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NC_070885.1__YP_010661734.1__PP936_gp096__00096

Bact-Vir

NC_070885.1__YP_010661734.1__PP936_gp096__00096

Identity

Accession:
NC_070885 ↗
Kingdom:
phage

Quality

87.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Trinifflemingvirus› Rhizobium_phage_RHph_I1_9

TaxID: 2509729

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 4-63
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1jx4A04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.66 48.0 4.16e-01 80.0% 60.2%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.62 45.0 3.78e-01 80.0% 48.6%
1fo0B00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 47.0 3.90e-01 85.0% 63.4%
2m2dA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 47.0 3.78e-01 85.0% 60.2%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.58 42.0 4.46e-01 80.0% 96.0%
2qhlD00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 45.0 3.73e-01 85.0% 65.1%
1tvdA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 44.0 3.61e-01 83.3% 62.1%
1q8mA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 44.0 3.50e-01 83.3% 54.5%
5xbfA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.57 39.0 3.56e-01 81.7% 50.6%
1bebA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 41.0 3.23e-01 83.3% 90.4%
3hnmA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 41.0 3.03e-01 78.3% 52.1%
1hxmB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 43.0 3.47e-01 85.0% 63.2%
4a3zA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.56 41.0 3.19e-01 78.3% 60.3%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.56 41.0 3.44e-01 81.7% 52.9%
2m6pA00 2.20.28.270 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › RNA polymerase-binding protein A 0.56 36.0 4.03e-01 75.0% 84.8%
3bcwA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 34.0 2.88e-01 78.3% 33.7%
4b6zA01 2.60.40.3120 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 37.0 3.09e-01 83.3% 36.3%
6lxgA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.56 39.0 3.71e-01 75.0% 100.0%
6rptC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 39.0 3.16e-01 76.7% 40.2%
4txwA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 39.0 3.02e-01 81.7% 46.5%
4limA00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.54 45.0 2.85e-01 98.3% 72.4%
2kd7A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 38.0 2.93e-01 81.7% 29.6%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.54 39.0 3.35e-01 81.7% 54.1%
2orzA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 38.0 2.91e-01 78.3% 97.4%
2gbmA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 41.0 3.75e-01 85.0% 91.4%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 39.0 2.96e-01 80.0% 88.5%
3h20A02 3.30.70.1790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RepB DNA-primase, N-terminal domain 0.53 43.0 3.77e-01 100.0% 99.0%
4jzjC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 39.0 3.37e-01 83.3% 54.8%
8gr2A01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.53 38.0 2.72e-01 78.3% 56.9%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 38.0 3.27e-01 80.0% 66.7%
2h7aA01 3.10.510.20 Alpha Beta › Roll › NE1680-like fold › YcgL domain 0.52 43.0 4.11e-01 100.0% 78.9%
2dk6A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.52 40.0 3.53e-01 86.7% 81.9%
2jdaB00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 42.0 3.37e-01 100.0% 62.7%
2o3iA01 3.40.1610.10 Alpha Beta › 3-Layer(aba) Sandwich › CV3147-like fold › CV3147-like domain 0.52 40.0 2.84e-01 93.3% 44.9%
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.52 38.0 3.21e-01 85.0% 75.8%
1kq1H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.52 38.0 3.72e-01 78.3% 71.2%
2i02A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 39.0 3.11e-01 86.7% 44.3%
3mb5A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.51 37.0 3.73e-01 78.3% 91.9%
4chkB00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 39.0 3.48e-01 85.0% 83.5%
3lgdA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.51 36.0 2.17e-01 75.0% 41.7%
3qnfC01 2.60.40.1730 Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain 0.51 36.0 2.57e-01 78.3% 22.4%
1wv4B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 37.0 2.91e-01 83.3% 39.6%
2wuhA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 36.0 2.75e-01 78.3% 53.4%
1u1sA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.51 37.0 3.64e-01 78.3% 71.2%
