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OR553913.1__WNN96012.1__SEA_HIRKO_62__00062

Bact-Vir

OR553913.1__WNN96012.1__SEA_HIRKO_62__00062

Identity

Accession:
OR553913 ↗
Kingdom:
phage

Quality

85.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Berryhillviridae› Vibakivirus› Arthrobacter_phage_Hirko

TaxID: 3077804

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 4-38
PDB
Domain cluster: representative
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3f6gA02 3.30.160.340 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.80 68.0 5.68e-01 100.0% 61.9%
5douA01 1.10.1030.10 Mainly Alpha › Orthogonal Bundle › Carbamoyl Phosphate Synthetase; Chain A, domain 4 › Carbamoyl-phosphate synthetase, large subunit oligomerisation domain 0.74 62.0 4.00e-01 97.1% 30.4%
3tzgA00 2.40.160.150 Mainly Beta › Beta Barrel › Porin › 0.72 52.0 3.16e-01 94.3% 11.7%
1xeaA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.68 50.0 3.06e-01 85.7% 14.6%
2p1jA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.67 54.0 3.69e-01 97.1% 41.3%
1huxA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.66 51.0 3.60e-01 97.1% 72.1%
4e4tA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.65 49.0 3.18e-01 97.1% 36.6%
1zbsA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.64 52.0 3.93e-01 97.1% 46.9%
3wknF00 6.20.50.120 Special › Other non-globular › N-terminal domain of TfIIb › 0.64 46.0 4.32e-01 94.3% 60.9%
4r8oA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.64 54.0 4.00e-01 100.0% 57.1%
8oqkA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.64 50.0 3.75e-01 97.1% 40.8%
2yx6D01 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.63 51.0 3.69e-01 91.4% 34.3%
1eyuA00 3.40.210.10 Alpha Beta › 3-Layer(aba) Sandwich › PvuII Endonuclease; Chain A › PVUII Endonuclease, subunit A 0.63 51.0 3.45e-01 100.0% 35.9%
8a9nA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.63 53.0 3.68e-01 100.0% 65.6%
2h3gX01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.63 53.0 4.05e-01 100.0% 42.0%
3mswA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.61 53.0 3.57e-01 100.0% 42.4%
1jcfA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.61 46.0 3.64e-01 97.1% 37.1%
2hjjA00 3.30.160.130 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › ykff protein like domains 0.60 43.0 3.60e-01 100.0% 42.4%
4hslA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.60 49.0 3.32e-01 100.0% 24.7%
2cxhA01 3.40.50.10480 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Brix domain 0.59 44.0 2.95e-01 94.3% 18.4%
4euyA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.59 52.0 3.88e-01 100.0% 66.3%
2vt1B00 3.40.1690.10 Alpha Beta › 3-Layer(aba) Sandwich › name from scop › secretion proteins EscU 0.58 50.0 3.81e-01 97.1% 43.2%
4p6bB00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.58 48.0 2.74e-01 94.3% 94.5%
5kfzA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.58 43.0 3.23e-01 100.0% 46.3%
3df7A02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.58 45.0 3.24e-01 100.0% 65.0%
5bv3D01 3.30.200.40 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Scavenger mRNA decapping enzyme, N-terminal domain 0.58 42.0 3.04e-01 82.9% 66.1%
2ffgA00 3.30.720.20 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Protein of unknown function DUF1797 0.58 46.0 3.71e-01 100.0% 60.0%
7o4xA01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 44.0 3.29e-01 91.4% 64.6%
3p8kA00 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.56 46.0 2.79e-01 100.0% 39.9%
3m05B01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 45.0 3.50e-01 97.1% 67.4%
2kcqA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.56 41.0 2.87e-01 88.6% 20.9%
6dxwA01 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.56 46.0 2.86e-01 97.1% 70.3%
4ctaA02 3.30.70.2860 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 46.0 3.68e-01 97.1% 78.7%
3qwmA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 42.0 3.00e-01 91.4% 27.6%
1y9kA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 46.0 3.33e-01 100.0% 46.0%
2pcrA02 3.40.190.80 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › 0.55 40.0 2.98e-01 100.0% 27.0%
2fl4A02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 40.0 3.10e-01 100.0% 94.2%
2y24A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 39.0 3.01e-01 97.1% 30.8%
3lzwA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 36.0 2.61e-01 71.4% 18.5%
4mybA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.52 41.0 2.63e-01 97.1% 35.0%
2anrA02 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.52 39.0 3.29e-01 94.3% 86.7%
3riqA00 2.160.20.20 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › 0.52 40.0 2.28e-01 100.0% 7.9%
4dwpA02 1.10.443.30 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Telomere resolvase 0.51 38.0 2.39e-01 80.0% 72.2%
4pwyA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 40.0 2.42e-01 88.6% 42.4%
6ryvA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 40.0 3.39e-01 97.1% 53.8%
