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NC_034248.1__YP_009352376.1__B7L88_gp125__00119

Bact-Vir

NC_034248.1__YP_009352376.1__B7L88_gp125__00119

Identity

Accession:
NC_034248 ↗
Kingdom:
phage

Quality

93.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_RHEph10

TaxID: 1220717

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 medium residues 1-68
PDB
Domain cluster: representative
CATH (55)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3htvA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.73 38.0 3.21e-01 80.9% 30.6%
2vtfA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.68 59.0 5.34e-01 97.1% 92.3%
3vmnA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.68 60.0 5.07e-01 98.5% 91.9%
5c71A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 59.0 5.27e-01 98.5% 92.7%
2yn5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 56.0 5.36e-01 92.6% 92.4%
1mvpA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.67 50.0 4.26e-01 80.9% 69.6%
1eerC01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 59.0 5.24e-01 100.0% 97.9%
1t3yA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.66 48.0 3.92e-01 79.4% 47.3%
4nn5C01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 58.0 5.39e-01 98.5% 91.7%
2w91A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 55.0 4.88e-01 98.5% 87.4%
2xwxA03 2.60.40.2550 Mainly Beta › Sandwich › Immunoglobulin-like › 0.64 56.0 4.97e-01 98.5% 92.9%
2fgzA01 2.60.40.1130 Mainly Beta › Sandwich › Immunoglobulin-like › Rab geranylgeranyltransferase alpha-subunit, insert domain 0.63 55.0 4.66e-01 98.5% 90.4%
4ka7A01 1.10.1370.40 Mainly Alpha › Orthogonal Bundle › Neurolysin; domain 3 › 0.63 45.0 2.78e-01 95.6% 12.5%
5c86A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 55.0 4.83e-01 100.0% 92.1%
2w1nA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 53.0 5.03e-01 97.1% 97.6%
2zuxA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 54.0 4.98e-01 100.0% 92.0%
4d8oA03 2.60.40.2660 Mainly Beta › Sandwich › Immunoglobulin-like › 0.61 54.0 4.44e-01 98.5% 90.5%
2vzsA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 54.0 4.46e-01 98.5% 74.8%
2je8A04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 54.0 4.75e-01 100.0% 99.0%
3pddA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 51.0 4.58e-01 97.1% 82.2%
2b39A03 2.60.40.1940 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 51.0 4.31e-01 100.0% 91.2%
3zyzA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 51.0 4.21e-01 98.5% 96.2%
1y8tA03 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.60 51.0 4.72e-01 97.1% 94.3%
4e19A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 36.0 2.91e-01 82.4% 30.8%
3u3gA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 36.0 2.81e-01 80.9% 28.6%
5yotA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 52.0 4.39e-01 100.0% 94.9%
3bgaA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 51.0 4.41e-01 98.5% 96.4%
2iayA00 3.30.1820.10 Alpha Beta › 2-Layer Sandwich › Lp2179-like fold › Lp2179-like 0.59 38.0 3.19e-01 85.3% 38.6%
1jzdC00 2.60.40.1250 Mainly Beta › Sandwich › Immunoglobulin-like › Thiol:disulfide interchange protein DsbD, N-terminal domain 0.57 49.0 4.16e-01 98.5% 89.8%
2x41A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 48.0 4.11e-01 100.0% 89.1%
1rp5A01 2.20.70.70 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.56 31.0 3.63e-01 79.4% 94.4%
4dm5A00 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.55 38.0 3.55e-01 100.0% 56.3%
3icyA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 40.0 3.41e-01 100.0% 44.9%
4kq7A01 2.60.120.1390 Mainly Beta › Sandwich › Jelly Rolls › Protein of unknown function DUF2961 0.55 49.0 3.73e-01 100.0% 80.9%
1oypA01 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.55 47.0 3.41e-01 100.0% 56.1%
6ryvA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 44.0 4.52e-01 95.6% 93.8%
2nn6C00 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.55 46.0 3.13e-01 97.1% 51.9%
2nn6E00 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.55 47.0 3.19e-01 100.0% 49.8%
1xffA00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.55 43.0 3.10e-01 92.6% 73.1%
3u1kC01 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.55 46.0 3.27e-01 97.1% 48.2%
2iafA00 3.30.1330.90 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › D-3-phosphoglycerate dehydrogenase; domain 3 0.54 47.0 3.73e-01 97.1% 82.1%
6eotD01 2.140.10.30 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Dipeptidylpeptidase IV, N-terminal domain 0.54 43.0 2.52e-01 85.3% 14.3%
5c82A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 39.0 3.01e-01 79.4% 85.9%
1xc3A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 37.0 3.28e-01 72.1% 91.3%
3d8pB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 39.0 3.03e-01 79.4% 83.7%
4ge1C00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 47.0 3.41e-01 100.0% 51.8%
1cb8A03 2.60.220.10 Mainly Beta › Sandwich › Chondroitinase Ac; Chain A, domain 3 › Polysaccharide lyase family 8-like, C-terminal 0.53 43.0 3.65e-01 88.2% 63.6%
4bc3A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 41.0 2.77e-01 89.7% 71.8%
1szqA02 3.30.1330.120 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › 2-methylcitrate dehydratase PrpD 0.51 43.0 3.48e-01 97.1% 90.8%
3bzcA03 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.51 38.0 3.24e-01 83.8% 95.3%
2itmA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 36.0 2.60e-01 76.5% 51.0%
2gupA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 35.0 3.18e-01 72.1% 92.8%
6p0wA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.50 37.0 2.99e-01 79.4% 77.0%