7eehA01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.51 35.0 2.39e-01 75.0% 40.6%
2ej9A02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.50 34.0 3.75e-01 71.7% 89.8%
4yn3A02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.50 39.0 3.14e-01 91.7% 97.8%
3wqbA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 36.0 2.78e-01 81.7% 39.8%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3607227 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.66 46.0 4.86e-01 75.0% 96.0%
4355655 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.65 48.0 3.84e-01 81.7% 97.6%
4971848 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.62 55.0 3.52e-01 100.0% 94.8%
4021064 10.9.1.0 ↗ beta sandwiches › jelly-roll › C-terminal domain of mullusc hemocyanin › C-terminal domain of mullusc hemocyanin 0.62 47.0 3.98e-01 83.3% 76.2%
5041794 206.1.3.40 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATPgrasp_YheCD 0.62 54.0 3.46e-01 100.0% 96.3%
5010420 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.62 48.0 3.96e-01 85.0% 99.1%
3917302 10.1.1.10 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › MAM 0.60 43.0 3.16e-01 81.7% 27.6%
4157339 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.60 43.0 3.51e-01 81.7% 39.2%
4082091 302.1.1.0 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.58 42.0 3.56e-01 80.0% 60.0%
4864730 11.1.1.99 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set 0.58 44.0 3.65e-01 85.0% 61.7%
3813787 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 42.0 3.42e-01 76.7% 96.5%
3227155 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.58 41.0 3.38e-01 80.0% 39.1%
5037200 303.1.1.1 ↗ a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.58 45.0 3.46e-01 90.0% 46.8%
None — 0.57 43.0 2.70e-01 83.3% 53.6%
4937253 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.57 42.0 3.39e-01 80.0% 48.7%
4990637 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.56 45.0 4.25e-01 100.0% 84.3%
185449 3342.1.1.1 ↗ beta sandwiches › C-terminal domain in a putative lipoprotein BACOVA_00967 › C-terminal domain in a putative lipoprotein BACOVA_00967 › C-terminal domain in a putative lipoprotein BACOVA_00967 › DUF4842 0.55 43.0 2.81e-01 91.7% 97.2%
3215161 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 40.0 3.66e-01 80.0% 65.5%
2323826 4187.2.1.1 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 › NAGPA 0.55 40.0 3.71e-01 78.3% 65.4%
4995671 3115.1.1.12 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › PF30567 0.55 38.0 3.99e-01 81.7% 92.0%
3366242 2487.1.1.0 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" 0.55 41.0 3.14e-01 80.0% 100.0%
4939879 315.1.1.15 ↗ a+b two layers › Tautomerase/MIF-like › Tautomerase/MIF › Tautomerase/MIF › DUF5402 0.54 41.0 3.37e-01 86.7% 49.2%
3426874 2487.1.1.7 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › PA 0.53 41.0 3.31e-01 91.7% 100.0%
3511375 4.1.1.349 ↗ beta barrels › SH3 › SH3 › SH3 › ROF 0.52 37.0 3.37e-01 76.7% 60.0%
4202760 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.52 37.0 3.34e-01 80.0% 88.4%
4463006 3115.2.1.0 ↗ a+b two layers › GP2-like › GP2 › GP2 0.52 35.0 3.75e-01 75.0% 97.8%
3678933 7590.1.1.3 ↗ a/b three-layered sandwiches › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Piwi,ArgoMid 0.52 39.0 2.88e-01 85.0% 62.7%
3464173 4004.1.1.5 ↗ beta sandwiches › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › DAGK_acc 0.52 38.0 2.63e-01 81.7% 93.0%
4206728 304.110.1.1 ↗ a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like › Acylphosphatase 0.51 41.0 3.76e-01 100.0% 93.5%
4063927 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.51 38.0 2.83e-01 86.7% 50.5%
3244570 304.7.1.4 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › S8_pro-domain 0.51 38.0 3.47e-01 81.7% 84.7%
5004463 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 37.0 2.45e-01 83.3% 97.5%
3164326 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.51 36.0 3.43e-01 76.7% 100.0%
3503404 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.51 37.0 3.15e-01 81.7% 49.1%
5054197 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.51 36.0 3.38e-01 80.0% 96.2%
3958601 217.1.1.2 ↗ a+b complex topology › FAD-binding domain-like › FAD-binding domain › FAD-binding domain › FAD_binding_4 0.51 35.0 2.98e-01 75.0% 44.0%
3321067 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 38.0 3.43e-01 88.3% 57.8%
3346140 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.50 37.0 3.34e-01 85.0% 86.3%