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NC_025426.1__YP_009099342.1__P108_0005__00005

Bact-Vir

NC_025426.1__YP_009099342.1__P108_0005__00005

Identity

Accession:
NC_025426 ↗
Kingdom:
phage

Quality

78.8 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 3-80
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1n5uA04 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.69 55.0 5.34e-01 85.9% 91.9%
3f2eA00 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 47.0 4.62e-01 71.8% 66.3%
4gmqA00 1.10.8.840 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ribosome-associated complex head domain 0.68 47.0 4.45e-01 71.8% 98.9%
2lwxA00 1.10.8.840 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ribosome-associated complex head domain 0.67 46.0 4.45e-01 71.8% 97.7%
2o7gA00 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.66 52.0 5.01e-01 84.6% 94.3%
4nqwA01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.64 51.0 4.98e-01 85.9% 98.8%
2uubT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.63 44.0 4.07e-01 71.8% 66.7%
1n5uA05 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.63 54.0 4.88e-01 98.7% 74.1%
5oklA01 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.63 50.0 4.66e-01 89.7% 80.2%
1kxpD02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.62 52.0 5.02e-01 93.6% 95.5%
4g12A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.62 52.0 4.32e-01 97.4% 78.5%
1zp2A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.62 44.0 3.96e-01 75.6% 62.5%
2lyiA01 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.60 52.0 4.32e-01 100.0% 59.5%
3nuqA01 1.10.150.450 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.60 43.0 4.04e-01 84.6% 60.6%
1ichA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.59 42.0 4.07e-01 97.4% 66.7%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.59 42.0 3.82e-01 73.1% 82.5%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.56 47.0 4.12e-01 91.0% 75.9%
4hhxA00 1.20.81.30 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › Type II secretion system (T2SS), domain F 0.55 43.0 3.96e-01 87.2% 64.4%
4bjzA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 43.0 3.44e-01 89.7% 94.6%
2pq7A00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.54 40.0 3.23e-01 83.3% 53.8%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1145724 601.21.1.4 alpha bundles › Four-helical up-and-down bundle › FAD-dependent thiol oxidase › FAD-dependent thiol oxidase › Baculo_p33 0.72 63.0 5.68e-01 94.9% 81.6%
4846312 1075.1.1.2 alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › LptF_LptG 0.71 49.0 4.10e-01 73.1% 88.8%
3222274 198.1.1.3 alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_1 0.59 44.0 4.16e-01 83.3% 74.0%
3271808 601.1.2.6 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Talin_IBS2B 0.55 46.0 3.73e-01 97.4% 61.8%
3494047 5001.1.1.1 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.54 42.0 2.89e-01 84.6% 38.1%
3641832 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.53 36.0 3.45e-01 71.8% 60.0%
4940134 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.52 42.0 3.19e-01 91.0% 52.3%
D2 high residues 234-373
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05257.23 best CHAP 78.0 8.70e-22 65.0% 96.3%
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2k3aA01 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.87 61.0 7.22e-01 78.6% 100.0%
4hz9A00 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.69 55.0 5.97e-01 97.9% 100.0%
6gbuD00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.68 32.0 4.68e-01 96.4% 100.0%
2btwA00 3.90.70.30 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Phytochelatin synthase, N-terminal domain 0.67 58.0 5.03e-01 92.9% 89.5%
3oisB00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.59 54.0 4.34e-01 100.0% 90.3%
2fb7A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.56 31.0 3.97e-01 74.3% 95.0%
6j5cA02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.55 28.0 3.42e-01 91.4% 78.3%
1xxmC01 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.54 30.0 3.78e-01 85.0% 98.6%
4bwcA01 2.10.70.60 Mainly Beta › Ribbon › Complement Module; domain 1 › Phospholipase B-like, domain 1 0.51 21.0 2.99e-01 71.4% 88.7%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4034057 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.95 70.0 8.12e-01 80.7% 100.0%
