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NC_041872.1__YP_009594061.1__FDG89_gp05__00005

Bact-Vir

NC_041872.1__YP_009594061.1__FDG89_gp05__00005

Identity

Accession:
NC_041872 ↗
Kingdom:
phage

Quality

91.2 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 63-105
PDB
Domain cluster: representative
CATH (64)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.96 88.0 6.25e-01 100.0% 37.7%
4in3B00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.92 84.0 4.60e-01 100.0% 7.3%
5mdtA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.92 74.0 4.95e-01 95.3% 25.0%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.90 82.0 6.41e-01 100.0% 69.8%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.90 79.0 7.11e-01 100.0% 71.9%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.90 75.0 6.54e-01 90.7% 64.5%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.89 80.0 7.11e-01 100.0% 73.3%
3fp3A01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.86 74.0 5.11e-01 97.7% 30.4%
1yfmA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.86 68.0 4.85e-01 90.7% 30.2%
3kd3A02 1.10.150.210 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Phosphoserine phosphatase; domain 2 0.85 65.0 5.82e-01 86.0% 60.0%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.84 71.0 6.14e-01 100.0% 61.5%
2zttA00 6.10.140.720 Special › Helix non-globular › Helix Hairpins › 0.84 72.0 6.06e-01 100.0% 57.5%
5c8aA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.84 70.0 5.85e-01 97.7% 55.1%
4ehsA00 1.10.860.10 Mainly Alpha › Orthogonal Bundle › DNAb Helicase; Chain A › DNAb Helicase; Chain A 0.83 67.0 4.81e-01 100.0% 31.5%
1wpbG01 1.10.287.680 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.83 62.0 5.78e-01 81.4% 64.8%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 65.0 4.91e-01 88.4% 39.2%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.82 69.0 6.13e-01 97.7% 93.8%
2c5iT00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 71.0 5.53e-01 100.0% 58.5%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.81 71.0 5.25e-01 100.0% 77.1%
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 0.80 65.0 6.20e-01 90.7% 82.0%
1cunA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 68.0 5.19e-01 100.0% 43.1%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.78 66.0 5.38e-01 100.0% 50.6%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.78 60.0 4.97e-01 86.0% 48.0%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.78 67.0 5.09e-01 100.0% 41.9%
5t1dB00 3.10.390.20 Alpha Beta › Roll › SAND domain › Viral glycoprotein L 0.78 64.0 4.89e-01 100.0% 40.4%
1zmbA02 6.10.170.10 Special › Helix non-globular › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.77 58.0 6.21e-01 86.0% 100.0%
3dmqA08 6.10.140.1500 Special › Helix non-globular › Helix Hairpins › 0.77 63.0 5.28e-01 100.0% 52.5%
1t7lB01 3.20.20.210 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.76 65.0 3.79e-01 100.0% 87.6%
2jaeA03 1.20.1440.240 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.76 67.0 5.06e-01 100.0% 49.5%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.75 65.0 4.76e-01 100.0% 76.9%
4cpgA00 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 0.75 61.0 5.27e-01 93.0% 60.9%
1y74A00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.75 65.0 5.97e-01 100.0% 80.7%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.75 62.0 5.79e-01 100.0% 75.9%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.75 60.0 5.13e-01 100.0% 54.3%
2o5iN07 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.74 65.0 4.80e-01 100.0% 37.9%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 57.0 5.03e-01 100.0% 56.3%
7ymiD01 1.20.85.10 Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like 0.74 60.0 4.08e-01 100.0% 52.2%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.74 58.0 5.48e-01 90.7% 79.2%
3g3oA00 3.20.100.30 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › VTC, catalytic tunnel domain 0.73 63.0 3.84e-01 100.0% 17.1%
2qkdA02 2.60.120.1040 Mainly Beta › Sandwich › Jelly Rolls › ZPR1, A/B domain 0.73 57.0 4.09e-01 100.0% 28.6%
1uddA00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.73 61.0 3.95e-01 100.0% 50.7%
2yf4F00 1.10.3420.10 Mainly Alpha › Orthogonal Bundle › putative ntp pyrophosphohydrolase like fold › putative ntp pyrophosphohydrolase like domain 0.71 59.0 4.22e-01 100.0% 30.8%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.71 63.0 4.62e-01 100.0% 77.5%
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 0.70 54.0 4.66e-01 93.0% 51.9%
4k7cA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.70 59.0 3.47e-01 100.0% 11.2%
2j5iA02 6.10.250.2850 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.70 53.0 5.60e-01 93.0% 94.7%
6t0bc01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 58.0 4.91e-01 100.0% 56.4%
4od8D00 6.10.140.1880 Special › Helix non-globular › Helix Hairpins › 0.70 54.0 5.17e-01 95.3% 74.5%
2cr7A01 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.69 51.0 4.68e-01 88.4% 58.7%
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 56.0 5.45e-01 97.7% 85.7%
1rsoB00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.69 58.0 5.38e-01 97.7% 75.0%
2fe1A00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.69 54.0 3.95e-01 93.0% 56.2%
3bemB00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.68 55.0 3.64e-01 97.7% 42.6%
