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KP881232.1__AKE44709.1__Sm_phiM9_079__00078

Bact-Vir

KP881232.1__AKE44709.1__Sm_phiM9_079__00078

Identity

Accession:
KP881232 ↗
Kingdom:
phage

Quality

76.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Emnonavirus› Sinorhizobium_phage_phiM9

TaxID: 1636182

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 3-57
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vx7X00 3.30.1360.210 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.68 59.0 4.97e-01 100.0% 95.9%
3u5eU00 3.30.1360.210 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.64 54.0 4.58e-01 100.0% 94.0%
2jwkA00 3.30.420.270 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.64 52.0 4.69e-01 89.1% 67.6%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.62 53.0 3.85e-01 100.0% 94.0%
4u13A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 52.0 4.26e-01 98.2% 70.6%
4k3bA02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.61 51.0 4.56e-01 100.0% 91.7%
3ar4A04 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.61 49.0 3.26e-01 92.7% 96.3%
3bb9B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 52.0 4.04e-01 98.2% 72.0%
2x8xX02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.61 50.0 4.63e-01 100.0% 93.4%
3nuhB02 3.30.300.370 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.60 48.0 3.80e-01 90.9% 92.6%
1n6zA00 3.10.20.250 Alpha Beta › Roll › Ubiquitin-like (UB roll) › YML108W-like 0.59 49.0 4.10e-01 100.0% 77.1%
5efrA01 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.58 47.0 4.30e-01 100.0% 98.8%
6njyA01 3.30.70.1900 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 47.0 3.63e-01 92.7% 100.0%
6j09A02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.57 46.0 4.24e-01 100.0% 98.7%
4ottA02 1.10.246.130 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain 0.55 40.0 3.13e-01 78.2% 66.9%
1x67A01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.55 41.0 3.28e-01 87.3% 63.2%
2pw9C02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.55 47.0 4.66e-01 100.0% 94.8%
3e59B02 3.30.60.140 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.55 35.0 3.80e-01 96.4% 94.7%
7uuim01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 45.0 3.32e-01 94.5% 89.9%
1wmhA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 47.0 4.16e-01 100.0% 96.4%
5tvfD00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.54 44.0 2.95e-01 100.0% 60.7%
2afcA00 3.40.220.10 Alpha Beta › 3-Layer(aba) Sandwich › Leucine Aminopeptidase, subunit E; domain 1 › Leucine Aminopeptidase, subunit E, domain 1 0.54 44.0 3.31e-01 96.4% 84.3%
2xzmT00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 39.0 2.88e-01 78.2% 44.7%
3h2zA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 40.0 2.89e-01 89.1% 93.0%
5ah5A01 3.10.20.590 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 44.0 4.35e-01 100.0% 95.1%
1d2oA02 2.60.40.1140 Mainly Beta › Sandwich › Immunoglobulin-like › Collagen-binding surface protein Cna, B-type domain 0.53 46.0 4.11e-01 100.0% 96.2%
4nrvA02 1.10.8.50 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.53 40.0 3.07e-01 85.5% 65.0%
2qdfA02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.53 43.0 3.93e-01 100.0% 91.6%
1qr0A02 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.52 40.0 3.46e-01 92.7% 100.0%
2hjhB01 3.40.50.1220 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › TPP-binding domain 0.51 40.0 2.77e-01 100.0% 24.3%
4bzaA01 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.51 40.0 3.87e-01 98.2% 95.6%
2x49A04 3.40.50.12790 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › FHIPEP family, domain 4 0.51 42.0 3.47e-01 90.9% 74.7%
1egaA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 41.0 2.93e-01 92.7% 42.0%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5077501 3715.1.1.0 ↗ a+b two layers › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal protein L22e 0.67 57.0 5.03e-01 98.2% 97.6%
5008091 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.64 56.0 5.14e-01 100.0% 75.7%
4979304 3715.1.1.1 ↗ a+b two layers › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal protein L22e › Ribosomal_L22e 0.63 52.0 4.45e-01 100.0% 86.9%
4541918 3121.1.1.1 ↗ a+b duplicates or obligate multimers › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › POTRA 0.60 50.0 4.57e-01 100.0% 93.8%
3995700 1021.1.1.0 ↗ a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.59 47.0 3.64e-01 87.3% 81.6%
5027955 4961.1.1.1 ↗ a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4 0.59 47.0 4.75e-01 100.0% 92.7%
2773896 4961.1.1.0 ↗ a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit 0.59 49.0 4.25e-01 100.0% 58.5%
5745 870.1.1.1 ↗ a+b two layers › Hypothetical protein Yml108w › Hypothetical protein Yml108w › Hypothetical protein Yml108w › DUF1892 0.59 49.0 4.10e-01 100.0% 77.1%
4282782 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.59 51.0 4.46e-01 100.0% 64.7%
4937778 4961.1.1.1 ↗ a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › RNA_pol_Rpb2_4 0.58 46.0 4.64e-01 100.0% 92.7%
4967731 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.58 49.0 4.74e-01 100.0% 84.6%
3496894 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 45.0 4.31e-01 92.7% 81.5%
1032929 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.54 46.0 4.00e-01 100.0% 61.1%
3276582 2006.1.6.39 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › Mat89Bb 0.54 44.0 2.87e-01 90.9% 37.5%
4037465 221.15.1.0 ↗ a+b two layers › beta-Grasp › beta-grasp fold domain in leucine-tRNA ligase › beta-grasp fold domain in leucine-tRNA ligase 0.54 45.0 4.38e-01 100.0% 92.1%
5020150 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.54 43.0 3.87e-01 100.0% 62.4%
3261872 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 45.0 4.13e-01 98.2% 92.0%
4105802 3121.1.1.2 ↗ a+b duplicates or obligate multimers › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › POTRA_1 0.53 42.0 3.98e-01 100.0% 92.0%
4943068 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 0.53 39.0 2.61e-01 85.5% 27.1%
4793136 2492.1.1.10 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.53 38.0 3.56e-01 76.4% 74.6%
5016620 267.1.1.3 ↗ a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Cation_ATPase 0.52 40.0 2.88e-01 92.7% 95.1%
4521188 221.1.1.1 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Fer2 0.52 44.0 3.79e-01 100.0% 100.0%
4206820 3121.1.1.2 ↗ a+b duplicates or obligate multimers › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › POTRA_1 0.52 41.0 3.68e-01 100.0% 74.4%
3584735 3698.1.1.1 ↗ beta sandwiches › Arginine methyltransferase oligomerization subdomain › Arginine methyltransferase oligomerization subdomain › Arginine methyltransferase oligomerization subdomain › PRMT5_C 0.50 42.0 2.87e-01 100.0% 91.3%