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KR052480.1__AKF12799.1__PHIM7_254__00254

Bact-Vir

KR052480.1__AKF12799.1__PHIM7_254__00254

Identity

Accession:
KR052480 ↗
Kingdom:
phage

Quality

76.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

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 10-60
PDB
Domain cluster: representative
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1h4rA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.78 50.0 4.12e-01 76.5% 37.4%
2fiaB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.75 42.0 2.91e-01 82.4% 18.2%
3fdfA02 6.10.140.550 Special › Helix non-globular › Helix Hairpins › 0.71 46.0 4.50e-01 74.5% 60.7%
7d27A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.71 59.0 3.84e-01 98.0% 20.9%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.71 48.0 4.39e-01 70.6% 54.5%
2ablA02 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.70 50.0 4.10e-01 78.4% 67.0%
4ehoB03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.69 60.0 4.15e-01 100.0% 55.9%
1qqgA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 50.0 4.03e-01 80.4% 45.6%
2fm8B00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.68 53.0 3.99e-01 86.3% 96.8%
1eqtA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.68 45.0 4.19e-01 70.6% 53.7%
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.66 45.0 2.95e-01 70.6% 20.0%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.65 52.0 4.27e-01 94.1% 47.6%
6fndA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.65 46.0 3.10e-01 74.5% 22.6%
3jtzA00 3.30.160.390 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Integrase, DNA-binding domain 0.64 55.0 4.86e-01 98.0% 75.3%
2yztA00 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.64 48.0 4.50e-01 96.1% 65.2%
4c12A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.64 53.0 3.48e-01 98.0% 20.6%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.63 48.0 4.64e-01 96.1% 73.7%
4ntqB00 3.30.2450.20 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.63 51.0 3.88e-01 100.0% 55.9%
3qpbF00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.63 54.0 3.51e-01 100.0% 91.6%
4ktwA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.63 56.0 3.92e-01 100.0% 33.1%
3rm5B01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.62 48.0 3.03e-01 84.3% 81.4%
3s6gA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.62 43.0 3.17e-01 80.4% 25.3%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.62 46.0 3.78e-01 84.3% 44.0%
1hf2A02 2.160.20.70 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › 0.62 42.0 3.34e-01 70.6% 47.2%
4gzuA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 49.0 3.49e-01 98.0% 29.3%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 47.0 3.52e-01 82.4% 79.3%
3qijB03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 49.0 4.05e-01 88.2% 88.8%
4hhvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 49.0 3.96e-01 90.2% 86.4%
1i3zA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.60 47.0 3.87e-01 90.2% 64.1%
2g3aA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.60 43.0 3.37e-01 74.5% 42.9%
7byjA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 47.0 3.85e-01 86.3% 92.6%
2dixA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.60 47.0 4.22e-01 92.2% 69.2%
1faoA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 47.0 3.77e-01 96.1% 44.0%
1ha6A00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.59 40.0 3.67e-01 70.6% 54.3%
6w0pA02 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.59 49.0 2.80e-01 88.2% 10.4%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.58 46.0 3.77e-01 86.3% 80.4%
3ml4C01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 45.0 3.60e-01 98.0% 41.7%
2a6aB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 45.0 3.46e-01 94.1% 37.8%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.56 46.0 3.38e-01 90.2% 74.0%
2yt4A03 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 42.0 3.47e-01 88.2% 43.3%
5ucoA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.54 46.0 3.36e-01 100.0% 78.4%
1je0C00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.54 45.0 2.99e-01 96.1% 61.7%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.53 43.0 3.89e-01 94.1% 66.2%
1pxfA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 43.0 3.51e-01 100.0% 82.9%
2zwrB00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.53 41.0 2.78e-01 86.3% 81.2%
3dcxA00 2.30.29.50 Mainly Beta › Roll › PH-domain like › Bacterial Pleckstrin homology domain 0.52 39.0 3.13e-01 86.3% 81.2%
1wp1B01 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.52 47.0 2.77e-01 100.0% 59.0%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.52 43.0 3.42e-01 90.2% 76.7%
1okjB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 40.0 3.14e-01 94.1% 36.2%
1wzaA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 36.0 3.18e-01 74.5% 60.8%
2lezA00 3.30.2450.10 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › Secreted effector protein pipB2 0.52 39.0 3.00e-01 82.4% 38.3%
3m4pA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 39.0 3.07e-01 84.3% 45.5%
4q0jA03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.51 39.0 2.97e-01 88.2% 35.9%
3u50C01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.50 35.0 2.84e-01 82.4% 66.1%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
None — 0.73 43.0 2.52e-01 90.2% 7.8%
3887159 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.69 46.0 4.29e-01 70.6% 58.5%
4952930 2.21.1.0 ↗ beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) 0.68 47.0 4.01e-01 72.5% 71.8%
