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NC_073375.1__YP_010751951.1__QDA11_gp15__00015

Bact-Vir

NC_073375.1__YP_010751951.1__QDA11_gp15__00015

Identity

Accession:
NC_073375 ↗
Kingdom:
phage

Quality

70.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Hodgkinviridae› Metamorphoovirus› Microbacterium_phage_Jayden

TaxID: 2656550

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 2-83
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qi2A01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.69 63.0 5.78e-01 100.0% 77.9%
3mcaB01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.69 59.0 5.59e-01 100.0% 79.2%
3oyyA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.59 44.0 4.80e-01 98.8% 100.0%
1j0hA04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.59 40.0 4.03e-01 100.0% 69.9%
3cpfA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.57 42.0 4.57e-01 98.8% 100.0%
1xkiA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 44.0 3.81e-01 82.9% 78.1%
2nwvA00 3.30.310.110 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › XisI-like 0.57 46.0 4.16e-01 89.0% 65.2%
1uebA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.56 40.0 4.42e-01 92.7% 100.0%
3hxlA05 3.30.360.90 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › 0.56 43.0 4.61e-01 85.4% 100.0%
1iz6A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.56 43.0 4.54e-01 98.8% 100.0%
1vwxT01 2.30.30.70 Mainly Beta › Roll › SH3 type barrels. › Ribosomal protein L21 0.54 42.0 4.05e-01 93.9% 73.2%
4aieA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 33.0 3.52e-01 100.0% 70.8%
1bebA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 45.0 3.72e-01 96.3% 93.6%
4l2iA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 44.0 3.40e-01 95.1% 80.0%
1gbgA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 41.0 3.10e-01 86.6% 95.8%
4mypA00 2.60.40.1850 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 41.0 3.62e-01 85.4% 99.2%
7k7jA02 2.60.40.1770 Mainly Beta › Sandwich › Immunoglobulin-like › ephrin a2 ectodomain 0.52 27.0 3.03e-01 87.8% 62.9%
1khiA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.52 40.0 4.13e-01 95.1% 90.7%
4yg6B00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.50 40.0 3.24e-01 86.6% 79.8%
2b39A10 2.60.120.1540 Mainly Beta › Sandwich › Jelly Rolls › 0.50 42.0 3.72e-01 100.0% 63.8%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
608 4.23.1.2 ↗ beta barrels › SH3 › Dom34/Pelota N-terminal domain-like › Dom34/Pelota N-terminal domain-like › PF26356 0.69 63.0 5.78e-01 100.0% 77.9%
4028885 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.61 45.0 4.95e-01 95.1% 100.0%
4345080 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.61 45.0 4.88e-01 95.1% 100.0%
4073200 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.60 45.0 4.87e-01 93.9% 100.0%
3265170 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.60 45.0 4.87e-01 95.1% 100.0%
3306779 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.60 44.0 4.83e-01 95.1% 100.0%
4158157 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.60 44.0 4.82e-01 95.1% 100.0%
4037383 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.59 44.0 4.78e-01 95.1% 100.0%
142633 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.59 44.0 4.80e-01 98.8% 100.0%
3599172 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 43.0 4.72e-01 95.1% 100.0%
4524363 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.59 43.0 4.74e-01 95.1% 100.0%
3608236 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.59 43.0 4.69e-01 95.1% 100.0%
3950208 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.59 43.0 4.69e-01 95.1% 100.0%
4051625 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.58 43.0 4.69e-01 95.1% 100.0%
4201878 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.58 43.0 4.66e-01 95.1% 100.0%
3948467 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.58 43.0 4.65e-01 92.7% 100.0%
4946993 4.1.1.479 ↗ beta barrels › SH3 › SH3 › SH3 › eIF-5a 0.58 45.0 4.75e-01 100.0% 100.0%
4213539 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.57 42.0 4.57e-01 98.8% 98.5%
4419948 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.57 42.0 4.59e-01 95.1% 100.0%
4292289 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.57 42.0 4.58e-01 95.1% 100.0%
4931072 4.1.1.139 ↗ beta barrels › SH3 › SH3 › SH3 › IF5A-like_N 0.57 44.0 4.72e-01 100.0% 100.0%
