←Back to structures
NC_047738.1__YP_009783914.1__HOQ88_gp12__00012
Bact-VirNC_047738.1__YP_009783914.1__HOQ88_gp12__00012
Identity
- Accession:
- NC_047738 ↗
- Kingdom:
- phage
Quality
73.0
mean pLDDT
Taxonomy
Heunggongvirae›
Uroviricota›
Caudoviricetes›
Autographivirales›
Paadamvirus›
Rhizobium_phage_RHEph01
TaxID: 1220601
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 3-49
Domain cluster:
representative
CATH (45)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3k3oA02 | 1.20.58.1360 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.80 | 72.0 | 5.91e-01 | 100.0% | 95.2% |
| 4ofzA01 | 1.20.58.1800 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.79 | 70.0 | 5.25e-01 | 100.0% | 77.0% |
| 3okqA00 | 1.20.58.1540 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain | 0.78 | 56.0 | 4.14e-01 | 78.7% | 32.0% |
| 1st6A03 | 1.20.120.810 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vinculin, Vh2 four-helix bundle | 0.76 | 55.0 | 3.52e-01 | 78.7% | 17.5% |
| 2wmmA01 | 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 | 0.76 | 56.0 | 5.54e-01 | 78.7% | 81.6% |
| 3fxdB00 | 1.20.58.90 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.75 | 53.0 | 5.01e-01 | 76.6% | 81.0% |
| 4nb5B02 | 1.10.287.160 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat | 0.75 | 53.0 | 4.83e-01 | 76.6% | 57.8% |
| 5jrcA00 | 1.20.58.2140 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.75 | 65.0 | 4.34e-01 | 100.0% | 38.7% |
| 3h5qA01 | 1.20.970.10 | Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C | 0.73 | 58.0 | 5.12e-01 | 89.4% | 68.6% |
| 2chnB03 | 1.20.58.460 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hyaluronidase post-catalytic domain-like | 0.72 | 62.0 | 4.20e-01 | 100.0% | 83.3% |
| 5yixA00 | 1.10.601.10 | Mainly Alpha › Orthogonal Bundle › RNA Polymerase Primary Sigma Factor › RNA Polymerase Primary Sigma Factor | 0.72 | 62.0 | 3.72e-01 | 97.9% | 44.8% |
| 3cbuA02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.70 | 50.0 | 3.66e-01 | 78.7% | 29.1% |
| 3gfaA00 | 3.40.109.10 | Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase | 0.69 | 50.0 | 3.26e-01 | 76.6% | 21.9% |
| 2yf4F00 | 1.10.3420.10 | Mainly Alpha › Orthogonal Bundle › putative ntp pyrophosphohydrolase like fold › putative ntp pyrophosphohydrolase like domain | 0.69 | 49.0 | 3.51e-01 | 76.6% | 25.9% |
| 2xqyA02 | 1.20.58.1340 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.69 | 57.0 | 4.18e-01 | 100.0% | 42.0% |
| 1dd5A01 | 1.10.132.20 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor | 0.69 | 53.0 | 4.14e-01 | 87.2% | 84.4% |
| 4f92B10 | 1.10.3380.10 | Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › Sec63 N-terminal domain-like domain | 0.69 | 49.0 | 3.49e-01 | 74.5% | 25.9% |
| 4hwdD00 | 1.20.58.120 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain | 0.69 | 58.0 | 4.79e-01 | 100.0% | 85.6% |
| 2hyjA01 | 1.10.10.60 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like | 0.68 | 50.0 | 5.06e-01 | 78.7% | 100.0% |
| 2wyhB04 | 1.20.1270.50 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain | 0.66 | 46.0 | 3.63e-01 | 76.6% | 34.7% |
| 1m62A00 | 1.20.58.120 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain | 0.66 | 55.0 | 4.62e-01 | 100.0% | 83.9% |
| 1lujB01 | 1.10.10.490 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Beta-catenin-interacting ICAT | 0.66 | 50.0 | 4.93e-01 | 89.4% | 81.1% |
| 1y74A00 | 1.10.287.650 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain | 0.65 | 48.0 | 4.49e-01 | 80.9% | 64.9% |
| 2oduA02 | 1.20.58.60 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.64 | 52.0 | 4.21e-01 | 100.0% | 81.9% |
| 2mpnA00 | 6.10.140.1340 | Special › Helix non-globular › Helix Hairpins › | 0.64 | 45.0 | 4.06e-01 | 76.6% | 66.2% |
| 2lf3A00 | 1.20.1280.220 | Mainly Alpha › Up-down Bundle › Monooxygenase › Effector protein HopAB, BAK1-interacting domain | 0.64 | 53.0 | 4.19e-01 | 97.9% | 51.4% |
| 3gziA00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.63 | 52.0 | 3.42e-01 | 93.6% | 28.6% |
| 2ys8A00 | 1.10.287.110 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain | 0.63 | 44.0 | 3.64e-01 | 74.5% | 46.7% |
