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NC_022765.1__YP_008770618.1__Riggi_61__00061

Bact-Vir

NC_022765.1__YP_008770618.1__Riggi_61__00061

Identity

Accession:
NC_022765 ↗
Kingdom:
phage

Quality

93.1 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 3-63
PDB
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4usaA02 1.10.150.120 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain 0.61 52.0 4.30e-01 100.0% 79.0%
2gxaE01 1.10.10.510 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Zinc finger, large T-antigen D1 domain 0.61 46.0 4.39e-01 88.5% 69.9%
3ceiA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.60 41.0 4.10e-01 72.1% 79.4%
2o57A01 1.10.287.840 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Mycolic acid cyclopropane synthase domain like 0.59 46.0 4.00e-01 90.2% 82.9%
4yzwA01 1.20.1370.10 Mainly Alpha › Up-down Bundle › Hemocyanin, N-terminal domain › Hemocyanin, N-terminal domain 0.58 43.0 3.37e-01 91.8% 34.9%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 45.0 4.53e-01 91.8% 95.2%
1gcvA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 45.0 3.55e-01 90.2% 95.7%
1t3qA02 1.10.150.120 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain 0.57 45.0 4.17e-01 91.8% 70.4%
3owaA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.55 44.0 3.49e-01 91.8% 61.6%
6o0aA01 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.55 41.0 3.22e-01 83.6% 89.9%
1bo9A00 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.55 41.0 3.88e-01 96.7% 68.5%
4jn7A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 42.0 3.56e-01 91.8% 65.5%
1mn8D00 1.10.150.180 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Gamma-retroviral matrix domain 0.54 43.0 3.81e-01 93.4% 79.4%
5eufA02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.54 43.0 3.15e-01 93.4% 75.3%
2gttC01 1.10.3570.10 Mainly Alpha › Orthogonal Bundle › Rhabdovirus nucleoprotein-like fold › Rhabdovirus nucleocapsid protein like domain 0.53 42.0 3.08e-01 93.4% 70.6%
2pmqA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 44.0 3.49e-01 95.1% 73.6%
2of7A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.52 41.0 3.36e-01 96.7% 75.0%
1zu4A01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.52 42.0 3.86e-01 95.1% 77.0%
2pg0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.52 36.0 2.73e-01 72.1% 77.2%
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.52 41.0 3.70e-01 98.4% 79.4%
2lsoA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 41.0 3.81e-01 95.1% 94.0%
1tm9A00 1.10.3960.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein MG354 fold › MG354-like 0.51 41.0 3.25e-01 91.8% 55.5%
1ej5A00 3.90.810.10 Alpha Beta › Alpha-Beta Complex › SerineThreonine-protein kinase PAK-alpha; Chain A › CRIB domain 0.51 37.0 3.14e-01 78.7% 79.4%
1x4qA01 1.20.1390.10 Mainly Alpha › Up-down Bundle › PWI domain › PWI domain 0.50 38.0 3.78e-01 93.4% 80.3%
2r7rA08 1.20.120.1400 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.50 38.0 3.54e-01 90.2% 69.8%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5044676 109.61.1.0 alpha superhelices › Repetitive alpha hairpins › Uncharacterized protein PF2048.1 › Uncharacterized protein PF2048.1 0.62 49.0 4.84e-01 90.2% 83.1%
4268846 218.1.1.8 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.62 50.0 4.30e-01 91.8% 84.0%
4355046 218.1.1.8 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.61 49.0 4.31e-01 90.2% 82.1%
2486293 8001.1.1.1 alpha arrays › N-terminal domain of large tumor antigen › N-terminal domain of large tumor antigen › N-terminal domain of large tumor antigen › PPV_E1_C 0.61 46.0 4.47e-01 91.8% 73.2%
4033427 639.2.1.0 alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) 0.61 50.0 4.80e-01 93.4% 85.7%
4271344 101.1.1.305 alpha arrays › HTH › HTH › Three-helical HTH › ALS2CR8 0.60 50.0 4.79e-01 93.4% 91.4%
4431372 218.1.1.8 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.59 47.0 4.10e-01 90.2% 83.2%
5066592 1030.1.1.0 alpha duplicates or obligate multimers › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 0.58 48.0 4.24e-01 100.0% 88.0%
3839957 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.58 46.0 2.97e-01 93.4% 17.1%
4295379 195.1.1.1 alpha complex topology › NusB-like › NusB-like › NusB-like › NusB 0.58 49.0 3.81e-01 100.0% 75.3%
4932863 101.1.2.947 alpha arrays › HTH › HTH › winged helix domain › PF27234 0.56 45.0 4.27e-01 98.4% 93.8%
3618386 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.55 38.0 4.06e-01 77.0% 100.0%
4930280 3930.1.1.3 alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical 0.55 42.0 3.55e-01 91.8% 91.2%
3956065 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.54 43.0 4.04e-01 93.4% 71.2%
4946543 2004.1.3.3 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR_N 0.53 39.0 2.88e-01 91.8% 26.2%
3942778 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.53 42.0 3.48e-01 93.4% 52.0%
4049391 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.52 41.0 3.71e-01 93.4% 66.3%
D2 medium residues 66-99
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1xjaB00 2.60.120.280 Mainly Beta › Sandwich › Jelly Rolls › Regulatory protein AraC 0.89 79.0 4.99e-01 100.0% 24.0%
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.88 76.0 4.62e-01 100.0% 18.5%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.84 72.0 6.37e-01 100.0% 66.7%
