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NC_055789.1__YP_010101296.1__KNU47_gp80__00080

Bact-Vir

NC_055789.1__YP_010101296.1__KNU47_gp80__00080

Identity

Accession:
NC_055789 ↗
Kingdom:
phage

Quality

78.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Zierdtviridae› Sukkupivirus› Gordonia_phage_IDyn

TaxID: 2510506

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 3-51
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2lf0A01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.81 69.0 6.53e-01 100.0% 85.0%
3pt1A02 1.20.930.60 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.76 65.0 4.85e-01 95.9% 66.7%
2o8pA00 1.20.190.20 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 14-3-3 domain 0.76 67.0 4.33e-01 100.0% 22.4%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.75 63.0 5.73e-01 100.0% 69.1%
2p4vA01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.74 64.0 5.49e-01 95.9% 67.1%
3keyA01 1.10.10.1080 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Stn1, N-terminal wHTH domain 0.74 46.0 3.78e-01 77.6% 35.6%
4gouA03 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.73 64.0 4.24e-01 100.0% 25.9%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 61.0 4.83e-01 95.9% 49.5%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 61.0 5.71e-01 95.9% 77.4%
1wpaA01 6.10.140.340 Special › Helix non-globular › Helix Hairpins › 0.72 63.0 4.98e-01 98.0% 49.5%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.72 57.0 4.54e-01 100.0% 42.7%
2z0qA01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.71 63.0 4.19e-01 100.0% 26.9%
1rq0A01 6.10.140.160 Special › Helix non-globular › Helix Hairpins › 0.68 59.0 5.03e-01 100.0% 98.8%
1k90B03 1.20.140.60 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.67 56.0 4.34e-01 95.9% 41.7%
5c9gA02 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 0.67 52.0 4.97e-01 87.8% 86.0%
4aifA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.66 54.0 3.98e-01 95.9% 33.3%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 57.0 4.99e-01 100.0% 70.3%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.64 53.0 4.55e-01 98.0% 57.0%
3k62A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.63 52.0 3.13e-01 100.0% 12.3%
3ic8A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.62 50.0 4.17e-01 100.0% 53.5%
2vx2G02 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 47.0 4.63e-01 100.0% 98.2%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5051266 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.84 75.0 4.74e-01 100.0% 21.3%
5041863 4163.1.1.0 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like 0.83 72.0 5.40e-01 98.0% 40.8%
4935546 4163.1.1.0 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like 0.82 73.0 5.27e-01 100.0% 36.3%
3577233 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.82 72.0 6.37e-01 98.0% 68.6%
5032045 4163.1.1.0 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like 0.82 73.0 5.73e-01 100.0% 49.0%
4977784 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.81 72.0 4.55e-01 100.0% 20.4%
4996586 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.81 71.0 5.03e-01 100.0% 34.3%
4941496 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.80 70.0 4.58e-01 100.0% 23.4%
5005094 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.80 69.0 4.57e-01 100.0% 24.6%
4542284 109.4.1.210 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_19 0.79 65.0 4.18e-01 89.8% 20.6%
4485576 1.1.17.4 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Peptidase_S64 0.79 69.0 4.25e-01 100.0% 33.8%
4999065 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.79 69.0 4.81e-01 100.0% 31.0%
3651038 192.29.1.221 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › PF29520 0.78 70.0 5.09e-01 100.0% 37.7%
3346803 5076.2.1.10 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › PF29520 0.78 69.0 4.20e-01 100.0% 16.1%
4998819 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.78 70.0 5.11e-01 100.0% 47.7%
5017725 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.78 67.0 4.48e-01 100.0% 24.6%
3956669 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.78 69.0 4.60e-01 100.0% 26.7%
4976428 4995.1.1.0 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like 0.78 66.0 5.59e-01 100.0% 61.2%
4972401 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.77 70.0 4.49e-01 100.0% 29.3%
3348106 5076.2.1.10 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › PF29520 0.77 69.0 4.29e-01 100.0% 18.1%
4213046 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 0.77 66.0 6.03e-01 95.9% 73.8%
4999337 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.76 68.0 4.75e-01 100.0% 32.3%
3955489 2484.1.1.211 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605, Cas12f1-like_TNB 0.76 68.0 4.40e-01 100.0% 34.3%
3646011 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.76 65.0 5.76e-01 95.9% 65.7%
2524047 601.14.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin › Hemerythrin 0.76 65.0 4.56e-01 98.0% 30.2%
3494602 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.76 67.0 3.66e-01 100.0% 54.6%
4202466 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.76 62.0 6.43e-01 91.8% 97.8%
4544002 192.6.1.1 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › ATP-synt_DE 0.76 63.0 6.25e-01 93.9% 88.0%
4978165 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.76 67.0 4.41e-01 100.0% 31.5%
3983659 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.75 62.0 5.62e-01 91.8% 67.7%
3924162 109.4.1.192 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8 0.72 57.0 3.32e-01 87.8% 10.8%
3286637 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.72 65.0 4.43e-01 100.0% 38.2%
4977429 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.72 64.0 4.58e-01 100.0% 44.3%
3615269 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.72 60.0 3.97e-01 95.9% 23.8%
4966687 192.3.1.1 ↗ alpha bundles › Long alpha-hairpin › Fe,Mn superoxide dismutase (SOD), N-terminal domain › Fe,Mn superoxide dismutase (SOD), N-terminal domain › Sod_Fe_N 0.69 56.0 4.76e-01 93.9% 83.5%