| 1lvfB00 | 1.20.58.90 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.63 | 50.0 | 4.11e-01 | 100.0% | 90.4% |
| 2rasA01 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.62 | 52.0 | 3.53e-01 | 97.9% | 57.6% |
| 1qv9A02 | 6.10.140.120 | Special › Helix non-globular › Helix Hairpins › | 0.61 | 43.0 | 3.39e-01 | 76.6% | 35.0% |
| 4tv7D01 | 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 | 0.60 | 52.0 | 4.28e-01 | 97.9% | 85.9% |
| 1ailA00 | 1.10.287.10 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding | 0.60 | 48.0 | 4.19e-01 | 87.2% | 98.6% |
| 3h37A02 | 1.10.110.30 | Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › | 0.59 | 49.0 | 4.09e-01 | 97.9% | 77.9% |
| 5tprA02 | 1.20.1090.10 | Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain | 0.58 | 48.0 | 3.21e-01 | 100.0% | 80.6% |
| 1dvhA00 | 1.10.760.10 | Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain | 0.58 | 38.0 | 3.26e-01 | 97.9% | 40.5% |
| 6a6fA00 | 3.90.1010.10 | Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › | 0.57 | 48.0 | 3.55e-01 | 100.0% | 46.3% |
| 2yqyA00 | 1.20.120.450 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain | 0.56 | 47.0 | 3.38e-01 | 91.5% | 34.9% |
| 1ds9A00 | 3.80.10.10 | Alpha Beta › Alpha-Beta Horseshoe › Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) › Ribonuclease Inhibitor | 0.55 | 41.0 | 2.82e-01 | 89.4% | 25.8% |
| 4w7sA02 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.54 | 45.0 | 3.08e-01 | 100.0% | 38.2% |
| 1xdxA01 | 3.30.1140.40 | Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › Tctex-1 | 0.53 | 43.0 | 3.52e-01 | 97.9% | 89.0% |
| 3tuiA00 | 1.10.3720.10 | Mainly Alpha › Orthogonal Bundle › MetI-like fold › MetI-like | 0.53 | 43.0 | 2.89e-01 | 100.0% | 43.1% |
| 1uhsA01 | 1.10.10.60 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like | 0.52 | 40.0 | 3.89e-01 | 91.5% | 85.2% |
| 3c1dA03 | 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 | 0.51 | 41.0 | 4.15e-01 | 87.2% | 87.0% |
| 2janA02 | 1.10.240.10 | Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase | 0.50 | 37.0 | 2.85e-01 | 76.6% | 35.6% |
ECOD (48)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3405975 | 633.21.1.42 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › DUF4781 | 0.90 | 81.0 | 5.27e-01 | 100.0% | 52.4% |
| 4177674 | 4992.1.1.23 ↗ | extended segments › RelB-like › RelB-like › RelB-like › Seryl_tRNA_N | 0.89 | 64.0 | 4.77e-01 | 76.6% | 33.6% |
| 3731064 | 633.6.1.0 ↗ | alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like | 0.88 | 64.0 | 4.73e-01 | 76.6% | 33.6% |
| 4000148 | 605.2.1.0 ↗ | alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 | 0.87 | 63.0 | 4.90e-01 | 76.6% | 38.9% |
| 3204414 | 1.1.17.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 | 0.86 | 62.0 | 3.58e-01 | 76.6% | 9.9% |
| 5055515 | 102.1.1.11 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › RNA_pol_Rpb4 | 0.85 | 63.0 | 4.64e-01 | 78.7% | 32.2% |
| 3587855 | 192.8.1.0 ↗ | alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain | 0.85 | 61.0 | 6.02e-01 | 76.6% | 74.0% |
| 3734558 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.84 | 61.0 | 3.21e-01 | 76.6% | 3.3% |
| 4209030 | 4336.1.1.1 ↗ | alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF | 0.84 | 60.0 | 4.47e-01 | 76.6% | 32.5% |
| 4634964 | 4336.1.1.1 ↗ | alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF | 0.82 | 59.0 | 4.46e-01 | 76.6% | 33.6% |
| 4493879 | 4992.1.1.23 ↗ | extended segments › RelB-like › RelB-like › RelB-like › Seryl_tRNA_N | 0.82 | 59.0 | 4.46e-01 | 76.6% | 33.6% |
| 4130073 | 4336.1.1.1 ↗ | alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF | 0.82 | 60.0 | 4.52e-01 | 78.7% | 33.6% |
| 2485668 | 7025.1.1.2 ↗ | alpha bundles › LIN9-LIN52 heterodimer › LIN9-LIN52 heterodimer › LIN9-LIN52 heterodimer › LIN9_C | 0.82 | 58.0 | 4.82e-01 | 76.6% | 42.9% |
| 3682846 | 109.4.1.2 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Arm | 0.81 | 72.0 | 4.16e-01 | 97.9% | 26.3% |
| 4453306 | 4336.1.1.1 ↗ | alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF | 0.81 | 58.0 | 4.33e-01 | 76.6% | 32.5% |
| 3754639 | 150.5.1.106 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › LIN9_C | 0.81 | 58.0 | 4.74e-01 | 76.6% | 43.5% |