3tthB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 41.0 3.21e-01 94.1% 40.9%
4htlA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.50 35.0 3.20e-01 73.5% 90.0%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4990440 2484.1.1.330 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF460 0.78 41.0 3.02e-01 86.8% 21.9%
3701860 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.76 39.0 3.47e-01 79.4% 35.8%
3244161 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.74 57.0 5.74e-01 95.6% 81.4%
1149586 2484.1.1.8 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.73 38.0 3.06e-01 80.9% 26.8%
3770717 5.1.4.12 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Sema 0.71 39.0 2.48e-01 85.3% 10.9%
3851509 5.1.4.12 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Sema 0.70 39.0 2.30e-01 85.3% 7.4%
5063667 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.70 36.0 3.10e-01 79.4% 31.4%
4420316 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.70 39.0 2.76e-01 83.8% 19.0%
3444038 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.69 53.0 4.93e-01 82.4% 69.4%
3354946 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.68 40.0 4.08e-01 80.9% 61.5%
3929846 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.67 38.0 2.45e-01 83.8% 12.3%
3274422 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 58.0 5.30e-01 98.5% 92.2%
3932273 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 59.0 5.46e-01 100.0% 90.6%
5022780 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 58.0 5.10e-01 98.5% 95.0%
3814983 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.66 39.0 3.75e-01 80.9% 53.3%
3937926 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.65 58.0 5.55e-01 100.0% 91.3%
3924126 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 57.0 5.23e-01 100.0% 87.8%
3715843 11.1.1.173 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CHB_HEX_C_1 0.63 54.0 5.28e-01 97.1% 96.0%
5078225 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.63 41.0 4.42e-01 85.3% 77.6%
3341735 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.63 37.0 2.64e-01 80.9% 20.0%
5056532 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 56.0 4.96e-01 98.5% 94.0%
3408539 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.63 43.0 3.90e-01 76.5% 51.6%
5070689 11.1.1.18 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › LTD 0.63 54.0 4.42e-01 98.5% 79.2%
5032845 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 53.0 4.16e-01 97.1% 96.7%
5076544 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 54.0 4.79e-01 95.6% 85.3%
5036649 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.61 42.0 4.06e-01 79.4% 65.3%
4930080 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.60 41.0 3.89e-01 79.4% 60.0%
3279541 10.37.1.1 ↗ beta sandwiches › jelly-roll › TerD › TerD › TerD 0.59 51.0 4.08e-01 97.1% 80.7%
5050316 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 50.0 4.63e-01 97.1% 91.1%
3923829 11.1.1.7 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › A2M,A2M_BRD 0.58 50.0 3.03e-01 100.0% 37.7%
3224158 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.58 42.0 3.93e-01 76.5% 64.7%
4089497 2484.1.1.8 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.57 39.0 3.17e-01 72.1% 93.6%
4012700 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.57 43.0 2.98e-01 80.9% 68.4%
3595729 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.57 40.0 3.82e-01 79.4% 63.7%
3193146 2485.1.1.30 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Phe_hydrox_dim 0.56 43.0 3.06e-01 80.9% 64.2%
3281300 4.1.1.426 ↗ beta barrels › SH3 › SH3 › SH3 › PF31188 0.56 36.0 3.73e-01 97.1% 69.2%
5048870 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.55 38.0 3.58e-01 80.9% 59.0%
4170578 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.55 38.0 3.47e-01 80.9% 54.4%
3204490 2485.1.1.30 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Phe_hydrox_dim 0.54 41.0 2.88e-01 80.9% 68.3%
4937838 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.54 40.0 2.85e-01 79.4% 99.5%
4861390 2484.1.1.6 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_N 0.54 38.0 2.65e-01 76.5% 50.6%
4165569 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.54 37.0 3.34e-01 80.9% 49.0%
1656448 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.54 36.0 3.25e-01 77.9% 47.1%
3611339 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 38.0 3.59e-01 94.1% 60.0%
5082492 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.53 40.0 3.77e-01 98.5% 63.5%
3627380 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 37.0 2.40e-01 73.5% 24.3%
3506427 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.53 34.0 2.81e-01 85.3% 36.0%
3575357 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.53 37.0 2.39e-01 73.5% 23.6%
3546198 5.1.4.149 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WDR54 0.53 37.0 2.35e-01 97.1% 15.0%
3179767 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 41.0 2.76e-01 91.2% 78.2%
5008587 2484.1.1.330 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF460 0.52 39.0 2.67e-01 83.8% 39.0%
4017407 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.52 36.0 3.65e-01 77.9% 72.9%
5079230 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.52 36.0 3.20e-01 97.1% 47.6%
4948119 5084.1.1.0 ↗ beta barrels › Outer membrane meander beta-barrels › OMPA-like › OMPA-like 0.52 46.0 3.84e-01 100.0% 84.2%
1884677 2484.1.1.8 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.51 34.0 2.95e-01 72.1% 84.4%
3196366 298.1.1.24 ↗ a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › GFO_IDH_MocA_C3 0.50 43.0 3.19e-01 97.1% 82.2%