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NC_070885.1__YP_010661705.1__PP936_gp067__00067

Bact-Vir

NC_070885.1__YP_010661705.1__PP936_gp067__00067

Identity

Accession:
NC_070885 ↗
Kingdom:
phage

Quality

96.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Trinifflemingvirus› Rhizobium_phage_RHph_I1_9

TaxID: 2509729

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 5-76
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1h6gA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.82 58.0 4.84e-01 75.0% 68.5%
1sj8A02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.77 69.0 5.79e-01 100.0% 82.0%
3sz7A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.77 49.0 3.85e-01 72.2% 31.1%
2ip6A00 1.20.1440.140 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.76 67.0 6.32e-01 100.0% 95.4%
2a0bA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.75 54.0 4.56e-01 76.4% 48.3%
1he1A00 1.20.120.260 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain 0.73 54.0 4.43e-01 79.2% 65.2%
3cazB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.72 51.0 3.67e-01 75.0% 81.0%
5h5mA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.72 52.0 4.32e-01 77.8% 73.1%
1r0dA00 1.20.1410.10 Mainly Alpha › Up-down Bundle › I/LWEQ domain › I/LWEQ domain 0.68 59.0 4.41e-01 100.0% 69.9%
4dmvA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 58.0 5.52e-01 94.4% 91.8%
3iqtA01 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.67 48.0 4.22e-01 77.8% 50.9%
7kdtA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.66 45.0 2.94e-01 72.2% 15.9%
2ff4A02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.66 45.0 3.42e-01 72.2% 40.1%
3i1aA03 1.20.58.840 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 49.0 4.23e-01 81.9% 73.3%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.65 47.0 4.85e-01 77.8% 92.4%
3agtA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.64 52.0 4.29e-01 90.3% 69.2%
5n17A01 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.63 54.0 4.91e-01 100.0% 83.7%
4wedA02 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.63 50.0 3.59e-01 87.5% 31.1%
5mq1A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.63 54.0 4.81e-01 100.0% 75.9%
2i6hA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.62 43.0 3.96e-01 72.2% 55.2%
4kjmA02 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.62 42.0 4.72e-01 79.2% 92.7%
5hayA02 1.25.40.440 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Nucleoporin, helical domain, central subdomain 0.62 42.0 4.17e-01 72.2% 67.1%
3e4bA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 45.0 2.81e-01 79.2% 98.5%
1x9bA00 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.60 41.0 4.50e-01 73.6% 96.2%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 42.0 4.43e-01 75.0% 95.2%
4od4A01 1.10.357.140 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › UbiA prenyltransferase 0.60 43.0 3.44e-01 77.8% 91.0%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.59 52.0 4.12e-01 100.0% 79.2%
3kh1A00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.59 46.0 3.40e-01 86.1% 73.8%
3caxA01 1.20.120.520 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like 0.58 49.0 3.60e-01 98.6% 80.6%
1tu9A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 49.0 4.13e-01 98.6% 90.8%
1ni3A03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.57 49.0 4.64e-01 100.0% 80.2%
2dkwA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.57 49.0 4.12e-01 100.0% 59.5%
5a1nB00 1.20.1050.130 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 45.0 3.34e-01 91.7% 77.0%
3dtoA01 1.10.472.50 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › HD-domain/PDEase-like 0.55 48.0 4.58e-01 100.0% 89.8%
2do9A01 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.55 45.0 4.41e-01 98.6% 100.0%
2ozbB01 1.10.287.4070 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 48.0 3.98e-01 100.0% 73.3%
4fqnC00 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.55 46.0 4.45e-01 100.0% 90.6%
3ma5A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.54 42.0 3.97e-01 84.7% 85.6%
2uv8A04 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 46.0 2.83e-01 100.0% 66.0%
6z4xA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.53 42.0 3.35e-01 88.9% 51.0%
3zilA00 1.25.10.60 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Rad61, Wapl domain 0.53 43.0 2.81e-01 94.4% 24.9%
2hoqA02 1.10.150.520 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.51 42.0 4.10e-01 91.7% 93.7%
2zcxA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 40.0 2.93e-01 86.1% 68.3%
1dliA03 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.51 36.0 3.46e-01 77.8% 100.0%
