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BML_08042016_6_5m_scaffold_3_prodigal-single.1__X__X__00012

Bact-Vir

BML_08042016_6_5m_scaffold_3_prodigal-single.1__X__X__00012

Identity

Kingdom:
phage

Quality

70.7 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 13-81
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2lqjA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.69 49.0 4.43e-01 75.4% 88.3%
4aw7A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.68 42.0 3.54e-01 79.7% 36.4%
2cveA02 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 46.0 4.79e-01 71.0% 98.5%
2rrnA01 3.30.70.2040 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 49.0 4.67e-01 79.7% 96.4%
2cuwA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.65 50.0 4.68e-01 81.2% 98.8%
1pu4A03 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.65 53.0 3.23e-01 91.3% 15.0%
1ksiA03 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.64 50.0 3.11e-01 91.3% 14.2%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.63 45.0 4.64e-01 76.8% 79.1%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.63 53.0 5.16e-01 94.2% 84.2%
2zaiA04 2.60.40.3030 Mainly Beta › Sandwich › Immunoglobulin-like › 0.63 51.0 4.13e-01 89.9% 65.2%
1vwxS01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.62 48.0 4.84e-01 85.5% 88.7%
2zw2A00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.61 47.0 4.41e-01 82.6% 98.8%
1x9tA02 3.90.1620.10 Alpha Beta › Alpha-Beta Complex › adenovirus 2 penton base, domain 2 › adenovirus 2 penton base, domain 2 0.61 44.0 2.98e-01 76.8% 42.5%
4ekuA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.61 39.0 3.33e-01 88.4% 38.5%
4njcA00 3.10.20.730 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like 0.61 45.0 4.74e-01 92.8% 91.7%
1hq6B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.61 48.0 3.37e-01 87.0% 35.5%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.61 51.0 4.95e-01 94.2% 84.2%
1mkfA02 2.60.40.1340 Mainly Beta › Sandwich › Immunoglobulin-like › Chemokine-binding protein M3-like 0.60 45.0 3.38e-01 79.7% 45.9%
1kf6B01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.60 41.0 3.62e-01 72.5% 82.7%
5jtwA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 43.0 3.81e-01 85.5% 52.0%
3pgbA01 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.59 48.0 2.90e-01 97.1% 12.2%
3e0jB00 3.90.1030.20 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain 0.59 49.0 3.88e-01 95.7% 44.1%
1j2vA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 46.0 4.12e-01 87.0% 90.1%
1n9eA01 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.59 47.0 2.86e-01 97.1% 12.3%
1uenA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 44.0 3.64e-01 87.0% 45.6%
2eenA00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.57 50.0 3.77e-01 100.0% 62.1%
2jheA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.57 39.0 3.77e-01 72.5% 88.9%
7oocE01 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.57 38.0 3.65e-01 71.0% 100.0%
3cjlA00 3.10.20.850 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Protein of unknown function DUF3861 0.56 31.0 2.90e-01 100.0% 39.8%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.56 45.0 3.25e-01 89.9% 36.3%
1s3rA04 2.60.40.1430 Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 0.56 43.0 3.78e-01 87.0% 57.7%
2mraA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.55 41.0 3.53e-01 82.6% 49.6%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 38.0 3.34e-01 87.0% 50.0%
3h7tB01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 37.0 3.12e-01 75.4% 61.5%
6p3xB01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.52 46.0 3.44e-01 100.0% 75.1%
5c86A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 41.0 3.66e-01 87.0% 59.4%
3wa7A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 42.0 2.64e-01 95.7% 75.8%
3agjF01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.52 38.0 3.24e-01 81.2% 62.2%
3hvnA01 3.90.840.10 Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain 0.52 39.0 3.02e-01 84.1% 38.4%
1egjA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.32e-01 87.0% 52.5%
5brrE01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 37.0 3.04e-01 76.8% 60.4%
5kfzA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.52 38.0 3.24e-01 81.2% 56.1%
3w1eA03 2.40.10.410 Mainly Beta › Beta Barrel › Thrombin, subunit H › FlgT, C-terminal domain 0.52 42.0 3.92e-01 95.7% 70.8%
1dfaA01 2.170.16.10 Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain 0.50 41.0 3.02e-01 92.8% 55.0%
1ciiA02 3.30.305.10 Alpha Beta › 2-Layer Sandwich › Colicin Ia; domain 2 › Colicin Ia; domain 2 0.50 35.0 3.23e-01 76.8% 83.2%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4642338 807.1.1.1 a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.73 52.0 5.84e-01 78.3% 96.2%
3508212 3115.1.1.6 a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.72 56.0 5.60e-01 84.1% 87.1%
3892842 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.71 53.0 5.49e-01 79.7% 92.3%
3280008 3115.1.1.2 a+b two layers › GP2-like › RplX-like › RplX-like › DUF4288 0.71 59.0 5.39e-01 91.3% 90.0%
3929121 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.71 60.0 5.04e-01 92.8% 55.7%
4084879 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.69 59.0 5.49e-01 94.2% 80.0%
4003316 10.7.1.0 beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.67 50.0 4.07e-01 79.7% 52.0%
3299532 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.66 49.0 4.17e-01 78.3% 50.0%
