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NC_054716.1__YP_010057190.1__KHO59_gp005__00005

Bact-Vir

NC_054716.1__YP_010057190.1__KHO59_gp005__00005

Identity

Accession:
NC_054716 ↗
Kingdom:
phage

Quality

80.4 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 3-68
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1owaA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.90 76.0 6.40e-01 100.0% 56.6%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.85 73.0 6.40e-01 100.0% 64.3%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.84 75.0 7.09e-01 100.0% 91.0%
1qgtB00 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.83 73.0 5.59e-01 97.0% 45.5%
3ztaA00 1.10.490.130 Mainly Alpha › Orthogonal Bundle › Globin-like › 0.81 73.0 5.67e-01 100.0% 49.6%
3vuqB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.80 65.0 4.70e-01 89.4% 33.0%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.77 64.0 5.38e-01 90.9% 70.9%
1kmiZ02 1.10.287.500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.77 67.0 5.38e-01 100.0% 79.9%
3syvA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.77 67.0 4.55e-01 100.0% 34.3%
1jadA00 1.20.1230.10 Mainly Alpha › Up-down Bundle › Phospholipase C Beta; Chain: A › Phospholipase C beta, distal C-terminal domain 0.76 67.0 4.55e-01 100.0% 77.3%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 65.0 6.60e-01 98.5% 100.0%
2rbdA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.76 66.0 5.00e-01 95.5% 74.7%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.76 67.0 5.80e-01 100.0% 83.3%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.75 54.0 5.81e-01 77.3% 94.3%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 62.0 6.40e-01 98.5% 98.4%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.75 66.0 6.24e-01 100.0% 87.3%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.75 65.0 6.10e-01 98.5% 85.2%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.74 65.0 5.60e-01 100.0% 96.2%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.74 52.0 4.97e-01 77.3% 62.8%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.74 63.0 4.86e-01 100.0% 43.4%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 65.0 6.26e-01 100.0% 93.4%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 65.0 5.50e-01 100.0% 70.5%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.72 61.0 5.81e-01 97.0% 87.2%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 55.0 5.34e-01 100.0% 75.7%
4bpxD00 1.20.930.80 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.70 51.0 3.59e-01 78.8% 35.7%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 62.0 5.94e-01 100.0% 90.7%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.70 54.0 5.71e-01 86.4% 96.5%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.69 57.0 5.69e-01 92.4% 95.5%
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 0.69 48.0 5.51e-01 87.9% 98.0%
4g12A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.68 53.0 4.16e-01 86.4% 39.6%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 56.0 5.51e-01 92.4% 90.1%
2wauA01 1.20.1310.20 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Duffy-antigen binding domain 0.67 53.0 4.09e-01 87.9% 46.5%
2bnlC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.67 54.0 4.38e-01 90.9% 47.0%
1wpaA01 6.10.140.340 Special › Helix non-globular › Helix Hairpins › 0.67 59.0 5.22e-01 100.0% 93.9%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.67 52.0 5.35e-01 87.9% 93.4%
3rc3A05 1.20.58.1080 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 56.0 4.70e-01 100.0% 55.8%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 54.0 5.24e-01 98.5% 82.9%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.64 50.0 5.12e-01 86.4% 96.8%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.63 48.0 4.80e-01 84.8% 78.6%
3n98A01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.62 53.0 3.28e-01 97.0% 25.7%
6ofuA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.62 45.0 3.05e-01 78.8% 33.6%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 51.0 4.37e-01 100.0% 66.7%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3503176 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.89 82.0 6.14e-01 100.0% 46.0%
3616669 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.88 80.0 6.51e-01 100.0% 56.5%
3947564 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 0.87 73.0 7.41e-01 90.9% 93.8%
3990182 3922.1.1.226 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 › Fy-3 0.85 76.0 6.30e-01 100.0% 63.5%
3164684 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 0.83 72.0 5.80e-01 97.0% 51.2%
3984016 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.82 72.0 6.47e-01 98.5% 72.2%
