Back to structures

BML_coassembly_scaffold_69_prodigal-single.1__X__X__00392

Bact-Vir

BML_coassembly_scaffold_69_prodigal-single.1__X__X__00392

Identity

Kingdom:
phage

Quality

90.0 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 1-52
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23987.2 best Phage_holin_10 53.3 3.10e-14 96.2% 94.2%
CATH (60)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.85 67.0 5.63e-01 86.5% 52.4%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.83 67.0 5.53e-01 92.3% 51.1%
3bjbD00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.83 67.0 4.62e-01 92.3% 27.0%
4aq4A02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.82 69.0 4.53e-01 96.2% 22.7%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.82 65.0 5.36e-01 94.2% 49.5%
3qnmA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.81 64.0 5.31e-01 88.5% 50.0%
3r0qA02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.80 72.0 4.71e-01 100.0% 91.8%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.78 69.0 6.14e-01 100.0% 70.3%
4k08A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.76 65.0 4.68e-01 94.2% 34.7%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.75 58.0 5.13e-01 86.5% 58.2%
3ilxA02 1.10.287.2170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.74 55.0 5.92e-01 84.6% 93.2%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.74 58.0 4.55e-01 88.5% 41.9%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.73 64.0 5.46e-01 100.0% 62.4%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.73 56.0 4.52e-01 86.5% 44.8%
3uo2B02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.72 56.0 4.73e-01 84.6% 51.2%
2gs4A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.71 61.0 4.37e-01 98.1% 72.8%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.71 59.0 5.14e-01 90.4% 66.2%
3agtA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.71 63.0 4.65e-01 100.0% 42.9%
2a2cA03 1.20.1440.340 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.71 59.0 4.30e-01 92.3% 34.8%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.70 59.0 5.28e-01 100.0% 73.1%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.70 51.0 4.61e-01 76.9% 60.6%
1cunA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 57.0 4.53e-01 90.4% 45.1%
4xpwA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.70 63.0 4.63e-01 100.0% 44.3%
3l1nA01 6.10.140.790 Special › Helix non-globular › Helix Hairpins › 0.69 57.0 5.82e-01 92.3% 100.0%
2rklF00 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 53.0 5.38e-01 86.5% 84.6%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 57.0 5.18e-01 92.3% 68.1%
1tjoB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.68 56.0 3.84e-01 92.3% 26.9%
5jc3A02 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.68 57.0 4.33e-01 96.2% 41.3%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.68 48.0 4.58e-01 78.8% 62.9%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.68 56.0 4.19e-01 92.3% 37.9%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.67 55.0 3.96e-01 92.3% 31.5%
4bpxD00 1.20.930.80 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.67 49.0 3.25e-01 78.8% 19.2%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.67 53.0 4.57e-01 98.1% 55.4%
1u5pA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 56.0 4.37e-01 96.2% 44.4%
2mpnA00 6.10.140.1340 Special › Helix non-globular › Helix Hairpins › 0.66 53.0 5.00e-01 98.1% 77.9%
1j30A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.66 53.0 3.92e-01 92.3% 33.3%
1op1A00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.66 53.0 4.67e-01 92.3% 59.8%
1ufhA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.65 51.0 3.78e-01 94.2% 31.0%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.64 49.0 4.64e-01 84.6% 69.4%
2e62A01 6.10.140.420 Special › Helix non-globular › Helix Hairpins › 0.64 49.0 4.91e-01 94.2% 96.2%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.64 52.0 4.22e-01 92.3% 73.5%
3c8tA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.63 54.0 4.43e-01 96.2% 56.7%
2i7uA00 6.10.250.1010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.63 52.0 5.05e-01 100.0% 96.8%
2kp8A00 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.63 54.0 4.91e-01 100.0% 77.8%
1aj3A00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 51.0 4.33e-01 100.0% 54.1%
2e9xA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 54.0 4.01e-01 100.0% 39.1%
4ap9A02 1.10.150.210 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Phosphoserine phosphatase; domain 2 0.62 43.0 4.12e-01 78.8% 63.3%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 54.0 4.84e-01 98.1% 84.9%
1hr5A00 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 0.61 49.0 5.04e-01 98.1% 97.9%
2chpA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.61 53.0 3.85e-01 100.0% 65.5%
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.60 55.0 4.83e-01 100.0% 75.7%
1vq8V00 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 53.0 4.93e-01 100.0% 78.5%