4013514 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.66 56.0 4.84e-01 92.8% 61.0%
4951473 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.66 51.0 5.30e-01 82.6% 93.7%
3517068 3115.1.1.6 a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.65 55.0 5.64e-01 94.2% 98.5%
4128974 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 55.0 5.24e-01 92.8% 85.0%
3634674 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.65 53.0 3.36e-01 91.3% 55.1%
3965010 3115.4.1.1 a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 0.65 53.0 4.82e-01 88.4% 76.7%
2106285 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 55.0 4.69e-01 94.2% 59.3%
4990637 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 55.0 5.19e-01 94.2% 78.3%
223776 3115.4.1.1 a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 0.64 51.0 5.08e-01 87.0% 84.5%
5010503 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 47.0 4.25e-01 79.7% 61.1%
3587109 304.5.1.7 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.63 55.0 5.00e-01 94.2% 87.8%
3702051 1116.1.1.0 a+b two layers › Polycystin-mucolipin domain › Polycystin-mucolipin domain › Polycystin-mucolipin domain 0.63 47.0 3.42e-01 81.2% 43.0%
3989610 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.63 49.0 4.65e-01 85.5% 97.6%
2831852 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.63 53.0 4.65e-01 94.2% 63.4%
3686997 304.9.1.6 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › Smg4_UPF3 0.63 45.0 4.52e-01 76.8% 98.6%
4332626 3532.1.1.0 alpha arrays › RNA-binding domain of telomerase › RNA-binding domain of telomerase › RNA-binding domain of telomerase 0.62 53.0 3.15e-01 100.0% 18.5%
3882425 511.1.1.0 beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.62 50.0 3.82e-01 91.3% 38.6%
3338688 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.61 46.0 4.75e-01 79.7% 92.3%
3211699 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.61 40.0 3.38e-01 75.4% 39.2%
1442393 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.61 51.0 4.40e-01 92.8% 59.6%
5045979 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.61 52.0 3.48e-01 95.7% 37.8%
3477515 11.1.1.179 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.61 42.0 3.64e-01 73.9% 53.9%
3242250 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.60 39.0 3.38e-01 76.8% 41.2%
3999001 10.7.1.0 beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.60 43.0 3.78e-01 76.8% 62.9%
3824339 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 47.0 3.60e-01 87.0% 37.0%
3484366 284.1.2.1 a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases › OSR1_C 0.59 42.0 3.75e-01 75.4% 100.0%
3896560 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.59 50.0 3.88e-01 100.0% 42.9%
4932514 4.23.1.2 beta barrels › SH3 › Dom34/Pelota N-terminal domain-like › Dom34/Pelota N-terminal domain-like › PF26356 0.59 44.0 3.69e-01 79.7% 79.2%
4556330 299.1.1.1 a+b complex topology › YbaK/ProRS associated domain › YbaK/ProRS associated domain › YbaK/ProRS associated domain › tRNA_edit 0.59 51.0 3.93e-01 98.6% 73.1%
3732370 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.59 44.0 4.69e-01 81.2% 95.0%
5011383 304.163.1.0 a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.58 43.0 4.57e-01 79.7% 96.7%
4978332 304.12.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.58 42.0 4.11e-01 79.7% 100.0%
3700518 4.23.1.2 beta barrels › SH3 › Dom34/Pelota N-terminal domain-like › Dom34/Pelota N-terminal domain-like › PF26356 0.58 43.0 3.54e-01 79.7% 76.2%
3991293 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.58 49.0 4.06e-01 94.2% 52.8%
3879431 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 43.0 3.85e-01 85.5% 54.3%
5005269 1.1.2.0 beta barrels › cradle loop barrel › RIFT-related › double psi 0.58 48.0 3.76e-01 89.9% 65.7%
3941308 4004.1.1.0 beta sandwiches › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like 0.57 44.0 3.23e-01 87.0% 99.1%
3939974 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 42.0 2.46e-01 85.5% 9.1%
3192440 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 45.0 3.83e-01 87.0% 53.6%
3493644 10.32.1.203 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.56 42.0 3.32e-01 85.5% 52.1%
3698884 304.46.1.1 a+b two layers › Alpha-beta plaits › eEF1-gamma domain › eEF1-gamma domain › EF1G 0.54 36.0 3.18e-01 71.0% 71.3%
4952672 4076.3.1.0 a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.53 38.0 4.15e-01 75.4% 96.4%
4456175 10.2.1.0 beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.53 40.0 2.91e-01 84.1% 29.1%
3794360 11.1.1.391 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › A2M,MG2,A2M_BRD,MG3 0.52 41.0 2.35e-01 89.9% 7.2%
1867336 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.52 40.0 4.12e-01 87.0% 95.2%
4943401 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.51 40.0 3.88e-01 92.8% 75.3%
3410774 382.1.1.14 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › DUF753 0.51 41.0 3.83e-01 87.0% 92.9%
4020185 4099.1.1.0 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.51 32.0 2.71e-01 91.3% 35.0%
3331566 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 41.0 3.53e-01 91.3% 59.1%
1503409 220.3.1.1 beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Rhabdo_glycop 0.51 41.0 3.40e-01 92.8% 80.3%
3700769 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.50 35.0 3.10e-01 73.9% 72.4%
3479321 5001.1.1.41 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srw 0.50 43.0 2.72e-01 98.6% 47.5%
5060239 7527.1.1.1 a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE 0.50 41.0 2.77e-01 89.9% 56.5%