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NC_054965.1__YP_010078854.1__KMC53_gp39__00039

Bact-Vir

NC_054965.1__YP_010078854.1__KMC53_gp39__00039

Identity

Accession:
NC_054965 ↗
Kingdom:
phage

Quality

70.3 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 1-45
PDB
Domain cluster: representative
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.87 77.0 6.70e-01 100.0% 66.2%
3pvuA02 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.85 73.0 5.96e-01 95.6% 53.8%
1z72A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.85 74.0 4.69e-01 100.0% 21.8%
2o8pA00 1.20.190.20 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 14-3-3 domain 0.85 74.0 4.69e-01 100.0% 20.5%
1vjxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 75.0 5.14e-01 100.0% 31.5%
1dd9A03 1.20.50.20 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › DnaG, RNA polymerase domain, helical bundle 0.83 64.0 5.88e-01 84.4% 64.4%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.83 63.0 5.73e-01 84.4% 61.3%
3anwA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 69.0 5.23e-01 100.0% 42.5%
1fioA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 69.0 4.53e-01 100.0% 27.4%
4i43B02 3.30.43.40 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain 0.80 68.0 5.08e-01 97.8% 71.1%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 69.0 5.91e-01 100.0% 64.4%
3i9wA00 1.20.58.920 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 64.0 3.98e-01 100.0% 16.3%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.79 67.0 5.08e-01 100.0% 40.4%
3uumA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 68.0 4.98e-01 100.0% 39.3%
4r42A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.78 66.0 4.41e-01 100.0% 24.6%
7k3zG01 3.50.7.10 Alpha Beta › 3-Layer(bba) Sandwich › GroEL › GroEL 0.78 63.0 4.06e-01 100.0% 19.2%
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 0.78 67.0 6.29e-01 97.8% 81.8%
3m1cB01 3.30.390.170 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.78 57.0 4.38e-01 91.1% 33.9%
3zdmB00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.78 62.0 6.03e-01 91.1% 86.0%
4fxdA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.77 65.0 4.54e-01 100.0% 30.1%
3g3oA00 3.20.100.30 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › VTC, catalytic tunnel domain 0.77 63.0 3.85e-01 93.3% 17.1%
3rqtA02 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.77 62.0 3.91e-01 88.9% 87.3%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.77 66.0 5.39e-01 97.8% 52.9%
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.76 62.0 6.15e-01 95.6% 91.7%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 64.0 5.89e-01 100.0% 77.4%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.75 63.0 6.15e-01 100.0% 94.1%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.75 63.0 5.90e-01 100.0% 76.3%
7vevA01 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.75 64.0 3.98e-01 97.8% 89.1%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.74 60.0 5.80e-01 100.0% 80.4%
4dloB02 1.25.40.610 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.74 60.0 4.60e-01 97.8% 38.5%
1wrdA00 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 64.0 5.03e-01 100.0% 48.0%
1r4gA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.74 54.0 5.27e-01 100.0% 71.7%
2wzkA01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.74 62.0 4.59e-01 100.0% 66.1%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.74 62.0 5.36e-01 100.0% 62.7%
6epyA01 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.73 62.0 3.86e-01 97.8% 85.9%
2a26B01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.73 58.0 5.85e-01 91.1% 93.2%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 56.0 4.81e-01 93.3% 51.3%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.73 63.0 5.05e-01 100.0% 74.4%
2ib0A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 61.0 4.47e-01 100.0% 34.8%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.73 63.0 5.04e-01 100.0% 51.6%
1o9gA02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 57.0 5.84e-01 88.9% 97.7%
1tmxB00 2.60.130.10 Mainly Beta › Sandwich › Protocatechuate 3,4-Dioxygenase, subunit A › Aromatic compound dioxygenase 0.72 60.0 3.68e-01 95.6% 15.0%
2cazC00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 57.0 5.27e-01 100.0% 71.9%
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 57.0 5.09e-01 100.0% 62.5%
3no6A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.70 58.0 3.72e-01 97.8% 24.3%
4hb1A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.69 56.0 5.69e-01 95.6% 95.5%
1v0dA01 6.10.140.170 Special › Helix non-globular › Helix Hairpins › 0.69 50.0 4.89e-01 84.4% 73.5%
1vp7A00 1.10.287.1040 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Exonuclease VII, small subunit 0.68 58.0 5.15e-01 100.0% 66.2%
2hepA00 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.66 50.0 5.12e-01 100.0% 97.6%
4dooA01 3.50.70.10 Alpha Beta › 3-Layer(bba) Sandwich › Chalcone isomerase › 0.64 44.0 3.06e-01 73.3% 42.3%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.62 52.0 3.68e-01 91.1% 33.3%
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.60 52.0 5.25e-01 100.0% 100.0%
1go3F02 6.10.140.10 Special › Helix non-globular › Helix Hairpins › 0.57 39.0 3.93e-01 100.0% 68.1%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3811835 7076.1.1.0 0.90 80.0 7.01e-01 100.0% 67.7%
4944568 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 0.85 73.0 6.49e-01 97.8% 100.0%
3358885 604.12.1.8 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › KATNA1_MIT 0.84 74.0 6.09e-01 100.0% 57.5%
3369775 5076.2.1.10 alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › PF29520 0.84 71.0 4.33e-01 100.0% 20.7%
