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OM868076.1__UPT53042.1__X__00008

Bact-Vir

OM868076.1__UPT53042.1__X__00008

Identity

Accession:
OM868076 ↗
Kingdom:
phage

Quality

84.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Synechococcus_phage_Yong-M3-232

TaxID: 2928847

Cluster

View cluster (166 members)

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 4-52
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.71 56.0 5.36e-01 89.8% 74.6%
2g7hA01 3.30.160.460 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.54 39.0 3.48e-01 81.6% 80.3%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4627507 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.75 61.0 5.07e-01 89.8% 78.8%
D2 medium residues 84-110_127-141_162-203
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4je3B00 3.10.20.720 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 33.0 3.45e-01 100.0% 62.3%
1neiA00 3.30.160.220 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › YoaG 0.55 31.0 3.58e-01 100.0% 76.7%
2fdoA00 3.30.1970.10 Alpha Beta › 2-Layer Sandwich › AF2331-like fold › AF2331-like 0.53 30.0 2.97e-01 72.6% 48.4%
4l8hB00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.53 47.0 4.11e-01 97.6% 89.4%
1mhxA00 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.50 25.0 2.81e-01 78.6% 56.9%
2qrdB01 2.20.25.290 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.50 22.0 2.86e-01 77.4% 73.0%
3ue3A01 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.50 32.0 3.09e-01 75.0% 55.7%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3475708 389.1.1.0 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin 0.56 27.0 3.75e-01 77.4% 90.9%
2418009 4955.1.1.0 ↗ a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.53 32.0 3.35e-01 81.0% 66.2%
3580978 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 42.0 2.97e-01 90.5% 68.6%
3289468 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.52 26.0 2.84e-01 81.0% 55.7%
3996083 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 43.0 3.12e-01 91.7% 82.1%
D3 medium residues 142-161_204-363
PDB
Domain cluster: rep: DQ340064.2__ABC61276.1__X__00022__D272-425
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09950.16 best Major_capside 183.8 5.70e-54 88.9% 64.3%
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7mh2A01 3.30.2320.10 Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain 0.82 43.0 5.97e-01 86.7% 100.0%
1ohgA02 3.30.2320.10 Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain 0.74 43.0 5.62e-01 88.9% 99.0%
3bjqA00 3.90.1690.10 Alpha Beta › Alpha-Beta Complex › phage-related protein like fold › phage-related protein like domain 0.71 67.0 5.56e-01 100.0% 74.0%
1yueA03 3.30.2320.40 Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › 0.64 42.0 5.02e-01 88.9% 97.5%
6xgpB01 3.30.1930.10 Alpha Beta › 2-Layer Sandwich › capsid protein of prophage fold › capsid protein of prophage domain 0.60 44.0 5.07e-01 87.8% 100.0%
1ygyB03 3.30.1330.90 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › D-3-phosphoglycerate dehydrogenase; domain 3 0.60 37.0 4.19e-01 80.0% 79.9%
3bn3B01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 28.0 3.95e-01 88.9% 93.0%
3n79A01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.59 22.0 3.24e-01 86.1% 74.4%
1zxqA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 27.0 3.89e-01 88.9% 92.9%
1iamA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 28.0 3.85e-01 88.9% 96.4%
3obyA03 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.56 28.0 3.61e-01 86.1% 84.8%
3d2uA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 28.0 3.67e-01 88.3% 96.7%
6tqdC01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 28.0 3.64e-01 88.9% 94.8%
2nykA02 2.60.40.2530 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 23.0 3.21e-01 88.9% 83.9%
2jheA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.52 20.0 2.81e-01 80.6% 71.6%
2c9aA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 27.0 3.54e-01 88.9% 91.8%
6lxgA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.51 21.0 3.10e-01 86.1% 87.7%
3nlcA01 3.30.70.2700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 23.0 3.25e-01 85.6% 93.4%
3cypB00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.50 34.0 3.93e-01 85.0% 96.1%
1cl7I00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 24.0 3.33e-01 83.3% 95.1%
