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pre3_saliva_scaffold_18_prodigal-single.1__X__X__00153

Bact-Vir

pre3_saliva_scaffold_18_prodigal-single.1__X__X__00153

Identity

Kingdom:
phage

Quality

86.5 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 1-82
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2x2vA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.75 52.0 5.68e-01 100.0% 88.2%
1w0bA01 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.73 45.0 4.38e-01 98.8% 55.4%
3l1nA02 1.20.1280.140 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.66 42.0 4.20e-01 95.1% 62.1%
3anwB00 1.20.58.2050 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 37.0 2.92e-01 89.0% 28.4%
3h3mA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.63 37.0 3.66e-01 93.9% 52.8%
1m6nA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.63 43.0 3.70e-01 100.0% 43.7%
6vudA01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.62 51.0 4.60e-01 100.0% 66.1%
4i43B02 3.30.43.40 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain 0.61 38.0 3.41e-01 90.2% 43.9%
2e9xA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 37.0 3.27e-01 100.0% 38.3%
3b9qA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.61 33.0 3.24e-01 81.7% 47.2%
8itfR01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.61 40.0 2.80e-01 98.8% 20.0%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.61 40.0 4.12e-01 96.3% 70.9%
3lnnB03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.60 36.0 3.90e-01 100.0% 71.6%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 49.0 4.52e-01 98.8% 72.9%
6xz3A01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.58 49.0 4.34e-01 92.7% 100.0%
3egoA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.57 34.0 3.02e-01 100.0% 39.7%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.57 42.0 3.72e-01 90.2% 51.6%
3ofnY00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.56 50.0 4.47e-01 100.0% 76.5%
2yinA03 1.20.58.740 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DOCK DHR2 domain, lobe C 0.56 38.0 3.39e-01 89.0% 46.1%
7zdtD01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.56 49.0 3.30e-01 100.0% 25.5%
1hs7A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 39.0 3.79e-01 96.3% 62.9%
2xokP00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.56 45.0 4.69e-01 97.6% 95.9%
5nx5B00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.55 49.0 3.35e-01 98.8% 47.9%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.54 49.0 4.91e-01 100.0% 98.8%
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.54 44.0 3.75e-01 100.0% 54.8%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.53 47.0 4.20e-01 97.6% 70.3%
3qweA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.53 47.0 3.35e-01 100.0% 32.3%
2odvA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 41.0 3.73e-01 97.6% 61.6%
3p8cF01 6.10.140.1620 Special › Helix non-globular › Helix Hairpins › 0.53 42.0 3.96e-01 98.8% 70.5%
4nqiD00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.53 45.0 3.32e-01 100.0% 34.5%
4i0xH00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.52 41.0 4.30e-01 97.6% 94.7%
2efkA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.52 45.0 3.22e-01 98.8% 38.5%
3g67A00 1.10.287.950 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Methyl-accepting chemotaxis protein 0.52 44.0 3.37e-01 98.8% 67.1%
5nl6B01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 41.0 3.66e-01 100.0% 59.5%
2v0xA01 1.10.287.3160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 46.0 3.66e-01 98.8% 57.1%
4nooB00 1.10.8.1160 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.51 38.0 3.72e-01 98.8% 70.5%
6vydA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.51 43.0 3.02e-01 98.8% 26.8%
4mh6A00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 42.0 3.45e-01 100.0% 48.4%
3ajwA00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 44.0 3.80e-01 100.0% 79.9%
7p3rA01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.51 43.0 2.99e-01 100.0% 37.8%
2p5tA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.50 37.0 3.60e-01 96.3% 69.6%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.50 44.0 4.09e-01 100.0% 82.2%
1zvzA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.50 40.0 3.52e-01 95.1% 58.1%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2323994 604.37.1.0 ↗ alpha bundles › Spectrin repeat-like › Legionella effector Lem22 › Legionella effector Lem22 0.71 40.0 3.90e-01 97.6% 48.9%
3977737 3831.1.1.1 ↗ alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › LprI 0.68 44.0 3.96e-01 100.0% 47.0%
5074955 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.66 41.0 4.00e-01 100.0% 56.7%
