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PLM4_65_coex_sep16_scaffold_0_prodigal-single.1__X__X__00424

Bact-Vir

PLM4_65_coex_sep16_scaffold_0_prodigal-single.1__X__X__00424

Identity

Kingdom:
phage

Quality

81.1 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 182-298
PDB
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vsrA00 3.40.960.10 Alpha Beta › 3-Layer(aba) Sandwich › Endonuclease; Chain A › VSR Endonuclease 0.81 75.0 7.10e-01 100.0% 85.8%
3r3pB00 3.40.960.10 Alpha Beta › 3-Layer(aba) Sandwich › Endonuclease; Chain A › VSR Endonuclease 0.80 60.0 6.52e-01 99.1% 92.9%
3ajvC02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.73 50.0 5.61e-01 100.0% 90.1%
6ln3A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 51.0 4.27e-01 100.0% 91.1%
1ob8A00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.56 49.0 4.89e-01 100.0% 92.4%
4i1tA02 3.30.70.2640 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Arenavirus RNA polymerase 0.56 39.0 4.57e-01 71.8% 100.0%
3fovA00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.56 43.0 4.59e-01 98.3% 93.1%
1khtB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 50.0 4.23e-01 98.3% 91.6%
3h4rA00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.55 50.0 4.03e-01 97.4% 61.6%
2b99C00 3.40.50.960 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Lumazine/riboflavin synthase 0.55 50.0 4.56e-01 100.0% 76.3%
1iq0A01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.55 43.0 3.12e-01 87.2% 65.1%
3v9pB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 48.0 4.08e-01 100.0% 94.1%
3geeA03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 47.0 4.48e-01 100.0% 82.0%
3skvA02 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.54 48.0 4.05e-01 100.0% 93.5%
2cxcA01 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.54 32.0 3.96e-01 81.2% 100.0%
1texA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 46.0 3.73e-01 97.4% 82.8%
3lucA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 45.0 4.39e-01 100.0% 84.4%
2bo4A01 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.53 39.0 3.28e-01 88.0% 46.4%
1q44A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 47.0 3.57e-01 100.0% 57.0%
4i0wB01 3.40.50.200 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain 0.52 47.0 3.44e-01 100.0% 87.2%
3vaaA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 46.0 4.06e-01 99.1% 92.0%
2haeA01 3.40.50.10380 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Malic enzyme, N-terminal domain 0.52 34.0 3.14e-01 82.1% 50.7%
3bs4A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 43.0 3.47e-01 93.2% 73.9%
1n3lA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.51 41.0 3.47e-01 88.9% 75.6%
4h5uA00 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.50 44.0 3.30e-01 96.6% 91.1%
2qg6A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 44.0 3.89e-01 100.0% 90.7%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4940296 2008.1.1.121 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › MTES_1575 0.86 65.0 7.18e-01 99.1% 95.8%
3673147 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.86 69.0 7.05e-01 100.0% 85.2%
4027358 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.86 68.0 6.70e-01 100.0% 77.6%
5053107 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.86 75.0 7.27e-01 100.0% 83.7%
3808239 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.85 68.0 7.33e-01 98.3% 96.0%
4025196 109.4.1.315 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RAP 0.85 69.0 4.26e-01 100.0% 17.3%
4026799 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.84 68.0 6.89e-01 100.0% 85.2%
4027449 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.84 68.0 7.20e-01 100.0% 94.3%
3163838 2008.1.1.17 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF559 0.83 66.0 6.68e-01 100.0% 83.5%
4028756 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.83 64.0 5.68e-01 100.0% 58.7%
3964655 2008.1.1.17 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF559 0.83 64.0 6.63e-01 100.0% 85.5%
4030733 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.82 64.0 6.82e-01 100.0% 91.3%
3964563 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.82 76.0 7.12e-01 100.0% 82.1%
5069856 2008.1.1.17 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF559 0.82 62.0 6.32e-01 97.4% 80.0%
4467650 2008.1.1.167 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr, DUF559 0.82 73.0 6.92e-01 100.0% 82.2%
3979018 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.82 77.0 6.98e-01 100.0% 78.0%
3235677 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.81 71.0 7.09e-01 91.5% 98.3%
4995722 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.81 64.0 6.92e-01 98.3% 96.0%
3958985 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.81 63.0 6.87e-01 98.3% 95.0%
4963568 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.80 50.0 5.92e-01 100.0% 91.3%
5056125 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.80 72.0 6.92e-01 100.0% 86.2%
5080733 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.79 66.0 6.35e-01 97.4% 79.2%
