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NC_041911.1__YP_009598863.1__FDH28_gp251__00170

Bact-Vir

NC_041911.1__YP_009598863.1__FDH28_gp251__00170

Identity

Accession:
NC_041911 ↗
Kingdom:
phage

Quality

78.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Ripduovirus› Ralstonia_phage_RP12

TaxID: 1923889

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 2-49
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.86 77.0 7.05e-01 100.0% 81.0%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.84 67.0 5.17e-01 100.0% 40.8%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.84 73.0 6.12e-01 100.0% 57.8%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.84 70.0 6.34e-01 100.0% 69.8%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.82 73.0 6.80e-01 100.0% 91.7%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.82 65.0 5.11e-01 100.0% 42.4%
2wmmA01 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 0.80 70.0 7.04e-01 97.9% 95.9%
2lmgA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.79 67.0 5.92e-01 100.0% 64.9%
4errB00 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 63.0 5.23e-01 100.0% 50.6%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.79 69.0 6.53e-01 100.0% 94.8%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.79 66.0 6.03e-01 100.0% 70.3%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.78 68.0 5.81e-01 100.0% 60.8%
1vx7301 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 68.0 5.95e-01 100.0% 70.3%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 67.0 5.33e-01 100.0% 48.0%
3ehfD01 1.20.5.1930 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.78 65.0 5.97e-01 100.0% 71.4%
3pyoY00 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.77 60.0 5.59e-01 87.5% 74.2%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.76 66.0 5.69e-01 100.0% 61.5%
4x5mA00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.76 64.0 5.30e-01 100.0% 53.5%
4a4kA01 1.20.1500.20 Mainly Alpha › Up-down Bundle › YheA-like fold › 0.76 67.0 5.08e-01 100.0% 44.2%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.75 65.0 5.42e-01 100.0% 55.8%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 63.0 5.65e-01 100.0% 67.6%
6xm1A02 3.90.830.10 Alpha Beta › Alpha-Beta Complex › Syntaxin Binding Protein 1; Chain A, domain 2 › Sec1/Munc18 (SM) protein, domain 3a 0.73 63.0 4.82e-01 100.0% 49.6%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.72 60.0 5.15e-01 100.0% 57.3%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.70 59.0 4.96e-01 100.0% 54.5%
3jcuZ00 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.69 58.0 5.44e-01 100.0% 96.7%
4a17U01 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 55.0 4.86e-01 100.0% 59.7%
1fouA01 1.10.246.30 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.68 58.0 5.10e-01 100.0% 64.9%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 56.0 4.98e-01 100.0% 69.9%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 52.0 4.22e-01 100.0% 49.1%
3ff5A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 50.0 4.88e-01 87.5% 81.5%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.60 46.0 4.55e-01 91.7% 86.8%
1bhaA00 1.10.287.170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 49.0 4.53e-01 100.0% 71.6%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4072921 192.5.1.20 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › Val_tRNA-synt_C 0.92 85.0 7.40e-01 100.0% 69.6%
4520081 192.5.1.20 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › Val_tRNA-synt_C 0.91 83.0 7.66e-01 100.0% 80.0%
3249513 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.90 82.0 8.12e-01 100.0% 96.0%
4147837 192.1.1.41 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › Val_tRNA-synt_C 0.90 83.0 7.38e-01 100.0% 73.8%
4070346 192.8.1.343 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Val_tRNA-synt_C 0.90 82.0 7.36e-01 100.0% 73.8%
4118522 605.1.1.137 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › RRP36 0.90 81.0 5.54e-01 100.0% 31.2%
