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MN364664.1__QFP93273.1__Xoosp15_8__00008

Bact-Vir

MN364664.1__QFP93273.1__Xoosp15_8__00008

Identity

Accession:
MN364664 ↗
Kingdom:
phage

Quality

76.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Caeruleovirus› Xanthomonas_phage_Xoo-sp15

TaxID: 2608370

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 3-64
PDB
Domain cluster: representative
CATH (56)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.85 71.0 6.83e-01 88.7% 79.7%
3hiuD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 67.0 4.94e-01 85.5% 42.8%
3uo2B02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.84 65.0 5.88e-01 88.7% 61.9%
1nfvA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 66.0 4.76e-01 85.5% 36.7%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.83 69.0 6.86e-01 88.7% 100.0%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.83 72.0 5.31e-01 93.5% 84.6%
2fb5A01 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.82 68.0 6.43e-01 88.7% 76.4%
3sjqC00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.82 67.0 6.15e-01 88.7% 72.5%
2etnB01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.81 71.0 6.57e-01 93.5% 77.6%
3jcuZ00 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.81 61.0 6.19e-01 88.7% 82.0%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.81 67.0 6.20e-01 88.7% 94.9%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 70.0 6.58e-01 93.5% 91.8%
6h9xA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.80 71.0 5.89e-01 95.2% 67.6%
1rv2D04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.80 61.0 5.89e-01 82.3% 92.9%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 66.0 5.44e-01 90.3% 86.0%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.79 61.0 6.10e-01 88.7% 81.2%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.79 65.0 5.07e-01 88.7% 79.0%
1x0tA01 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 58.0 5.90e-01 85.5% 80.3%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.78 58.0 5.81e-01 88.7% 78.1%
4xpwA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.77 62.0 4.86e-01 88.7% 42.0%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.76 61.0 5.41e-01 88.7% 67.8%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 66.0 5.56e-01 96.8% 90.2%
3ehfD01 1.20.5.1930 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.75 61.0 6.11e-01 88.7% 87.3%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.75 60.0 5.61e-01 88.7% 72.7%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 59.0 5.46e-01 88.7% 67.9%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.74 67.0 6.00e-01 100.0% 94.1%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 59.0 5.63e-01 88.7% 86.3%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.74 63.0 5.35e-01 100.0% 57.8%
1op1A00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.74 59.0 5.39e-01 98.4% 67.1%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.74 62.0 5.28e-01 91.9% 77.3%
1vx7301 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 60.0 5.71e-01 93.5% 77.0%
5dn6J00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.72 53.0 5.02e-01 79.0% 100.0%
1jalA03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.72 53.0 4.92e-01 82.3% 61.7%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.72 64.0 5.94e-01 100.0% 78.2%
1quuA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 56.0 4.56e-01 88.7% 44.4%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.71 59.0 5.40e-01 93.5% 70.4%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.71 60.0 5.11e-01 95.2% 66.7%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 57.0 5.47e-01 91.9% 97.2%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.70 58.0 4.19e-01 93.5% 39.4%
3t98B00 6.10.140.1350 Special › Helix non-globular › Helix Hairpins › 0.69 61.0 5.49e-01 100.0% 84.9%
2a2cA03 1.20.1440.340 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.69 53.0 4.20e-01 87.1% 62.3%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.69 57.0 4.59e-01 90.3% 80.3%
6vudA01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.69 53.0 4.38e-01 82.3% 49.5%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.67 51.0 4.87e-01 82.3% 73.0%
4finB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.66 47.0 3.10e-01 90.3% 17.3%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.66 52.0 5.36e-01 90.3% 98.3%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 51.0 4.88e-01 90.3% 74.4%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.65 48.0 4.91e-01 88.7% 86.4%
4kn7D01 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.64 53.0 4.20e-01 93.5% 96.2%
2o5iN07 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.64 53.0 4.38e-01 93.5% 92.2%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.64 51.0 5.11e-01 95.2% 87.7%
2e62A01 6.10.140.420 Special › Helix non-globular › Helix Hairpins › 0.61 46.0 5.02e-01 80.6% 96.2%
