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NC_054984.1__YP_010080184.1__KMC72_gp31__00031

Bact-Vir

NC_054984.1__YP_010080184.1__KMC72_gp31__00031

Identity

Accession:
NC_054984 ↗
Kingdom:
phage

Quality

88.2 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 8-62
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.96 87.0 8.06e-01 96.4% 94.0%
1oksA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.92 53.0 5.43e-01 72.7% 60.4%
6lumD01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.90 68.0 5.07e-01 80.0% 68.0%
4heoA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.88 55.0 5.54e-01 78.2% 63.6%
4fxdA06 1.10.132.60 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain 0.88 65.0 4.53e-01 78.2% 75.0%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.86 78.0 6.07e-01 98.2% 84.7%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.85 77.0 6.04e-01 98.2% 84.4%
4hfvA01 1.20.1440.330 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.85 62.0 4.81e-01 78.2% 36.8%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.83 62.0 4.82e-01 80.0% 38.8%
2lqxA00 6.10.250.1700 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.82 54.0 6.01e-01 72.7% 90.2%
4eqyA02 1.20.1180.10 Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain 0.82 54.0 5.00e-01 70.9% 54.3%
4l8iB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.81 72.0 5.66e-01 98.2% 83.9%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.81 70.0 5.73e-01 94.5% 83.5%
2au3A04 1.20.50.30 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › 0.79 58.0 5.82e-01 85.5% 78.2%
2qsbA00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.77 55.0 4.79e-01 78.2% 49.4%
2ynqB00 1.25.40.680 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type VII secretion system EssB, C-terminal-like domain 0.77 63.0 4.56e-01 89.1% 35.8%
1fkwA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.75 58.0 3.52e-01 83.6% 98.6%
7vkcA01 1.10.1070.20 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › 0.75 66.0 4.57e-01 94.5% 73.3%
3itfA00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.74 55.0 4.30e-01 78.2% 58.6%
4edgA03 1.20.50.20 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › DnaG, RNA polymerase domain, helical bundle 0.73 58.0 5.69e-01 87.3% 85.0%
1iurA01 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.73 63.0 6.09e-01 100.0% 92.1%
4zvaA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.72 64.0 4.65e-01 100.0% 87.2%
4rg8A04 1.10.287.1240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 49.0 4.79e-01 85.5% 64.5%
3cqcB01 1.20.58.1380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 60.0 5.12e-01 94.5% 61.1%
4ehsA00 1.10.860.10 Mainly Alpha › Orthogonal Bundle › DNAb Helicase; Chain A › DNAb Helicase; Chain A 0.71 60.0 4.51e-01 90.9% 72.6%
1rqgA02 2.170.220.10 Mainly Beta › Beta Complex › Methionyl-trna Synthetase; domain 2 › 0.71 47.0 3.42e-01 78.2% 24.7%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.69 56.0 4.97e-01 87.3% 74.0%
2qywA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.69 56.0 4.81e-01 94.5% 83.2%
3bkxA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.67 52.0 3.36e-01 87.3% 34.1%
4c0eA02 1.25.40.800 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.65 56.0 3.77e-01 100.0% 25.3%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 47.0 4.28e-01 90.9% 56.4%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 56.0 3.90e-01 98.2% 34.9%
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 0.65 49.0 5.32e-01 87.3% 100.0%
1lfkA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.64 52.0 3.27e-01 100.0% 33.6%
2wmmA01 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 0.63 47.0 4.99e-01 89.1% 91.8%
3msuB03 1.10.230.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450-Terp; domain 2 › Cytochrome P450-Terp, domain 2 0.63 51.0 4.18e-01 96.4% 100.0%
2rkkA01 1.25.40.270 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Vacuolar protein sorting-associated protein vta1 0.62 53.0 3.88e-01 98.2% 41.0%
1y79101 1.10.1370.40 Mainly Alpha › Orthogonal Bundle › Neurolysin; domain 3 › 0.61 52.0 3.14e-01 96.4% 19.5%
1v9dB00 1.20.58.2220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Formin, FH2 domain 0.61 54.0 3.30e-01 98.2% 46.4%
4o8uA00 3.30.420.440 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF4152 0.61 54.0 3.56e-01 100.0% 59.5%
3i2fA02 1.10.3020.10 Mainly Alpha › Orthogonal Bundle › alpha-amino acid ester hydrolase ( Helical cap domain) › alpha-amino acid ester hydrolase ( Helical cap domain) 0.59 47.0 3.97e-01 89.1% 90.5%
4gf0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 43.0 3.53e-01 81.8% 41.6%
3w1oA00 3.40.1760.20 Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical protein yfbM fold › 0.58 48.0 3.83e-01 92.7% 93.0%
1dj2A02 1.10.300.10 Mainly Alpha › Orthogonal Bundle › Adenylosuccinate Synthetase, subunit A; domain 2 › Adenylosuccinate Synthetase, subunit A, domain 2 0.55 46.0 3.93e-01 98.2% 91.9%
2va8A03 1.10.3380.30 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › 0.54 49.0 3.20e-01 98.2% 36.0%
4r16A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 42.0 3.05e-01 94.5% 28.6%
2y0eB03 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 41.0 2.87e-01 92.7% 23.3%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3751351 3796.1.1.0 alpha arrays › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain 0.90 71.0 6.60e-01 81.8% 69.2%
