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NC_048028.1__YP_009807721.1__HOT82_gp025__00025

Bact-Vir

NC_048028.1__YP_009807721.1__HOT82_gp025__00025

Identity

Accession:
NC_048028 ↗
Kingdom:
phage

Quality

55.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Ronaldovirus› Gordonia_phage_Ronaldo

TaxID: 2250397

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 88-160
PDB
D2 high residues 218-271
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ixkA01 3.30.70.1170 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sun protein; domain 3 0.72 51.0 4.11e-01 79.6% 39.0%
2of5H00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.70 54.0 4.41e-01 85.2% 47.0%
2ltuA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.69 49.0 4.74e-01 74.1% 66.1%
2l3nA00 1.10.1050.20 Mainly Alpha › Orthogonal Bundle › Ribosomal Protein S4 Delta 41; Chain A, domain 1 › 0.69 54.0 4.38e-01 96.3% 45.2%
1v92A00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.68 51.0 5.43e-01 88.9% 97.8%
2l2dA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.68 55.0 5.06e-01 92.6% 72.6%
1oaiA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.68 53.0 5.18e-01 90.7% 79.7%
2yviA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.67 49.0 4.23e-01 79.6% 85.4%
2g3bA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.67 48.0 3.33e-01 85.2% 22.5%
1wxpA01 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.65 47.0 4.21e-01 81.5% 88.1%
1iv8A03 1.10.150.200 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Maltooligosyl trehalose synthase; domain 3 0.65 52.0 4.43e-01 87.0% 71.8%
1ctfA00 3.30.1390.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS 0.65 44.0 4.13e-01 74.1% 55.9%
2l4eA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.64 52.0 5.15e-01 100.0% 89.5%
1u9lB00 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.63 46.0 4.27e-01 77.8% 85.7%
2mqkA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.63 44.0 4.10e-01 72.2% 70.8%
2oap202 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 50.0 3.15e-01 87.0% 23.1%
3ivpD01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.61 41.0 3.70e-01 70.4% 60.0%
2o38A01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.60 42.0 3.92e-01 72.2% 66.2%
7fsfA02 3.30.56.80 Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › 0.60 42.0 3.94e-01 75.9% 76.8%
5eoxB03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 43.0 3.24e-01 75.9% 43.8%
3ezqA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.59 49.0 3.97e-01 100.0% 73.9%
1aipH03 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.58 47.0 4.75e-01 100.0% 100.0%
2ld7A00 6.10.160.20 Special › Helix non-globular › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.57 38.0 3.22e-01 77.8% 40.4%
3oc2A01 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.56 46.0 3.31e-01 94.4% 40.5%
3l0oA01 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.56 38.0 3.92e-01 79.6% 79.6%
7o06C01 3.30.1470.10 Alpha Beta › 2-Layer Sandwich › Photosystem 1 Reaction Centre Subunit Ii; Chain: D; › Photosystem I PsaD, reaction center subunit II 0.56 41.0 3.55e-01 81.5% 82.4%
1t90A01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.54 47.0 2.97e-01 96.3% 31.4%
4g6dB02 6.10.140.1800 Special › Helix non-globular › Helix Hairpins › 0.51 41.0 3.52e-01 98.1% 56.8%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4332288 4095.1.1.1 ↗ alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › DNA_ligase_A_N 0.79 62.0 4.80e-01 83.3% 42.7%
3702894 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.78 62.0 6.47e-01 87.0% 100.0%
None — 0.76 52.0 3.08e-01 75.9% 10.3%
3561384 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.75 50.0 5.62e-01 74.1% 100.0%
3706294 103.1.1.103 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › PF29442 0.74 52.0 5.56e-01 79.6% 88.9%
3226566 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.71 50.0 4.91e-01 75.9% 68.3%
4239182 103.13.1.1 ↗ alpha arrays › RuvA-C › C-terminal lid domain of glucokinase regulatory protein › C-terminal lid domain of glucokinase regulatory protein › GKRP-like_C 0.70 53.0 4.77e-01 83.3% 58.7%
3516806 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.70 51.0 3.15e-01 75.9% 14.6%
3781465 103.1.1.88 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › PF27606 0.67 51.0 4.99e-01 90.7% 75.0%
3166932 130.1.1.10 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP30_Sin3_bdg 0.67 39.0 4.50e-01 77.8% 82.1%
4264894 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.66 55.0 4.89e-01 96.3% 66.3%
3740975 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.66 51.0 5.01e-01 88.9% 81.7%
3737617 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.65 53.0 5.20e-01 96.3% 85.0%
4207508 103.1.1.84 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › PF28540 0.65 53.0 5.29e-01 92.6% 89.1%
4081317 103.13.1.0 ↗ alpha arrays › RuvA-C › C-terminal lid domain of glucokinase regulatory protein › C-terminal lid domain of glucokinase regulatory protein 0.64 47.0 4.36e-01 83.3% 61.4%
4008313 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.62 45.0 4.23e-01 77.8% 78.5%
4269992 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.61 47.0 4.36e-01 90.7% 70.7%
4465202 103.1.1.1 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › UBA 0.60 51.0 5.12e-01 96.3% 94.5%
3258982 103.1.1.2 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › CUE 0.60 43.0 4.61e-01 77.8% 97.8%
3306298 101.1.4.53 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › PF29035 0.58 42.0 4.10e-01 75.9% 71.7%
3659756 3238.1.1.1 ↗ alpha superhelices › Mitochondrial mTERF-like › Mitochondrial mTERF › Mitochondrial mTERF › mTERF 0.57 45.0 3.25e-01 96.3% 42.1%
4034109 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.52 39.0 3.70e-01 79.6% 67.7%
D3 medium residues 3-65
PDB