2au3A04 1.20.50.30 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › 0.83 59.0 5.02e-01 100.0% 47.3%
3m1cB01 3.30.390.170 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.82 63.0 4.42e-01 88.2% 33.9%
2py5A04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.82 63.0 6.28e-01 100.0% 83.3%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.81 68.0 5.64e-01 100.0% 53.1%
1kaeA03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.80 65.0 5.60e-01 94.1% 61.8%
3mzlB02 6.10.140.1600 Special › Helix non-globular › Helix Hairpins › 0.79 60.0 5.30e-01 100.0% 55.4%
1gw5A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.79 60.0 3.26e-01 97.1% 5.1%
2p18A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.79 62.0 3.68e-01 100.0% 11.7%
2xevB00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.78 64.0 4.39e-01 97.1% 26.6%
4hkaA02 1.10.287.3810 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 58.0 5.44e-01 100.0% 74.5%
2jqtA00 1.20.1280.40 Mainly Alpha › Up-down Bundle › Monooxygenase › HHA 0.75 59.0 5.26e-01 100.0% 61.4%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.75 58.0 5.37e-01 100.0% 66.7%
4g09A03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.73 58.0 5.12e-01 97.1% 60.0%
1dc1A02 1.10.238.90 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Restriction endonuclease BsobI, helical domain 0.69 55.0 4.12e-01 91.2% 93.2%
1ufhA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.65 53.0 3.55e-01 100.0% 72.9%
1jqjD03 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.64 49.0 3.71e-01 85.3% 33.7%
3fdqA01 1.20.120.1030 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Motility repressor MogR, DNA-binding domain 0.63 48.0 3.46e-01 97.1% 27.0%
2lqxA00 6.10.250.1700 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.63 48.0 4.62e-01 91.2% 82.9%
1k8kA04 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.62 46.0 3.41e-01 82.4% 31.5%
3k3wA02 1.10.287.150 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 44.0 4.56e-01 79.4% 96.7%
3kyzA00 3.30.450.170 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Two-component histidine kinase, sensor domain 0.61 48.0 3.57e-01 97.1% 29.5%
3no6A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.61 49.0 3.05e-01 100.0% 53.2%
2qr4A02 1.10.287.830 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › putative peptidase helix hairpin domain like 0.61 47.0 4.47e-01 100.0% 95.7%
3l0mA02 1.20.1280.280 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.60 52.0 4.01e-01 100.0% 69.2%
3u4qB04 6.10.140.1030 Special › Helix non-globular › Helix Hairpins › 0.59 48.0 3.91e-01 100.0% 46.4%
3vzbB02 2.60.200.40 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.50 41.0 2.58e-01 100.0% 82.7%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5072052 3718.1.1.0 alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT 0.89 78.0 6.27e-01 100.0% 52.3%
5077460 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.88 75.0 6.00e-01 100.0% 55.9%
4640528 4146.1.1.0 alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like 0.87 76.0 7.21e-01 100.0% 85.0%
4964847 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 0.86 72.0 6.70e-01 100.0% 84.4%
3280308 192.11.1.0 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB 0.85 75.0 7.44e-01 100.0% 97.1%
3778560 109.4.1.401 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › NRDE-2 0.83 71.0 3.86e-01 100.0% 5.8%
3703251 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.82 69.0 4.49e-01 97.1% 24.8%
3230775 192.1.1.25 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › VPS18_RING_C 0.81 70.0 4.87e-01 100.0% 30.9%
4179301 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.80 65.0 4.67e-01 100.0% 41.8%
3900350 7005.1.1.2 a+b duplicates or obligate multimers › LUBAC-tethering domain › LUBAC-tethering domain › LUBAC-tethering domain › LTM 0.79 62.0 5.74e-01 91.2% 68.9%
5073502 159.1.1.0 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 0.78 65.0 4.86e-01 100.0% 41.1%
3182754 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 0.76 60.0 5.39e-01 100.0% 67.3%
4973347 515.1.1.4 alpha arrays › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › EMC3_TMCO1 0.75 62.0 3.97e-01 100.0% 20.0%
4831662 5043.1.1.1 extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like › Htr2 0.74 57.0 4.90e-01 100.0% 51.5%
4178707 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 0.72 61.0 5.46e-01 100.0% 92.0%
3586047 2004.1.1.5 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.67 51.0 2.99e-01 100.0% 8.9%
3462586 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 0.66 52.0 4.83e-01 91.2% 73.3%
3612104 310.2.1.70 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › CBP110 0.65 52.0 3.46e-01 100.0% 21.8%
3193662 592.1.1.1 alpha arrays › PWI domain-like › PWI domain › PWI domain › PWI 0.63 55.0 4.17e-01 100.0% 50.0%
3798279 821.1.1.0 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.62 50.0 3.64e-01 94.1% 33.0%
3578019 821.1.1.8 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › ANKLE2_3rd 0.62 51.0 3.60e-01 94.1% 31.4%
3798777 592.1.1.0 alpha arrays › PWI domain-like › PWI domain › PWI domain 0.62 53.0 4.25e-01 100.0% 57.1%
3589429 4159.1.1.0 alpha arrays › SP0561-like › SP0561-like › SP0561-like 0.61 44.0 3.76e-01 94.1% 46.7%
4317833 2.1.1.264 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › BrxL_N 0.61 48.0 3.33e-01 97.1% 34.6%
3224794 150.5.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.59 44.0 3.65e-01 94.1% 100.0%