2k3nA00 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.51 41.0 3.29e-01 93.1% 59.4%
1bqbA02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.51 42.0 3.45e-01 98.6% 47.2%
3rc3A05 1.20.58.1080 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 38.0 3.34e-01 80.6% 69.9%
1eyvB00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.50 39.0 3.34e-01 88.9% 51.1%
4u72A01 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 42.0 3.09e-01 98.6% 66.2%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3954422 633.5.1.0 ↗ alpha bundles › Bromodomain-like › LemA-like › LemA-like 0.77 69.0 5.48e-01 100.0% 80.7%
182184 109.4.1.1288 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_11 0.77 49.0 3.89e-01 72.2% 32.2%
None — 0.77 68.0 3.70e-01 100.0% 8.6%
3914072 633.23.1.19 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › TMEM37 0.76 67.0 5.01e-01 100.0% 96.7%
3181692 109.4.1.95 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_2 0.75 48.0 3.64e-01 72.2% 27.6%
3639820 109.4.1.1264 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_16 0.74 47.0 3.50e-01 72.2% 25.4%
4364663 633.12.1.0 ↗ alpha bundles › Bromodomain-like › Ta0600-like › Ta0600-like 0.72 64.0 5.57e-01 100.0% 77.3%
3602825 633.12.1.0 ↗ alpha bundles › Bromodomain-like › Ta0600-like › Ta0600-like 0.71 63.0 5.21e-01 100.0% 60.8%
4979632 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.71 59.0 4.42e-01 100.0% 36.7%
4950911 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.71 62.0 5.02e-01 100.0% 61.4%
3346328 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.68 49.0 3.92e-01 76.4% 43.4%
3969284 633.28.1.2 ↗ alpha bundles › Bromodomain-like › Tsi6 › Tsi6 › DUF4404 0.67 55.0 5.41e-01 95.8% 97.5%
4546706 109.2.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid 0.66 46.0 3.29e-01 73.6% 25.0%
3692017 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.63 47.0 3.80e-01 79.2% 77.1%
3741297 633.31.1.0 ↗ alpha bundles › Bromodomain-like › Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase › Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase 0.62 53.0 5.36e-01 100.0% 98.6%
4169890 5.1.11.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed › Beta_propel 0.60 48.0 2.90e-01 88.9% 22.2%
4965784 3455.1.1.17 ↗ alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors › DUF7853 0.59 51.0 4.86e-01 100.0% 92.9%
3961048 4953.1.1.7 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › AI-2E_transport 0.58 48.0 4.57e-01 97.2% 86.7%
3467296 558.1.1.0 ↗ alpha duplicates or obligate multimers › Lis-homology dimerization domain › Lis-homology dimerization domain › Lis-homology dimerization domain 0.57 42.0 2.54e-01 79.2% 14.4%
3438234 509.1.1.0 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain 0.57 43.0 4.51e-01 91.7% 95.4%
3794915 3065.1.1.1 ↗ alpha bundles › Fatty acid- and retinoid-binding proteins › Fatty acid- and retinoid-binding proteins › Fatty acid- and retinoid-binding proteins › ANIS5_cation-bd 0.56 44.0 3.68e-01 88.9% 57.0%
3917586 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 39.0 3.21e-01 75.0% 47.9%
3675734 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.55 42.0 3.83e-01 84.7% 87.0%
5000894 2004.1.1.76 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.55 41.0 2.64e-01 81.9% 70.6%
3594741 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 40.0 2.94e-01 80.6% 45.4%
4118464 4030.1.1.1 ↗ alpha bundles › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › F_actin_cap_B 0.54 37.0 3.99e-01 91.7% 94.5%
3578718 101.1.6.0 ↗ alpha arrays › HTH › HTH › TrpR 0.54 44.0 4.04e-01 91.7% 84.2%
5072397 4095.1.1.1 ↗ alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › DNA_ligase_A_N 0.54 42.0 3.76e-01 86.1% 81.9%
3630023 188.1.1.1 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.53 44.0 3.14e-01 100.0% 78.4%
3214917 188.1.1.1 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.53 46.0 3.13e-01 100.0% 80.6%
3203269 109.4.1.1478 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_11, TPR_16 0.53 41.0 2.99e-01 84.7% 37.6%
3788815 109.4.1.1441 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, TPR_11, TPR_16 0.53 40.0 2.91e-01 84.7% 35.0%
3961071 101.1.1.536 ↗ alpha arrays › HTH › HTH › Three-helical HTH › PF27122 0.51 29.0 2.96e-01 100.0% 54.3%
3815745 592.6.1.1 ↗ alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain › BRR2_plug 0.51 45.0 4.38e-01 100.0% 96.2%
3898240 592.6.1.1 ↗ alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain › BRR2_plug 0.50 44.0 3.72e-01 100.0% 62.4%
3786647 592.6.1.1 ↗ alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain › BRR2_plug 0.50 44.0 4.26e-01 100.0% 100.0%