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NC_041911.1__YP_009598947.1__FDH28_gp167__00254

Bact-Vir

NC_041911.1__YP_009598947.1__FDH28_gp167__00254

Identity

Accession:
NC_041911 ↗
Kingdom:
phage

Quality

77.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Ripduovirus› Ralstonia_phage_RP12

TaxID: 1923889

Cluster

View cluster (2 members)

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 82-144
PDB
Domain cluster: rep: S2_006_000_R2_scaffold_44_prodigal-single.1__X__X__00157__D47-100
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 56.0 5.31e-01 77.8% 64.4%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.78 58.0 5.16e-01 77.8% 60.5%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.77 51.0 5.29e-01 73.0% 74.1%
3lphC00 6.10.140.630 Special › Helix non-globular › Helix Hairpins › 0.76 47.0 4.86e-01 71.4% 67.2%
1o7dC01 1.20.1270.50 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain 0.74 50.0 5.15e-01 71.4% 77.0%
1jogA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.74 54.0 4.25e-01 79.4% 38.5%
2gsqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.70 48.0 3.96e-01 74.6% 41.7%
3whjA00 6.10.140.1710 Special › Helix non-globular › Helix Hairpins › 0.68 48.0 4.01e-01 74.6% 46.8%
4gczA03 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.68 49.0 4.94e-01 79.4% 75.4%
2rdcA00 1.10.287.800 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › protein ne1242 0.68 50.0 3.99e-01 81.0% 39.1%
1on2A02 1.10.60.10 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Iron dependent repressor, metal binding and dimerisation domain 0.68 49.0 4.95e-01 77.8% 84.1%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.68 49.0 4.66e-01 79.4% 64.9%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.67 47.0 4.67e-01 74.6% 70.8%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.67 56.0 4.58e-01 93.7% 85.6%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 47.0 4.78e-01 76.2% 82.5%
1ykhA00 6.10.140.200 Special › Helix non-globular › Helix Hairpins › 0.66 48.0 4.25e-01 79.4% 60.0%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.64 45.0 4.61e-01 76.2% 78.3%
2dodA00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.63 42.0 3.92e-01 95.2% 53.7%
3m1mA03 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.63 42.0 3.51e-01 74.6% 40.0%
4jzaA02 1.10.520.60 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › 0.61 43.0 3.58e-01 93.7% 41.4%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.61 44.0 4.02e-01 79.4% 64.8%
1v8bA01 3.40.50.1480 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Adenosylhomocysteinase-like 0.60 45.0 2.91e-01 81.0% 66.7%
7wj9A01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.60 48.0 3.15e-01 90.5% 92.3%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.60 40.0 4.14e-01 73.0% 72.9%
2x6hA03 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.60 44.0 3.14e-01 79.4% 48.0%
4nv0A02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.59 41.0 3.78e-01 73.0% 74.4%
3egeA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 40.0 2.66e-01 73.0% 90.3%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
54483 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.78 58.0 4.48e-01 79.4% 38.5%
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 0.78 55.0 5.32e-01 74.6% 71.4%
4299170 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.77 54.0 5.21e-01 73.0% 68.6%
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 0.76 53.0 5.14e-01 73.0% 68.6%
4387824 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.75 52.0 5.04e-01 73.0% 68.6%
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 0.74 52.0 5.07e-01 74.6% 70.0%
4946898 375.1.9.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase 0.74 57.0 5.38e-01 82.5% 69.3%
3804939 192.2.1.3 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Rad50_zn_hook 0.74 58.0 4.41e-01 92.1% 37.9%
4420423 5094.1.1.1 ↗ a+b duplicates or obligate multimers › OmpH-like › OmpH-like › OmpH-like › OmpH 0.73 55.0 4.12e-01 81.0% 51.6%
3355246 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.73 54.0 5.02e-01 79.4% 65.0%
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 0.73 50.0 5.03e-01 73.0% 73.8%
3177225 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.73 52.0 4.70e-01 77.8% 57.8%
4214525 632.22.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.73 61.0 5.25e-01 93.7% 100.0%
3781441 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.73 53.0 4.63e-01 77.8% 54.7%
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 0.71 49.0 4.81e-01 73.0% 70.0%
4072921 192.5.1.20 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › Val_tRNA-synt_C 0.70 49.0 4.84e-01 74.6% 72.5%
3641422 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.70 53.0 4.45e-01 82.5% 47.3%
3474600 4207.1.2.48 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region › Med14 0.70 51.0 4.44e-01 81.0% 50.0%
5049361 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.69 47.0 4.39e-01 71.4% 56.2%
4563674 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.69 48.0 4.73e-01 74.6% 70.0%
4013585 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.69 48.0 4.66e-01 73.0% 70.0%
3210369 603.1.1.108 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF27599 0.69 49.0 3.81e-01 74.6% 45.4%
4146694 192.29.1.277 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Dynamitin 0.68 48.0 4.81e-01 77.8% 72.3%
4520081 192.5.1.20 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › Val_tRNA-synt_C 0.67 46.0 4.74e-01 73.0% 76.7%
185014 3393.1.1.1 ↗ extended segments › CAA3-type cytochrome c oxidase subunit IV › CAA3-type cytochrome c oxidase subunit IV › CAA3-type cytochrome c oxidase subunit IV › CAA3_Cox_suIV 0.66 47.0 4.76e-01 76.2% 81.2%
3973636 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.66 47.0 4.53e-01 77.8% 72.0%
4857846 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.66 55.0 3.75e-01 95.2% 59.3%
3687276 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.64 47.0 4.31e-01 81.0% 57.6%
5017280 2002.1.1.172 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PHP_C 0.63 51.0 3.24e-01 85.7% 40.0%
1632108 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.63 45.0 4.04e-01 77.8% 59.8%
3222020 7579.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.52 38.0 2.67e-01 79.4% 22.7%
D2 medium residues 1-76
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hkoA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.58 49.0 3.64e-01 100.0% 75.7%
5yksB02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.56 46.0 3.59e-01 93.4% 69.1%
3dlsB02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.53 43.0 3.42e-01 94.7% 69.8%
3pm2A00 1.10.238.270 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › 0.52 41.0 3.24e-01 88.2% 95.4%
1ej6A01 3.90.1810.10 Alpha Beta › Alpha-Beta Complex › Reovirus components fold › Reovirus components 0.51 42.0 2.81e-01 97.4% 32.3%
1oglA01 1.20.1680.10 Mainly Alpha › Up-down Bundle › all-alpha NTP pyrophosphatases › Type II deoxyuridine triphosphatase 0.51 38.0 3.34e-01 80.3% 53.4%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3808315 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.56 45.0 3.05e-01 90.8% 42.5%
4660205 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.55 38.0 3.20e-01 72.4% 91.1%
3610682 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.54 45.0 3.07e-01 94.7% 48.5%
3596729 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.53 44.0 3.02e-01 94.7% 47.5%