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NC_055027.1__YP_010082124.1__KMD16_gp30__00030

Bact-Vir

NC_055027.1__YP_010082124.1__KMD16_gp30__00030

Identity

Accession:
NC_055027 ↗
Kingdom:
phage

Quality

56.3 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 medium residues 8-59
PDB
Domain cluster: representative
CATH (61)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.96 89.0 5.72e-01 98.1% 28.0%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.95 88.0 8.18e-01 98.1% 85.5%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.92 85.0 6.52e-01 100.0% 48.1%
1rq0A01 6.10.140.160 Special › Helix non-globular › Helix Hairpins › 0.91 83.0 7.00e-01 100.0% 68.7%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.89 79.0 7.64e-01 96.2% 89.7%
4adzA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.89 77.0 6.29e-01 94.2% 63.3%
2g2dA00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.88 78.0 5.33e-01 94.2% 31.9%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.88 76.0 6.38e-01 94.2% 63.5%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.88 81.0 7.49e-01 100.0% 84.4%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.87 74.0 6.54e-01 100.0% 65.8%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.87 78.0 7.26e-01 100.0% 79.7%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.86 77.0 6.37e-01 100.0% 58.2%
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 0.86 69.0 7.15e-01 86.5% 100.0%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.85 70.0 6.20e-01 92.3% 64.8%
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 0.84 66.0 6.79e-01 84.6% 88.0%
1t7sA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.84 74.0 5.51e-01 100.0% 52.7%
2itbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 74.0 4.95e-01 100.0% 27.3%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.84 73.0 6.35e-01 100.0% 79.0%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.83 72.0 6.67e-01 96.2% 87.7%
3pt1A02 1.20.930.60 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.83 76.0 5.68e-01 100.0% 47.5%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.83 64.0 5.34e-01 82.7% 87.2%
4aurA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.83 70.0 4.28e-01 100.0% 17.3%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.83 76.0 6.54e-01 100.0% 75.6%
3k29A00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.83 73.0 5.11e-01 100.0% 36.0%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.82 73.0 6.97e-01 100.0% 85.0%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.82 63.0 5.88e-01 86.5% 67.7%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.82 73.0 6.51e-01 98.1% 73.2%
7bi4A01 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.82 59.0 3.97e-01 84.6% 21.5%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.82 73.0 6.42e-01 98.1% 68.9%
3uumA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 72.0 5.45e-01 100.0% 44.3%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.81 70.0 6.36e-01 98.1% 84.5%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.81 71.0 6.77e-01 98.1% 90.2%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.81 69.0 5.71e-01 100.0% 58.2%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.81 69.0 5.21e-01 98.1% 50.0%
5dn6J00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.80 71.0 6.32e-01 100.0% 98.6%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.80 73.0 6.80e-01 100.0% 87.3%
3jcuZ00 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.80 70.0 6.65e-01 100.0% 83.6%
4jvyB00 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.80 62.0 4.11e-01 82.7% 88.4%
4asvA00 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 5.39e-01 88.5% 57.0%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.78 67.0 6.53e-01 100.0% 87.9%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.77 67.0 5.74e-01 100.0% 67.1%
4oe8C00 1.10.8.1170 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.75 65.0 5.50e-01 98.1% 63.2%
1bhaA00 1.10.287.170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.74 66.0 6.09e-01 100.0% 80.6%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 62.0 6.04e-01 100.0% 93.2%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.73 62.0 4.82e-01 94.2% 44.5%
2kkmA01 1.20.1440.170 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Translation machinery-associated protein 16-like 0.73 57.0 4.34e-01 86.5% 72.8%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.73 66.0 4.50e-01 100.0% 29.9%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.73 62.0 5.51e-01 100.0% 67.1%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 62.0 4.98e-01 100.0% 49.5%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 60.0 5.77e-01 98.1% 90.0%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.72 60.0 4.77e-01 100.0% 53.8%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.71 58.0 5.08e-01 100.0% 95.5%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 56.0 4.74e-01 100.0% 52.0%