1vh6A01 6.10.140.1940 Special › Helix non-globular › Helix Hairpins › 0.60 52.0 4.20e-01 96.2% 92.8%
1pd3A00 1.10.287.230 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 49.0 4.89e-01 100.0% 92.6%
1p49A02 1.10.287.550 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.59 54.0 5.14e-01 100.0% 96.6%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.59 51.0 4.76e-01 96.2% 76.9%
2b3tB01 6.10.140.1980 Special › Helix non-globular › Helix Hairpins › 0.57 45.0 4.29e-01 90.4% 92.3%
4q5qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 50.0 3.86e-01 94.2% 60.0%
1b48A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.56 46.0 3.79e-01 100.0% 51.4%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.54 42.0 3.62e-01 98.1% 56.6%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3446460 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 0.88 79.0 4.68e-01 100.0% 14.6%
4936252 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 0.87 78.0 6.33e-01 100.0% 54.7%
4478129 166.1.1.1 alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.83 67.0 5.55e-01 88.5% 51.1%
4024271 3871.1.1.1 alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.82 70.0 5.19e-01 100.0% 37.8%
4142372 2006.1.1.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.81 72.0 4.66e-01 100.0% 23.1%
1676535 3989.1.1.1 alpha arrays › SidC C-terminal domain › SidC C-terminal domain › SidC C-terminal domain › SidC_C 0.80 59.0 4.42e-01 82.7% 33.3%
2674763 5041.1.1.1 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.79 69.0 6.14e-01 100.0% 69.3%
4333013 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.78 68.0 5.93e-01 100.0% 70.0%
4149728 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.78 68.0 5.95e-01 100.0% 70.0%
3740910 1008.1.1.0 alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain 0.78 66.0 6.55e-01 100.0% 94.5%
3971072 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 0.76 65.0 5.44e-01 100.0% 60.0%
4180835 5041.1.1.1 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.76 66.0 6.06e-01 100.0% 75.7%
3610088 5086.1.1.105 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › Flagellar_rod 0.75 58.0 3.93e-01 84.6% 23.9%
5039692 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 0.75 62.0 5.26e-01 100.0% 54.7%
3993361 622.4.1.41 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › DUF7753 0.75 63.0 5.97e-01 100.0% 87.7%
3561370 106.1.1.10 alpha arrays › Globin-like › Globin-like › Globin-like › BCD_RFX 0.74 66.0 4.82e-01 100.0% 37.1%
4860885 633.6.1.6 alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACAD9-ACADV_C 0.74 59.0 4.58e-01 84.6% 43.8%
3988447 5043.1.1.0 extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like 0.74 60.0 5.99e-01 98.1% 92.7%
4275409 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 55.0 4.26e-01 80.8% 38.2%
3589830 5043.2.1.8 extended segments › Sensor proteins transmembrane domains › NarQ transmembrane domain › NarQ transmembrane domain › DUF5592 0.73 63.0 5.76e-01 100.0% 80.0%
4401282 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.72 57.0 4.33e-01 84.6% 40.0%
4940986 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 0.71 60.0 5.05e-01 100.0% 58.9%
4942772 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 55.0 5.13e-01 84.6% 70.8%
3520403 633.6.1.6 alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACAD9-ACADV_C 0.71 60.0 4.69e-01 92.3% 46.7%
4975050 3843.1.1.0 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.68 55.0 4.89e-01 90.4% 61.3%
3697800 3559.1.1.0 a+b complex topology › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 0.68 57.0 4.38e-01 92.3% 42.6%
3725506 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 0.68 57.0 4.41e-01 92.3% 44.5%
5066847 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 55.0 4.56e-01 94.2% 51.1%
3503989 162.1.1.1 alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.67 57.0 4.68e-01 96.2% 55.8%
3967901 192.15.1.91 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › COX4_pro 0.65 57.0 4.79e-01 100.0% 63.3%
4618805 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 0.65 57.0 5.66e-01 98.1% 90.9%
3504889 604.22.1.1 alpha bundles › Spectrin repeat-like › tubulin binding cofactor C N-terminal domain › tubulin binding cofactor C N-terminal domain › TBCC_N 0.65 57.0 4.82e-01 98.1% 62.4%
4459223 605.1.1.162 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › COX4_pro 0.65 53.0 4.36e-01 100.0% 50.5%
3583102 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.64 51.0 4.54e-01 96.2% 58.7%
3214189 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.63 57.0 4.49e-01 100.0% 50.5%
3625492 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.63 54.0 3.83e-01 98.1% 33.1%
4522608 3812.1.1.15 alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › COX4_pro 0.61 53.0 4.46e-01 98.1% 64.4%
4005270 3718.1.1.15 alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT › COX4_pro 0.61 49.0 4.26e-01 100.0% 65.3%
5077460 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.60 53.0 4.83e-01 98.1% 77.9%
4025 150.5.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.54 42.0 3.62e-01 98.1% 56.6%