4882197 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.93 72.0 7.84e-01 78.6% 93.2%
4031159 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.91 78.0 7.56e-01 90.7% 80.5%
4015238 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.81 71.0 7.50e-01 90.7% 100.0%
184711 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.78 66.0 6.37e-01 97.9% 78.7%
3590884 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.78 68.0 7.03e-01 91.4% 99.2%
3990071 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.74 68.0 6.83e-01 95.0% 95.0%
1905738 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.73 67.0 6.63e-01 97.1% 98.6%
3784612 219.1.1.115 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › AIM3_BBC1_C 0.69 65.0 6.05e-01 100.0% 93.5%
3615365 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.69 60.0 5.02e-01 92.9% 95.2%
3448975 4.1.1.66 beta barrels › SH3 › SH3 › SH3 › LBR_tudor 0.69 33.0 4.77e-01 92.1% 100.0%
3698096 219.1.1.115 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › AIM3_BBC1_C 0.68 64.0 5.81e-01 100.0% 89.4%
3344796 4.1.1.42 beta barrels › SH3 › SH3 › SH3 › Agenet 0.68 31.0 3.98e-01 97.9% 72.3%
3389662 4.1.1.219 beta barrels › SH3 › SH3 › SH3 › LSM12_LSM 0.66 34.0 4.41e-01 99.3% 87.5%
3207081 4.1.1.92 beta barrels › SH3 › SH3 › SH3 › SH3_9 0.64 31.0 4.47e-01 87.9% 100.0%
3782999 219.1.1.115 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › AIM3_BBC1_C 0.62 57.0 5.68e-01 99.3% 97.9%
3339162 4.1.1.330 beta barrels › SH3 › SH3 › SH3 › SH3-B_UBE2O, SH3-C_UBE2O 0.61 35.0 3.67e-01 100.0% 60.8%
3940729 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.61 37.0 4.59e-01 81.4% 100.0%
3675653 4.1.1.239 beta barrels › SH3 › SH3 › SH3 › SH3-B_UBE2O 0.60 33.0 4.41e-01 100.0% 100.0%
3218349 4.1.1.9 beta barrels › SH3 › SH3 › SH3 › TUDOR 0.59 37.0 4.34e-01 97.1% 91.6%
3354076 4.1.1.330 beta barrels › SH3 › SH3 › SH3 › SH3-B_UBE2O, SH3-C_UBE2O 0.59 34.0 3.59e-01 100.0% 61.5%
3585492 4.1.1.103 beta barrels › SH3 › SH3 › SH3 › SH3_12 0.57 42.0 4.74e-01 97.1% 99.1%
3721062 4.1.1.225 beta barrels › SH3 › SH3 › SH3 › DUF7025 0.55 33.0 4.23e-01 97.1% 100.0%
1527468 4.1.1.51 beta barrels › SH3 › SH3 › SH3 › SGF29_Tudor 0.53 39.0 4.30e-01 99.3% 95.5%
3786518 4.8.1.18 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Myosin_N 0.53 27.0 3.55e-01 96.4% 100.0%
3930210 1.1.17.1 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.52 33.0 2.74e-01 100.0% 35.1%
3974649 243.19.1.0 a+b two layers › Cystatin-like › Phi ETA orf 56-like protein C-terminal domains › Phi ETA orf 56-like protein C-terminal domains 0.52 32.0 3.83e-01 92.1% 94.4%
3188712 4.1.1.225 beta barrels › SH3 › SH3 › SH3 › DUF7025 0.51 35.0 4.06e-01 98.6% 97.0%
3492018 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.50 36.0 4.12e-01 80.7% 100.0%
D3 medium residues 86-184
PDB
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d37B01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.75 48.0 3.92e-01 76.8% 37.4%
1k28D03 2.40.30.150 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacteriophage T4, Gp27, baseplate hub, domain 3 0.73 48.0 4.97e-01 78.8% 69.5%
2p5zX01 2.30.110.50 Mainly Beta › Roll › Pnp Oxidase; Chain A › 0.69 43.0 3.59e-01 75.8% 37.3%
6vbkA01 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.63 44.0 4.26e-01 72.7% 87.4%
4ci2B02 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.61 46.0 4.31e-01 80.8% 92.8%
2q9kA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 43.0 3.79e-01 74.7% 78.2%
5ejlA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.59 43.0 3.98e-01 75.8% 86.3%
3q0bX00 2.30.280.10 Mainly Beta › Roll › PUA domain-like › SRA-YDG 0.59 42.0 3.66e-01 73.7% 57.4%
2cc6A00 3.30.1660.10 Alpha Beta › 2-Layer Sandwich › Dodecin subunit-like › Flavin-binding protein dodecin 0.58 36.0 4.27e-01 75.8% 96.9%
3lvtA03 2.60.40.2210 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 38.0 3.49e-01 71.7% 73.6%
1twfB07 2.40.50.150 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II, Rpb2 subunit, wall domain 0.53 40.0 3.73e-01 79.8% 89.5%
1vs3A02 3.30.70.660 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Pseudouridine synthase I, catalytic domain, C-terminal subdomain 0.53 36.0 3.27e-01 70.7% 84.0%
4m4xA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 37.0 3.46e-01 73.7% 91.3%
