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MK493321.1__QBQ74924.1__RW110999_046__00039

Bact-Vir

MK493321.1__QBQ74924.1__RW110999_046__00039

Identity

Accession:
MK493321 ↗
Kingdom:
phage

Quality

91.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Shandvirus› Cyanophage_S-RIM4

TaxID: 2530169

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 medium residues 28-80
PDB
Domain cluster: rep: LacPavin_0818_WC50_scaffold_3810_prodigal-single.1__X__X__00013__D8-52
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3vpbE00 2.20.28.160 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.68 46.0 4.55e-01 75.5% 67.9%
2cr4A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.67 52.0 4.28e-01 86.8% 89.9%
1yu0A01 2.10.10.30 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › 0.65 53.0 5.42e-01 94.3% 96.1%
1v6zA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.62 49.0 4.67e-01 88.7% 93.8%
6mzoA01 3.40.50.11970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 46.0 3.61e-01 86.8% 51.6%
1o9aA01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.60 40.0 4.24e-01 75.5% 81.8%
4nqrA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.60 51.0 3.66e-01 94.3% 71.0%
1clwA00 2.160.20.20 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › 0.59 48.0 2.79e-01 96.2% 10.3%
4h40A01 2.60.40.3730 Mainly Beta › Sandwich › Immunoglobulin-like › Fimbrillin-like 0.58 43.0 3.12e-01 81.1% 55.7%
4paaA03 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.58 41.0 2.98e-01 81.1% 24.3%
6pzjA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.58 43.0 3.28e-01 86.8% 53.4%
3cpxA02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.57 43.0 4.13e-01 83.0% 82.3%
2iecD00 3.30.1300.20 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 7,8-dihydroneopterin aldolase (MptD) 0.57 43.0 3.40e-01 83.0% 88.9%
3j7yD01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 41.0 3.29e-01 77.4% 50.0%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.56 42.0 3.22e-01 84.9% 47.1%
6biqC01 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.55 45.0 3.57e-01 96.2% 47.9%
5hy7B02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 47.0 2.95e-01 100.0% 97.5%
5i7pA02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.55 37.0 3.87e-01 71.7% 81.2%
1vq8A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 40.0 3.60e-01 81.1% 65.4%
1tpmA00 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.54 37.0 3.76e-01 75.5% 76.0%
1vw3B01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 42.0 3.55e-01 86.8% 91.4%
4g2sA00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.54 38.0 3.19e-01 79.2% 71.7%
2im9A02 2.30.260.10 Mainly Beta › Roll › putative xylanase like fold › putative xylanase like domain 0.53 45.0 3.33e-01 98.1% 70.1%
4perB00 3.10.130.10 Alpha Beta › Roll › P-30 Protein › Ribonuclease A-like domain 0.53 38.0 3.09e-01 79.2% 55.0%
3fgbA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 40.0 2.47e-01 84.9% 25.5%
2m1hA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 35.0 2.91e-01 71.7% 52.7%
1kw3B02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.51 37.0 2.72e-01 79.2% 60.4%
5aykA07 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 39.0 3.27e-01 94.3% 84.3%
3a32A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.51 40.0 3.09e-01 94.3% 46.8%
4i79A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.50 40.0 2.62e-01 98.1% 81.0%
3gqbA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.50 39.0 3.62e-01 88.7% 78.9%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2495545 207.2.1.22 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Beta_helix 0.81 65.0 3.76e-01 94.3% 10.1%
3528795 3761.1.1.0 ↗ beta duplicates or obligate multimers › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related 0.75 56.0 6.00e-01 90.6% 95.6%
4955635 375.1.1.63 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › LysW-like_globular 0.69 48.0 4.59e-01 79.2% 62.5%
3517867 214.1.1.9 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7063 0.67 56.0 4.30e-01 98.1% 76.2%
3226032 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.65 48.0 4.80e-01 79.2% 88.7%
1107990 3761.1.1.1 ↗ beta duplicates or obligate multimers › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Mtd_N 0.65 53.0 5.46e-01 94.3% 98.0%
None — 0.64 52.0 3.14e-01 90.6% 13.7%
5069323 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 44.0 4.53e-01 79.2% 78.0%
4927153 375.1.1.63 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › LysW-like_globular 0.63 42.0 4.24e-01 77.4% 67.3%
3509348 214.1.1.15 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7063, DUF7145 0.62 51.0 3.25e-01 98.1% 53.3%
3650304 66.1.1.0 ↗ beta sandwiches › ISP domain › ISP domain › ISP domain 0.61 44.0 4.33e-01 81.1% 75.0%
5028514 375.1.1.63 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › LysW-like_globular 0.61 43.0 4.18e-01 79.2% 68.3%
4991056 375.1.1.63 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › LysW-like_globular 0.61 41.0 4.11e-01 77.4% 69.1%
5071089 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.60 42.0 4.30e-01 77.4% 80.0%
3271846 391.1.2.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related 0.59 42.0 4.25e-01 77.4% 87.3%
4627221 4.1.1.175 ↗ beta barrels › SH3 › SH3 › SH3 › MSSS 0.58 40.0 3.77e-01 71.7% 58.5%
3874321 389.1.2.7 ↗ few secondary structure elements › EGF-like › EGF-related › Complement control module/SCR domain › THBD 0.58 45.0 4.16e-01 86.8% 74.3%
4218318 2484.1.1.295 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, RNase_H_2 0.57 40.0 2.48e-01 75.5% 13.8%
3595236 7563.1.1.0 ↗ a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related 0.57 43.0 2.75e-01 84.9% 44.8%
5045717 286.1.1.2 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › PhzC-PhzF 0.56 43.0 3.37e-01 88.7% 56.9%
4680376 4.1.1.175 ↗ beta barrels › SH3 › SH3 › SH3 › MSSS 0.56 38.0 3.80e-01 71.7% 69.1%
3834352 3075.1.1.0 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA 0.56 45.0 2.69e-01 92.5% 11.2%
5051933 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 41.0 2.91e-01 79.2% 44.7%
3459983 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.56 44.0 2.72e-01 92.5% 12.3%
3633382 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.55 46.0 3.33e-01 94.3% 69.7%
3190369 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.55 45.0 3.67e-01 94.3% 84.8%
3256917 4.8.1.2 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.55 41.0 3.66e-01 81.1% 72.0%
4861411 5.1.4.58 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › DUF5074 0.54 39.0 2.50e-01 81.1% 96.2%
3637504 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.54 40.0 2.35e-01 84.9% 15.0%
223688 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.54 39.0 4.24e-01 79.2% 100.0%
5073026 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 38.0 3.90e-01 77.4% 80.0%
4656410 1.1.9.32 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › TnpB_IS66 0.53 41.0 3.61e-01 90.6% 97.8%
3609095 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 36.0 3.41e-01 73.6% 67.7%
3656396 219.1.1.16 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C48 0.50 36.0 2.64e-01 79.2% 29.7%
D2 medium residues 81-135
PDB
Domain cluster: representative