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pre1_saliva_scaffold_4_prodigal-single.1__X__X__00038

Bact-Vir

pre1_saliva_scaffold_4_prodigal-single.1__X__X__00038

Identity

Kingdom:
phage

Quality

80.7 mean pLDDT

Cluster

View cluster (9 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 6-114
PDB
Domain cluster: rep: PHAGE-A8--js4906-27-3_S30_scaffold_1_curated_closed_complete_prodigal-single.1__X__X__00090__D4-132
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2e9xB02 1.20.58.1020 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 35.0 3.55e-01 100.0% 49.5%
2oznB01 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.65 36.0 4.19e-01 95.4% 75.0%
1p8dB00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.58 46.0 3.63e-01 85.3% 77.4%
2guzA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.55 35.0 4.16e-01 77.1% 97.2%
3nt7A00 3.40.470.10 Alpha Beta › 3-Layer(aba) Sandwich › Uracil-DNA Glycosylase, subunit E › Uracil-DNA glycosylase-like domain 0.55 43.0 3.53e-01 85.3% 71.0%
4btfA01 1.20.930.20 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Adaptor protein Cbl, N-terminal domain 0.55 33.0 3.44e-01 100.0% 64.0%
6tqfA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.54 44.0 3.04e-01 90.8% 50.1%
1f2uB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 37.0 3.44e-01 90.8% 55.2%
1nt4A02 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.53 41.0 3.76e-01 83.5% 81.6%
1psyA01 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.53 36.0 3.80e-01 76.1% 78.0%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.52 46.0 4.68e-01 100.0% 98.2%
2r31A02 1.10.3580.10 Mainly Alpha › Orthogonal Bundle › ATP12-like fold › ATP12 ATPase 0.52 46.0 4.01e-01 100.0% 95.3%
4b6lA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.52 45.0 3.88e-01 96.3% 78.0%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3632799 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.68 37.0 3.44e-01 96.3% 43.0%
4977335 604.12.1.139 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › DUF1844 0.64 38.0 4.29e-01 100.0% 77.1%
3605711 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.61 35.0 3.95e-01 100.0% 75.0%
3896239 102.1.2.10 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase › Q_salvage 0.61 47.0 3.35e-01 81.7% 37.8%
3968363 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.60 34.0 4.24e-01 96.3% 100.0%
3699724 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.58 35.0 4.18e-01 99.1% 92.9%
3323680 5051.1.1.10 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › AA_permease_2 0.57 46.0 3.02e-01 84.4% 83.0%
3939282 650.1.1.10 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › PF30912 0.57 35.0 4.03e-01 75.2% 86.7%
4271879 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.55 33.0 4.09e-01 74.3% 100.0%
None — 0.55 46.0 3.03e-01 90.8% 99.6%
3670391 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.53 42.0 3.04e-01 85.3% 71.6%
5030008 3930.2.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in endoribonuclease Dicer › Helical bundle in endoribonuclease Dicer 0.52 43.0 3.73e-01 89.0% 82.4%
3527261 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.52 36.0 2.68e-01 72.5% 99.0%
3781626 171.1.1.0 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like 0.52 39.0 3.33e-01 78.9% 98.9%
2753367 219.1.1.43 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CoV_peptidase 0.51 39.0 3.26e-01 83.5% 76.0%
D2 high residues 124-236
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4kn7D01 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.71 57.0 5.45e-01 86.7% 100.0%
1gwiA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.52 47.0 3.23e-01 100.0% 49.5%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.52 37.0 3.61e-01 73.5% 69.8%
2olsA01 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.52 40.0 3.48e-01 84.1% 69.9%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.51 36.0 3.84e-01 72.6% 97.9%
3q5dA02 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.51 36.0 3.87e-01 79.6% 85.6%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
82329 372.2.1.0 ↗ a+b complex topology › RNase A-like › EndoU-like › EndoU-like 0.54 47.0 3.61e-01 99.1% 89.5%
D3 high residues 379-507
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4epcA01 2.30.30.170 Mainly Beta › Roll › SH3 type barrels. › 0.53 28.0 3.37e-01 89.9% 77.8%
4hdoA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 34.0 3.88e-01 91.5% 92.4%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5041029 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.69 43.0 5.22e-01 98.4% 100.0%
D4 medium residues 263-351_539-567
PDB
Domain cluster: rep: PHAGE-A8--js4906-27-3_S30_scaffold_1_curated_closed_complete_prodigal-single.1__X__X__00090__D278-372
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1k78I00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 21.0 2.81e-01 92.4% 65.5%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3185635 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.55 48.0 3.10e-01 100.0% 88.3%
4013654 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.53 46.0 2.96e-01 98.3% 90.1%
3952691 3156.1.1.8 ↗ beta sandwiches › Cupredoxin-like › Cupredoxin-related › Cupredoxin-related › Cu-oxidase_2 0.50 35.0 3.48e-01 94.9% 67.7%
D5 medium residues 601-646
PDB