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SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00212

Bact-Vir

SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00212

Identity

Kingdom:
phage

Quality

75.2 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 1-53
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.90 66.0 7.03e-01 77.4% 95.7%
3t9oB00 1.20.120.30 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartate receptor, ligand-binding domain 0.89 65.0 4.85e-01 77.4% 36.7%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.82 60.0 5.62e-01 77.4% 64.1%
5xfaA04 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.82 59.0 4.97e-01 75.5% 48.2%
3c1yA02 1.20.1260.110 Mainly Alpha › Up-down Bundle › Ferritin › DNA integrity scanning linker region 0.81 73.0 5.20e-01 100.0% 77.0%
4d3dB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.78 65.0 4.74e-01 88.7% 46.5%
1siqA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.78 70.0 4.90e-01 98.1% 52.9%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.78 57.0 4.53e-01 79.2% 41.1%
1v9vA01 1.20.1480.20 Mainly Alpha › Up-down Bundle › hypothetical protein mp506/mpn330, domain 1 › MAST3 pre-PK domain-like 0.77 56.0 4.61e-01 77.4% 46.3%
8hk0B03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.76 68.0 4.99e-01 100.0% 62.3%
2ix5A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.74 66.0 4.69e-01 100.0% 52.9%
4rm7A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.74 66.0 4.82e-01 100.0% 59.0%
2jifA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.73 64.0 4.59e-01 100.0% 53.2%
5iduC03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.72 64.0 4.53e-01 100.0% 51.6%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.70 55.0 4.80e-01 84.9% 72.2%
3q18A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.70 59.0 4.59e-01 94.3% 70.7%
2gf2A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.69 56.0 4.14e-01 88.7% 41.8%
6wfqC01 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.69 57.0 4.35e-01 100.0% 37.3%
6q9jB02 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.68 48.0 4.09e-01 75.5% 47.7%
5lb3B02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 55.0 3.60e-01 90.6% 24.6%
2ynqB00 1.25.40.680 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type VII secretion system EssB, C-terminal-like domain 0.66 51.0 3.68e-01 94.3% 29.8%
3w8hB00 1.10.12.70 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › 0.66 47.0 4.45e-01 81.1% 62.1%
4ofzA01 1.20.58.1800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 54.0 4.28e-01 100.0% 65.5%
3cnhB02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.60 42.0 3.98e-01 94.3% 60.3%
3u62A01 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.60 43.0 3.44e-01 96.2% 35.2%
2o5iN07 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.59 52.0 4.06e-01 100.0% 80.2%
2rfqB01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.59 47.0 3.89e-01 96.2% 99.1%
2uxwA02 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.56 44.0 3.63e-01 100.0% 90.1%
4nphA02 1.20.1270.330 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.55 44.0 3.97e-01 88.7% 82.4%
1zvwA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.55 40.0 3.80e-01 81.1% 97.0%
2jbrA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.51 39.0 3.27e-01 98.1% 88.2%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2429105 4992.1.1.0 ↗ extended segments › RelB-like › RelB-like › RelB-like 0.92 69.0 6.07e-01 79.2% 59.5%
3530272 632.22.1.175 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › DUF4527 0.85 62.0 5.61e-01 77.4% 61.4%
4112959 7512.1.1.1 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDPGT 0.84 73.0 4.53e-01 92.5% 58.9%
3900175 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 0.84 75.0 4.53e-01 96.2% 32.8%
3501709 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.83 60.0 5.36e-01 77.4% 60.0%
5035458 632.1.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid 0.82 60.0 4.87e-01 77.4% 43.2%
1780824 6075.1.1.1 ↗ alpha bundles › DisA helical linker domain › DisA helical linker domain › DisA helical linker domain › DisA-linker 0.81 73.0 5.03e-01 100.0% 66.7%
3905839 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 0.80 71.0 4.81e-01 98.1% 53.5%
3481369 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.79 71.0 4.44e-01 98.1% 42.7%
3981675 633.6.1.1 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA_dh_1 0.79 72.0 5.09e-01 100.0% 54.7%
4600937 633.6.1.0 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like 0.79 72.0 5.08e-01 100.0% 54.7%
3858204 633.6.1.1 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA_dh_1 0.76 68.0 4.90e-01 100.0% 56.6%
3451546 633.6.1.1 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA_dh_1 0.75 67.0 4.72e-01 100.0% 52.9%
3958074 633.6.1.0 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like 0.74 67.0 4.96e-01 100.0% 65.4%
1481961 633.6.1.1 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA_dh_1 0.74 66.0 4.65e-01 100.0% 51.6%
3693342 129.1.1.0 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like 0.74 61.0 4.57e-01 90.6% 49.6%
4521765 604.29.1.1 ↗ alpha bundles › Spectrin repeat-like › Trehalose-6-phosphate phosphatase N-terminal helical bundle › Trehalose-6-phosphate phosphatase N-terminal helical bundle › T6PP_N 0.73 62.0 4.79e-01 98.1% 75.2%
