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NC_054723.1__YP_010058846.1__KHQ83_gp219__00057

Bact-Vir

NC_054723.1__YP_010058846.1__KHQ83_gp219__00057

Identity

Accession:
NC_054723 ↗
Kingdom:
phage

Quality

89.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Puppervirus› Gordonia_phage_Pupper

TaxID: 2571249

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 5-55
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4iluA02 1.20.58.1290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › CarD-like, C-terminal domain 0.86 66.0 5.03e-01 82.4% 37.8%
5jjxA01 1.25.40.1040 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.84 58.0 3.51e-01 72.5% 12.5%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 65.0 6.07e-01 84.3% 69.4%
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 71.0 6.06e-01 98.0% 72.6%
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.82 63.0 6.45e-01 86.3% 87.5%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 63.0 6.11e-01 84.3% 74.1%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.81 63.0 5.81e-01 84.3% 73.4%
1go3F02 6.10.140.10 Special › Helix non-globular › Helix Hairpins › 0.80 54.0 5.61e-01 88.2% 76.6%
4g1tA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.79 60.0 5.65e-01 92.2% 68.9%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.78 59.0 5.31e-01 82.4% 59.2%
1wrdA00 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 67.0 5.36e-01 96.1% 65.3%
5x8tT00 3.90.470.10 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › Ribosomal protein L22/L17 0.77 58.0 4.17e-01 90.2% 29.2%
1o9gA02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.75 57.0 6.11e-01 86.3% 100.0%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.73 54.0 5.04e-01 82.4% 68.7%
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 0.73 59.0 5.06e-01 96.1% 55.3%
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 0.73 60.0 5.01e-01 96.1% 53.4%
2itbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.72 59.0 4.00e-01 94.1% 28.8%
5lb3B02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.72 50.0 3.16e-01 72.5% 50.4%
2bnlC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.70 50.0 3.66e-01 76.5% 60.4%
5c8aA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.68 51.0 4.50e-01 82.4% 55.1%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.68 59.0 4.54e-01 100.0% 86.6%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.68 55.0 4.79e-01 96.1% 63.5%
2r0cA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.66 50.0 3.13e-01 80.4% 20.4%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.65 47.0 3.58e-01 84.3% 30.4%
3k2nA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.63 47.0 3.34e-01 84.3% 81.4%
2iw3A02 1.20.1390.20 Mainly Alpha › Up-down Bundle › PWI domain › 0.63 49.0 4.08e-01 84.3% 76.7%
1np7A02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.63 46.0 3.63e-01 82.4% 38.7%
1h99A01 1.10.1790.10 Mainly Alpha › Orthogonal Bundle › PTS-regulatory domain, PRD › PRD domain 0.62 47.0 3.73e-01 82.4% 76.0%
2nr5A00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.59 46.0 4.44e-01 86.3% 79.3%
4fzwA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.59 44.0 4.34e-01 88.2% 94.8%
3sllA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.58 44.0 4.23e-01 88.2% 93.4%
2fe1A00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.51 43.0 3.22e-01 94.1% 48.5%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4675076 192.19.1.1 ↗ alpha bundles › Long alpha-hairpin › YnzC-like › YnzC-like › DUF896 0.96 77.0 6.61e-01 84.3% 57.3%
4477969 192.19.1.1 ↗ alpha bundles › Long alpha-hairpin › YnzC-like › YnzC-like › DUF896 0.95 76.0 7.74e-01 84.3% 86.0%
3740829 192.19.1.3 ↗ alpha bundles › Long alpha-hairpin › YnzC-like › YnzC-like › Wbp11 0.95 77.0 6.64e-01 86.3% 58.7%
4673830 192.19.1.1 ↗ alpha bundles › Long alpha-hairpin › YnzC-like › YnzC-like › DUF896 0.94 76.0 6.36e-01 84.3% 54.4%
3163958 507.1.1.2 ↗ alpha arrays › DnaB helicase N-terminal domain-related › DnaB helicase N-terminal domain-related › DnaB helicase N-terminal domain-related › DnaG_DnaB_bind 0.94 75.0 5.26e-01 84.3% 30.7%
4186571 192.19.1.1 ↗ alpha bundles › Long alpha-hairpin › YnzC-like › YnzC-like › DUF896 0.94 75.0 7.62e-01 84.3% 88.0%
