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Filtrate_w_scaffold_3_prodigal-single.1__X__X__00297

Bact-Vir

Filtrate_w_scaffold_3_prodigal-single.1__X__X__00297

Identity

Kingdom:
phage

Quality

78.9 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 medium residues 1-15_83-149
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3w1oA00 3.40.1760.20 Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical protein yfbM fold › 0.76 58.0 5.16e-01 80.5% 99.1%
6xasW01 3.90.940.10 Alpha Beta › Alpha-Beta Complex › Eukaryotic RPB6 RNA polymerase subunit › RNA polymerase subunit, RPB6/omega 0.63 20.0 2.62e-01 81.7% 40.8%
1t6cA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.63 45.0 3.51e-01 75.6% 88.4%
3d85C00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.56 40.0 3.41e-01 73.2% 87.2%
8b70A01 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.51 40.0 2.58e-01 86.6% 57.4%
2vl7A02 1.10.275.30 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › 0.50 35.0 3.26e-01 74.4% 95.5%
4nwbA01 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.50 38.0 3.28e-01 81.7% 53.8%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
224413 618.1.1.0 a+b complex topology › DNA mimic protein DMP12-like › DNA mimic protein DMP12-related › DNA mimic protein DMP12-related 0.76 58.0 5.16e-01 80.5% 99.1%
3897876 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.57 50.0 3.81e-01 100.0% 42.0%
4464715 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.56 41.0 3.70e-01 79.3% 88.7%
4347463 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.55 40.0 3.56e-01 75.6% 88.7%
4271696 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.55 41.0 3.55e-01 80.5% 85.4%
4141108 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.54 39.0 3.46e-01 75.6% 87.5%
4423474 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.54 38.0 3.41e-01 73.2% 90.4%
4628544 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.54 41.0 3.63e-01 80.5% 88.7%
4318194 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.53 40.0 3.59e-01 80.5% 88.7%
4234798 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.53 38.0 3.39e-01 74.4% 87.8%
3630321 304.60.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.52 39.0 3.29e-01 81.7% 49.7%
4573350 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.52 39.0 3.52e-01 80.5% 90.4%
4304796 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.52 37.0 3.34e-01 75.6% 88.7%
4539710 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.51 38.0 3.42e-01 79.3% 88.7%
4153998 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.51 37.0 3.33e-01 78.0% 88.3%
4504658 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.51 37.0 3.38e-01 78.0% 87.8%
3599173 304.60.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like 0.51 38.0 3.34e-01 81.7% 55.4%
4613951 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.51 38.0 3.33e-01 80.5% 89.6%
3494104 304.60.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.50 38.0 3.43e-01 81.7% 61.7%
D2 medium residues 16-82
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3beyD00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.82 49.0 4.30e-01 77.6% 42.6%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.82 56.0 4.55e-01 70.1% 51.3%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.79 54.0 4.77e-01 70.1% 57.6%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.78 58.0 5.63e-01 79.1% 81.3%
2hs5A02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.78 56.0 4.29e-01 74.6% 70.0%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.78 50.0 5.56e-01 71.6% 84.6%
1vkeB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.77 50.0 4.28e-01 77.6% 43.6%
3craB01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.77 52.0 4.78e-01 70.1% 66.3%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.77 57.0 5.44e-01 79.1% 75.3%
1cpqA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.77 63.0 4.95e-01 86.6% 69.8%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.76 55.0 5.00e-01 74.6% 60.9%
7y4rB01 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.76 49.0 4.14e-01 77.6% 41.5%
4agsB04 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.76 55.0 4.38e-01 77.6% 74.4%
3nrxA00 1.20.58.1520 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 56.0 4.57e-01 79.1% 65.9%
1dkxA02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.75 57.0 5.33e-01 79.1% 75.0%
3ihuA02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.75 56.0 4.41e-01 80.6% 72.7%
4i1mB01 1.20.120.1700 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.74 56.0 4.45e-01 79.1% 67.4%
2yb5F01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.74 55.0 5.07e-01 79.1% 62.8%
3ls1A00 1.20.120.290 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle 0.74 59.0 4.66e-01 85.1% 59.4%
1fioA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 54.0 3.88e-01 79.1% 46.3%
1vjxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 53.0 4.14e-01 79.1% 85.9%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.72 53.0 4.14e-01 79.1% 86.6%
1x04A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.72 54.0 3.77e-01 79.1% 78.0%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.70 53.0 4.65e-01 82.1% 79.4%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.70 53.0 4.60e-01 82.1% 78.6%
4xriA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.68 50.0 2.79e-01 79.1% 6.1%
3unoE00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.68 49.0 3.65e-01 76.1% 95.8%
3r2kA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.68 49.0 3.83e-01 79.1% 75.3%
6axfA01 1.20.870.10 Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 0.67 49.0 4.14e-01 79.1% 50.4%
1nafA02 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 49.0 4.56e-01 79.1% 82.4%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.67 45.0 3.96e-01 70.1% 93.2%
2i0mA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.66 48.0 4.19e-01 79.1% 73.6%
1sziA02 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.65 49.0 3.95e-01 82.1% 59.1%
2gd5A00 6.10.140.1230 Special › Helix non-globular › Helix Hairpins › 0.65 56.0 4.47e-01 100.0% 86.6%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.65 47.0 4.51e-01 76.1% 86.8%
3tulB00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.65 50.0 4.05e-01 85.1% 91.0%
2v5cA03 1.20.58.460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hyaluronidase post-catalytic domain-like 0.64 55.0 4.53e-01 100.0% 70.8%
1gqeA01 1.20.58.410 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Release factor 0.64 48.0 4.07e-01 80.6% 99.1%
3r2qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.63 46.0 3.94e-01 79.1% 66.4%
3i2wA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.62 44.0 3.02e-01 76.1% 73.3%
2chnB03 1.20.58.460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hyaluronidase post-catalytic domain-like 0.62 54.0 4.01e-01 100.0% 61.1%
6axgA01 1.20.870.10 Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 0.62 46.0 4.22e-01 86.6% 60.7%
1hqoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 42.0 3.50e-01 79.1% 64.1%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.58 43.0 3.24e-01 80.6% 74.9%
1k04A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.58 45.0 3.91e-01 85.1% 82.7%
3gonA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.57 51.0 4.06e-01 100.0% 79.9%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.54 44.0 3.78e-01 94.0% 89.3%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4511641 109.4.1.3388 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_16, PF30363 0.84 57.0 3.21e-01 70.1% 11.1%
3904792 109.4.1.2788 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_2, TPR_6, PF30363, PF30475 0.81 56.0 3.16e-01 71.6% 11.2%
3868214 109.4.1.1302 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF30363 0.80 60.0 4.45e-01 79.1% 46.9%
5041256 601.4.1.91 alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › PF30769 0.78 58.0 4.99e-01 79.1% 93.3%
5058485 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.77 57.0 4.75e-01 79.1% 73.0%
3632454 650.1.1.0 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.75 57.0 5.20e-01 79.1% 83.5%
3578554 3877.1.1.0 alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.75 51.0 3.00e-01 71.6% 9.3%
4465072 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.74 52.0 4.30e-01 73.1% 93.9%
3972329 633.5.1.0 alpha bundles › Bromodomain-like › LemA-like › LemA-like 0.74 65.0 4.82e-01 95.5% 55.2%
3775375 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.74 56.0 4.34e-01 82.1% 60.0%
5013248 601.3.1.1 alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › Hpt 0.74 53.0 4.37e-01 77.6% 63.2%
3578466 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.72 54.0 5.09e-01 79.1% 80.0%
3605285 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.71 53.0 4.09e-01 79.1% 52.4%
3232875 11.2.1.7 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › Anillin 0.71 53.0 3.61e-01 79.1% 69.1%
3246117 1075.4.1.2 alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › ABC_membrane_2 0.69 54.0 3.39e-01 85.1% 88.1%
3821843 3291.1.1.1 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.69 52.0 3.87e-01 79.1% 81.3%
3920960 604.8.1.2 alpha bundles › Spectrin repeat-like › Smac/diablo › Smac/diablo › Mitofilin 0.68 49.0 4.04e-01 79.1% 68.5%
3714029 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.68 49.0 3.60e-01 79.1% 39.5%
4988301 3877.1.1.0 alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.62 46.0 3.65e-01 82.1% 85.3%
4345017 2004.1.1.433 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23 0.57 49.0 2.88e-01 100.0% 16.0%
4542972 3755.4.1.0 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.51 43.0 3.14e-01 100.0% 61.0%