3967123 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.81 66.0 6.25e-01 98.5% 73.8%
3851320 376.1.1.0 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.81 74.0 4.74e-01 100.0% 52.9%
5056427 3843.1.1.38 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › T4SS_pilin 0.79 69.0 5.89e-01 100.0% 60.9%
3957419 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.79 68.0 6.53e-01 97.0% 85.3%
3837404 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.78 69.0 5.51e-01 100.0% 50.8%
3253283 192.5.1.14 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.77 69.0 6.09e-01 100.0% 69.5%
3671258 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.77 67.0 5.45e-01 100.0% 53.8%
4645372 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 69.0 6.09e-01 100.0% 70.5%
5063166 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.77 68.0 5.84e-01 100.0% 66.7%
5048093 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.77 68.0 5.75e-01 100.0% 90.9%
3725261 4177.1.1.1 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.76 66.0 4.34e-01 100.0% 32.2%
3240682 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.76 69.0 5.77e-01 100.0% 66.4%
4045132 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.76 65.0 5.49e-01 100.0% 57.3%
4329615 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.76 63.0 6.26e-01 100.0% 88.6%
4937739 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.76 68.0 5.35e-01 100.0% 64.4%
5030302 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 0.76 66.0 5.85e-01 97.0% 67.4%
3376917 192.24.1.8 alpha bundles › Long alpha-hairpin › RPC62 helical hairpin domain › RPC62 helical hairpin domain › CDK5RAP3 0.75 68.0 6.34e-01 100.0% 81.2%
3339561 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.75 63.0 5.58e-01 97.0% 65.0%
5029642 5058.1.1.0 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.75 62.0 5.55e-01 93.9% 65.3%
3736652 192.29.1.102 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Fung_rhodopsin 0.75 61.0 5.75e-01 92.4% 75.0%
3971224 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.74 64.0 4.43e-01 97.0% 28.9%
4980095 310.2.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.74 64.0 5.59e-01 100.0% 64.8%
3971539 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 0.74 62.0 6.00e-01 97.0% 82.7%
3909017 192.5.1.1 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.74 65.0 5.89e-01 100.0% 78.9%
3415405 2004.1.1.87 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.74 64.0 3.88e-01 100.0% 20.0%
4042007 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.74 66.0 5.55e-01 100.0% 92.7%
3294437 5086.1.1.110 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HisKA 0.74 62.0 5.90e-01 97.0% 81.2%
3733140 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.73 63.0 4.88e-01 100.0% 43.9%
3231463 632.8.1.2 alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › Alpha-2-MRAP_C 0.73 62.0 5.50e-01 100.0% 65.3%
4349607 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 63.0 5.42e-01 100.0% 60.0%
3251379 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.73 62.0 5.75e-01 95.5% 74.1%
2055367 650.1.1.3 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › HsbA 0.73 58.0 5.80e-01 95.5% 85.7%
4250162 3755.4.1.0 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.73 62.0 5.04e-01 100.0% 57.0%
4947351 601.33.1.0 alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain 0.72 64.0 4.67e-01 100.0% 42.9%
3781350 5041.1.1.20 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › PF26669 0.71 63.0 5.17e-01 98.5% 62.5%
3969538 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 0.71 54.0 5.76e-01 83.3% 100.0%
3646011 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 0.71 57.0 5.65e-01 89.4% 85.7%
4883924 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.70 56.0 5.32e-01 93.9% 75.0%
3586032 605.1.1.237 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Patched 0.70 60.0 5.21e-01 98.5% 63.8%
4021036 3826.1.1.0 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.69 58.0 5.10e-01 95.5% 71.0%
4940229 2004.1.1.87 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.69 59.0 3.73e-01 100.0% 18.1%
3530949 3291.1.1.231 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › PF27745 0.69 60.0 4.66e-01 100.0% 47.3%
3573038 4207.1.1.99 alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › PF28139 0.67 55.0 5.03e-01 100.0% 68.9%
3588172 10.12.1.0 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.67 57.0 4.46e-01 98.5% 72.0%
3189791 601.19.1.18 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Mmc1_C 0.65 54.0 3.86e-01 100.0% 29.1%
3858340 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.63 54.0 4.31e-01 100.0% 54.3%