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term1_saliva_scaffold_3_curated_closed_complete_prodigal-single.1__X__X__00213

Bact-Vir

term1_saliva_scaffold_3_curated_closed_complete_prodigal-single.1__X__X__00213

Identity

Kingdom:
phage

Quality

73.9 mean pLDDT

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 medium residues 38-58_155-280
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5bw0F00 3.30.1300.30 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › GSPII I/J protein-like 0.68 24.0 3.05e-01 79.6% 50.5%
3wo4C02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 26.0 3.22e-01 76.9% 62.6%
2covG00 2.60.40.2450 Mainly Beta › Sandwich › Immunoglobulin-like › Beta-1,3-xylanase, CBM31 domain 0.59 26.0 3.29e-01 79.6% 67.0%
3ubfA03 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.59 28.0 3.35e-01 76.9% 64.7%
3fn9C04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 25.0 3.16e-01 77.6% 64.1%
6m9yA00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.58 19.0 2.96e-01 76.9% 71.9%
7q61A01 2.60.40.1940 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 30.0 3.50e-01 77.6% 68.8%
3oq3B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 27.0 3.22e-01 76.9% 65.0%
2qkdA01 2.20.25.420 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ZPR1, zinc finger domain 0.56 18.0 2.86e-01 72.8% 75.0%
4r6uA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 23.0 2.84e-01 76.9% 58.0%
4kc3B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 26.0 3.09e-01 76.9% 65.3%
4gafB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 26.0 3.00e-01 76.9% 60.4%
3o4oC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 27.0 3.09e-01 78.9% 63.6%
7skhB01 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.53 26.0 3.11e-01 76.9% 68.0%
2iteA00 2.60.40.1850 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 28.0 3.06e-01 81.6% 60.3%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3940678 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.76 22.0 2.74e-01 76.2% 40.0%
4935472 330.4.1.0 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain 0.70 21.0 3.05e-01 77.6% 55.7%
3578102 11.1.1.102 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › A2M_BRD 0.63 29.0 3.55e-01 79.6% 66.0%
1822815 6173.1.1.1 ↗ beta barrels › V1/V2 domain in HIV gp120 › V1/V2 domain in HIV gp120 › V1/V2 domain in HIV gp120 › GP120 0.59 21.0 3.44e-01 79.6% 91.7%
3594714 259.1.1.0 ↗ a+b two layers › Ribosomal protein L31e-like › Ribosomal protein L31e/gp120 outer domain › Ribosomal protein L31e/gp120 outer domain 0.55 38.0 4.35e-01 84.4% 95.4%
3932817 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 3.23e-01 82.3% 60.0%
4950602 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 28.0 3.13e-01 83.7% 62.7%
3499841 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 20.0 2.47e-01 78.2% 47.8%
4927548 331.3.1.9 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › AHSA1 0.52 26.0 2.86e-01 72.8% 55.8%
4030088 206.1.3.18 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › D123 0.52 40.0 3.34e-01 96.6% 45.0%
3561724 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.50 32.0 3.40e-01 78.9% 71.5%
5065314 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 26.0 3.11e-01 76.9% 73.7%
D2 medium residues 59-110_141-154
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.62 46.0 3.01e-01 78.8% 88.8%
3pgbA01 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.61 44.0 2.66e-01 78.8% 63.5%
1ksiA03 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.60 43.0 2.72e-01 78.8% 79.6%
1fm2B03 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.54 39.0 3.99e-01 78.8% 93.9%
1n9eA01 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.54 47.0 2.77e-01 97.0% 13.1%
2zewB00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 41.0 3.14e-01 100.0% 36.7%
2py5A05 4.10.80.20 Few Secondary Structures › Irregular › Rhinovirus 14, subunit 4 › DNA polymerase; domain 5 0.54 25.0 3.21e-01 77.3% 80.0%
3nqzA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 35.0 3.31e-01 86.4% 53.6%
4yfbC02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.53 38.0 3.64e-01 77.3% 94.9%
3n77A00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.53 38.0 3.05e-01 78.8% 49.6%
1ae2A00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 42.0 3.97e-01 100.0% 73.3%
3rd4B00 2.40.50.660 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 44.0 4.12e-01 100.0% 78.0%
1kf6A04 4.10.80.40 Few Secondary Structures › Irregular › Rhinovirus 14, subunit 4 › succinate dehydrogenase protein domain 0.51 25.0 3.11e-01 77.3% 80.0%
3ua0A00 6.20.280.10 Special › Other non-globular › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.50 34.0 3.25e-01 77.3% 58.2%
6toaE01 2.40.10.270 Mainly Beta › Beta Barrel › Thrombin, subunit H › Bacteriophage SPP1 head-tail adaptor protein 0.50 36.0 3.25e-01 78.8% 100.0%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5045979 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.81 42.0 2.70e-01 93.9% 12.6%
3633076 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.71 42.0 3.64e-01 77.3% 37.1%
3544841 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.60 49.0 3.78e-01 93.9% 42.2%
3268156 223.2.1.4 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › DENN,uDENN 0.57 50.0 3.60e-01 98.5% 61.6%
4029824 2484.1.1.20 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_A_exo1 0.55 39.0 2.62e-01 77.3% 71.8%
2034 12.3.1.2 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Cu_amine_oxid 0.54 47.0 2.82e-01 97.0% 14.3%
3737341 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.54 38.0 3.11e-01 75.8% 70.0%