2i6vA00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.50 40.0 3.17e-01 100.0% 86.2%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4386515 330.1.1.30 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF27148 0.85 70.0 5.77e-01 97.1% 56.9%
3702613 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.79 62.0 5.70e-01 100.0% 66.0%
4984224 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.79 62.0 4.68e-01 97.1% 38.9%
4980279 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.77 64.0 5.18e-01 97.1% 50.0%
4616494 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.77 63.0 4.93e-01 97.1% 80.0%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.75 66.0 5.87e-01 100.0% 74.0%
4322692 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.74 60.0 4.78e-01 100.0% 81.2%
3671443 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.67 53.0 4.31e-01 97.1% 46.2%
3886813 233.1.1.0 ↗ a+b two layers › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC antigen-recognition domain 0.66 47.0 3.71e-01 88.6% 34.1%
5046873 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.66 57.0 4.05e-01 100.0% 81.9%
138513 2484.1.1.4 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.64 52.0 3.53e-01 97.1% 24.5%
5081301 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.63 49.0 2.82e-01 94.3% 15.4%
3899773 221.4.1.1 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.62 46.0 2.92e-01 100.0% 14.8%
4995146 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.62 49.0 3.63e-01 100.0% 34.4%
4854856 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.62 51.0 3.81e-01 100.0% 82.2%
3753029 221.15.1.0 ↗ a+b two layers › beta-Grasp › beta-grasp fold domain in leucine-tRNA ligase › beta-grasp fold domain in leucine-tRNA ligase 0.62 51.0 4.92e-01 97.1% 85.0%
4966228 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.61 49.0 4.05e-01 100.0% 46.7%
3586214 4019.1.1.1 ↗ alpha complex topology › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › Beta-lactamase 0.61 42.0 2.54e-01 71.4% 69.8%
3978376 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.61 47.0 3.60e-01 97.1% 36.0%
3238115 389.1.1.145 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin › PF29138 0.61 45.0 3.98e-01 85.7% 52.7%
3909399 233.1.1.0 ↗ a+b two layers › MHC antigen-recognition domain › MHC antigen-recognition domain › MHC antigen-recognition domain 0.61 54.0 4.10e-01 100.0% 56.2%
185414 3347.1.1.1 ↗ beta meanders › Uncharacterized protein BF3112 › Uncharacterized protein BF3112 › Uncharacterized protein BF3112 › DUF3836 0.61 53.0 3.58e-01 100.0% 42.8%
3842593 221.4.1.1 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.61 44.0 2.86e-01 100.0% 15.9%
3362984 10.1.1.11 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Glyco_hydro_16 0.60 48.0 3.11e-01 97.1% 27.4%
3958972 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.60 49.0 3.73e-01 100.0% 38.9%
4235551 221.15.1.0 ↗ a+b two layers › beta-Grasp › beta-grasp fold domain in leucine-tRNA ligase › beta-grasp fold domain in leucine-tRNA ligase 0.60 42.0 4.25e-01 74.3% 68.6%
5067477 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.60 47.0 3.56e-01 97.1% 34.0%
5074741 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.60 49.0 3.57e-01 100.0% 49.1%
4978486 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.59 49.0 3.45e-01 100.0% 69.2%
5021465 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.58 49.0 2.93e-01 100.0% 20.0%
3512071 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.58 44.0 2.67e-01 100.0% 29.0%
3935086 7512.1.1.0 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.58 48.0 3.21e-01 100.0% 93.5%
3473631 109.6.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Ras GEF › Ras GEF › RasGEF 0.58 47.0 2.64e-01 97.1% 10.6%
3336611 2004.1.1.26 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin 0.57 46.0 2.82e-01 97.1% 92.7%
4642817 3326.1.1.1 ↗ alpha arrays › DNA-binding domain in UvrA › DNA-binding domain in UvrA › DNA-binding domain in UvrA › UvrA_DNA-bind 0.56 39.0 2.76e-01 71.4% 18.3%
5025065 2004.1.1.100 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NTPase_1 0.54 43.0 2.86e-01 100.0% 27.2%
3362573 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.53 39.0 2.39e-01 77.1% 9.2%
2325417 3012.1.1.0 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.53 39.0 3.13e-01 94.3% 62.1%
4170819 4070.1.1.3 ↗ alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like › DUF3267 0.52 43.0 2.82e-01 100.0% 48.4%
3357798 3082.1.1.3 ↗ extended segments › C-terminal region of nonsense mediated decay factor UPF2 › C-terminal region of nonsense mediated decay factor UPF2 › C-terminal region of nonsense mediated decay factor UPF2 › Pro_isomerase 0.51 36.0 3.51e-01 80.0% 77.3%
4479761 7.1.1.0 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain 0.51 39.0 3.03e-01 97.1% 72.0%
4958890 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.50 36.0 3.10e-01 97.1% 82.5%
3494714 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.50 35.0 2.97e-01 74.3% 82.9%
4982514 304.162.1.0 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain 0.50 38.0 3.26e-01 88.6% 82.7%