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LC554890.1__BCG50291.1__X__00273

Bact-Vir

LC554890.1__BCG50291.1__X__00273

Identity

Accession:
LC554890 ↗
Kingdom:
phage

Quality

71.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Ralstonia_phage_RP13

TaxID: 2743402

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 6-59
PDB
Domain cluster: rep: KC699836.1__AGK86975.1__SIOphi_00835__00167__D38-90
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00476.27 best DNA_pol_A 36.7 3.40e-09 100.0% 11.3%
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3py8A04 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.80 70.0 5.08e-01 96.3% 41.7%
2ltuA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.72 53.0 5.08e-01 77.8% 85.5%
4gltA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.68 37.0 2.88e-01 83.3% 24.6%
3hx3A01 1.10.8.20 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › N-terminal domain of phosphatidylinositol transfer protein sec14p 0.66 47.0 4.41e-01 100.0% 61.2%
1bh9B00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.66 50.0 4.27e-01 83.3% 51.7%
2gwlA00 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.64 51.0 3.47e-01 94.4% 24.0%
1xb2B01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.60 38.0 3.71e-01 98.1% 56.7%
4bfmA00 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.58 47.0 2.94e-01 88.9% 79.6%
4dbgB02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.58 40.0 3.90e-01 100.0% 65.6%
2lklA01 1.10.1900.40 Mainly Alpha › Orthogonal Bundle › c-terminal domain of poly(a) binding protein › Acidic terminal segments, variant surface antigen of PfEMP1 0.56 40.0 3.78e-01 100.0% 59.7%
4a17O01 1.10.1650.10 Mainly Alpha › Orthogonal Bundle › 50s Ribosomal Protein L19e, Chain O, domain 1 › 0.56 38.0 3.85e-01 85.2% 69.1%
4c9yA00 1.10.10.1890 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Ska1 microtubule binding domain-like 0.55 39.0 2.91e-01 100.0% 32.5%
3qvmB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 46.0 2.95e-01 96.3% 24.3%
7zhgO01 1.10.8.50 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.54 44.0 4.17e-01 90.7% 90.9%
6ifsB02 1.10.8.100 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › rRNA adenine dimethylase, C-terminal domain 0.54 45.0 4.17e-01 94.4% 100.0%
2yqzA02 1.10.8.900 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.54 38.0 3.59e-01 77.8% 89.7%
2l22A01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.53 38.0 3.32e-01 77.8% 60.4%
4gkfA00 1.10.520.30 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › AF1862-like domain 0.53 46.0 3.43e-01 100.0% 65.8%
3q9oA02 3.90.1350.10 Alpha Beta › Alpha-Beta Complex › Exotoxin A, middle domain › Exotoxin A, middle domain 0.53 44.0 3.19e-01 96.3% 75.4%
5ejdA00 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.52 41.0 3.65e-01 85.2% 72.0%
1uqtA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.51 43.0 2.87e-01 98.1% 100.0%
3id7A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.51 36.0 2.23e-01 74.1% 12.0%
1z6tA03 1.10.8.430 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Helical domain of apoptotic protease-activating factors 0.50 41.0 3.62e-01 92.6% 100.0%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3969341 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.93 68.0 4.98e-01 79.6% 32.8%
4456463 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.91 66.0 4.79e-01 79.6% 31.5%
4237263 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.90 65.0 4.88e-01 79.6% 34.2%
4169333 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.89 65.0 4.79e-01 79.6% 32.8%
4027630 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.89 65.0 4.84e-01 79.6% 34.2%
4876668 304.48.1.6 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_A 0.87 63.0 4.67e-01 79.6% 33.1%
3277186 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.86 65.0 4.80e-01 79.6% 34.4%
3001792 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.85 62.0 4.73e-01 79.6% 35.6%
4995740 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.79 64.0 4.77e-01 87.0% 48.8%
3333780 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.79 65.0 4.68e-01 88.9% 45.0%
2970332 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.78 70.0 5.04e-01 98.1% 42.0%
