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NC_070888.1__YP_010662453.1__PP939_gp045__00045

Bact-Vir

NC_070888.1__YP_010662453.1__PP939_gp045__00045

Identity

Accession:
NC_070888 ↗
Kingdom:
phage

Quality

83.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Innesvirus› Rhizobium_phage_RL38J1

TaxID: 2663232

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 3-85
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2dk7A00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.68 37.0 3.89e-01 90.4% 58.9%
1sgoA01 3.30.2280.10 Alpha Beta › 2-Layer Sandwich › copper amine oxidase-like fold › Hypothetical protein (hspc210) 0.67 46.0 4.21e-01 96.4% 54.6%
1f9cA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.66 53.0 4.67e-01 86.7% 94.3%
3rr1A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.64 53.0 4.48e-01 90.4% 83.9%
2oztA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.61 48.0 4.31e-01 86.7% 97.5%
2q18X01 3.10.330.40 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.59 43.0 4.66e-01 90.4% 91.4%
2vw9B00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.59 46.0 4.26e-01 84.3% 83.8%
4e4tA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.58 42.0 3.30e-01 79.5% 89.1%
1stzA03 3.30.390.60 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Heat-inducible transcription repressor hrca homolog; domain 3 0.58 40.0 4.00e-01 74.7% 89.9%
1mmuA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.57 46.0 3.01e-01 85.5% 85.3%
7q04F01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.56 43.0 3.94e-01 81.9% 88.1%
2zylA01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.55 46.0 3.96e-01 92.8% 71.9%
3vcaA02 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.55 44.0 3.98e-01 89.2% 83.2%
7ylsB01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.55 41.0 3.86e-01 81.9% 88.0%
3kk7A01 3.30.420.400 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.52 40.0 3.73e-01 85.5% 81.7%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3291683 4221.1.1.0 ↗ a+b two layers › YkuJ-like › YkuJ-like › YkuJ-like 0.73 49.0 4.81e-01 73.5% 64.4%
4566718 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.65 45.0 4.45e-01 72.3% 94.4%
4059525 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.63 44.0 4.21e-01 72.3% 91.6%
4072334 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.63 45.0 4.24e-01 75.9% 98.0%
4380331 295.1.1.27 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PF25991 0.62 36.0 3.92e-01 81.9% 68.6%
134801 218.1.1.5 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MenC_N 0.61 45.0 4.22e-01 78.3% 98.0%
4069377 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.61 45.0 4.32e-01 78.3% 97.9%
3170675 1013.1.1.0 ↗ beta duplicates or obligate multimers › WD repeat-containing protein 48 ancillary domain › WD repeat-containing protein 48 ancillary domain › WD repeat-containing protein 48 ancillary domain 0.61 40.0 3.08e-01 96.4% 28.0%
4031599 101.1.2.584 ↗ alpha arrays › HTH › HTH › winged helix domain › HrcA 0.60 43.0 4.20e-01 77.1% 95.8%
4303869 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.60 42.0 4.15e-01 74.7% 92.2%
4385005 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.59 41.0 4.01e-01 74.7% 94.7%
3924546 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.58 42.0 3.71e-01 77.1% 73.1%
3838444 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 35.0 3.64e-01 91.6% 62.5%
4643582 330.1.1.12 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › LIX1 0.57 44.0 3.48e-01 83.1% 91.4%
3827622 12.2.1.7 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Hyaluronate lyase-like, C-terminal domain › Hyaluronate lyase-like, C-terminal domain › BRX 0.57 36.0 4.29e-01 88.0% 91.7%
3346566 1.1.7.85 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › BRX 0.56 35.0 4.32e-01 86.7% 98.2%
3376285 706.1.1.4 ↗ beta complex topology › Head domain of nucleotide exchange factor GrpE › Head domain of nucleotide exchange factor GrpE › Head domain of nucleotide exchange factor GrpE › BRX 0.54 34.0 4.21e-01 85.5% 100.0%
3827130 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.53 45.0 2.98e-01 95.2% 57.1%
3371900 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.52 45.0 3.10e-01 100.0% 57.0%
None — 0.52 34.0 2.46e-01 94.0% 19.5%
3215728 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.51 31.0 3.45e-01 86.7% 81.7%
3379673 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 43.0 3.01e-01 94.0% 62.6%
4182428 220.1.1.191 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF28624 0.51 41.0 3.38e-01 88.0% 68.0%