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NC_041929.1__YP_009601126.1__FDH46_gp001__00001

Bact-Vir

NC_041929.1__YP_009601126.1__FDH46_gp001__00001

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

55.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 5-90
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3bdrA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.70 43.0 3.49e-01 95.3% 34.0%
3t4nA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.69 43.0 4.18e-01 88.4% 56.2%
1k8kD01 3.30.1460.20 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.65 47.0 3.89e-01 75.6% 68.9%
1lkeA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.61 47.0 3.86e-01 94.2% 45.2%
6f91A01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.60 47.0 3.26e-01 83.7% 53.6%
6serA01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.60 47.0 3.47e-01 97.7% 32.0%
4aghA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.59 41.0 4.20e-01 97.7% 76.2%
1jy1A01 3.30.870.10 Alpha Beta › 2-Layer Sandwich › Endonuclease; Chain A › Endonuclease Chain A 0.58 46.0 3.55e-01 87.2% 76.4%
2w4yA00 2.40.160.220 Mainly Beta › Beta Barrel › Porin › 0.58 52.0 4.61e-01 98.8% 72.1%
6f90A01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.58 46.0 3.18e-01 84.9% 36.5%
1pzdA01 2.60.40.1480 Mainly Beta › Sandwich › Immunoglobulin-like › Coatomer, gamma subunit, appendage domain 0.56 46.0 3.77e-01 89.5% 64.1%
4p02A03 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.55 40.0 3.65e-01 77.9% 83.6%
2wvxA01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.55 44.0 3.09e-01 89.5% 68.2%
2i99A01 3.30.1780.10 Alpha Beta › 2-Layer Sandwich › ornithine cyclodeaminase, domain 1 › ornithine cyclodeaminase, domain 1 0.54 46.0 3.88e-01 100.0% 54.7%
4ccvA00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 48.0 4.36e-01 98.8% 89.6%
8aa0E01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.53 46.0 3.18e-01 97.7% 42.5%
2giaB00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.53 43.0 3.68e-01 90.7% 73.3%
1xszA03 3.30.310.140 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › sec7 domains 0.53 43.0 3.51e-01 88.4% 58.6%
6zhhA01 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.53 47.0 3.71e-01 100.0% 58.3%
3gkeA02 3.90.380.10 Alpha Beta › Alpha-Beta Complex › Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 › Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 0.52 47.0 3.53e-01 100.0% 73.8%
1cruA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.52 45.0 2.89e-01 98.8% 36.2%
7clgA01 3.30.870.10 Alpha Beta › 2-Layer Sandwich › Endonuclease; Chain A › Endonuclease Chain A 0.52 42.0 3.27e-01 88.4% 62.1%
3w9kA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 44.0 3.78e-01 93.0% 59.3%
1d7bA00 2.60.40.1210 Mainly Beta › Sandwich › Immunoglobulin-like › Cellobiose dehydrogenase, cytochrome domain 0.52 44.0 3.43e-01 94.2% 92.4%
2z6oA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.51 45.0 3.67e-01 98.8% 77.1%
1vavA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 45.0 3.38e-01 100.0% 77.0%
5bncB01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 38.0 3.28e-01 82.6% 83.9%
4jgwA01 1.20.870.10 Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 0.50 35.0 2.90e-01 75.6% 40.4%
5brqA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.50 40.0 4.13e-01 93.0% 91.4%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4944962 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.69 44.0 4.17e-01 89.5% 55.0%
3408795 12.1.1.60 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Chitin_bind_4 0.68 46.0 5.39e-01 97.7% 98.4%
3752441 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.65 44.0 3.96e-01 94.2% 50.0%
3729312 9.14.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Uncharacterized protein YLR301W › Uncharacterized protein YLR301W › HRI1 0.65 48.0 4.47e-01 79.1% 80.9%
5014277 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.64 44.0 4.45e-01 97.7% 71.8%
5074323 331.10.2.0 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.63 40.0 3.71e-01 89.5% 47.8%
3645476 295.1.1.1 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PC4 0.63 41.0 3.95e-01 91.9% 57.0%
3282173 2004.1.1.689 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15, AAA_21 0.62 54.0 3.53e-01 95.3% 42.1%
3248630 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.62 51.0 3.34e-01 88.4% 27.5%
3823242 216.1.1.5 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › BRE 0.61 47.0 4.21e-01 100.0% 59.2%
3455686 844.1.1.5 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › DUF3527 0.61 54.0 3.86e-01 100.0% 47.7%
3171956 9.1.1.45 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › FBO_C 0.60 46.0 3.88e-01 100.0% 47.3%
3192104 3385.1.1.0 ↗ beta barrels › Allergen Alt a 1 › Allergen Alt a 1 › Allergen Alt a 1 0.60 51.0 4.53e-01 93.0% 69.6%
3615124 5.1.3.28 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › BNR_3 0.58 52.0 3.42e-01 100.0% 45.3%
135591 265.1.1.4 ↗ a+b two layers › RNA bacteriophage capsid protein › RNA bacteriophage capsid protein › RNA bacteriophage capsid protein › PhiCb5_coat 0.58 52.0 4.61e-01 98.8% 72.1%
3743439 897.1.1.1 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 › MAM33 0.57 52.0 4.03e-01 100.0% 70.3%
3368132 4099.1.1.4 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › CENP-O 0.57 48.0 4.37e-01 100.0% 68.3%
3934735 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.55 49.0 4.74e-01 100.0% 98.0%
3730272 301.7.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › YjgF-like › YjgF-like 0.55 44.0 3.75e-01 87.2% 99.3%
3328470 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.55 48.0 4.22e-01 100.0% 65.4%
3715886 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.55 44.0 2.88e-01 87.2% 24.1%
3558274 4096.1.1.1 ↗ a+b two layers › NAP-like › NAP-like › NAP-like › NAP 0.54 45.0 3.17e-01 94.2% 53.7%
4864166 5.1.3.22 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › GSDH 0.53 46.0 3.43e-01 100.0% 66.3%
3479226 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.53 42.0 4.01e-01 100.0% 75.0%
3700517 5.1.2.33 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › BNR_3 0.52 45.0 3.12e-01 100.0% 45.9%
3827202 5.1.11.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed › eIF2A 0.51 44.0 3.38e-01 100.0% 50.9%
3297404 243.1.1.2 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › NTF2 0.51 45.0 3.85e-01 97.7% 100.0%
3608101 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 38.0 3.74e-01 80.2% 74.7%
3917491 331.4.1.5 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › KA1_BRSK 0.51 41.0 3.59e-01 89.5% 58.5%
D2 high residues 98-149
PDB
D3 high residues 294-341
PDB
D4 medium residues 224-284
PDB