3742795 7022.1.1.1 ↗ alpha bundles › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › MBOAT 0.64 44.0 3.80e-01 100.0% 43.7%
4200387 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.64 43.0 4.19e-01 93.9% 63.3%
4940598 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.62 39.0 4.09e-01 98.8% 70.7%
4102807 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.61 39.0 3.67e-01 97.6% 50.5%
3175421 3922.1.1.312 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › PF30554 0.59 53.0 4.47e-01 100.0% 71.4%
4037982 5076.2.1.7 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › UPF0259 0.59 44.0 3.16e-01 78.0% 94.7%
5036645 5058.1.1.16 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.59 55.0 4.75e-01 100.0% 68.3%
3638634 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.58 48.0 4.35e-01 98.8% 67.0%
3498964 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.57 50.0 4.16e-01 100.0% 92.7%
4969464 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.57 36.0 3.51e-01 97.6% 58.9%
3880840 375.1.1.246 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rad50_zn_hook 0.57 46.0 4.34e-01 100.0% 73.0%
3410407 3745.1.1.1 ↗ alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex 0.56 45.0 3.04e-01 89.0% 57.3%
4998415 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.56 50.0 3.83e-01 97.6% 45.7%
3943069 3291.1.1.136 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › PF27688 0.55 48.0 4.02e-01 100.0% 57.0%
3400571 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.55 47.0 3.92e-01 100.0% 87.7%
4175809 5086.1.1.88 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_CyaD 0.55 47.0 3.85e-01 100.0% 95.2%
3883667 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 35.0 3.27e-01 97.6% 50.5%
3287601 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.54 44.0 4.26e-01 97.6% 78.7%
3591530 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.54 49.0 4.17e-01 100.0% 68.5%
3477880 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.54 47.0 3.26e-01 100.0% 27.9%
3282443 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.54 42.0 4.11e-01 97.6% 76.7%
3285241 192.29.1.52 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Anthrone_oxy 0.53 49.0 3.83e-01 100.0% 50.3%
3275656 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.53 46.0 3.88e-01 100.0% 95.3%
5037963 1079.1.1.0 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA 0.53 44.0 3.35e-01 98.8% 68.9%
3551506 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.53 48.0 3.23e-01 100.0% 67.3%
3259751 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.53 43.0 4.42e-01 100.0% 93.8%
3575692 633.7.1.5 ↗ alpha bundles › Bromodomain-like › Bacillus cereus metalloprotein-like › Bacillus cereus metalloprotein-like › Piezo_TM1-24 0.53 45.0 3.77e-01 98.8% 58.7%
3171466 3755.3.1.459 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › AIM11_N 0.53 46.0 4.26e-01 100.0% 85.5%
4128438 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.53 44.0 3.80e-01 100.0% 57.0%
3570651 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.53 37.0 3.56e-01 100.0% 63.2%
4964044 5058.1.1.16 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.53 46.0 4.35e-01 96.3% 87.0%
3256577 633.22.1.1 ↗ alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) › VKOR 0.53 45.0 3.66e-01 97.6% 80.6%
3267401 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.52 45.0 3.37e-01 95.1% 56.1%
1291200 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.52 46.0 3.16e-01 100.0% 27.9%
3688474 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.52 45.0 3.40e-01 100.0% 58.2%
3953975 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 0.52 37.0 3.60e-01 96.3% 65.3%
3584894 605.1.1.238 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › CNNM 0.52 43.0 4.19e-01 92.7% 86.7%
3183532 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.52 35.0 3.23e-01 97.6% 50.0%
3354876 5076.2.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › EI24 0.51 45.0 3.08e-01 100.0% 30.8%
5069014 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.51 45.0 3.82e-01 100.0% 87.9%
3288436 150.5.1.11 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › T7SS_ESX_EspC 0.51 42.0 3.94e-01 97.6% 73.3%
3282208 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.51 44.0 4.32e-01 93.9% 86.7%
3595321 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.51 45.0 4.35e-01 100.0% 89.5%
4349607 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.51 44.0 4.08e-01 100.0% 78.2%
3513364 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.50 44.0 3.68e-01 100.0% 92.0%
3235363 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.50 44.0 3.27e-01 100.0% 49.5%