04 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.54 38.0 3.67e-01 97.0% 64.1%
3c2qA01 2.40.420.10 Mainly Beta › Beta Barrel › conserved putative lor/sdh protein from methanococcus maripaludis s2 fold › conserved putative lor/sdh protein from methanococcus maripaludis s2 domain 0.54 36.0 3.41e-01 71.6% 96.6%
2e9xD02 3.40.5.60 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.52 32.0 3.41e-01 95.5% 70.0%
4ak8A00 3.10.100.10 Alpha Beta › Roll › Mannose-Binding Protein A; Chain A › Mannose-Binding Protein A, subunit A 0.51 44.0 3.61e-01 98.5% 91.5%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2559744 70.4.1.2 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.84 61.0 6.50e-01 92.5% 86.4%
3948608 70.4.1.7 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › XM1_gp53_minor_capsid 0.81 65.0 6.67e-01 86.6% 93.8%
5083816 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.79 70.0 6.88e-01 94.0% 92.9%
3602933 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.79 66.0 6.71e-01 91.0% 90.8%
5016125 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.78 59.0 6.45e-01 94.0% 98.2%
3981037 70.4.1.9 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement_2 0.74 56.0 6.09e-01 92.5% 98.2%
2526359 70.4.1.2 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.73 58.0 6.08e-01 95.5% 95.0%
3398750 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.71 60.0 5.71e-01 92.5% 93.8%
3490658 70.1.1.0 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like 0.71 61.0 5.47e-01 95.5% 91.6%
5075574 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.71 61.0 5.75e-01 94.0% 92.5%
4948446 7541.1.1.2 ↗ a/b three-layered sandwiches › Molybdenum cofactor biosynthesis proteins › Molybdenum cofactor biosynthesis proteins › Molybdenum cofactor biosynthesis proteins › MoeA_C 0.71 64.0 4.22e-01 100.0% 33.8%
4975521 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.71 61.0 5.59e-01 94.0% 90.6%
4938684 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 63.0 5.80e-01 100.0% 91.8%
5017350 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 61.0 6.07e-01 95.5% 97.1%
4933166 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 59.0 5.58e-01 92.5% 93.8%
4935036 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 61.0 5.91e-01 95.5% 95.9%
4930449 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 57.0 5.54e-01 89.6% 93.3%
5049149 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 58.0 5.70e-01 91.0% 97.3%
3959516 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 60.0 5.79e-01 95.5% 97.3%
4617493 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 61.0 5.75e-01 97.0% 95.0%
4953517 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 59.0 5.76e-01 94.0% 93.2%
4990371 70.1.1.0 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like 0.69 59.0 5.81e-01 92.5% 95.7%
3516152 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 59.0 5.46e-01 95.5% 95.3%
2389830 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.68 57.0 5.20e-01 94.0% 87.9%
1176847 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.68 59.0 5.65e-01 97.0% 94.8%
5016905 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.64 53.0 5.31e-01 91.0% 95.6%
D2 high residues 91-147
PDB
Domain cluster: rep: NC_074638__YP_010772018.1__QIT35-gp28__00028__D11-63
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6xgqb01 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.86 79.0 6.59e-01 100.0% 64.5%
1c5eA00 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.78 71.0 5.94e-01 100.0% 90.5%
1g8lA04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.71 62.0 5.68e-01 96.5% 98.6%
6ethA04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.70 63.0 5.43e-01 100.0% 89.9%
8bveA03 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.70 62.0 5.73e-01 98.2% 100.0%
2w5eA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.65 45.0 4.18e-01 100.0% 56.8%
4fw1A02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.59 35.0 3.63e-01 80.7% 61.1%
1yu0A02 2.80.20.10 Mainly Beta › Trefoil › Tail fiber receptor-binding protein › Tail fiber receptor-binding protein 0.59 48.0 3.75e-01 100.0% 72.6%
1vloA04 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.58 47.0 4.02e-01 100.0% 56.0%
1kk1A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 46.0 3.29e-01 100.0% 95.9%
2f2hA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 31.0 3.34e-01 100.0% 64.6%
3mmlE02 2.40.100.10 Mainly Beta › Beta Barrel › Cyclophilin › Cyclophilin-like 0.54 43.0 3.62e-01 100.0% 78.3%
2k2dA00 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.51 34.0 3.67e-01 82.5% 85.1%
