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NC_070814.1__YP_010654685.1__PP510_gp53__00053

Bact-Vir

NC_070814.1__YP_010654685.1__PP510_gp53__00053

Identity

Accession:
NC_070814 ↗
Kingdom:
phage

Quality

67.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Beenievirus› Gordonia_phage_Easley

TaxID: 2182395

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 8-54
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4z32A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.75 44.0 3.41e-01 72.3% 28.1%
4flnA02 3.20.190.20 Alpha Beta › Alpha-Beta Barrel › N-terminal domain of MutM-like DNA repair proteins › 0.74 49.0 3.43e-01 70.2% 28.9%
7kfuC02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.72 49.0 3.11e-01 72.3% 14.6%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 45.0 3.60e-01 70.2% 36.8%
5xpyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 42.0 3.19e-01 70.2% 26.9%
3luuA00 3.30.2020.30 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › 0.67 46.0 3.66e-01 72.3% 50.6%
4c5wA01 3.30.2020.30 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › 0.66 46.0 3.53e-01 72.3% 58.8%
2auwA01 3.30.2020.10 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › NE0471-like N-terminal domain 0.66 41.0 3.40e-01 70.2% 35.4%
1hyuA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.63 46.0 3.07e-01 78.7% 57.1%
2a5hA03 6.20.120.40 Special › Other non-globular › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.62 38.0 3.55e-01 72.3% 46.8%
1v57A03 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.61 42.0 2.90e-01 72.3% 31.2%
3fm8D03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 39.0 2.98e-01 70.2% 87.0%
3f4lA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.59 44.0 2.86e-01 83.0% 19.3%
3jyyA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.58 51.0 3.71e-01 100.0% 52.2%
1x9mA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 41.0 2.64e-01 76.6% 17.3%
1b9mA03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.56 37.0 3.24e-01 70.2% 43.7%
2vszB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 37.0 2.86e-01 70.2% 98.3%
4tyzA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 39.0 2.97e-01 74.5% 33.0%
1x1fA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 37.0 2.53e-01 70.2% 61.7%
3vz9B00 3.30.457.50 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › Chromosome segregation protein Spc25 0.55 39.0 3.18e-01 80.9% 87.4%
3ezjA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.55 38.0 3.38e-01 74.5% 52.9%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.54 42.0 3.05e-01 87.2% 67.9%
1iwmA00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.54 39.0 2.67e-01 78.7% 27.7%
5xuhA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.54 39.0 2.99e-01 83.0% 55.2%
1nkiA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.53 44.0 3.32e-01 100.0% 85.1%
2wweA01 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.53 41.0 3.21e-01 85.1% 39.4%
4py5A01 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.53 39.0 3.32e-01 76.6% 50.0%
4hstA01 1.10.439.10 Mainly Alpha › Orthogonal Bundle › Penicillin Amidohydrolase; domain 1 › Penicillin Amidohydrolase, domain 1 0.52 42.0 3.09e-01 100.0% 31.1%
4p79A00 1.20.140.150 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.51 44.0 2.97e-01 97.9% 27.6%
1xtfA00 3.90.1240.10 Alpha Beta › Alpha-Beta Complex › Zincin-like › "Metalloproteases (""zincins""), catalytic domain like" 0.50 42.0 2.45e-01 93.6% 11.2%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3959944 3826.1.1.95 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › RNA_pol_Rpb1_1 0.83 55.0 4.26e-01 76.6% 33.7%
4072958 2.1.1.9 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_S4e 0.75 45.0 3.95e-01 70.2% 43.1%
4943272 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.74 44.0 4.02e-01 70.2% 46.7%
3256547 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.72 43.0 3.32e-01 70.2% 28.0%
4026595 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.71 43.0 3.46e-01 70.2% 31.8%
3576046 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.70 45.0 4.44e-01 70.2% 60.0%
3708219 331.23.1.4 ↗ a+b two layers › TBP-like › Integrator IntS9/IntS11 C-terminal domain › Integrator IntS9/IntS11 C-terminal domain › CPSF100_C 0.70 42.0 3.65e-01 78.7% 40.0%
4025931 377.1.1.6 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › Ribosomal_L24e 0.68 41.0 2.95e-01 87.2% 22.3%
3364309 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.68 46.0 3.24e-01 70.2% 25.4%
3998421 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.67 45.0 4.02e-01 70.2% 55.4%
5049640 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 44.0 3.67e-01 72.3% 41.8%
3552232 377.1.1.6 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › Ribosomal_L24e 0.66 37.0 2.60e-01 87.2% 18.9%
4565519 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.65 43.0 3.20e-01 70.2% 50.8%
3598207 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 42.0 3.05e-01 70.2% 25.6%
