←Back to structures

NC_014260.1__YP_003734180.1__IME08_gp030__00030

Bact-Vir

NC_014260.1__YP_003734180.1__IME08_gp030__00030

Identity

Accession:
NC_014260 ↗
Kingdom:
phage

Quality

73.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Dhakavirus› Escherichia_phage_IME08

TaxID: 698728

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 22-75
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23945.2 best DUF7279 59.3 3.60e-16 79.6% 79.2%
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1e3hA03 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.75 56.0 3.72e-01 79.6% 65.3%
2il5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.74 63.0 4.58e-01 100.0% 96.3%
3wxmB02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.73 54.0 4.08e-01 77.8% 51.6%
2v0uA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.71 61.0 4.49e-01 98.1% 38.4%
2ivnA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.70 52.0 3.73e-01 83.3% 32.1%
3o5yB00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.68 58.0 4.32e-01 100.0% 36.7%
3qcpA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.66 59.0 4.09e-01 98.1% 83.0%
2nn6C00 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.66 53.0 3.41e-01 90.7% 58.9%
4du5B00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.66 45.0 2.84e-01 92.6% 13.2%
1c9rA04 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.66 57.0 4.54e-01 96.3% 48.6%
1jkxA00 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.64 52.0 3.66e-01 100.0% 28.2%
1s3iA01 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.64 54.0 3.73e-01 100.0% 28.8%
3p9xA00 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.64 53.0 3.72e-01 100.0% 29.7%
3e9mB02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.64 51.0 3.47e-01 88.9% 98.0%
3da8B00 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.63 52.0 3.66e-01 100.0% 27.8%
5nckA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.63 49.0 4.01e-01 88.9% 43.8%
4a2bA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.63 50.0 3.82e-01 90.7% 41.3%
2xzmZ00 3.30.1230.20 Alpha Beta › 2-Layer Sandwich › Hypothetical Cytosolic Protein; Chain: A; › Ribosomal protein S21 0.63 44.0 3.71e-01 75.9% 47.4%
4iqfB01 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.63 52.0 3.62e-01 100.0% 27.9%
4d10F01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.62 45.0 3.24e-01 81.5% 27.9%
1hjrA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.62 45.0 3.32e-01 81.5% 31.0%
3k2nA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.62 53.0 3.78e-01 100.0% 31.1%
5cjjB00 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.61 51.0 3.59e-01 100.0% 29.5%
4zg5A00 3.40.1210.10 Alpha Beta › 3-Layer(aba) Sandwich › Stationary-phase Survival Protein Sure Homolog; Chain: A, › Survival protein SurE-like phosphatase/nucleotidase 0.61 48.0 3.18e-01 90.7% 58.7%
2je6A01 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.61 48.0 3.16e-01 90.7% 60.9%
6jptA00 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.60 47.0 3.67e-01 87.0% 40.5%
3wa7A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 49.0 2.90e-01 94.4% 15.6%
3dluA00 3.30.56.30 Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › Signal recognition particle, SRP19-like subunit 0.59 52.0 4.30e-01 98.1% 98.9%
1xvwA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.59 39.0 2.92e-01 83.3% 24.1%
4mt1A06 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.58 47.0 3.94e-01 94.4% 90.1%
3uuwB02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.57 38.0 2.71e-01 70.4% 20.7%
1dpgA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.57 48.0 3.03e-01 98.1% 90.9%
4mfzA02 3.40.630.120 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › 0.57 45.0 3.35e-01 90.7% 33.3%
7uclA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 43.0 3.51e-01 83.3% 51.0%
3r8eA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 42.0 3.25e-01 88.9% 34.3%
6dgiA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 46.0 3.36e-01 92.6% 50.7%
2ge3A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 42.0 3.11e-01 88.9% 56.1%
1eo1A00 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.53 37.0 3.02e-01 79.6% 35.5%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.52 44.0 3.30e-01 92.6% 46.6%
1kf6B01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.52 38.0 3.19e-01 81.5% 44.2%
