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pre4_saliva_scaffold_3_prodigal-single.1__X__X__00088

Bact-Vir

pre4_saliva_scaffold_3_prodigal-single.1__X__X__00088

Identity

Kingdom:
phage

Quality

89.3 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 high residues 2-104
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ifvC00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.59 50.0 3.91e-01 97.1% 50.4%
3d31A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 25.0 3.27e-01 86.4% 89.1%
3go5A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 30.0 3.41e-01 94.2% 72.2%
2k52A00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 29.0 3.28e-01 90.3% 71.6%
1uebA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 29.0 3.45e-01 86.4% 85.7%
3hfnA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.52 25.0 3.20e-01 84.5% 78.3%
2eifA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 28.0 3.38e-01 86.4% 88.1%
2uvaG11 6.10.60.10 Special › Helix non-globular › Hydrophobic Seed Protein › 0.51 28.0 3.50e-01 87.4% 98.2%
4oonA03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.50 30.0 3.00e-01 95.1% 55.8%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4980359 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.62 53.0 5.07e-01 94.2% 99.2%
4995027 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.61 52.0 4.95e-01 95.1% 98.4%
4426056 227.1.1.4 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.61 52.0 4.59e-01 97.1% 99.4%
4026073 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.60 45.0 4.23e-01 78.6% 98.4%
4998584 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.60 50.0 4.66e-01 94.2% 98.5%
3292092 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.60 47.0 4.35e-01 85.4% 96.3%
5059299 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.59 51.0 4.89e-01 95.1% 99.2%
2392884 227.1.1.14 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › gp45-slide_C 0.59 47.0 4.47e-01 86.4% 95.0%
5990 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.59 48.0 4.65e-01 92.2% 99.2%
4232371 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.58 45.0 4.34e-01 83.5% 99.2%
5035697 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.58 31.0 3.66e-01 89.3% 78.5%
4956739 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.56 48.0 4.59e-01 97.1% 98.4%
5017215 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 29.0 3.60e-01 89.3% 87.3%
5039027 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.56 45.0 4.30e-01 87.4% 100.0%
4947996 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 28.0 3.65e-01 90.3% 89.1%
3238130 227.1.1.12 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.56 48.0 4.35e-01 98.1% 92.4%
3719304 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.55 43.0 4.00e-01 85.4% 94.0%
3507499 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.55 43.0 3.99e-01 85.4% 82.2%
3256386 227.1.1.4 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.54 44.0 4.09e-01 90.3% 97.8%
3789625 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.54 42.0 3.92e-01 86.4% 80.7%
3862483 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.52 23.0 3.13e-01 71.8% 97.5%
5053579 206.1.3.16 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Ins134_P3_kin 0.51 44.0 3.25e-01 98.1% 67.6%
4385597 2.1.1.7 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › S1 0.51 29.0 3.07e-01 91.3% 61.1%
D2 high residues 106-190
PDB
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.76 42.0 3.55e-01 98.8% 33.6%
4exrA01 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.73 44.0 4.50e-01 100.0% 63.0%
1lf7A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.73 46.0 3.62e-01 97.6% 32.3%
4hgzA02 2.20.25.570 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.73 42.0 4.85e-01 97.6% 80.0%
4l9cA00 3.40.1000.30 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › 0.70 41.0 3.39e-01 100.0% 32.7%
4exrA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.70 41.0 4.46e-01 100.0% 70.4%
1y8cA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.69 39.0 4.58e-01 96.5% 80.0%
3wjcA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.68 42.0 3.44e-01 98.8% 34.6%
3bxoA02 2.20.130.10 Mainly Beta › Single Sheet › S-adenosyl-L-methionine-dependent methyltransferases › CAC2371-like domains 0.66 41.0 4.74e-01 96.5% 89.8%
2gr7A00 3.30.1300.30 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › GSPII I/J protein-like 0.64 39.0 3.74e-01 97.6% 51.5%
3esiA00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.63 56.0 4.96e-01 100.0% 85.5%
4r80A00 3.10.450.630 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 41.0 4.32e-01 100.0% 75.0%
5t5lA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.60 53.0 3.91e-01 97.6% 57.2%
6obtA00 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.60 52.0 3.73e-01 100.0% 38.8%
2xklA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.59 41.0 3.48e-01 95.3% 41.6%
1s3rA03 3.40.30.40 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Perfringolysin 0.59 53.0 4.61e-01 98.8% 79.1%
2eigA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.59 50.0 3.76e-01 97.6% 56.5%
5a67A00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.59 53.0 3.98e-01 100.0% 69.9%
5w8mA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.58 51.0 3.95e-01 100.0% 98.0%
