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NC_051725.1__YP_009964102.1__I5J35_gp77__00077

Bact-Vir

NC_051725.1__YP_009964102.1__I5J35_gp77__00077

Identity

Accession:
NC_051725 ↗
Kingdom:
phage

Quality

56.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Trigintaduovirus› Mycobacterium_phage_Rem711

TaxID: 2079285

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 medium residues 25-89
PDB
Domain cluster: representative
CATH (56)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.75 52.0 5.24e-01 76.9% 72.7%
5u55A02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.71 44.0 3.53e-01 76.9% 32.8%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.70 52.0 4.59e-01 80.0% 92.6%
1wmhA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.68 43.0 4.02e-01 73.8% 50.6%
1yqsA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.61 45.0 2.91e-01 81.5% 72.5%
3tg9A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.61 44.0 2.86e-01 78.5% 73.6%
2npnA02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.60 47.0 3.99e-01 86.2% 88.1%
1b04A02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.60 43.0 3.85e-01 78.5% 53.5%
2mp4A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.60 50.0 3.88e-01 100.0% 52.7%
1u3eM02 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 0.60 44.0 4.39e-01 78.5% 85.3%
3hu1A01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.60 43.0 3.81e-01 76.9% 57.3%
2yn5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 41.0 3.93e-01 80.0% 60.8%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.60 44.0 4.25e-01 81.5% 69.7%
2jz6A01 2.30.170.40 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L28/L24 0.59 37.0 3.98e-01 81.5% 80.0%
2vfrA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.59 36.0 2.93e-01 72.3% 31.5%
2r6fA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.58 42.0 4.11e-01 80.0% 70.8%
2greF02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.58 40.0 3.79e-01 72.3% 66.7%
3pihA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.58 41.0 4.03e-01 80.0% 69.4%
2htdB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 41.0 3.38e-01 78.5% 51.6%
5escA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 41.0 3.41e-01 78.5% 53.8%
3nd1A02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.56 44.0 3.76e-01 87.7% 88.2%
2l9dA00 3.30.70.2340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Uncharacterised protein PF12112 family, DUF3579 0.56 40.0 3.51e-01 78.5% 81.5%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 39.0 3.51e-01 75.4% 50.0%
4he6A00 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 39.0 3.55e-01 73.8% 65.2%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.55 39.0 3.50e-01 75.4% 58.3%
3l5iA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 41.0 3.77e-01 80.0% 59.1%
1rfeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 40.0 3.23e-01 80.0% 48.5%
6b9tF01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.55 43.0 3.49e-01 86.2% 50.4%
2fg9A01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 41.0 3.15e-01 81.5% 47.2%
4a0tA03 2.60.320.30 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › 0.55 43.0 3.93e-01 87.7% 97.8%
1vl7A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 40.0 3.24e-01 80.0% 52.6%
3gd0A01 2.60.110.10 Mainly Beta › Sandwich › Thaumatin › Thaumatin 0.55 41.0 2.80e-01 83.1% 29.2%
2hhzA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 41.0 3.22e-01 80.0% 47.8%
2l72A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.54 46.0 3.87e-01 98.5% 55.9%
1ywlA00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.54 41.0 3.69e-01 84.6% 83.3%
1wx9A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 43.0 3.92e-01 86.2% 82.6%
2ig6A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 39.0 3.13e-01 80.0% 43.4%
3dnhA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 40.0 3.08e-01 80.0% 46.4%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.54 40.0 3.52e-01 84.6% 92.7%
4qd4A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 39.0 2.52e-01 78.5% 46.2%
3bh1A03 3.40.140.40 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Domain of unknown function (DUF1846), C-terminal subdomain 0.53 41.0 3.30e-01 87.7% 91.8%
4dguA01 2.60.40.2680 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 38.0 3.23e-01 83.1% 44.6%
2xf1A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.53 44.0 3.67e-01 95.4% 53.3%
3ec6A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 39.0 3.20e-01 80.0% 48.4%
2eixA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 40.0 3.41e-01 81.5% 58.5%
5jv4A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 38.0 3.03e-01 78.5% 55.6%
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.53 39.0 3.27e-01 81.5% 79.2%
2hq9B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 37.0 2.99e-01 78.5% 46.0%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.52 38.0 3.35e-01 84.6% 87.4%
2fhqA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 39.0 3.16e-01 84.6% 81.5%
1xffA00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.51 38.0 2.66e-01 83.1% 55.5%
3zq5A03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.51 36.0 2.84e-01 76.9% 33.3%
7bjkA02 3.55.40.20 Alpha Beta › 3-Layer(bab) Sandwich › minor pseudopilin epsh fold › Iron/manganese superoxide dismutase, C-terminal domain 0.51 42.0 3.54e-01 93.8% 66.4%
1xreA02 3.55.40.20 Alpha Beta › 3-Layer(bab) Sandwich › minor pseudopilin epsh fold › Iron/manganese superoxide dismutase, C-terminal domain 0.51 42.0 3.55e-01 93.8% 65.2%