8d8lN01 1.10.287.1480 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 57.0 4.88e-01 94.2% 61.6%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.68 56.0 4.38e-01 98.1% 44.6%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 53.0 4.85e-01 94.2% 64.5%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.66 55.0 5.53e-01 98.1% 96.2%
4mk3A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.66 53.0 4.31e-01 100.0% 47.0%
2jaeA03 1.20.1440.240 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.63 52.0 4.16e-01 90.4% 57.4%
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.61 46.0 4.85e-01 88.5% 97.9%
1yfmA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.54 41.0 3.32e-01 96.2% 38.1%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3218199 192.4.1.0 alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.98 93.0 7.45e-01 100.0% 60.0%
3623143 192.4.1.0 alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.97 92.0 7.56e-01 100.0% 63.5%
3671626 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.96 91.0 5.96e-01 100.0% 70.6%
3892002 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.96 90.0 6.15e-01 100.0% 34.8%
3594586 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.95 89.0 7.06e-01 100.0% 56.8%
3471215 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 0.95 89.0 7.69e-01 100.0% 72.0%
4949863 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 0.94 88.0 7.64e-01 100.0% 74.7%
3491738 632.8.1.0 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 0.94 88.0 6.89e-01 100.0% 57.6%
4576425 4207.1.1.112 alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › ING 0.94 90.0 6.73e-01 100.0% 49.1%
3223800 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 0.94 87.0 5.98e-01 100.0% 34.8%
3436926 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.94 85.0 7.44e-01 98.1% 71.6%
3740547 5086.1.1.87 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › ING 0.93 89.0 6.66e-01 100.0% 49.1%
3249849 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.93 86.0 6.56e-01 100.0% 49.1%
3705545 3755.4.1.0 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.93 86.0 5.73e-01 100.0% 32.6%
2456957 192.13.1.1 alpha bundles › Long alpha-hairpin › ISY1 N-terminal domain-like › ISY1 N-terminal domain-like › Isy1 0.91 80.0 7.82e-01 94.2% 91.1%
3192393 2004.1.1.430 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, ABC_tran_Xtn 0.91 84.0 4.65e-01 100.0% 8.8%
3962991 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.91 84.0 5.48e-01 100.0% 27.7%
3679373 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.90 83.0 7.60e-01 100.0% 87.7%
3626569 633.10.1.0 alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.89 80.0 5.62e-01 100.0% 34.8%
3725377 192.15.1.44 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › DUF6604 0.89 80.0 6.55e-01 98.1% 75.6%
3398320 632.7.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.88 79.0 7.10e-01 98.1% 72.9%
4146694 192.29.1.277 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Dynamitin 0.88 79.0 7.26e-01 98.1% 81.5%
4940797 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 0.87 79.0 6.61e-01 100.0% 63.5%
3783731 2004.1.1.505 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, AAA_30 0.86 80.0 4.60e-01 100.0% 12.6%
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 0.86 78.0 4.46e-01 100.0% 12.1%
5064396 2004.1.1.198 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.85 77.0 4.57e-01 100.0% 15.8%
4249161 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 0.85 75.0 6.99e-01 100.0% 83.1%
3276221 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.85 75.0 5.56e-01 100.0% 42.3%
4396464 605.1.1.305 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Exonuc_VII_S 0.84 70.0 6.65e-01 90.4% 81.7%
3988454 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 73.0 6.62e-01 100.0% 80.0%
4140524 604.11.1.1 alpha bundles › Spectrin repeat-like › XseB-like › XseB-like › Exonuc_VII_S 0.80 64.0 6.16e-01 88.5% 83.3%
4030667 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.80 68.0 5.69e-01 100.0% 55.6%
4971843 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.79 67.0 5.71e-01 100.0% 68.5%
3608012 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 5.63e-01 98.1% 80.0%
3869913 2004.1.1.442 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_21 0.77 67.0 3.92e-01 100.0% 12.4%
3607086 4992.1.1.0 extended segments › RelB-like › RelB-like › RelB-like 0.77 66.0 5.79e-01 100.0% 86.3%
4395939 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.76 65.0 4.20e-01 100.0% 21.2%
5070736 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.75 62.0 4.28e-01 100.0% 40.5%
4171766 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.71 59.0 5.09e-01 100.0% 62.2%
3973636 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.71 59.0 5.36e-01 100.0% 74.7%
3941960 5086.1.1.86 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_YBHG 0.70 58.0 4.55e-01 100.0% 44.8%
3473827 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.69 58.0 5.64e-01 100.0% 91.7%
3944323 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 55.0 4.61e-01 100.0% 88.0%