4985007 7581.1.1.6 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Chal_sti_synt_C 0.64 43.0 3.00e-01 70.2% 25.9%
4942265 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 42.0 3.64e-01 74.5% 40.0%
3260618 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.61 42.0 3.11e-01 72.3% 50.0%
3538471 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 41.0 3.01e-01 70.2% 33.3%
3897880 3935.1.1.1 ↗ extended segments › 4E-BP2 › 4E-BP2 › 4E-BP2 › eIF_4EBP 0.60 38.0 3.59e-01 70.2% 54.5%
3962772 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.60 43.0 3.05e-01 74.5% 27.1%
3540263 377.1.1.50 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › ZMYM4 0.59 42.0 4.29e-01 74.5% 91.1%
4855695 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.59 41.0 2.69e-01 74.5% 19.1%
5048050 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 37.0 2.26e-01 93.6% 10.5%
5045224 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.58 41.0 3.39e-01 74.5% 88.2%
3616361 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.57 44.0 2.95e-01 91.5% 20.5%
3722860 2004.1.1.463 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin, Kinesin_assoc, Microtub_bd 0.57 47.0 2.77e-01 97.9% 64.3%
5004414 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.56 40.0 3.23e-01 83.0% 75.7%
3439923 1.1.11.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain 0.56 41.0 3.66e-01 83.0% 54.7%
4653150 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.56 41.0 3.20e-01 80.9% 53.6%
3995979 220.1.1.34 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_9 0.56 39.0 2.90e-01 72.3% 79.2%
3938900 3346.1.1.5 ↗ a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › ODR4-like 0.55 46.0 3.09e-01 93.6% 46.5%
3691304 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.55 46.0 2.93e-01 97.9% 29.1%
5062120 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 37.0 2.89e-01 70.2% 43.8%
4428289 301.8.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › 4'-phosphopantetheinyl transferase › 4'-phosphopantetheinyl transferase › ACPS 0.54 38.0 2.93e-01 78.7% 59.2%
4080950 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.54 41.0 2.88e-01 91.5% 63.7%
3238035 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.54 36.0 3.54e-01 70.2% 62.0%
3418933 2004.1.1.414 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GTP_EFTU, MMR_HSR1 0.54 41.0 2.68e-01 83.0% 29.8%
3701382 312.1.1.8 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › DcpS_C 0.53 43.0 2.76e-01 95.7% 76.7%
2507513 210.1.2.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › Penicil_amidase 0.53 42.0 2.91e-01 100.0% 24.6%
5014724 295.1.1.51 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › FtsQ_DivIB_C 0.53 42.0 3.20e-01 91.5% 40.0%
3180103 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.52 41.0 2.39e-01 97.9% 90.4%
4942722 377.1.1.6 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › Ribosomal_L24e 0.52 43.0 3.60e-01 91.5% 57.5%
3657220 2004.1.1.73 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.52 46.0 2.66e-01 100.0% 20.5%
4033043 616.1.1.41 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Terminase_4 0.51 36.0 2.93e-01 74.5% 38.9%
3271906 377.1.1.4 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › GATA 0.51 44.0 4.06e-01 93.6% 84.7%
None — 0.51 45.0 2.62e-01 100.0% 18.1%
3269367 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.51 42.0 3.41e-01 95.7% 96.8%
4959884 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.50 39.0 3.75e-01 100.0% 72.7%
5083877 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.50 45.0 3.23e-01 100.0% 57.8%
4164380 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.50 42.0 3.58e-01 95.7% 91.3%
D2 medium residues 63-156
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
8e9gK01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 46.0 4.69e-01 85.1% 65.9%
2fp1B00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.68 47.0 3.85e-01 100.0% 40.2%
1cunA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 45.0 4.37e-01 86.2% 62.7%
1h7cA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 48.0 4.71e-01 85.1% 70.9%
1vh6A01 6.10.140.1940 Special › Helix non-globular › Helix Hairpins › 0.58 46.0 4.57e-01 87.2% 80.4%
3buxB01 1.20.930.20 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Adaptor protein Cbl, N-terminal domain 0.55 42.0 3.83e-01 100.0% 59.7%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4007316 3291.1.1.4 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › PspA_IM30 0.78 55.0 4.56e-01 72.3% 73.5%
4963794 3755.4.1.90 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › PspA_IM30 0.73 51.0 4.26e-01 72.3% 45.0%
4974450 3291.1.1.4 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › PspA_IM30 0.72 66.0 5.33e-01 100.0% 85.7%
3489767 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.71 46.0 4.16e-01 85.1% 48.8%
3940779 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 45.0 4.36e-01 71.3% 62.9%
3292425 3291.1.1.4 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › PspA_IM30 0.64 47.0 3.65e-01 78.7% 35.6%