3sllA02 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 0.68 56.0 5.15e-01 100.0% 98.4%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.67 58.0 4.20e-01 100.0% 61.9%
3iylU02 1.10.287.1520 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.67 57.0 5.34e-01 97.7% 79.2%
1vfrA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.65 52.0 3.35e-01 90.7% 54.4%
2x0qA04 1.10.510.40 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › 0.64 52.0 3.50e-01 100.0% 63.9%
6dv2G02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.64 52.0 3.51e-01 100.0% 38.0%
3qxzA02 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 0.63 53.0 4.85e-01 100.0% 95.0%
4jylA02 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 0.63 51.0 4.98e-01 100.0% 83.7%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.62 47.0 4.17e-01 86.0% 91.0%
2r18A02 1.10.8.880 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Birnavirus VP3 protein, domain 2 0.60 45.0 4.16e-01 86.0% 62.7%
2kkmA01 1.20.1440.170 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Translation machinery-associated protein 16-like 0.59 47.0 3.61e-01 100.0% 60.8%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5051746 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.98 91.0 7.19e-01 100.0% 53.8%
5054079 192.4.1.0 alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.97 90.0 7.08e-01 100.0% 53.8%
4971500 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.96 89.0 6.22e-01 100.0% 35.8%
4971062 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.96 88.0 6.85e-01 100.0% 50.6%
3555742 103.1.1.0 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.95 88.0 6.81e-01 100.0% 56.5%
3931480 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.95 87.0 6.66e-01 100.0% 47.8%
4948496 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 85.0 6.08e-01 100.0% 38.2%
5065070 192.15.1.3 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Vps23_core 0.94 84.0 7.23e-01 97.7% 64.6%
4947371 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.94 86.0 6.06e-01 100.0% 35.8%
3511354 4146.1.1.0 alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like 0.94 73.0 7.60e-01 83.7% 90.0%
3486312 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.94 85.0 6.01e-01 100.0% 36.1%
4008053 4168.1.1.7 alpha duplicates or obligate multimers › HAMP domain › HAMP domain › HAMP domain › PF26769 0.93 84.0 5.49e-01 100.0% 26.7%
5043437 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.93 84.0 6.17e-01 100.0% 41.0%
4945691 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.93 84.0 6.70e-01 100.0% 53.8%
5029911 604.3.1.0 alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.92 79.0 7.01e-01 93.0% 67.8%
4220406 375.1.9.14 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase › GvpG 0.92 83.0 7.03e-01 100.0% 64.7%
3377698 192.15.1.2 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Mod_r 0.92 82.0 5.99e-01 100.0% 39.1%
3438984 192.15.1.176 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Cornichon 0.91 81.0 6.45e-01 100.0% 51.8%
5036455 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 0.90 79.0 4.67e-01 97.7% 14.8%
3355246 192.1.1.0 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.90 80.0 6.45e-01 100.0% 53.8%
3783055 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.90 81.0 5.88e-01 100.0% 40.0%
4946898 375.1.9.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase 0.88 80.0 6.56e-01 100.0% 57.3%
3725377 192.15.1.44 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › DUF6604 0.83 72.0 5.71e-01 100.0% 50.0%
3337903 108.1.1.23 alpha arrays › EF-hand › EF-hand-related › EF-hand › RST 0.81 63.0 5.52e-01 86.0% 56.9%
3821967 509.1.1.1 alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.81 63.0 5.27e-01 88.4% 49.3%
4641055 2004.1.1.6 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran,oligo_HPY 0.79 69.0 3.97e-01 100.0% 11.8%
2772104 103.1.1.13 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RNA_pol_Rpo13 0.78 63.0 6.31e-01 93.0% 93.2%
5013989 5069.1.3.0 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.77 65.0 5.08e-01 100.0% 44.9%
3769584 4146.1.1.4 alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like › FAM216B 0.77 62.0 5.09e-01 97.7% 48.8%
3218210 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 0.74 63.0 3.85e-01 100.0% 15.7%
3720672 109.4.1.1591 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U-box 0.74 64.0 3.91e-01 100.0% 15.7%
3691750 376.1.1.8 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › U-box 0.74 65.0 4.45e-01 100.0% 29.5%
4227989 604.9.1.1 alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.73 63.0 5.04e-01 100.0% 57.3%
4934254 2006.1.4.2 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.73 61.0 4.32e-01 97.7% 56.8%
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 0.73 58.0 4.56e-01 90.7% 44.2%
4996648 2006.1.4.2 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.72 61.0 4.13e-01 97.7% 49.1%
4012698 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.71 58.0 4.52e-01 95.3% 61.0%
3386456 3718.1.1.0 alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT 0.71 59.0 4.90e-01 97.7% 72.5%
4076608 109.4.1.924 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_CcmH_CycH 0.70 59.0 3.58e-01 100.0% 14.9%
3988447 5043.1.1.0 extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like 0.66 55.0 5.21e-01 100.0% 81.8%