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PPR_Contig_984988_prodigal-single.1__X__X__00292

Bact-Vir

PPR_Contig_984988_prodigal-single.1__X__X__00292

Identity

Kingdom:
phage

Quality

71.1 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 1402-1567
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3oonA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.77 47.0 5.59e-01 100.0% 88.5%
5m38C00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.75 50.0 6.01e-01 100.0% 99.1%
3cypB00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.73 48.0 5.48e-01 99.4% 86.0%
5wtpA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.72 49.0 5.66e-01 100.0% 91.9%
4rhaA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.66 47.0 5.31e-01 100.0% 93.1%
6aeoB01 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.66 45.0 4.98e-01 99.4% 85.9%
1r1mA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.62 48.0 5.19e-01 100.0% 95.0%
1dihA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.61 36.0 4.34e-01 84.3% 88.9%
1vdyA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.60 34.0 3.69e-01 73.5% 65.0%
3h8gA01 3.40.220.10 Alpha Beta › 3-Layer(aba) Sandwich › Leucine Aminopeptidase, subunit E; domain 1 › Leucine Aminopeptidase, subunit E, domain 1 0.53 30.0 3.13e-01 74.7% 55.9%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3385657 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.76 51.0 5.88e-01 100.0% 90.3%
3386470 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.76 51.0 5.94e-01 100.0% 93.3%
3386253 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.74 49.0 5.24e-01 100.0% 75.9%
1347936 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.73 48.0 5.47e-01 98.8% 87.9%
4273645 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.73 50.0 5.51e-01 100.0% 84.1%
None 0.72 49.0 5.14e-01 100.0% 75.3%
3981506 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.72 49.0 4.99e-01 100.0% 70.6%
3962237 301.3.1.0 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like 0.71 48.0 5.75e-01 98.8% 99.1%
2798263 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.70 47.0 4.98e-01 100.0% 75.8%
2773879 301.3.1.1 a+b three layers › Bacillus chorismate mutase-like › OmpA-like › OmpA-like › OmpA 0.61 51.0 5.41e-01 100.0% 96.7%
4988570 2005.1.1.0 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.57 39.0 4.55e-01 98.8% 96.7%
3481082 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 36.0 2.98e-01 73.5% 35.7%
3345073 298.3.1.2 a+b two layers › FwdE/GAPDH domain-like › Serine dehydratase beta chain-like › Serine dehydratase beta chain-like › PGDH_inter 0.51 38.0 3.92e-01 92.8% 81.9%
3212577 246.2.1.7 a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › DNA_pol_E_B 0.51 43.0 3.50e-01 89.2% 79.3%
D2 medium residues 89-108_234-288_461-473_540-589_1339-1362
PDB
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3kyfA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.65 40.0 4.68e-01 96.9% 86.3%
4kktA02 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.63 37.0 4.55e-01 73.5% 90.5%
3cddA01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.60 57.0 5.45e-01 99.4% 96.2%
1wruA01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.59 56.0 5.43e-01 98.8% 98.3%
1qz8A01 2.40.10.250 Mainly Beta › Beta Barrel › Thrombin, subunit H › Replicase NSP9 0.59 32.0 3.82e-01 74.1% 79.0%
3d37B01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.57 54.0 5.32e-01 100.0% 98.3%
2p5zX01 2.30.110.50 Mainly Beta › Roll › Pnp Oxidase; Chain A › 0.55 51.0 5.09e-01 97.5% 100.0%
3qw9B00 2.60.40.4100 Mainly Beta › Sandwich › Immunoglobulin-like › Zona pellucida, ZP-C domain 0.53 37.0 3.73e-01 70.4% 97.6%
3q0bX00 2.30.280.10 Mainly Beta › Roll › PUA domain-like › SRA-YDG 0.52 40.0 4.25e-01 95.1% 89.9%
2e8yA04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 26.0 3.45e-01 74.1% 88.9%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3968713 1.1.13.5 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_GPD 0.75 42.0 5.55e-01 72.8% 98.9%