4hwxA00 3.30.350.10 Alpha Beta › 2-Layer Sandwich › Subtilisin Inhibitor › Subtilisin inhibitor-like 0.51 36.0 2.96e-01 77.8% 94.7%
2mcqA01 3.30.300.90 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › BolA-like 0.51 34.0 3.18e-01 72.2% 81.3%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5007978 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.76 69.0 5.02e-01 98.1% 39.3%
4945650 878.1.1.0 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 0.76 65.0 5.26e-01 94.4% 99.0%
4980707 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.74 62.0 5.11e-01 98.1% 50.5%
4469636 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.73 60.0 5.22e-01 92.6% 89.4%
3597121 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.73 59.0 3.62e-01 87.0% 24.4%
4438376 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.72 57.0 4.46e-01 88.9% 40.8%
3591691 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.70 59.0 4.90e-01 94.4% 86.3%
3429580 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.70 56.0 3.99e-01 88.9% 35.0%
3512065 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.69 52.0 5.03e-01 88.9% 72.3%
3928228 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.69 56.0 3.64e-01 90.7% 23.7%
4082205 7571.1.1.1 ↗ a/b three-layered sandwiches › Formyltransferase › Formyltransferase › Formyltransferase › Formyl_trans_N 0.68 58.0 3.97e-01 100.0% 29.5%
4397552 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.68 59.0 4.45e-01 96.3% 96.8%
3740761 2492.1.1.4 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.67 59.0 3.93e-01 98.1% 27.3%
5024957 7089.1.1.0 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD 0.67 56.0 4.95e-01 92.6% 67.1%
4871776 4019.1.1.0 ↗ alpha complex topology › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › alpha-helical domain in beta-lactamase/transpeptidase-like proteins 0.66 46.0 4.90e-01 85.2% 91.1%
3931735 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.66 55.0 4.68e-01 100.0% 56.7%
3953212 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.65 49.0 3.69e-01 81.5% 34.1%
3939681 5001.1.1.41 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srw 0.65 55.0 3.40e-01 98.1% 32.7%
4604112 213.1.1.8 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › HlyC 0.65 55.0 3.91e-01 94.4% 66.3%
5054600 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.64 51.0 4.10e-01 90.7% 44.3%
4022567 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.64 53.0 4.11e-01 100.0% 40.0%
4883002 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.62 53.0 5.13e-01 100.0% 85.2%
3284357 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.61 47.0 3.55e-01 83.3% 65.4%
1002449 3662.1.1.1 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC3 0.59 46.0 3.63e-01 87.0% 40.2%
3684154 327.5.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C 0.59 42.0 3.76e-01 77.8% 82.5%
3940192 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.59 51.0 4.37e-01 98.1% 60.2%
None — 0.59 48.0 2.68e-01 88.9% 32.4%
5058066 2484.1.1.38 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 0.58 48.0 3.80e-01 92.6% 42.6%
3830727 109.4.1.1493 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Zw10_middle, ZW10_C, ZW10_C2 0.58 53.0 3.05e-01 100.0% 16.1%
3224683 221.1.1.2 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › ubiquitin 0.58 41.0 3.59e-01 77.8% 47.7%
5074340 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.58 47.0 3.38e-01 87.0% 48.6%
3651779 109.21.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain 0.58 48.0 2.66e-01 90.7% 32.6%
4218926 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.57 45.0 3.61e-01 90.7% 40.8%
3438711 221.1.1.2 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › ubiquitin 0.57 43.0 3.75e-01 87.0% 100.0%
5056801 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.56 45.0 3.49e-01 100.0% 38.4%
3722015 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.56 52.0 2.99e-01 100.0% 82.6%
5026550 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 43.0 3.53e-01 90.7% 42.6%
3199443 2002.1.1.4 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Alpha-amylase 0.55 41.0 2.50e-01 81.5% 89.4%
3499681 292.2.1.1 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › POLO_box 0.55 44.0 3.67e-01 87.0% 89.2%
5031007 2484.1.1.38 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 0.53 41.0 3.28e-01 88.9% 44.0%
5075397 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.52 44.0 3.46e-01 100.0% 45.6%