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NC_004735.1__NP_835590.1__Rm378p003__00003

Bact-Vir

NC_004735.1__NP_835590.1__Rm378p003__00003

Identity

Accession:
NC_004735 ↗
Kingdom:
phage

Quality

80.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhodothermus_phage_RM378

TaxID: 148943

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 3-83
PDB
Domain cluster: representative
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3gpvA00 1.10.1660.10 Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › 0.74 52.0 4.60e-01 79.0% 52.2%
1yf2A02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.72 66.0 5.97e-01 100.0% 77.6%
4nsmA00 6.10.250.2770 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.71 50.0 5.35e-01 88.9% 83.1%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 52.0 5.50e-01 90.1% 87.7%
2qywA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.69 49.0 4.69e-01 86.4% 64.2%
1wp1B01 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.69 62.0 3.96e-01 100.0% 26.0%
1qoyA00 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.69 62.0 4.15e-01 100.0% 36.0%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 56.0 5.75e-01 91.4% 100.0%
6nyyE01 1.20.58.760 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Peptidase M41 0.66 52.0 4.10e-01 86.4% 80.3%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 58.0 5.29e-01 100.0% 79.2%
4iloA00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 57.0 4.09e-01 100.0% 36.4%
1fxkC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 59.0 4.92e-01 100.0% 88.7%
4o7iA01 3.30.540.10 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › Fructose-1,6-Bisphosphatase, subunit A, domain 1 0.63 46.0 3.51e-01 76.5% 34.6%
1go4A00 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.62 46.0 3.53e-01 80.2% 53.6%
2pg0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.62 47.0 3.87e-01 81.5% 44.3%
1f02T00 4.10.820.10 Few Secondary Structures › Irregular › Translocated Intimin Receptor; Chain T › Translocated intimin receptor, central domain 0.61 43.0 4.74e-01 85.2% 89.4%
1f1mA00 1.20.120.240 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Lipoprotein, type 6 0.60 55.0 4.35e-01 100.0% 90.7%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 51.0 4.46e-01 98.8% 61.7%
1w07A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.60 50.0 4.02e-01 97.5% 45.8%
1l8dA00 1.10.287.510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.58 51.0 4.75e-01 100.0% 79.6%
6ks6A02 3.30.260.10 Alpha Beta › 2-Layer Sandwich › GROEL; domain 2 › TCP-1-like chaperonin intermediate domain 0.56 40.0 3.66e-01 75.3% 100.0%
1llaA03 1.10.1280.10 Mainly Alpha › Orthogonal Bundle › di-copper center containing domain from catechol oxidase › Di-copper center containing domain from catechol oxidase 0.55 43.0 3.08e-01 87.7% 33.7%
2o0jA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 38.0 2.72e-01 74.1% 42.9%
3ragB00 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.54 43.0 3.20e-01 90.1% 83.6%
3hwcA01 1.10.3140.10 Mainly Alpha › Orthogonal Bundle › 4-hydroxybutyryl-coa dehydratase, domain 1 › 4-hydroxybutyryl-coa dehydratase, domain 1 0.54 37.0 3.13e-01 72.8% 42.9%
1dosA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 45.0 3.02e-01 100.0% 78.8%
1j7gA00 3.50.80.10 Alpha Beta › 3-Layer(bba) Sandwich › D-tyrosyl-trna(Tyr) Deacylase; Chain: A; › D-tyrosyl-tRNA(Tyr) deacylase 0.52 37.0 3.14e-01 77.8% 67.4%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3201554 150.1.1.98 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Vwaint 0.77 49.0 4.32e-01 81.5% 44.2%
3925968 109.4.1.162 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Nup192 0.76 66.0 3.54e-01 100.0% 5.4%
3271984 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.75 61.0 4.97e-01 87.7% 49.0%
3498567 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.73 66.0 4.83e-01 96.3% 59.0%
3287147 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.71 63.0 4.93e-01 100.0% 46.5%
1885522 3834.1.1.1 ↗ alpha bundles › TcA alpha pore-forming domain › TcA alpha pore-forming domain › TcA alpha pore-forming domain › TcA_TcB_BD 0.71 63.0 4.02e-01 100.0% 21.7%
3547409 604.1.1.153 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › DUF4455 0.70 63.0 4.71e-01 100.0% 61.5%
3903618 219.1.1.54 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C98 0.70 49.0 3.29e-01 80.2% 20.3%
5070087 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 0.70 56.0 5.53e-01 86.4% 85.9%
3290286 150.8.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PPE › PPE 0.69 63.0 4.75e-01 100.0% 83.8%
3237589 1203.1.2.0 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 0.67 56.0 4.91e-01 90.1% 64.2%
3277618 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 0.67 45.0 4.72e-01 95.1% 74.7%
3743565 109.4.1.313 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › UTP20_N 0.67 41.0 2.70e-01 71.6% 15.3%
5047150 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.67 61.0 4.51e-01 100.0% 41.5%
3976270 601.27.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › MW0975(SA0943)-like › MW0975(SA0943)-like › DUF3053 0.65 59.0 4.65e-01 100.0% 55.8%
3731212 192.24.1.0 ↗ alpha bundles › Long alpha-hairpin › RPC62 helical hairpin domain › RPC62 helical hairpin domain 0.64 55.0 5.44e-01 95.1% 87.1%
3611776 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.64 57.0 4.70e-01 96.3% 92.1%
3693554 4957.1.1.0 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit 0.64 56.0 4.53e-01 97.5% 52.0%
3916642 192.2.1.56 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › KIF9 0.64 56.0 4.63e-01 100.0% 54.0%
3729874 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.63 56.0 4.38e-01 96.3% 80.0%
3917696 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.63 56.0 4.19e-01 98.8% 40.0%
3717247 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.63 57.0 4.12e-01 100.0% 57.3%
4025072 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.61 54.0 4.79e-01 95.1% 81.7%
3613695 3922.1.1.230 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › DRC10_N 0.61 55.0 4.30e-01 96.3% 86.3%
4011414 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.61 56.0 4.07e-01 100.0% 79.5%
3706007 633.6.1.0 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like 0.61 51.0 3.93e-01 92.6% 41.1%
3744587 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.61 53.0 4.79e-01 100.0% 76.5%
4115648 3671.1.1.1 ↗ alpha duplicates or obligate multimers › Translocated intimin receptor Tir extracellular domain › Translocated intimin receptor Tir extracellular domain › Translocated intimin receptor Tir extracellular domain › Tir_receptor_M 0.61 53.0 5.25e-01 100.0% 92.9%
3775826 4016.1.1.0 ↗ alpha bundles › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase 0.60 49.0 4.04e-01 90.1% 49.7%
3614292 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.59 51.0 3.96e-01 97.5% 44.1%
3193128 4957.1.1.0 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit 0.59 51.0 4.08e-01 93.8% 58.1%
4025655 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.59 50.0 4.81e-01 98.8% 82.1%
3498627 7015.1.1.1 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › DHHC 0.57 52.0 3.62e-01 100.0% 34.1%
4251053 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.57 50.0 3.55e-01 98.8% 59.2%
4939027 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.56 42.0 3.74e-01 81.5% 60.8%
3222232 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.56 40.0 2.99e-01 80.2% 28.8%
3717499 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 41.0 2.65e-01 82.7% 58.2%