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NC_028928.1__YP_009210417.1__SEA_NERUJAY_66__00066

Bact-Vir

NC_028928.1__YP_009210417.1__SEA_NERUJAY_66__00066

Identity

Accession:
NC_028928 ↗
Kingdom:
phage

Quality

86.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Fromanvirus› Mycobacterium_phage_Nerujay

TaxID: 1647308

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 2-67
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d9wA02 2.40.128.150 Mainly Beta › Beta Barrel › Lipocalin › Cysteine proteinases 0.63 52.0 4.51e-01 92.4% 98.0%
2eyqA05 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.60 44.0 4.63e-01 83.3% 89.8%
1wuoA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.58 43.0 3.04e-01 80.3% 89.5%
2jzlA00 2.30.60.10 Mainly Beta › Roll › HIV-inactivating Protein, Cyanovirin-n › Cyanovirin-N 0.58 38.0 3.16e-01 98.5% 39.6%
2i0rA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 49.0 3.13e-01 100.0% 88.4%
1mdaH00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 48.0 3.01e-01 97.0% 80.7%
2kd2A01 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.55 46.0 4.31e-01 95.5% 98.8%
4ebgA00 3.10.450.560 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 43.0 3.86e-01 92.4% 60.8%
2n8xA00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.54 37.0 2.86e-01 72.7% 60.2%
3plsA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 37.0 3.25e-01 71.2% 75.0%
4ic5A02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 37.0 3.29e-01 72.7% 79.8%
6qpwA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 38.0 3.00e-01 84.8% 32.7%
2daxA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.54 40.0 3.25e-01 81.8% 55.3%
2e12A00 2.30.30.720 Mainly Beta › Roll › SH3 type barrels. › Protein of unknown function (DUF3247) 0.54 40.0 3.70e-01 84.8% 78.5%
1ixdA00 2.30.30.190 Mainly Beta › Roll › SH3 type barrels. › CAP Gly-rich-like domain 0.54 45.0 3.93e-01 95.5% 71.2%
1h4iA00 2.140.10.10 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Quinoprotein alcohol dehydrogenase-like superfamily 0.54 46.0 2.69e-01 100.0% 83.5%
6ruiB04 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.54 44.0 3.28e-01 93.9% 88.5%
4az3A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 40.0 2.78e-01 84.8% 30.9%
4irzA01 2.130.10.130 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Integrin alpha, N-terminal 0.53 40.0 2.52e-01 84.8% 23.6%
7c5wA01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 36.0 2.85e-01 71.2% 34.5%
1vkdA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.53 42.0 2.75e-01 90.9% 59.8%
4qiwB04 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.53 42.0 3.22e-01 89.4% 79.1%
3ugfB02 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.53 43.0 3.22e-01 92.4% 57.6%
4b6mB00 2.30.30.190 Mainly Beta › Roll › SH3 type barrels. › CAP Gly-rich-like domain 0.51 44.0 4.23e-01 100.0% 93.7%
3m9qA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 38.0 3.73e-01 83.3% 90.3%
1bcrA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 39.0 2.69e-01 86.4% 31.5%
1twfB04 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.50 40.0 3.00e-01 89.4% 79.7%
1xfdA01 2.140.10.30 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Dipeptidylpeptidase IV, N-terminal domain 0.50 38.0 2.38e-01 86.4% 19.2%
8in8C01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.50 37.0 2.63e-01 86.4% 86.3%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3974170 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 56.0 4.89e-01 90.9% 67.0%
3897030 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 48.0 4.13e-01 89.4% 83.5%
3611119 719.1.1.4 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › SAS-6_N 0.61 46.0 3.75e-01 83.3% 85.9%
3673878 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.59 50.0 3.13e-01 95.5% 89.7%
3935079 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.59 45.0 4.55e-01 86.4% 95.4%
None — 0.58 44.0 2.81e-01 81.8% 16.8%
3689291 220.1.1.69 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Meiotic_rec114 0.58 45.0 3.56e-01 89.4% 81.9%
4416106 2.1.1.1 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosom_S12_S23 0.58 40.0 3.24e-01 74.2% 55.2%
3958888 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 42.0 3.33e-01 81.8% 63.9%
3659202 1.1.11.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain 0.57 37.0 3.48e-01 72.7% 53.8%
3826506 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.57 47.0 3.16e-01 93.9% 26.3%
3698492 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.56 43.0 3.48e-01 81.8% 68.0%
5079843 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.55 42.0 4.28e-01 86.4% 100.0%
197051 4.1.1.74 ↗ beta barrels › SH3 › SH3 › SH3 › DUF3247 0.54 40.0 3.70e-01 84.8% 78.5%
572 4.1.1.18 ↗ beta barrels › SH3 › SH3 › SH3 › CAP_GLY 0.54 45.0 3.93e-01 95.5% 71.2%
5028865 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 36.0 3.99e-01 74.2% 92.0%
5054449 375.1.1.7 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › TFIIS_C 0.53 36.0 3.58e-01 72.7% 68.1%
3831450 4.1.1.18 ↗ beta barrels › SH3 › SH3 › SH3 › CAP_GLY 0.53 43.0 3.89e-01 90.9% 80.0%
3912173 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.51 40.0 3.82e-01 87.9% 77.5%
3801858 252.1.1.0 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD 0.51 36.0 3.78e-01 83.3% 85.0%
4015526 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.51 38.0 2.77e-01 84.8% 28.8%
4970648 375.1.1.21 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-ZPR1 0.50 34.0 3.82e-01 71.2% 92.0%
3807468 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.50 40.0 2.91e-01 93.9% 47.6%