| 3972084 | 3755.3.1.0 ↗ | alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin | 0.80 | 57.0 | 4.17e-01 | 76.6% | 28.8% |
| 3718035 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.80 | 58.0 | 5.16e-01 | 76.6% | 56.9% |
| 4343661 | 4336.1.1.1 ↗ | alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF | 0.79 | 58.0 | 4.33e-01 | 78.7% | 32.5% |
| 4066056 | 4336.1.1.1 ↗ | alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF | 0.79 | 57.0 | 4.30e-01 | 78.7% | 32.2% |
| 3697800 | 3559.1.1.0 ↗ | a+b complex topology › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 | 0.78 | 55.0 | 4.10e-01 | 74.5% | 34.8% |
| 3477418 | 4992.1.1.12 ↗ | extended segments › RelB-like › RelB-like › RelB-like › LIN9_C | 0.78 | 56.0 | 4.44e-01 | 76.6% | 38.9% |
| 3380823 | 109.4.1.1146 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ARM_PUB | 0.78 | 69.0 | 3.95e-01 | 100.0% | 26.7% |
| 4209288 | 4336.1.1.1 ↗ | alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF | 0.78 | 56.0 | 4.15e-01 | 76.6% | 33.0% |
| 3840952 | 601.19.1.39 ↗ | alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › LIN9_C | 0.78 | 55.0 | 4.76e-01 | 76.6% | 49.3% |
| 3179180 | 632.22.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats | 0.77 | 55.0 | 3.66e-01 | 76.6% | 20.5% |
| 3725506 | 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 | 0.76 | 55.0 | 4.14e-01 | 76.6% | 37.3% |
| 3270031 | 5000.4.1.1 ↗ | alpha arrays › Toxins' membrane translocation domains › delta-Endotoxin (insectocide), N-terminal domain › delta-Endotoxin (insectocide), N-terminal domain › Endotoxin_N | 0.76 | 59.0 | 3.65e-01 | 87.2% | 30.9% |
| 4992790 | 601.2.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes | 0.75 | 65.0 | 5.21e-01 | 100.0% | 78.9% |
| 3784566 | 604.1.1.191 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF29057 | 0.74 | 62.0 | 4.85e-01 | 93.6% | 85.0% |
| 3611632 | 192.7.1.0 ↗ | alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm | 0.73 | 52.0 | 4.09e-01 | 76.6% | 38.0% |
| 3260684 | 377.1.1.0 ↗ | few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like | 0.72 | 52.0 | 5.00e-01 | 78.7% | 70.9% |
| 3678263 | 109.4.1.1266 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Arm, ARM_PUB | 0.72 | 61.0 | 3.53e-01 | 100.0% | 25.6% |
| 4522608 | 3812.1.1.15 ↗ | alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › COX4_pro | 0.71 | 50.0 | 4.09e-01 | 76.6% | 48.9% |
| 4870601 | 3016.1.1.5 ↗ | a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SHMT | 0.71 | 51.0 | 3.92e-01 | 76.6% | 47.0% |
| 3497418 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.70 | 60.0 | 4.80e-01 | 100.0% | 84.0% |
| 4946497 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.70 | 61.0 | 4.04e-01 | 100.0% | 29.5% |
| 3513381 | 4082.1.1.0 ↗ | alpha duplicates or obligate multimers › Hairy Orange domain › Hairy Orange domain › Hairy Orange domain | 0.69 | 45.0 | 4.13e-01 | 97.9% | 53.3% |
| 3783773 | 109.4.1.32 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G | 0.67 | 55.0 | 3.16e-01 | 100.0% | 11.4% |
| 3224423 | 101.1.4.0 ↗ | alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like | 0.65 | 44.0 | 4.22e-01 | 72.3% | 87.3% |
| 1247969 | 101.1.1.5 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › TetR_N | 0.63 | 54.0 | 4.74e-01 | 97.9% | 84.5% |
| 3529255 | 1067.1.1.1 ↗ | few secondary structure elements › pheromone Ep-1 › pheromone Ep-1 › pheromone Ep-1 › DUF4536 | 0.62 | 44.0 | 4.13e-01 | 76.6% | 63.3% |
| 4508282 | 195.1.1.1 ↗ | alpha complex topology › NusB-like › NusB-like › NusB-like › NusB | 0.62 | 55.0 | 3.76e-01 | 97.9% | 49.4% |
| 4797659 | 632.1.1.3 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid | 0.62 | 44.0 | 4.26e-01 | 78.7% | 67.3% |
| 3912246 | 604.1.1.1 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin | 0.60 | 48.0 | 3.84e-01 | 100.0% | 79.1% |
| 3483235 | 2485.1.1.0 ↗ | a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like | 0.59 | 43.0 | 3.18e-01 | 76.6% | 44.3% |
| 3177141 | 6155.1.1.2 ↗ | alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop | 0.58 | 47.0 | 3.93e-01 | 100.0% | 89.5% |
| 5050286 | 632.1.1.3 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid | 0.55 | 49.0 | 3.81e-01 | 100.0% | 85.0% |