4027159 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.78 66.0 6.69e-01 100.0% 90.4%
4927469 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.75 64.0 6.28e-01 100.0% 84.0%
5081837 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.74 56.0 5.92e-01 100.0% 89.3%
4025795 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.73 68.0 6.52e-01 100.0% 87.7%
4970785 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.73 47.0 5.40e-01 86.3% 89.4%
5073529 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.71 55.0 5.75e-01 100.0% 89.5%
3603694 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.66 61.0 5.86e-01 100.0% 88.5%
4946865 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.62 55.0 5.70e-01 94.0% 100.0%
3610413 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 54.0 4.18e-01 94.9% 56.8%
3287525 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 57.0 5.19e-01 100.0% 90.7%
3969697 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 51.0 4.64e-01 100.0% 68.4%
3594690 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 56.0 4.54e-01 100.0% 57.2%
5010842 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 55.0 4.97e-01 100.0% 82.6%
3717618 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.57 37.0 3.52e-01 88.9% 55.0%
1144868 2008.1.1.66 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › ArenaCapSnatch 0.56 48.0 4.25e-01 92.3% 63.9%
4281154 2004.1.1.191 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.56 51.0 4.40e-01 100.0% 88.6%
4982187 2004.1.1.51 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Sulfotransfer_1 0.56 50.0 4.32e-01 100.0% 79.9%
5009348 2008.1.1.108 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF234 0.56 46.0 4.79e-01 93.2% 98.1%
4929242 2004.1.1.191 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.56 51.0 4.31e-01 100.0% 91.3%
4520759 2004.1.1.191 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.56 50.0 4.21e-01 98.3% 88.7%
4971453 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 49.0 4.09e-01 99.1% 92.4%
5058443 2004.1.1.191 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.55 49.0 4.18e-01 99.1% 92.8%
4093593 2007.1.14.3 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like › Ferrochelatase 0.55 41.0 3.67e-01 99.1% 53.7%
3924732 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.55 49.0 4.21e-01 100.0% 76.3%
4959013 2008.1.1.182 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF26351 0.55 51.0 4.59e-01 100.0% 98.7%
2887772 7590.1.1.3 a/b three-layered sandwiches › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Piwi,ArgoMid 0.54 47.0 4.11e-01 100.0% 63.1%
4375784 2008.1.1.6 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › UPF0102 0.54 44.0 4.63e-01 100.0% 98.1%
3645022 2005.1.1.43 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_2nd 0.53 44.0 3.90e-01 87.2% 69.7%
4947598 2004.1.1.191 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.53 48.0 4.05e-01 100.0% 93.3%
3261619 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.53 44.0 3.78e-01 91.5% 95.3%
5069576 3008.1.1.0 a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.53 33.0 3.63e-01 73.5% 80.0%
5048439 2004.1.1.79 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Thymidylate_kin 0.53 46.0 3.84e-01 99.1% 85.1%
4929046 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.52 46.0 3.82e-01 100.0% 93.6%
4385057 2004.1.1.41 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ADK 0.52 46.0 3.98e-01 100.0% 91.6%
3499873 2004.1.1.192 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_18 0.52 46.0 3.88e-01 99.1% 85.0%
3688078 2004.1.1.191 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.52 46.0 3.93e-01 100.0% 86.2%
3479767 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 45.0 3.66e-01 99.1% 86.7%
4652309 2004.1.1.105 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinase-PPPase 0.51 46.0 4.30e-01 100.0% 88.3%
3368127 2005.1.1.41 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.51 40.0 4.05e-01 96.6% 86.1%
3829621 2004.1.1.105 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinase-PPPase 0.51 44.0 3.93e-01 99.1% 75.8%
4101322 2004.1.1.60 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SKI 0.51 44.0 3.80e-01 100.0% 81.9%
D2 medium residues 14-71
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2pw9C02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.55 38.0 3.82e-01 86.2% 74.1%
5vmzA03 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.51 28.0 3.10e-01 70.7% 67.5%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3435613 3014.1.1.3 alpha duplicates or obligate multimers › Middle operon regulator dimerization domain › Middle operon regulator dimerization domain › Middle operon regulator dimerization domain › DUF1677 0.59 46.0 4.45e-01 84.5% 92.3%
3678066 101.1.11.40 alpha arrays › HTH › HTH › Ribbon-helix-helix › DUF1677 0.59 45.0 4.30e-01 84.5% 82.9%
D3 medium residues 72-123
PDB
D4 medium residues 124-181
PDB
Domain cluster: representative
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4101567 7525.1.1.2 a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_2 0.61 47.0 2.90e-01 84.5% 14.5%