4563674 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.90 82.0 7.12e-01 100.0% 68.6%
3528259 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.90 81.0 7.13e-01 100.0% 69.6%
3885007 3922.1.1.67 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Val_tRNA-synt_C 0.90 81.0 7.09e-01 100.0% 68.6%
4387824 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.90 81.0 7.10e-01 100.0% 68.6%
3393826 3812.1.1.0 ↗ alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE 0.90 81.0 7.13e-01 100.0% 69.6%
4383676 3922.1.1.67 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Val_tRNA-synt_C 0.89 81.0 7.06e-01 100.0% 68.6%
4367294 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.89 81.0 7.76e-01 100.0% 88.9%
3186805 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.89 80.0 7.02e-01 100.0% 68.6%
4373203 605.1.1.131 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Val_tRNA-synt_C 0.89 80.0 7.20e-01 100.0% 73.8%
4503822 3922.1.1.67 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Val_tRNA-synt_C 0.88 80.0 7.05e-01 100.0% 70.6%
4587769 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.88 80.0 7.16e-01 100.0% 73.8%
4299170 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.88 80.0 6.98e-01 100.0% 68.6%
3177225 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.88 79.0 6.33e-01 100.0% 53.3%
3595063 192.8.1.343 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Val_tRNA-synt_C 0.88 80.0 7.16e-01 100.0% 73.8%
4185385 605.2.1.6 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Val_tRNA-synt_C 0.87 78.0 6.82e-01 100.0% 68.6%
3708367 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.87 79.0 6.88e-01 100.0% 68.6%
3569037 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.86 76.0 6.18e-01 100.0% 53.3%
4181677 192.29.1.272 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Val_tRNA-synt_C 0.86 76.0 6.72e-01 100.0% 68.6%
4484919 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.86 76.0 6.15e-01 100.0% 53.3%
2773864 3615.1.1.1 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Fzo_mitofusin 0.83 64.0 5.88e-01 100.0% 64.1%
1956188 3615.1.1.1 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Fzo_mitofusin 0.82 63.0 5.52e-01 100.0% 56.2%
5006936 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 0.82 63.0 5.75e-01 100.0% 63.1%
2518028 5044.1.1.1 ↗ extended segments › PsbZ-like › PsbZ-like › PsbZ-like › Ycf9 0.81 73.0 6.74e-01 100.0% 90.2%
1927453 3615.1.1.0 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain 0.79 61.0 5.53e-01 100.0% 62.1%
4241935 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.74 64.0 5.05e-01 100.0% 47.0%
3619865 10.28.1.1 ↗ beta sandwiches › jelly-roll › Jelly-roll domain in Zinc finger protein ZPR1 › Jelly-roll domain in Zinc finger protein ZPR1 › jr-ZPR1 0.73 60.0 4.36e-01 95.8% 31.7%
1002194 192.23.1.1 ↗ alpha bundles › Long alpha-hairpin › DUF683 › DUF683 › Rop-like 0.73 61.0 5.50e-01 100.0% 67.6%
4428645 3826.1.1.80 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › GrpE 0.72 63.0 5.85e-01 97.9% 78.3%
3975851 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.72 61.0 5.50e-01 100.0% 75.7%
3619662 192.12.1.3 ↗ alpha bundles › Long alpha-hairpin › Transcriptional repressor TraM › Transcriptional repressor TraM › DUF747 0.72 60.0 5.21e-01 100.0% 60.0%
3731028 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.71 57.0 4.67e-01 100.0% 45.7%
3518386 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.70 60.0 5.25e-01 100.0% 64.0%
3483986 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 52.0 4.40e-01 100.0% 48.4%
3167450 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.63 53.0 3.14e-01 100.0% 11.2%
4443506 101.1.2.517 ↗ alpha arrays › HTH › HTH › winged helix domain › RNA_pol_Rpc82, HTH_9, POLR3C_WHD 0.58 53.0 3.07e-01 100.0% 95.0%
4022243 101.1.2.517 ↗ alpha arrays › HTH › HTH › winged helix domain › RNA_pol_Rpc82, HTH_9, POLR3C_WHD 0.57 53.0 2.96e-01 100.0% 96.0%
D2 medium residues 67-123
PDB
D3 medium residues 124-179
PDB
Domain cluster: rep: NC_041911.1__YP_009598868.1__FDH28_gp246__00175__D52-102