4810019 1.1.13.57 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › PF30637 0.74 46.0 5.66e-01 73.5% 92.7%
3968432 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.66 41.0 5.01e-01 95.7% 96.2%
4319057 1.1.5.25 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.65 41.0 4.82e-01 96.9% 89.6%
3949052 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.65 35.0 4.53e-01 75.3% 93.3%
4565791 1.1.7.87 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25954 0.64 35.0 4.49e-01 75.9% 93.3%
4036849 1.1.5.25 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.63 43.0 4.71e-01 96.9% 84.2%
4514734 1.1.13.42 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Tail_tube 0.62 41.0 4.95e-01 75.3% 99.1%
4157825 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.62 45.0 5.01e-01 74.1% 95.4%
4562905 1.1.5.25 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.62 41.0 4.64e-01 96.3% 87.2%
4214150 1.1.5.25 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.61 36.0 4.30e-01 95.7% 85.5%
3909822 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.61 40.0 4.75e-01 79.6% 97.3%
3501491 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.60 38.0 4.09e-01 75.9% 74.1%
3299946 1.1.7.81 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SEN1_barrel 0.57 38.0 4.45e-01 83.3% 93.9%
3256920 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 40.0 4.50e-01 79.6% 92.8%
4957560 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.56 43.0 4.73e-01 87.7% 98.5%
3844943 11.1.1.117 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › EpoR_lig-bind 0.52 28.0 3.47e-01 75.9% 84.2%
D3 medium residues 109-154_289-308_320-460
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.65 29.0 3.57e-01 93.7% 63.7%
4ke2A00 6.10.140.1860 Special › Helix non-globular › Helix Hairpins › 0.60 30.0 3.15e-01 89.9% 49.5%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.57 30.0 4.13e-01 87.9% 99.1%
2oexA02 1.20.140.50 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › alix/aip1 like domains 0.56 32.0 3.34e-01 95.2% 58.4%
1fxkC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 34.0 4.18e-01 91.8% 97.7%
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 34.0 3.13e-01 93.7% 51.1%
8a1gC01 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 33.0 3.50e-01 93.7% 70.7%
4iloA00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 30.0 2.90e-01 95.2% 47.9%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4930606 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.66 34.0 2.79e-01 91.3% 29.7%
3271459 4323.1.1.1 alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.54 37.0 4.29e-01 95.7% 94.0%
3990696 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.53 34.0 3.51e-01 92.8% 66.5%
3735933 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.53 30.0 3.51e-01 92.3% 77.9%
3582569 3755.3.1.348 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › zf-C4H2 0.53 32.0 3.08e-01 90.3% 51.0%
4338795 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.52 31.0 3.44e-01 93.7% 69.4%
3943772 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.52 30.0 3.20e-01 86.5% 62.6%
4564040 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.51 32.0 3.86e-01 90.3% 94.1%
4963973 1203.1.2.0 alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 0.51 32.0 3.55e-01 79.2% 75.9%
3225949 4323.1.1.1 alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.50 34.0 3.92e-01 91.3% 92.7%
D4 medium residues 593-684
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7wezA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.52 33.0 3.65e-01 71.7% 80.0%
3hi9D00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.50 32.0 3.42e-01 72.8% 73.2%
4iufA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.50 31.0 3.36e-01 72.8% 74.0%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3584644 304.9.1.59 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › CEBP_ZZ 0.53 30.0 2.92e-01 70.7% 45.5%