6gbuD00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.58 36.0 4.07e-01 91.8% 84.4%
4oocA00 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.57 49.0 3.56e-01 100.0% 38.4%
1omoA01 3.30.1780.10 Alpha Beta › 2-Layer Sandwich › ornithine cyclodeaminase, domain 1 › ornithine cyclodeaminase, domain 1 0.57 39.0 3.23e-01 100.0% 40.3%
3d2lA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.56 34.0 3.84e-01 95.3% 82.5%
2wuqB00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.55 43.0 3.12e-01 88.2% 94.7%
4pn0C00 3.20.100.10 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › mRNA triphosphatase Cet1-like 0.55 49.0 3.50e-01 100.0% 49.2%
2giaA00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.53 40.0 3.25e-01 78.8% 57.8%
1vavA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 46.0 3.44e-01 98.8% 46.4%
3tzgA00 2.40.160.150 Mainly Beta › Beta Barrel › Porin › 0.52 41.0 2.98e-01 84.7% 30.5%
2joxA00 2.60.40.4240 Mainly Beta › Sandwich › Immunoglobulin-like › Transcription activator, Churchill 0.51 39.0 3.64e-01 98.8% 66.0%
4ewfA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.50 41.0 3.00e-01 94.1% 94.8%
1n9eA01 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.50 46.0 2.80e-01 100.0% 28.2%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3731233 220.1.1.202 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_FT_N 0.79 45.0 3.60e-01 100.0% 32.0%
3890928 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.78 44.0 3.36e-01 98.8% 26.1%
3992540 79.1.1.24 ↗ beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Mlf1IP 0.73 42.0 4.02e-01 97.6% 51.6%
3961706 4.1.1.161 ↗ beta barrels › SH3 › SH3 › SH3 › DUF4178 0.70 44.0 4.98e-01 98.8% 83.1%
5043752 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.70 43.0 3.03e-01 100.0% 22.0%
4955671 7089.1.1.0 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD 0.68 44.0 4.59e-01 100.0% 70.0%
3997324 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.68 45.0 3.60e-01 97.6% 35.6%
3576360 9.1.1.12 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › THAP4_heme-bd 0.68 45.0 3.53e-01 98.8% 33.1%
3453561 10.1.1.2 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Lectin_legB 0.67 60.0 4.27e-01 97.6% 58.0%
3286735 243.3.1.3 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › PepSY 0.67 42.0 4.25e-01 100.0% 63.5%
5036897 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.66 46.0 3.77e-01 100.0% 42.1%
3625919 9.1.1.12 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › THAP4_heme-bd 0.66 43.0 3.34e-01 98.8% 31.7%
3888428 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.65 38.0 3.74e-01 98.8% 53.3%
4321969 222.1.1.0 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.64 56.0 4.57e-01 100.0% 72.1%
3228242 4210.1.1.1 ↗ a+b two layers › WGR domain › WGR domain › WGR domain › WGR 0.63 43.0 4.06e-01 98.8% 60.0%
2388236 246.2.1.9 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos_2 0.61 55.0 4.23e-01 100.0% 95.9%
3069457 1053.1.1.0 ↗ beta barrels › Factor H-binding protein (fHbp) N-terminal beta-barrel domain › Factor H-binding protein (fHbp) N-terminal beta-barrel domain › Factor H-binding protein (fHbp) N-terminal beta-barrel domain 0.61 39.0 4.62e-01 97.6% 96.5%
3949953 222.1.1.17 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › PKS_DH_N 0.61 53.0 4.60e-01 100.0% 79.3%
4129272 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 54.0 4.55e-01 100.0% 60.0%
4087213 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.60 38.0 4.07e-01 95.3% 73.3%
5035423 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.59 43.0 4.36e-01 75.3% 78.8%
3938069 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.59 49.0 4.16e-01 98.8% 55.6%
3991063 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.58 50.0 3.90e-01 97.6% 53.2%
3179848 241.15.1.2 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › PI31_Prot_N 0.57 40.0 3.48e-01 74.1% 57.6%
4013569 246.2.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases 0.56 51.0 3.89e-01 100.0% 99.5%
3962989 222.1.1.0 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.55 40.0 3.88e-01 77.6% 96.0%
3606318 897.1.1.0 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 0.55 40.0 2.98e-01 100.0% 30.0%
3379458 5084.5.1.2 ↗ beta barrels › Outer membrane meander beta-barrels › Porins › Porin › Omp85 0.54 43.0 2.86e-01 84.7% 37.9%
3718669 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 46.0 2.92e-01 100.0% 19.5%
3714031 5.1.3.66 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Pep3_Vps18 0.54 42.0 3.39e-01 87.1% 75.1%
3712989 897.1.1.1 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 › MAM33 0.53 39.0 2.94e-01 100.0% 31.4%
3967320 5084.5.1.0 ↗ beta barrels › Outer membrane meander beta-barrels › Porins › Porin 0.53 38.0 2.49e-01 97.6% 17.6%
4999447 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.52 49.0 3.31e-01 100.0% 38.6%
3924939 4210.1.1.1 ↗ a+b two layers › WGR domain › WGR domain › WGR domain › WGR 0.52 42.0 3.78e-01 100.0% 63.5%
3567279 243.3.1.4 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › Latexin_N 0.50 43.0 3.91e-01 95.3% 77.4%
3454721 5.1.3.142 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Beta-prop_AT5G49610-like 0.50 45.0 3.01e-01 100.0% 71.8%