6hj2A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.50 42.0 2.86e-01 98.5% 56.2%
4e6xB00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.50 38.0 2.61e-01 89.2% 81.4%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4030243 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.69 53.0 4.59e-01 84.6% 80.0%
3518750 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.69 46.0 3.98e-01 80.0% 43.8%
4632256 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 49.0 4.70e-01 76.9% 100.0%
5049794 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.67 57.0 4.42e-01 95.4% 57.2%
3552754 304.163.1.1 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › R1_ABCA1 0.66 49.0 4.62e-01 80.0% 100.0%
4959407 304.163.1.3 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › PF31118 0.65 44.0 4.87e-01 78.5% 92.0%
3802146 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.64 46.0 3.94e-01 76.9% 70.0%
3475431 133.1.1.0 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) 0.64 47.0 3.16e-01 78.5% 52.5%
3611587 4342.1.1.0 ↗ alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like 0.63 45.0 3.16e-01 76.9% 23.6%
4979507 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.62 52.0 4.08e-01 96.9% 57.0%
3994984 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.62 45.0 4.55e-01 76.9% 93.8%
3998938 6110.1.1.1 ↗ alpha superhelices › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › Linker domain of cytoplasmic dynein heavy chain › DHC_N2 0.61 41.0 2.47e-01 70.8% 19.8%
3941506 2002.1.1.16 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Bac_luciferase 0.60 49.0 3.09e-01 89.2% 51.6%
3911204 382.1.1.16 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › CD59 0.60 48.0 4.63e-01 95.4% 78.7%
3783481 11.1.1.642 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig-like_Pom152_1 0.60 43.0 3.49e-01 75.4% 55.0%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.59 41.0 4.56e-01 75.4% 96.0%
4961379 4176.1.1.2 ↗ a/b three-layered sandwiches › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › S-Me-THD_N 0.59 43.0 3.09e-01 81.5% 47.3%
3612075 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.59 43.0 3.00e-01 78.5% 30.5%
4011483 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 41.0 3.45e-01 75.4% 53.0%
4031603 1.1.7.22 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Peptidase_M42 0.59 41.0 3.55e-01 72.3% 73.7%
3988217 241.12.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › YktB/PF0168-like › YktB/PF0168-like 0.58 49.0 3.44e-01 92.3% 39.5%
5075402 210.1.3.3 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_4 0.58 43.0 2.89e-01 83.1% 40.4%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.57 42.0 3.86e-01 81.5% 95.6%
57 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.57 41.0 3.17e-01 78.5% 40.6%
3700302 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.57 44.0 3.43e-01 84.6% 66.2%
5052496 1.1.5.36 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyrid_ox_like 0.57 42.0 3.27e-01 81.5% 51.6%
3289401 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.56 43.0 3.50e-01 84.6% 73.8%
1392732 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.56 39.0 3.37e-01 75.4% 44.3%
3817222 221.1.1.1 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Fer2 0.56 42.0 3.85e-01 81.5% 84.3%
3487190 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.56 36.0 3.29e-01 73.8% 45.3%
3179826 11.1.1.642 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig-like_Pom152_1 0.56 40.0 3.26e-01 76.9% 56.0%
3383616 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.56 40.0 2.33e-01 76.9% 18.6%
3284440 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.55 41.0 3.29e-01 80.0% 46.4%
4954188 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.55 43.0 3.40e-01 89.2% 66.4%
4935672 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.55 43.0 3.46e-01 89.2% 72.1%
3702727 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.54 37.0 3.30e-01 72.3% 47.0%
3369564 130.1.1.39 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › DUF7086 0.54 38.0 3.05e-01 75.4% 57.1%
4930766 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.54 42.0 3.53e-01 93.8% 75.6%
3607484 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.54 40.0 3.03e-01 80.0% 86.7%
3782443 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.53 41.0 3.21e-01 89.2% 75.8%
4953373 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.53 39.0 3.15e-01 80.0% 47.4%
3242062 3680.1.1.1 ↗ a+b complex topology › Zinc finger FYVE domain-containing protein 9 C-terminal domain › Zinc finger FYVE domain-containing protein 9 C-terminal domain › Zinc finger FYVE domain-containing protein 9 C-terminal domain › SARA_C 0.52 37.0 2.82e-01 73.8% 88.7%
4053553 11.13.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Leukocidin-like › Leukocidin-like › Leukocidin 0.52 42.0 2.76e-01 93.8% 42.6%
2775442 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 39.0 4.13e-01 83.1% 91.5%
3298909 109.4.1.1599 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase 0.51 42.0 2.67e-01 93.8% 79.7%
5081134 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.51 37.0 3.77e-01 81.5% 90.0%
3358129 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.50 40.0 2.30e-01 90.8% 15.3%
3628791 3680.1.1.1 ↗ a+b complex topology › Zinc finger FYVE domain-containing protein 9 C-terminal domain › Zinc finger FYVE domain-containing protein 9 C-terminal domain › Zinc finger FYVE domain-containing protein 9 C-terminal domain › SARA_C 0.50 39.0 3.13e-01 92.3% 82.6%
D2 medium residues 187-251
PDB
D3 medium residues 269-350
PDB