3321816 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.52 32.0 3.43e-01 75.0% 70.0%
D5 medium residues 705-782_905-1019
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1wruA02 3.55.50.10 Alpha Beta › 3-Layer(bab) Sandwich › Phage tail protein beta-alpha-beta fold › Baseplate protein-like domains 0.75 31.0 4.56e-01 85.5% 84.1%
3d37A02 3.55.50.10 Alpha Beta › 3-Layer(bab) Sandwich › Phage tail protein beta-alpha-beta fold › Baseplate protein-like domains 0.74 30.0 4.55e-01 85.5% 87.1%
4jtmA00 3.55.50.30 Alpha Beta › 3-Layer(bab) Sandwich › Phage tail protein beta-alpha-beta fold › 0.70 29.0 4.45e-01 85.5% 91.4%
3tj8A02 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.52 20.0 3.08e-01 78.2% 86.5%
2p5kA00 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 0.52 20.0 3.19e-01 73.6% 100.0%
3t15A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 28.0 3.09e-01 84.5% 63.9%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4846239 3070.1.1.12 a+b complex topology › N0 domain in phage tail proteins and secretins-like › N0 domain in phage tail proteins and secretins › N0 domain in phage tail proteins and secretins › Gp44-like_2nd 0.81 32.0 5.03e-01 87.6% 88.1%
185933 3070.1.1.12 a+b complex topology › N0 domain in phage tail proteins and secretins-like › N0 domain in phage tail proteins and secretins › N0 domain in phage tail proteins and secretins › Gp44-like_2nd 0.75 31.0 4.56e-01 85.5% 84.1%
3972068 3070.1.1.0 a+b complex topology › N0 domain in phage tail proteins and secretins-like › N0 domain in phage tail proteins and secretins › N0 domain in phage tail proteins and secretins 0.74 32.0 4.73e-01 87.0% 88.9%
184487 3070.1.1.12 a+b complex topology › N0 domain in phage tail proteins and secretins-like › N0 domain in phage tail proteins and secretins › N0 domain in phage tail proteins and secretins › Gp44-like_2nd 0.74 30.0 4.55e-01 85.5% 87.1%
1070142 3070.1.1.11 a+b complex topology › N0 domain in phage tail proteins and secretins-like › N0 domain in phage tail proteins and secretins › N0 domain in phage tail proteins and secretins › type_II_gspD_N0 0.71 29.0 4.49e-01 85.5% 91.4%
3974451 3070.1.1.0 a+b complex topology › N0 domain in phage tail proteins and secretins-like › N0 domain in phage tail proteins and secretins › N0 domain in phage tail proteins and secretins 0.69 29.0 4.19e-01 86.0% 85.9%
4929757 3070.1.1.0 a+b complex topology › N0 domain in phage tail proteins and secretins-like › N0 domain in phage tail proteins and secretins › N0 domain in phage tail proteins and secretins 0.65 34.0 4.44e-01 86.0% 88.2%
5056954 305.1.1.0 a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase 0.54 16.0 2.64e-01 77.2% 68.0%
3314359 320.1.1.11 a+b two layers › R3H domain-like › R3H domain › R3H domain › PF27261 0.51 17.0 2.77e-01 85.0% 77.3%
3300188 101.1.2.496 alpha arrays › HTH › HTH › winged helix domain › WH_eIF2D 0.51 25.0 3.34e-01 88.1% 88.0%
3482679 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.50 18.0 2.66e-01 87.6% 71.8%
D6 medium residues 783-828_843-904
PDB
D7 medium residues 1020-1205
PDB
D8 medium residues 1206-1338_1363-1390
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1dgjA05 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.56 29.0 3.67e-01 79.5% 84.0%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4889790 3071.1.1.7 a+b complex topology › C-terminal insertion domain in phage tail proteins › C-terminal insertion domain in phage tail proteins › C-terminal insertion domain in phage tail proteins › PF30637 0.63 48.0 4.81e-01 78.9% 81.3%
2475125 3071.1.1.7 a+b complex topology › C-terminal insertion domain in phage tail proteins › C-terminal insertion domain in phage tail proteins › C-terminal insertion domain in phage tail proteins › PF30637 0.62 46.0 4.68e-01 78.3% 77.8%