4633524 192.19.1.1 ↗ alpha bundles › Long alpha-hairpin › YnzC-like › YnzC-like › DUF896 0.93 74.0 6.57e-01 84.3% 61.4%
3590808 192.19.1.1 ↗ alpha bundles › Long alpha-hairpin › YnzC-like › YnzC-like › DUF896 0.92 73.0 7.42e-01 84.3% 88.0%
3721752 5086.1.1.170 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › Not3 0.88 70.0 5.09e-01 84.3% 35.2%
3714271 109.4.1.192 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8 0.86 66.0 4.43e-01 82.4% 23.3%
4981549 102.1.1.11 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › RNA_pol_Rpb4 0.86 64.0 4.98e-01 94.1% 40.0%
3462297 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.86 67.0 5.86e-01 84.3% 57.3%
4031046 192.7.1.1 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › FemAB 0.85 66.0 6.29e-01 86.3% 71.7%
4009505 7079.1.1.1 ↗ a+b complex topology › Phage tail fiber assembly protein › Phage tail fiber assembly protein › Phage tail fiber assembly protein › Caudo_TAP 0.85 67.0 5.94e-01 84.3% 61.4%
4007897 3809.1.1.2 ↗ alpha bundles › Uncharacterized protein CV0426 › Uncharacterized protein CV0426 › Uncharacterized protein CV0426 › Caudo_TAP 0.85 67.0 5.94e-01 84.3% 61.4%
3975852 192.8.1.466 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Caudo_TAP 0.85 66.0 6.09e-01 84.3% 66.2%
3330916 3846.1.1.0 ↗ alpha bundles › IcmR › IcmR › IcmR 0.84 66.0 6.42e-01 84.3% 80.0%
3985321 3579.1.1.29 ↗ extended segments › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › ThrE_2 0.83 64.0 4.59e-01 84.3% 29.7%
3202914 3846.1.1.0 ↗ alpha bundles › IcmR › IcmR › IcmR 0.83 63.0 6.02e-01 82.4% 70.0%
4674 192.7.1.1 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › FemAB 0.83 65.0 5.97e-01 84.3% 66.2%
3721483 109.4.1.681 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans_2 0.83 73.0 4.39e-01 96.1% 19.2%
3415944 109.4.1.1324 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › P4Ha_N, TPR_P4H 0.83 64.0 4.41e-01 84.3% 26.1%
5040510 304.48.1.3 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.82 72.0 4.50e-01 96.1% 46.5%
4019713 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.82 64.0 5.71e-01 84.3% 61.4%
3724838 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.81 64.0 5.70e-01 84.3% 61.4%
3891006 109.4.1.2301 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, TPR_6, TPR_16, TPR_19 0.81 74.0 4.58e-01 100.0% 19.6%
5006188 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 0.79 61.0 5.80e-01 84.3% 73.3%
3639366 109.4.1.1978 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1, TPR_2, ANAPC3, TPR_8, TPR_16, PF29407 0.79 61.0 3.66e-01 84.3% 12.5%
3614452 1021.1.1.0 ↗ a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.75 57.0 4.80e-01 84.3% 47.8%
5061885 298.2.1.0 ↗ a+b two layers › FwdE/GAPDH domain-like › FwdE-like › FwdE-like 0.75 66.0 4.33e-01 98.0% 23.8%
3775580 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.71 55.0 4.91e-01 86.3% 60.0%
3615716 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.67 55.0 4.25e-01 94.1% 59.2%
4076265 3390.1.1.0 ↗ extended segments › Photosystem II reaction center protein T, PsbT › Photosystem II reaction center protein T, PsbT › Photosystem II reaction center protein T, PsbT 0.67 52.0 5.27e-01 84.3% 90.0%
3178037 109.4.1.2223 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF29062 0.65 52.0 3.27e-01 100.0% 23.5%
4015147 2004.1.1.430 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, ABC_tran_Xtn 0.65 46.0 2.65e-01 84.3% 7.0%
4130511 6026.1.1.19 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › GrpE 0.63 49.0 4.68e-01 84.3% 73.3%
3755839 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.62 52.0 4.54e-01 96.1% 95.0%
2474881 397.7.1.0 ↗ few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 0.60 47.0 4.83e-01 98.0% 91.5%
3168913 228.1.1.1 ↗ a+b three layers › Fe,Mn superoxide dismutase (SOD)-C › Fe,Mn superoxide dismutase (SOD)-C › Fe,Mn superoxide dismutase (SOD)-C › Sod_Fe_C 0.60 48.0 3.24e-01 86.3% 23.7%
3675439 5059.1.1.52 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › PAP2 0.59 51.0 3.84e-01 100.0% 53.8%
D2 high residues 59-122
PDB
Domain cluster: rep: NC_028653.1__YP_009187121.1__AU099_gp59__00059__D21-72