4q9bA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 28.0 3.59e-01 88.9% 96.0%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2995627 2485.3.1.7 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Major_capside 0.90 87.0 7.09e-01 100.0% 71.7%
3944238 2485.3.1.7 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Major_capside 0.89 87.0 7.20e-01 100.0% 75.3%
3942344 2485.3.1.19 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › PF30928 0.84 81.0 6.59e-01 100.0% 71.3%
4815223 2485.3.1.7 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Major_capside 0.83 79.0 7.48e-01 97.8% 100.0%
4873245 2485.3.1.2 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 0.82 57.0 6.73e-01 85.0% 100.0%
4884207 2485.3.1.7 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Major_capside 0.80 76.0 6.34e-01 99.4% 71.0%
2841509 2485.3.1.12 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › DUF6260 0.76 72.0 5.97e-01 98.9% 71.4%
5083051 2485.3.1.12 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › DUF6260 0.76 72.0 5.98e-01 100.0% 73.1%
3965498 2485.3.1.0 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 0.71 67.0 5.41e-01 100.0% 74.1%
3603036 2485.3.1.0 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 0.71 67.0 5.88e-01 100.0% 71.0%
3583655 2485.3.1.5 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Gp23 0.71 67.0 5.41e-01 100.0% 69.7%
3090875 2485.3.1.14 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Gp10A-like 0.71 66.0 5.47e-01 100.0% 76.1%
5081698 2485.3.1.18 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid_4 0.71 66.0 5.48e-01 100.0% 73.1%
5082710 2485.3.1.9 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › DUF4043 0.70 66.0 5.31e-01 100.0% 77.5%
194954 2485.3.1.2 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 0.70 65.0 5.85e-01 98.9% 74.6%
4988094 2485.3.1.18 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid_4 0.70 66.0 5.79e-01 100.0% 77.6%
2968064 2485.3.1.0 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 0.69 64.0 5.14e-01 100.0% 76.0%
4890673 2485.3.1.9 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › DUF4043 0.69 65.0 5.12e-01 100.0% 71.9%
5011908 2485.3.1.2 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 0.69 62.0 5.60e-01 100.0% 71.2%
3946670 2485.3.1.3 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid 0.68 65.0 5.51e-01 100.0% 75.3%
2989340 2485.3.1.3 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid 0.68 63.0 5.20e-01 99.4% 72.7%
2988313 2485.3.1.18 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid_4 0.68 64.0 5.50e-01 100.0% 69.9%
4991535 2485.3.1.2 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 0.68 63.0 5.64e-01 98.9% 73.5%
4955362 2485.3.1.2 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 0.67 62.0 5.65e-01 98.9% 76.5%
2639625 2485.3.1.18 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid_4 0.67 62.0 5.31e-01 100.0% 69.6%
5002389 2485.3.1.0 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 0.66 62.0 5.24e-01 100.0% 71.4%
2989372 2485.3.1.3 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid 0.65 61.0 5.08e-01 100.0% 71.1%
2989356 2485.3.1.3 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid 0.65 60.0 5.08e-01 100.0% 73.5%
2989363 2485.3.1.3 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid 0.65 60.0 4.99e-01 100.0% 73.7%
4031028 2485.3.1.3 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid 0.62 58.0 4.95e-01 100.0% 70.0%
2831773 2485.3.1.2 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 0.62 57.0 5.01e-01 100.0% 70.3%
5083777 2485.3.1.3 ↗ a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid 0.60 56.0 4.67e-01 99.4% 97.3%
1222169 11.1.1.64 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ICAM_N 0.59 28.0 3.95e-01 88.9% 92.0%
3525469 11.1.1.64 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ICAM_N 0.59 28.0 3.93e-01 88.9% 94.1%
3522049 298.3.1.2 ↗ a+b two layers › FwdE/GAPDH domain-like › Serine dehydratase beta chain-like › Serine dehydratase beta chain-like › PGDH_inter 0.58 37.0 4.22e-01 78.9% 84.4%
5068937 11.1.1.249 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Big_9 0.55 28.0 3.66e-01 88.9% 89.5%
5040305 11.1.1.249 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Big_9 0.54 27.0 3.61e-01 88.9% 90.5%
3537321 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.52 28.0 3.59e-01 88.9% 91.0%
3172782 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.52 24.0 3.30e-01 88.3% 88.2%