5swiD01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.52 38.0 2.91e-01 76.8% 43.9%
3o1lB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.52 35.0 3.72e-01 72.7% 78.4%
4wsqB00 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.52 39.0 2.80e-01 80.8% 60.0%
3u83A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 33.0 3.30e-01 71.7% 63.4%
4dpoB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.62e-01 74.7% 76.2%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3973341 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.81 47.0 5.10e-01 75.8% 68.2%
4957568 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.74 49.0 5.29e-01 74.7% 78.8%
4982501 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.72 47.0 4.80e-01 73.7% 68.4%
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 0.71 56.0 4.70e-01 82.8% 92.4%
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 0.70 55.0 4.56e-01 81.8% 74.1%
3944430 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.70 46.0 4.55e-01 78.8% 62.9%
5079927 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.70 46.0 4.83e-01 70.7% 73.3%
5031599 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.70 49.0 4.42e-01 72.7% 92.6%
4950972 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.69 48.0 4.67e-01 72.7% 78.2%
5056723 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.67 44.0 4.47e-01 73.7% 68.4%
4954540 1.1.9.0 beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.66 47.0 4.58e-01 73.7% 84.5%
1914511 1.1.5.25 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.64 44.0 4.07e-01 73.7% 55.1%
5078127 1.1.9.0 beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.61 42.0 4.51e-01 70.7% 98.8%
3990367 389.4.1.7 few secondary structure elements › EGF-like › Fibulin-4 EGF-like 1 domain › Fibulin-4 EGF-like 1 domain › TIL_2 0.58 36.0 3.93e-01 75.8% 75.0%
3991838 389.1.1.47 few secondary structure elements › EGF-like › EGF-related › EGF/Laminin › TIL_2 0.58 35.0 4.26e-01 75.8% 96.8%
4201836 304.102.1.3 a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › PseudoU_synth_1 0.57 39.0 2.97e-01 70.7% 49.2%
4944741 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 40.0 3.61e-01 74.7% 93.6%
5049138 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 40.0 3.64e-01 74.7% 97.0%
3556801 325.1.7.2 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › RNA_pol_Rpb2_6 0.56 41.0 3.80e-01 76.8% 98.4%
5053150 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.56 40.0 3.46e-01 74.7% 91.6%
4002415 389.2.1.3 few secondary structure elements › EGF-like › Serine protease inhibitors › Serine protease inhibitors › TIL_2 0.56 34.0 4.11e-01 75.8% 93.8%
3997235 389.4.1.7 few secondary structure elements › EGF-like › Fibulin-4 EGF-like 1 domain › Fibulin-4 EGF-like 1 domain › TIL_2 0.56 34.0 2.99e-01 75.8% 40.0%
4970832 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.55 41.0 3.83e-01 78.8% 100.0%
3223282 223.2.1.22 a+b three layers › Profilin-like › profilin-like › profilin-like › Folliculin 0.54 39.0 3.25e-01 74.7% 98.2%
4030042 325.1.7.2 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › RNA_pol_Rpb2_6 0.54 41.0 3.71e-01 79.8% 99.2%
3625217 223.2.1.37 a+b three layers › Profilin-like › profilin-like › profilin-like › C9orf72-like 0.54 40.0 3.22e-01 78.8% 81.5%
3786933 325.1.7.2 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › RNA_pol_Rpb2_6 0.54 40.0 3.72e-01 78.8% 100.0%
3514909 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 38.0 2.77e-01 74.7% 92.8%
3574420 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 38.0 3.29e-01 74.7% 96.2%
3929223 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 38.0 3.27e-01 74.7% 96.2%
3711910 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 38.0 3.24e-01 74.7% 90.0%
3774553 223.2.1.22 a+b three layers › Profilin-like › profilin-like › profilin-like › Folliculin 0.53 38.0 2.81e-01 74.7% 92.7%
3474976 331.9.1.0 a+b two layers › TBP-like › Subdomain of clathrin and coatomer appendage domain › Subdomain of clathrin and coatomer appendage domain 0.53 39.0 3.59e-01 78.8% 92.3%
3614450 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 37.0 3.02e-01 74.7% 55.1%
3244287 223.2.1.34 a+b three layers › Profilin-like › profilin-like › profilin-like › NPR2 0.51 36.0 3.05e-01 74.7% 92.9%