3230196 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.89 70.0 5.31e-01 83.6% 53.3%
3522359 639.2.1.0 alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) 0.88 67.0 6.75e-01 83.6% 80.0%
2625677 310.2.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.86 78.0 6.07e-01 98.2% 84.7%
4094836 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.86 78.0 5.27e-01 98.2% 90.6%
3270632 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.85 76.0 5.13e-01 98.2% 86.7%
4044098 3352.1.1.1 alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3 0.82 66.0 3.80e-01 85.5% 22.2%
1144608 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.82 74.0 5.70e-01 98.2% 82.5%
4253707 170.1.1.0 alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C 0.81 71.0 5.66e-01 96.4% 65.7%
3645559 650.1.1.1 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.80 74.0 6.17e-01 100.0% 68.9%
3379819 6164.1.1.4 alpha bundles › Bestrophin › Bestrophin › Bestrophin › Bestrophin_2 0.80 72.0 4.35e-01 100.0% 33.5%
4400236 170.1.1.0 alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C 0.80 70.0 5.58e-01 96.4% 65.7%
2849677 129.1.1.10 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › Mannitol_dh_C 0.80 67.0 4.70e-01 96.4% 32.2%
4812867 6164.1.1.4 alpha bundles › Bestrophin › Bestrophin › Bestrophin › Bestrophin_2 0.78 69.0 4.53e-01 100.0% 47.0%
1826909 396.2.1.1 few secondary structure elements › CCHC-type 1 zinc finger › Chromatin remodeling factor Mit1 C-terminal Zn fingers › Chromatin remodeling factor Mit1 C-terminal Zn fingers › zf-CCCH_6 0.78 57.0 5.77e-01 87.3% 78.2%
3634796 604.11.1.4 alpha bundles › Spectrin repeat-like › XseB-like › XseB-like › zf-CCCH_6 0.78 63.0 5.56e-01 98.2% 61.3%
3690358 109.6.1.2 alpha superhelices › Repetitive alpha hairpins › Ras GEF › Ras GEF › RasGEF,RasGEF_N 0.76 67.0 3.93e-01 98.2% 16.0%
4594465 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 0.76 69.0 5.67e-01 100.0% 81.1%
3596608 1134.1.1.0 alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.74 65.0 5.61e-01 98.2% 69.4%
3531403 3914.1.1.0 alpha bundles › TMEM16 lipid scramblase transmembrane domain › TMEM16 lipid scramblase transmembrane domain › TMEM16 lipid scramblase transmembrane domain 0.74 56.0 5.90e-01 87.3% 90.0%
3659127 2002.1.1.41 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › A_deaminase 0.74 64.0 3.88e-01 98.2% 94.9%
3498448 604.3.1.0 alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.73 65.0 5.74e-01 100.0% 86.3%
3389963 1134.1.1.0 alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.73 66.0 6.05e-01 100.0% 85.7%
4497642 150.1.2.20 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Heme oxygenase/Ribonucleotide reductase › Rubrerythrin 0.73 55.0 3.38e-01 81.8% 14.4%
3269094 1134.1.1.0 alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.73 60.0 5.87e-01 94.5% 83.3%
3505507 1134.1.1.0 alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.71 62.0 5.69e-01 96.4% 87.1%
3213165 198.1.1.0 alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.71 59.0 5.33e-01 98.2% 68.8%
3592737 1134.1.1.0 alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.71 60.0 5.74e-01 98.2% 81.5%
4597664 2002.1.1.41 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › A_deaminase 0.70 60.0 3.68e-01 96.4% 96.8%
5072863 2004.1.3.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.69 59.0 4.18e-01 100.0% 31.9%
3353941 1134.1.1.7 alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain › ALA1 0.69 58.0 5.55e-01 100.0% 81.5%
4600185 3602.1.1.15 alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › DUF444 0.69 53.0 4.74e-01 85.5% 60.0%
4180990 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.69 59.0 5.31e-01 100.0% 87.5%
3673509 4048.1.1.1 alpha bundles › Second alpha-helical domain in heme-dependent catalases › Second alpha-helical domain in heme-dependent catalases › Second alpha-helical domain in heme-dependent catalases › Catalase-rel 0.68 50.0 4.81e-01 90.9% 67.7%
4206596 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 0.68 51.0 5.57e-01 80.0% 100.0%
3607639 10.12.1.9 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › JmjC 0.66 59.0 3.54e-01 100.0% 25.6%
3387205 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 0.66 51.0 4.32e-01 92.7% 51.1%
4010384 361.1.1.0 few secondary structure elements › DnaJ/Hsp40 cysteine-rich domain › DnaJ/Hsp40 cysteine-rich domain › DnaJ/Hsp40 cysteine-rich domain 0.64 54.0 5.09e-01 92.7% 86.2%
3482349 604.12.1.2 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.63 53.0 5.03e-01 92.7% 83.1%
4033612 101.35.1.4 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.63 45.0 4.71e-01 87.3% 88.0%
3753969 622.4.1.0 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.62 51.0 4.23e-01 90.9% 80.0%
4034201 192.7.1.1 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › FemAB 0.61 50.0 4.89e-01 92.7% 83.3%
3501752 2007.2.3.2 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › DSPc 0.58 50.0 3.91e-01 98.2% 70.0%
4536901 563.1.1.1 alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.58 45.0 3.36e-01 94.5% 58.8%
5079633 7094.1.1.4 alpha bundles › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › PF27273 0.57 48.0 4.22e-01 100.0% 61.2%