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NC_019550.1__YP_007011107.1__F489_gp12__00012

Bact-Vir

NC_019550.1__YP_007011107.1__F489_gp12__00012

Identity

Accession:
NC_019550 ↗
Kingdom:
phage

Quality

89.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Liberibacter_phage_SC2

TaxID: 941970

Cluster

View cluster (24 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 medium residues 1-58
PDB
Domain cluster: rep: NC_020205.1__YP_007392909.1__H390_gp20__00020__D1-53
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2iz4A01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.56 27.0 2.93e-01 72.4% 42.9%
4id8A00 3.30.70.20 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 28.0 2.78e-01 79.3% 43.1%
1vjwA00 3.30.70.20 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 28.0 2.85e-01 81.0% 49.2%
3kepA00 3.30.1610.10 Alpha Beta › 2-Layer Sandwich › c-terminal autoproteolytic domain of nucleoporin nup98 › Peptidase S59, nucleoporin 0.51 36.0 2.84e-01 75.9% 89.6%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3388594 389.1.1.0 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin 0.58 28.0 3.29e-01 74.1% 57.5%
3480298 101.1.2.69 ↗ alpha arrays › HTH › HTH › winged helix domain › La 0.52 31.0 2.79e-01 86.2% 38.8%
D2 medium residues 162-313
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6tdyD01 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.77 38.0 5.32e-01 94.7% 96.0%
1fx0B01 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.77 40.0 5.43e-01 100.0% 96.2%
2l1tA00 2.30.110.70 Mainly Beta › Roll › Pnp Oxidase; Chain A › 0.68 36.0 4.27e-01 91.4% 72.5%
3okxB00 2.40.30.70 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › YaeB-like 0.64 49.0 4.99e-01 95.4% 80.5%
2gk6A02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.64 36.0 4.58e-01 100.0% 98.8%
2nv4A00 2.40.30.70 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › YaeB-like 0.64 48.0 5.16e-01 95.4% 90.9%
4i86A00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.64 36.0 4.32e-01 94.1% 82.4%
1kjzA03 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.61 32.0 3.98e-01 89.5% 82.6%
2dn7A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 32.0 3.69e-01 98.0% 73.8%
2imlA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 34.0 3.86e-01 91.4% 77.9%
1lwrA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 30.0 3.65e-01 97.4% 81.2%
2erjB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 31.0 3.62e-01 99.3% 77.9%
1bquA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 30.0 3.45e-01 99.3% 71.3%
5t89Y06 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 30.0 3.73e-01 91.4% 88.0%
1wfoA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 30.0 3.50e-01 100.0% 76.0%
2v5yA05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 29.0 3.40e-01 94.1% 75.3%
2dm4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 28.0 3.44e-01 99.3% 79.8%
2dmkA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 32.0 3.69e-01 96.1% 84.5%
8owfA01 2.60.40.290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 36.0 4.05e-01 97.4% 92.8%
1e62A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 41.0 4.42e-01 100.0% 96.1%
2r6hA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 45.0 4.66e-01 100.0% 97.9%
1wisA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 32.0 3.70e-01 94.7% 91.1%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4660673 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.79 41.0 5.39e-01 97.4% 89.4%
4854964 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.78 40.0 5.24e-01 95.4% 88.4%
3967745 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.78 38.0 5.33e-01 100.0% 96.0%
4366483 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.77 42.0 5.48e-01 98.0% 94.1%
2556060 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.77 39.0 5.37e-01 97.4% 96.2%
4883586 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.77 38.0 5.02e-01 100.0% 84.9%
3596642 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.75 40.0 5.27e-01 100.0% 92.9%
3561733 5.1.3.253 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › CATSPERB_head 0.75 42.0 5.43e-01 100.0% 94.4%
4072878 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.74 39.0 5.24e-01 99.3% 97.5%
3728657 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.72 43.0 5.52e-01 94.1% 100.0%
4668791 1.1.8.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › eIF2_C 0.68 34.0 4.04e-01 89.5% 69.5%
5000763 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.68 39.0 4.97e-01 100.0% 95.6%
3267574 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.67 44.0 5.25e-01 96.1% 97.1%
4946423 1.1.7.138 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › NAD_binding_1 0.65 39.0 4.75e-01 98.7% 91.0%
140548 1.1.7.13 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › TrmO 0.65 48.0 4.81e-01 95.4% 75.0%
4080655 1.1.8.5 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › tRNA_Me_trans_C 0.63 32.0 3.93e-01 87.5% 76.8%
3967128 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.58 22.0 3.19e-01 96.1% 72.9%
3540700 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.56 31.0 3.62e-01 98.7% 78.0%
4942281 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.55 29.0 3.50e-01 94.7% 77.9%
3918983 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.54 30.0 3.52e-01 99.3% 78.0%
3099010 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.54 37.0 4.05e-01 96.7% 86.6%
3250327 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 31.0 3.68e-01 98.0% 83.0%
3780447 11.1.1.866 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_Rha78A_N 0.54 31.0 3.29e-01 98.0% 60.7%
3906165 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.53 27.0 3.34e-01 98.0% 77.8%
3924429 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 32.0 3.66e-01 98.7% 82.9%
3541118 11.1.1.3 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ig 0.53 29.0 3.15e-01 96.7% 61.6%
3905580 11.1.1.127 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › IL6Ra-bind 0.52 30.0 3.46e-01 99.3% 79.0%
4405629 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 33.0 3.64e-01 96.7% 82.6%
4515092 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.51 34.0 3.80e-01 97.4% 92.7%
D3 medium residues 329-379_416-444
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2y9fA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.58 40.0 3.29e-01 71.2% 88.6%
2otrA00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.58 32.0 3.07e-01 72.5% 46.7%
1h10A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 29.0 2.61e-01 73.8% 33.3%
1ntyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 35.0 3.06e-01 90.0% 41.1%
1tfkA00 3.10.450.200 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 32.0 3.06e-01 87.5% 50.0%
2bkkA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.50 37.0 3.59e-01 78.8% 80.0%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3919234 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.57 50.0 3.17e-01 100.0% 23.5%
1349153 5.1.11.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed › eIF2A 0.52 45.0 2.82e-01 100.0% 25.5%
4021102 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.50 43.0 2.72e-01 100.0% 27.3%