1cqxA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 41.0 3.42e-01 100.0% 48.6%
1u3bA02 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.50 42.0 3.82e-01 100.0% 96.3%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2559744 70.4.1.2 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.88 76.0 7.52e-01 100.0% 88.1%
2640772 70.4.1.1 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › HDPD 0.85 79.0 6.42e-01 100.0% 60.0%
3945811 70.4.1.7 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › XM1_gp53_minor_capsid 0.85 77.0 7.58e-01 98.2% 96.7%
5083817 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.83 73.0 6.98e-01 96.5% 98.5%
3513462 70.4.1.8 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement 0.82 74.0 7.33e-01 100.0% 96.7%
5007190 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.80 67.0 7.11e-01 96.5% 100.0%
4963571 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.79 70.0 6.69e-01 100.0% 83.1%
5033307 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.79 72.0 5.28e-01 100.0% 43.6%
5002645 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.78 72.0 7.13e-01 100.0% 98.3%
4937267 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.78 69.0 5.31e-01 96.5% 48.3%
5022524 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.78 69.0 6.44e-01 100.0% 78.6%
5016125 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.78 67.0 6.83e-01 98.2% 96.4%
5024766 7550.1.1.5 ↗ a/b three-layered sandwiches › Tetrapyrrole methylase N-terminal domain › Tetrapyrrole methylase N-terminal domain › Tetrapyrrole methylase N-terminal domain › DUF7839 0.78 65.0 4.59e-01 94.7% 31.9%
5002644 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.77 70.0 6.36e-01 100.0% 96.0%
5039270 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.76 65.0 6.69e-01 98.2% 96.4%
2808420 70.4.1.1 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › HDPD 0.76 68.0 5.46e-01 100.0% 78.9%
4930420 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.76 67.0 6.27e-01 100.0% 78.6%
3986892 70.4.1.8 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement 0.76 67.0 6.15e-01 100.0% 93.3%
5083816 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.76 69.0 6.41e-01 100.0% 92.9%
3602933 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.74 68.0 6.46e-01 100.0% 93.8%
3205316 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.73 65.0 5.59e-01 100.0% 93.3%
3970970 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.71 64.0 5.83e-01 100.0% 97.3%
5075574 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 63.0 5.62e-01 100.0% 92.5%
3398750 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 63.0 5.63e-01 100.0% 95.0%
3516152 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.70 63.0 5.46e-01 100.0% 92.9%
3227803 70.1.1.0 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like 0.70 62.0 5.95e-01 98.2% 100.0%
3959516 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 63.0 5.69e-01 100.0% 96.0%
4617493 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.69 62.0 5.53e-01 100.0% 92.5%
2526359 70.4.1.2 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.68 60.0 5.98e-01 100.0% 95.0%
4217249 375.1.1.204 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › PolC_DP2_central 0.66 45.0 3.76e-01 71.9% 68.0%
5056460 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.64 44.0 4.08e-01 100.0% 56.0%
3283905 70.1.1.0 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like 0.64 53.0 5.05e-01 98.2% 97.1%
3255841 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.59 45.0 3.16e-01 84.2% 89.0%
1107991 4166.1.1.4 ↗ beta sandwiches › Lactophage receptor-binding protein N-terminal domain-like › Lactophage receptor-binding protein N-terminal domain-like › Lactophage receptor-binding protein N-terminal domain-like › mtd_2nd 0.59 48.0 4.00e-01 100.0% 91.4%
2984229 70.1.1.1 ↗ beta barrels › beta-clip › MoeA C-terminal domain-like › MoeA C-terminal domain-like › MoeA_C 0.58 49.0 4.53e-01 100.0% 94.9%
4512779 75.1.1.2 ↗ beta barrels › Cyclophilin-like › Cyclophilin-like › Cyclophilin-like › CT_A_B 0.55 45.0 3.52e-01 100.0% 62.1%
3741680 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 37.0 3.74e-01 84.2% 74.5%
3704784 325.1.7.1 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › Biotin_lipoyl 0.53 47.0 4.14e-01 100.0% 91.8%
4581802 377.1.1.11 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › RecO_C 0.52 42.0 3.14e-01 96.5% 41.2%
3556811 391.1.1.1 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › fn1 0.51 35.0 3.70e-01 93.0% 84.0%
3229874 708.1.1.18 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › DUF7747 0.51 43.0 3.07e-01 96.5% 69.1%