5053066 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.83 72.0 4.50e-01 100.0% 19.1%
4040184 605.1.1.4 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.83 71.0 6.97e-01 100.0% 96.0%
4954852 101.1.2.136 alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.83 72.0 4.80e-01 100.0% 26.0%
3219646 3826.1.1.0 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.83 71.0 6.74e-01 100.0% 85.5%
3414767 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.82 71.0 5.91e-01 100.0% 56.2%
3922888 109.4.1.889 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_M 0.82 72.0 4.59e-01 100.0% 22.0%
5015362 5076.2.1.3 alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › DUF4013 0.82 70.0 4.26e-01 100.0% 16.4%
4156333 109.4.1.206 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › YfiO 0.82 70.0 4.88e-01 100.0% 30.0%
3258150 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.82 64.0 6.72e-01 91.1% 100.0%
4945817 10.28.1.0 beta sandwiches › jelly-roll › Jelly-roll domain in Zinc finger protein ZPR1 › Jelly-roll domain in Zinc finger protein ZPR1 0.81 70.0 5.05e-01 100.0% 35.2%
4115372 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.81 71.0 5.34e-01 100.0% 42.7%
1389183 6161.1.1.1 a+b two layers › Uncharacterized virus protein A-100 › Uncharacterized virus protein A-100 › Uncharacterized virus protein A-100 › DUF5517 0.81 70.0 5.69e-01 100.0% 52.3%
3599922 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.80 71.0 4.17e-01 100.0% 13.4%
3638713 2003.1.2.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.80 69.0 3.90e-01 100.0% 9.2%
5048590 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.80 69.0 5.21e-01 100.0% 42.7%
3699985 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.80 69.0 4.09e-01 100.0% 13.8%
3956906 605.1.1.4 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.80 68.0 5.83e-01 100.0% 62.7%
3249106 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 0.80 69.0 6.70e-01 100.0% 90.0%
4154114 192.29.1.164 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › RRP36 0.79 67.0 4.87e-01 100.0% 33.8%
3504474 192.5.1.1 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.79 67.0 5.26e-01 100.0% 46.0%
3480097 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.78 67.0 5.90e-01 100.0% 67.1%
3879987 601.48.1.0 alpha bundles › Four-helical up-and-down bundle › vWA2 C-terminal domain › vWA2 C-terminal domain 0.78 63.0 5.64e-01 91.1% 66.2%
4598021 148.1.1.63 alpha arrays › Histone-like › Histone-related › Histone › RRP36 0.78 68.0 4.95e-01 100.0% 37.6%
4160609 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 0.78 66.0 6.49e-01 100.0% 90.0%
3385229 2003.1.9.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.78 67.0 3.94e-01 100.0% 12.3%
4667226 3877.1.1.1 alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC › 60KD_IMP 0.78 68.0 4.25e-01 97.8% 73.2%
4519110 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 0.78 66.0 6.46e-01 100.0% 89.8%
3253331 6132.1.1.0 alpha bundles › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain 0.78 66.0 5.83e-01 100.0% 67.1%
3570403 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.78 66.0 4.86e-01 100.0% 37.6%
3976663 3812.1.1.1 alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › T3SS_needle_E 0.78 65.0 5.89e-01 100.0% 70.8%
3724988 2004.1.1.184 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.78 66.0 3.89e-01 100.0% 12.2%
3692897 3922.1.1.0 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.77 65.0 5.64e-01 100.0% 61.3%
3394272 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.77 66.0 4.44e-01 100.0% 26.3%
3640083 2004.1.1.185 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11,AAA_12 0.77 65.0 3.89e-01 100.0% 13.4%
4127368 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 0.77 63.0 6.20e-01 100.0% 88.0%
3690329 2004.1.1.473 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ResIII, AAA_11 0.77 65.0 3.85e-01 100.0% 12.3%
3266812 3291.1.1.211 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › EMC3_TMCO1 0.77 65.0 4.48e-01 100.0% 29.4%
3565241 5.1.4.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.77 65.0 3.81e-01 100.0% 11.4%
1948638 4970.1.1.1 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_B 0.76 65.0 6.19e-01 100.0% 85.2%
3492118 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.76 64.0 4.01e-01 100.0% 18.1%
5081365 601.33.1.0 alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain 0.76 64.0 4.57e-01 100.0% 31.7%
4137062 507.1.1.1 alpha arrays › DnaB helicase N-terminal domain-related › DnaB helicase N-terminal domain-related › DnaB helicase N-terminal domain-related › DnaB 0.76 60.0 4.24e-01 91.1% 28.8%
3965569 150.1.1.183 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Transposase_20 0.75 63.0 4.28e-01 100.0% 26.1%
57654 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 64.0 6.08e-01 100.0% 85.2%
4568335 3812.1.1.8 alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › DUF5398 0.75 63.0 5.58e-01 100.0% 78.3%
2161989 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 0.74 62.0 6.18e-01 100.0% 93.6%
3290879 3922.1.1.155 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › DUF4349 0.74 63.0 5.52e-01 100.0% 67.1%
4041347 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.74 61.0 4.77e-01 100.0% 42.7%
4261003 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 0.74 60.0 6.02e-01 97.8% 95.6%
4419515 150.1.1.59 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Coat_F 0.74 63.0 5.28e-01 100.0% 58.7%
3503933 192.14.1.1 alpha bundles › Long alpha-hairpin › Siah interacting protein N terminal domain-like › Siah interacting protein N terminal domain-like › Siah-Interact_N 0.73 61.0 6.17e-01 100.0% 97.8%