3214850 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.54 37.0 2.35e-01 71.2% 67.7%
3639466 4.23.1.2 ↗ beta barrels › SH3 › Dom34/Pelota N-terminal domain-like › Dom34/Pelota N-terminal domain-like › PF26356 0.54 38.0 3.02e-01 75.8% 77.2%
3304525 4.1.1.173 ↗ beta barrels › SH3 › SH3 › SH3 › DUF4216 0.53 47.0 3.93e-01 97.0% 94.5%
3299532 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.53 41.0 3.51e-01 90.9% 50.9%
3784604 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.53 46.0 3.45e-01 97.0% 46.1%
3620606 385.1.1.1 ↗ few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines › Cys_knot 0.53 43.0 3.95e-01 89.4% 98.8%
3589333 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 44.0 3.85e-01 90.9% 76.8%
3517068 3115.1.1.6 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.52 43.0 4.40e-01 92.4% 100.0%
4932882 4.23.1.2 ↗ beta barrels › SH3 › Dom34/Pelota N-terminal domain-like › Dom34/Pelota N-terminal domain-like › PF26356 0.51 43.0 3.39e-01 90.9% 60.0%
3923851 385.1.1.8 ↗ few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines › DAN 0.51 42.0 3.67e-01 93.9% 84.8%
5010503 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 40.0 3.53e-01 89.4% 58.9%
3477515 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.50 46.0 3.80e-01 100.0% 60.9%
3778719 385.1.1.8 ↗ few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines › DAN 0.50 42.0 3.66e-01 93.9% 85.4%
4027717 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.50 42.0 2.86e-01 95.5% 38.8%
3881856 385.1.1.8 ↗ few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines › DAN 0.50 41.0 3.64e-01 92.4% 85.0%
D3 medium residues 111-140_281-349
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gvnA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.67 47.0 4.98e-01 71.7% 96.6%
1w36C04 1.10.486.10 Mainly Alpha › Orthogonal Bundle › PCRA; domain 4 › PCRA; domain 4 0.62 40.0 3.14e-01 72.7% 31.6%
3if8B02 1.20.58.730 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 51.0 5.10e-01 90.9% 90.0%
3bk2A03 3.10.20.580 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.60 40.0 4.05e-01 76.8% 67.7%
6xpdA01 1.20.1510.10 Mainly Alpha › Up-down Bundle › Alpha-lytic protease prodomain-like › Cation efflux protein transmembrane domain 0.60 54.0 4.27e-01 100.0% 95.5%
6xj1A01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.58 40.0 3.00e-01 70.7% 86.1%
1or7B01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.56 38.0 3.96e-01 76.8% 74.5%
4mndA02 1.20.120.1760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain 0.55 48.0 3.94e-01 100.0% 58.1%
3ez0C00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 46.0 3.63e-01 93.9% 88.5%
3oz2A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 47.0 3.57e-01 98.0% 79.7%
4nwpD00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.53 41.0 3.55e-01 80.8% 63.1%
6a3kA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.53 47.0 4.33e-01 99.0% 93.0%
5zbqA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.53 46.0 3.38e-01 100.0% 45.9%
2yn7A00 1.10.3160.10 Mainly Alpha › Orthogonal Bundle › Bbcrasp-1 › Bbcrasp-1 0.52 44.0 3.55e-01 99.0% 94.4%
3bg2A03 1.10.3410.10 Mainly Alpha › Orthogonal Bundle › putative deoxyguanosinetriphosphate triphosphohydrolase fold › putative deoxyguanosinetriphosphate triphosphohydrolase like domain 0.52 38.0 3.93e-01 77.8% 95.8%
6d5xA00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.51 39.0 3.44e-01 81.8% 61.6%
1op1A00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.51 37.0 3.99e-01 88.9% 90.2%
2v0oB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.51 39.0 2.90e-01 81.8% 75.6%
3frrA00 1.20.1260.60 Mainly Alpha › Up-down Bundle › Ferritin › Vacuolar protein sorting-associated protein Ist1 0.51 40.0 3.25e-01 82.8% 77.4%
1foeA01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.51 40.0 3.22e-01 85.9% 47.0%
1binA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.50 39.0 3.40e-01 80.8% 76.2%
1dtoA01 1.10.287.30 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › E2 (early) protein, N terminal domain, subdomain 1 0.50 37.0 3.73e-01 77.8% 96.1%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4941191 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.67 47.0 4.50e-01 70.7% 93.6%
3719613 1189.1.1.0 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor 0.64 44.0 3.37e-01 70.7% 85.8%
3812310 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.58 40.0 3.45e-01 70.7% 60.0%
3741872 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.58 40.0 3.23e-01 71.7% 76.2%
5035275 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.57 40.0 3.96e-01 71.7% 89.5%
3270186 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 0.57 41.0 3.85e-01 74.7% 95.8%
4045999 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.56 47.0 3.83e-01 96.0% 96.0%
1299701 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.55 48.0 3.89e-01 100.0% 55.5%
3723192 5069.1.3.55 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DUF202 0.53 41.0 3.89e-01 81.8% 89.2%
3770274 603.1.1.198 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › DUF4716 0.53 40.0 4.10e-01 78.8% 100.0%
3631038 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.52 45.0 3.62e-01 99.0% 93.8%
3494198 328.7.1.0 ↗ a+b two layers › IF3-like › Smr domain › Smr domain 0.51 44.0 3.56e-01 92.9% 87.4%
3339772 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.51 38.0 3.43e-01 78.8% 95.0%
4155141 1079.1.1.14 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › MarC 0.51 40.0 3.28e-01 85.9% 56.9%
3252688 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.51 39.0 3.25e-01 78.8% 83.6%