4942589 4.1.1.139 ↗ beta barrels › SH3 › SH3 › SH3 › IF5A-like_N 0.57 44.0 4.69e-01 96.3% 100.0%
4863266 4.1.1.139 ↗ beta barrels › SH3 › SH3 › SH3 › IF5A-like_N 0.56 40.0 4.30e-01 97.6% 96.9%
3509252 12.1.1.34 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Glyco_hydro38C2 0.56 41.0 3.86e-01 100.0% 64.0%
4027469 4246.1.1.2 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 0.56 46.0 3.11e-01 92.7% 37.9%
4968081 375.1.1.299 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › CPxCG_zf 0.55 36.0 4.27e-01 73.2% 100.0%
2884215 2005.1.1.10 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ETF 0.55 45.0 3.43e-01 91.5% 79.1%
3483489 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 42.0 4.32e-01 100.0% 90.7%
4997059 4.1.1.139 ↗ beta barrels › SH3 › SH3 › SH3 › IF5A-like_N 0.55 44.0 4.58e-01 100.0% 98.7%
3719304 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.55 45.0 3.83e-01 90.2% 79.1%
4419521 243.1.1.108 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › NTF2_YvbJ 0.54 39.0 3.33e-01 75.6% 92.6%
3643549 4.1.1.139 ↗ beta barrels › SH3 › SH3 › SH3 › IF5A-like_N 0.54 41.0 4.17e-01 97.6% 86.3%
3702616 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 42.0 3.63e-01 84.1% 87.2%
5018514 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 40.0 3.35e-01 79.3% 83.0%
4445317 9.1.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Lipocalin 0.53 41.0 3.40e-01 86.6% 76.8%
3702171 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 40.0 3.15e-01 84.1% 58.0%
3814058 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.51 42.0 3.60e-01 89.0% 80.0%
3614237 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.51 42.0 3.59e-01 91.5% 88.2%
4313210 283.1.1.3 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › Creatinase/aminopeptidase › Creatinase/aminopeptidase › Pantoate_ligase 0.50 40.0 3.73e-01 89.0% 72.4%
D2 high residues 133-189
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4an6B00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.66 45.0 3.24e-01 71.9% 24.0%
3zx7A02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.61 51.0 4.00e-01 100.0% 90.5%
3e8lC00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.60 51.0 3.72e-01 100.0% 85.2%
1avwB00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.60 41.0 2.97e-01 71.9% 24.0%
2k2jA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 38.0 3.05e-01 98.2% 34.2%
1k07A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.55 38.0 2.51e-01 73.7% 19.8%
1qmgB01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 37.0 2.55e-01 71.9% 80.6%
2nutB04 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.53 42.0 2.93e-01 96.5% 25.8%
2h9fA02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.51 35.0 2.56e-01 73.7% 65.6%
4d10F01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.50 41.0 2.98e-01 93.0% 43.6%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4414458 6.1.1.2 ↗ beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › Kunitz_legume 0.70 47.0 3.34e-01 70.2% 23.4%
4007983 252.2.1.5 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_3 0.63 42.0 3.60e-01 96.5% 42.1%
3982540 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.58 38.0 2.55e-01 87.7% 16.2%
4026577 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.58 39.0 3.97e-01 96.5% 72.7%
3738714 220.1.1.74 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PIG-H 0.57 39.0 3.16e-01 70.2% 95.5%
4219215 2.1.1.14 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RuvA_N 0.56 33.0 3.06e-01 93.0% 42.7%
5064517 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.54 39.0 2.99e-01 77.2% 71.9%
4644945 246.1.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Carbon-nitrogen hydrolase › Carbon-nitrogen hydrolase 0.54 43.0 2.92e-01 89.5% 99.1%
5003161 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 41.0 2.90e-01 91.2% 73.6%
4483491 2004.1.1.73 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.53 38.0 2.68e-01 77.2% 70.9%
3942396 4.1.1.412 ↗ beta barrels › SH3 › SH3 › SH3 › DUF1062 0.52 41.0 3.68e-01 93.0% 100.0%
5004588 2011.2.1.1 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › PNP_UDP_1 0.51 42.0 2.78e-01 93.0% 89.6%
3589594 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.51 38.0 2.92e-01 86.0% 92.9%
4947164 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 40.0 2.91e-01 87.7% 69.4%
3666731 2003.1.5.26 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_28 0.50 37.0 2.30e-01 80.7% 24.3%