3983052 300.1.1.8 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › PLDc_2 0.68 53.0 3.43e-01 86.3% 69.2%
3499134 2485.1.1.1 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin 0.68 52.0 3.81e-01 84.3% 68.6%
3889621 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.68 46.0 4.41e-01 70.6% 60.0%
3623534 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.67 47.0 4.00e-01 76.5% 73.3%
3390566 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.67 55.0 4.61e-01 100.0% 54.0%
3678841 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.67 57.0 4.90e-01 100.0% 64.7%
3344139 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.66 50.0 4.89e-01 84.3% 76.4%
3239418 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 53.0 3.50e-01 92.2% 33.5%
3260733 220.1.1.158 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_LRR1 0.66 47.0 3.70e-01 76.5% 53.6%
5069121 4.6.1.0 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain 0.66 46.0 4.43e-01 74.5% 75.0%
3620293 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.65 51.0 3.82e-01 100.0% 33.8%
5001238 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.65 52.0 4.21e-01 100.0% 43.6%
3979711 252.2.1.6 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_2 0.64 56.0 5.22e-01 98.0% 76.9%
3598612 220.1.1.230 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26289 0.64 49.0 4.06e-01 82.4% 100.0%
3891749 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.63 52.0 3.77e-01 100.0% 32.9%
4341865 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.63 51.0 5.04e-01 94.1% 96.4%
3629491 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 42.0 4.19e-01 70.6% 76.4%
3907024 260.1.1.1 ↗ a+b duplicates or obligate multimers › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › Plectin 0.63 48.0 2.95e-01 84.3% 18.8%
3362766 386.1.1.4 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-BED 0.63 50.0 5.05e-01 92.2% 96.0%
3479661 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.63 50.0 4.05e-01 94.1% 44.5%
3209694 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.63 50.0 4.15e-01 94.1% 53.0%
5018724 872.3.1.0 ↗ a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like 0.63 50.0 4.15e-01 100.0% 48.4%
3408937 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.63 49.0 4.41e-01 94.1% 63.7%
3516025 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.63 55.0 4.33e-01 100.0% 47.6%
3323471 386.1.1.4 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-BED 0.63 47.0 4.65e-01 90.2% 80.0%
4944397 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 45.0 4.57e-01 86.3% 82.0%
3514660 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.62 48.0 4.13e-01 88.2% 55.6%
5079725 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.62 52.0 5.01e-01 100.0% 86.7%
3549045 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.62 49.0 3.99e-01 94.1% 44.5%
3584575 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 52.0 3.61e-01 100.0% 28.2%
3933098 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.61 47.0 4.44e-01 88.2% 73.8%
3926600 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 51.0 3.97e-01 92.2% 78.2%
5018514 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 40.0 2.99e-01 70.6% 28.9%
3742185 2003.1.5.26 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_28 0.60 47.0 2.82e-01 86.3% 13.9%
3925738 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 46.0 3.83e-01 94.1% 45.5%
4942828 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 0.60 47.0 3.30e-01 86.3% 97.0%
3623273 101.1.2.712 ↗ alpha arrays › HTH › HTH › winged helix domain › FNIP_C 0.60 53.0 3.31e-01 100.0% 72.0%
3307718 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.59 41.0 3.18e-01 72.5% 50.8%
4956750 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.59 52.0 3.13e-01 100.0% 82.4%
5028212 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.59 52.0 3.76e-01 100.0% 87.2%
3582821 220.1.1.5 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PID 0.58 49.0 4.09e-01 100.0% 53.3%
3282977 300.1.1.12 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › DUF5753 0.58 45.0 3.01e-01 98.0% 22.2%
3290052 101.1.9.42 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › DUF6319 0.56 46.0 3.94e-01 88.2% 80.0%
3286982 330.6.1.0 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain 0.55 47.0 3.81e-01 100.0% 94.2%
3604204 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.55 43.0 3.07e-01 90.2% 95.0%
3426675 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.54 43.0 4.19e-01 92.2% 84.7%
3276465 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.54 45.0 3.12e-01 100.0% 73.7%
3269549 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 43.0 3.10e-01 90.2% 61.9%
3461521 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.54 44.0 3.42e-01 98.0% 40.9%
None — 0.53 48.0 2.63e-01 100.0% 29.5%
3616718 207.1.1.85 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › F-box-like 0.53 37.0 2.22e-01 74.5% 23.6%
4995163 2006.1.1.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.53 46.0 2.99e-01 100.0% 22.1%
3287378 601.23.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III 0.53 47.0 2.96e-01 100.0% 77.3%
3254676 2004.1.1.16 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Arf 0.52 42.0 3.03e-01 98.0% 77.2%
3965157 2003.1.2.58 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox, Pyr_redox_2 0.52 45.0 3.03e-01 100.0% 25.8%
3926998 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.51 34.0 3.09e-01 70.6% 50.0%
5071748 318.1.1.1 ↗ a+b two layers › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal_L6 0.51 45.0 3.89e-01 96.1% 100.0%
3700743 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.50 44.0 4.00e-01 98.0% 94.3%