1wpbG01 1.10.287.680 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.61 39.0 4.06e-01 79.0% 74.1%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.56 48.0 4.46e-01 98.4% 75.9%
1vibA00 1.10.287.120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Neurotoxin B-IV-like 0.55 41.0 4.25e-01 85.5% 92.7%
2x6hA03 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.54 46.0 3.27e-01 98.4% 92.5%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3735607 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.87 73.0 6.58e-01 88.7% 75.0%
3363051 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.86 70.0 6.11e-01 88.7% 60.0%
4275409 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.85 70.0 5.69e-01 88.7% 61.8%
3292032 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.84 70.0 5.69e-01 88.7% 52.7%
4025445 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.84 69.0 5.76e-01 88.7% 54.0%
3595968 605.2.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 0.84 69.0 6.25e-01 88.7% 67.5%
5056100 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.84 69.0 6.49e-01 88.7% 86.7%
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 0.84 68.0 4.76e-01 88.7% 30.0%
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 0.83 69.0 5.67e-01 88.7% 54.3%
3468553 328.7.1.0 ↗ a+b two layers › IF3-like › Smr domain › Smr domain 0.83 68.0 4.99e-01 88.7% 35.9%
3930829 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.83 68.0 6.37e-01 88.7% 86.7%
4315986 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.82 68.0 5.94e-01 88.7% 80.0%
4619538 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.82 68.0 5.44e-01 88.7% 49.6%
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 0.82 67.0 5.55e-01 88.7% 53.3%
4206858 4992.1.1.23 ↗ extended segments › RelB-like › RelB-like › RelB-like › Seryl_tRNA_N 0.82 68.0 5.41e-01 88.7% 49.6%
5079947 4323.1.1.0 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C 0.82 66.0 5.04e-01 88.7% 40.0%
5059270 4323.1.1.0 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C 0.82 72.0 5.55e-01 95.2% 46.4%
3554799 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.82 71.0 5.50e-01 93.5% 46.4%
3742112 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.81 71.0 5.79e-01 91.9% 78.8%
4214525 632.22.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.80 66.0 5.55e-01 88.7% 55.0%
3615244 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.80 69.0 5.00e-01 93.5% 36.9%
4857117 632.8.1.1 ↗ 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_N 0.80 61.0 5.88e-01 87.1% 72.2%
3703141 109.4.1.3264 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Flagellar_rod 0.80 72.0 4.83e-01 100.0% 76.9%
3231045 101.1.1.117 ↗ alpha arrays › HTH › HTH › Three-helical HTH › CHDCT2 0.79 65.0 5.44e-01 90.3% 58.1%
3298167 5086.1.1.62 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › XH 0.78 69.0 5.16e-01 95.2% 46.4%
3991599 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.78 63.0 5.37e-01 88.7% 61.0%
4989575 2004.1.1.29 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD 0.78 67.0 3.75e-01 95.2% 8.9%
4406905 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 0.78 62.0 6.01e-01 88.7% 77.1%
3808476 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 0.78 60.0 5.75e-01 88.7% 72.9%
4051951 605.2.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 0.77 61.0 5.45e-01 88.7% 73.3%
3269863 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.76 56.0 3.41e-01 79.0% 13.4%
3601441 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.76 67.0 5.66e-01 96.8% 70.0%
3309583 604.12.1.65 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT_ATG1 0.74 62.0 5.69e-01 91.9% 77.5%
3167271 192.8.1.385 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Med11 0.74 58.0 5.42e-01 88.7% 68.8%
4447644 2004.1.1.514 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23, AAA_29, SbcC_Walker_B 0.73 66.0 3.97e-01 100.0% 24.1%
3282651 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 0.73 60.0 3.48e-01 88.7% 11.2%
4106620 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 0.72 57.0 5.37e-01 88.7% 72.0%
3486312 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.72 58.0 4.68e-01 88.7% 47.1%
3725377 192.15.1.44 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › DUF6604 0.72 58.0 5.14e-01 90.3% 70.0%
3264853 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.71 59.0 4.65e-01 93.5% 72.6%
3691750 376.1.1.8 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › U-box 0.71 54.0 4.07e-01 82.3% 36.2%
4401282 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.71 57.0 4.67e-01 88.7% 48.7%
3927738 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 0.70 55.0 4.88e-01 88.7% 57.9%
3976071 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.70 51.0 4.44e-01 80.6% 52.2%
3417475 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 0.68 54.0 3.26e-01 88.7% 13.3%
5076400 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 0.68 55.0 4.73e-01 87.1% 56.8%
4505260 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.64 55.0 3.99e-01 100.0% 37.3%