3963837 633.6.1.0 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like 0.72 62.0 4.58e-01 100.0% 56.6%
3416186 3855.1.1.2 ↗ alpha arrays › Serum amyloid A-1 protein › Serum amyloid A-1 protein › Serum amyloid A-1 protein › DM4_12 0.70 62.0 4.63e-01 100.0% 78.4%
4029405 109.4.1.584 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fis1_TPR_C 0.70 61.0 4.43e-01 96.2% 60.7%
3793850 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.68 56.0 4.19e-01 100.0% 54.7%
3848061 109.4.1.593 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HPS6_C 0.63 55.0 3.69e-01 100.0% 55.7%
3429732 109.7.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Cytochrome c oxidase subunit E › Cytochrome c oxidase subunit E 0.62 50.0 4.21e-01 96.2% 53.3%
3213319 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.58 39.0 3.80e-01 73.6% 63.1%
D2 high residues 105-162
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3zxsC02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.68 58.0 4.31e-01 98.3% 49.4%
4i2zA03 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.63 50.0 3.09e-01 91.4% 19.4%
4eqyA02 1.20.1180.10 Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain 0.61 43.0 4.05e-01 84.5% 61.4%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 49.0 4.19e-01 87.9% 87.0%
3o2tA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.60 52.0 3.34e-01 100.0% 49.0%
4kwaB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.60 48.0 3.56e-01 100.0% 58.9%
4ks9A01 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.60 50.0 4.02e-01 100.0% 71.4%
3fp3A01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.58 52.0 3.95e-01 100.0% 43.7%
3ismC01 1.25.40.240 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ku, C-terminal domain 0.58 49.0 3.68e-01 98.3% 53.9%
2hzdA00 6.10.20.40 Special › Helix non-globular › Arc Repressor Mutant, subunit A › TEA/ATTS domain 0.58 44.0 4.00e-01 84.5% 76.8%
3vw7A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.58 48.0 3.04e-01 91.4% 39.7%
7t2rC01 1.10.10.1590 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › NADH-quinone oxidoreductase subunit E 0.57 44.0 4.47e-01 94.8% 91.2%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.57 43.0 3.51e-01 84.5% 55.2%
1kewA02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.56 45.0 4.09e-01 93.1% 64.3%
3anwA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 45.0 3.60e-01 89.7% 55.8%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.55 41.0 3.44e-01 84.5% 76.9%
7n1nB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 36.0 3.52e-01 91.4% 61.9%
1pu6A01 1.10.1670.10 Mainly Alpha › Orthogonal Bundle › Endonuclease Iii, domain 2 › Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 0.54 42.0 3.74e-01 93.1% 84.0%
4c6rA00 3.40.50.10140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Toll/interleukin-1 receptor homology (TIR) domain 0.53 44.0 3.33e-01 100.0% 74.1%
1jvmB00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 38.0 3.24e-01 77.6% 63.0%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.53 42.0 3.46e-01 93.1% 83.8%
2yqdA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.51 37.0 2.99e-01 77.6% 70.0%
3d1bB00 1.20.920.40 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.50 41.0 3.50e-01 100.0% 64.8%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.50 37.0 3.13e-01 84.5% 98.2%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5040466 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.67 51.0 4.72e-01 82.8% 82.4%
3335640 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 49.0 4.80e-01 87.9% 95.4%
3195100 6155.1.1.2 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.62 43.0 3.41e-01 74.1% 53.6%
3765901 109.4.1.470 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › INTS2 0.60 50.0 3.14e-01 100.0% 26.1%
3358974 109.4.1.1524 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_ZFYVE26 0.59 49.0 3.60e-01 98.3% 34.3%
3582393 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.58 43.0 3.11e-01 82.8% 61.1%
3741700 109.40.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › Ctf4_C 0.56 46.0 3.83e-01 100.0% 51.3%
3919095 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.55 47.0 3.33e-01 93.1% 37.1%
3239343 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 43.0 3.65e-01 93.1% 51.8%
3189353 548.1.1.1 ↗ alpha duplicates or obligate multimers › GRIP domain › GRIP domain › GRIP domain › GRIP 0.55 36.0 3.85e-01 94.8% 80.0%
4970733 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.55 45.0 3.42e-01 89.7% 45.2%
4277373 4994.1.1.1 ↗ alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507 0.55 45.0 3.89e-01 93.1% 80.6%
4289855 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.54 45.0 4.36e-01 93.1% 87.7%
3741246 3343.1.1.1 ↗ alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal 0.54 45.0 2.59e-01 93.1% 34.1%
4270503 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.54 42.0 3.81e-01 89.7% 65.9%
3993014 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.54 40.0 3.02e-01 84.5% 90.9%
3895658 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.51 43.0 3.58e-01 98.3% 83.6%
4524825 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.50 41.0 3.57e-01 94.8% 70.5%
3562237 4953.1.1.21 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › PP1_inhibitor 0.50 36.0 3.29e-01 77.6% 81.2%