4848450 304.48.1.6 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_A 0.76 68.0 4.93e-01 98.1% 43.9%
4975020 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.76 67.0 4.91e-01 96.3% 45.9%
3562851 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.75 62.0 4.49e-01 90.7% 44.8%
4889886 4970.1.1.2 ↗ 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 › DNA_pol_A 0.72 50.0 3.68e-01 72.2% 37.9%
4964800 101.1.2.925 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF7344 0.72 51.0 4.12e-01 87.0% 39.0%
4962468 101.1.2.925 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF7344 0.72 52.0 4.20e-01 87.0% 40.0%
4997208 2004.1.1.146 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase 0.69 46.0 2.89e-01 70.4% 18.6%
4489811 103.17.1.0 ↗ alpha arrays › RuvA-C › HMG-CoA reductase flap domain › HMG-CoA reductase flap domain 0.68 43.0 4.46e-01 98.1% 70.0%
3832446 178.1.1.1 ↗ alpha arrays › SWIB/MDM2 domain › SWIB/MDM2 domain › SWIB/MDM2 domain › SWIB 0.67 44.0 3.86e-01 75.9% 46.2%
3551458 103.1.1.3 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › CRAL_TRIO_N 0.67 48.0 4.23e-01 100.0% 51.2%
4985569 873.1.1.12 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27313 0.67 48.0 3.62e-01 87.0% 31.1%
3423103 178.1.1.1 ↗ alpha arrays › SWIB/MDM2 domain › SWIB/MDM2 domain › SWIB/MDM2 domain › SWIB 0.66 44.0 3.73e-01 77.8% 43.5%
4038795 186.1.1.1 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 0.65 51.0 4.11e-01 87.0% 42.7%
3237008 2484.1.1.233 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF1280 0.65 40.0 2.72e-01 85.2% 17.4%
5021128 873.1.1.12 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27313 0.63 51.0 3.96e-01 92.6% 40.8%
4959470 873.1.1.12 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27313 0.63 51.0 3.99e-01 92.6% 42.5%
3502241 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.61 42.0 4.55e-01 79.6% 86.7%
3973713 159.1.1.1 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › MazG 0.61 46.0 2.97e-01 92.6% 16.7%
5051872 873.1.1.12 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27313 0.60 45.0 3.58e-01 83.3% 37.5%
4399694 7531.1.1.1 ↗ a/b three-layered sandwiches › Carbamate kinase-like › Carbamate kinase-like › Carbamate kinase-like › AA_kinase 0.60 50.0 3.20e-01 96.3% 30.9%
5068344 6102.1.1.1 ↗ alpha arrays › N-terminal domain of segregation and condensation protein A, ScpA › N-terminal domain of segregation and condensation protein A, ScpA › N-terminal domain of segregation and condensation protein A, ScpA › SMC_ScpA 0.60 42.0 3.36e-01 88.9% 33.1%
3412952 103.1.1.85 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › PF28528 0.60 41.0 4.03e-01 100.0% 66.7%
4043052 3949.1.1.1 ↗ alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › IPPT 0.59 48.0 4.39e-01 94.4% 73.3%
3623379 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.59 52.0 4.32e-01 100.0% 75.8%
4270025 3949.1.1.1 ↗ alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › IPPT 0.58 47.0 4.39e-01 94.4% 78.6%
3629758 577.1.1.1 ↗ alpha arrays › CRIB domain › CRIB domain › CRIB domain › PBD 0.58 42.0 3.92e-01 83.3% 58.9%
4235656 2005.1.1.1 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1 0.57 48.0 3.03e-01 100.0% 57.8%
5006337 4120.1.1.0 ↗ few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP 0.57 39.0 3.02e-01 79.6% 28.9%
5083870 375.1.1.1 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › tRNA-synt_1 0.57 47.0 3.12e-01 96.3% 32.2%
3386629 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.56 40.0 3.59e-01 81.5% 54.7%
3666334 2004.1.1.44 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › PRK 0.56 45.0 2.88e-01 100.0% 71.4%
5061104 2005.1.1.1 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1 0.53 43.0 2.69e-01 100.0% 22.2%
4336243 3949.1.1.1 ↗ alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › IPPT 0.52 42.0 4.04e-01 94.4% 78.5%
4942351 2004.1.1.191 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.52 41.0 3.03e-01 100.0% 40.8%
3594966 3614.1.2.0 ↗ alpha arrays › T4 RNA ligase › T4 RNA ligase 0.51 41.0 3.48e-01 98.1% 51.0%
4976386 2007.1.3.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › Oxidored_q6 0.50 43.0 2.83e-01 96.3% 31.5%