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NC_041911.1__YP_009598944.1__FDH28_gp170__00251

Bact-Vir

NC_041911.1__YP_009598944.1__FDH28_gp170__00251

Identity

Accession:
NC_041911 ↗
Kingdom:
phage

Quality

88.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Ripduovirus› Ralstonia_phage_RP12

TaxID: 1923889

Cluster

View cluster (11 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 15-143_439-463
PDB
Domain cluster: rep: SRR1747027_scaffold_2_prodigal-single.1__X__X__00109__D20-149
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5odnC00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.69 28.0 3.48e-01 81.2% 57.8%
3hx8A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.60 26.0 2.89e-01 78.6% 48.4%
4ikbA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.54 35.0 3.78e-01 83.1% 76.7%
4gs3A00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 29.0 3.82e-01 82.5% 92.2%
6lofA00 2.40.155.10 Mainly Beta › Beta Barrel › Green Fluorescent Protein › Green fluorescent protein 0.53 31.0 3.06e-01 86.4% 53.7%
2r76A00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.53 31.0 3.36e-01 83.1% 66.7%
1aqbA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 41.0 3.95e-01 97.4% 72.6%
3iq2A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.52 33.0 3.63e-01 83.1% 78.9%
3f6gA02 3.30.160.340 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 24.0 3.33e-01 81.2% 98.4%
3n8bA00 3.10.450.700 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 23.0 3.06e-01 96.1% 81.3%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3279764 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.80 29.0 4.41e-01 81.8% 75.7%
3252847 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.69 30.0 3.97e-01 81.8% 74.1%
4593266 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.62 26.0 3.65e-01 79.9% 78.7%
5081878 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 56.0 4.22e-01 99.4% 97.2%
3382312 192.18.1.0 ↗ alpha bundles › Long alpha-hairpin › MxiH-like › MxiH-like 0.56 31.0 2.58e-01 86.4% 29.3%
5055184 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.55 24.0 3.09e-01 82.5% 69.4%
3368394 4325.1.1.11 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › PF27041 0.55 29.0 3.52e-01 94.2% 77.9%
3439646 284.1.3.2 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › OSR1_C 0.54 26.0 3.03e-01 90.3% 62.9%
3741279 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.53 35.0 3.73e-01 83.1% 73.6%
3475901 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.53 24.0 3.04e-01 78.6% 68.9%
5004462 3454.1.1.0 ↗ beta barrels › GspC HR domain/PilP-like › GspC HR domain/PilP-like › GspC HR domain/PilP-like 0.53 28.0 3.42e-01 74.0% 83.3%
3658323 284.1.2.1 ↗ a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases › OSR1_C 0.51 25.0 2.93e-01 90.3% 64.8%
3218206 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.50 39.0 3.77e-01 97.4% 70.6%
D2 medium residues 145-267_360-438
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1noyB02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.66 59.0 5.64e-01 92.1% 100.0%
4qclA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.65 62.0 5.55e-01 100.0% 88.2%
1vz6A01 3.60.70.12 Alpha Beta › 4-Layer Sandwich › L-amino peptidase D-ALA esterase/amidase › L-amino peptidase D-ALA esterase/amidase 0.65 37.0 3.41e-01 91.6% 44.7%
1d5aA02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.59 57.0 5.54e-01 100.0% 97.2%
1q8iA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 50.0 5.30e-01 91.1% 100.0%
3zyvC06 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.54 43.0 3.91e-01 97.0% 62.0%
3gv0A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 34.0 4.07e-01 78.7% 92.6%
1ffvB04 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.54 43.0 4.36e-01 97.0% 84.8%
2w3sB04 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.52 43.0 4.30e-01 97.5% 84.5%
4xxhA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 32.0 3.79e-01 78.2% 91.3%
3il0A00 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.51 29.0 3.62e-01 70.3% 89.1%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4649118 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.67 64.0 4.97e-01 100.0% 57.0%
3605750 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.67 64.0 4.01e-01 100.0% 24.7%
None — 0.67 63.0 4.07e-01 100.0% 26.9%
None — 0.66 63.0 4.06e-01 99.0% 27.8%
3802227 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.66 63.0 4.04e-01 100.0% 26.4%
3798596 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.66 63.0 6.09e-01 100.0% 99.6%
3266685 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.66 63.0 3.82e-01 100.0% 19.4%
3584771 2484.1.1.197 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.66 63.0 5.46e-01 100.0% 76.3%
3619240 304.48.1.59 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_exo1, DNA_pol_B_exo2 0.66 63.0 4.10e-01 99.5% 29.3%
5054032 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.64 61.0 4.87e-01 100.0% 58.4%
4002044 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.64 60.0 4.98e-01 100.0% 74.1%
4282509 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 57.0 4.03e-01 100.0% 37.3%
4452101 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.60 57.0 5.57e-01 100.0% 95.9%
2801086 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.60 57.0 4.60e-01 100.0% 58.6%
3759576 2484.1.1.288 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PML_C 0.58 45.0 4.16e-01 100.0% 63.9%
3569539 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 45.0 4.82e-01 100.0% 91.1%
4975018 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 44.0 4.56e-01 99.0% 84.6%
3719170 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 49.0 4.65e-01 94.6% 98.7%
3656569 2484.1.1.20 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_A_exo1 0.54 43.0 4.30e-01 97.5% 79.5%
4139730 2484.1.1.153 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF1744 0.53 48.0 3.98e-01 97.0% 88.6%
4962882 2484.3.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Creatinase/prolidase N-terminal domain › Creatinase/prolidase N-terminal domain 0.51 27.0 3.46e-01 88.1% 85.0%
4945305 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.51 17.0 2.63e-01 80.7% 69.4%
3600160 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 47.0 4.29e-01 99.5% 87.3%
3496749 2484.1.1.83 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNApol_Exo 0.50 45.0 3.89e-01 95.5% 74.2%
D3 medium residues 268-359
PDB
Domain cluster: representative
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4323378 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.60 48.0 3.36e-01 100.0% 27.2%
3608759 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 34.0 3.56e-01 96.7% 62.4%
3738589 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.51 38.0 3.65e-01 79.3% 98.1%
3743164 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.50 40.0 2.68e-01 88.0% 37.2%
D4 medium residues 479-540
PDB
Domain cluster: representative