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SR-VP_0-2_scaffold_141_316084_prodigal-single.1__X__X__00031

Bact-Vir

SR-VP_0-2_scaffold_141_316084_prodigal-single.1__X__X__00031

Identity

Kingdom:
phage

Quality

76.9 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 13-75
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.89 76.0 7.28e-01 100.0% 80.6%
2rdcA00 1.10.287.800 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › protein ne1242 0.89 81.0 6.19e-01 100.0% 46.6%
3nyjA00 1.20.120.770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Amyloid precursor protein, E2 domain 0.88 78.0 5.51e-01 100.0% 33.7%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.84 67.0 5.46e-01 98.4% 47.4%
6lumD01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.81 65.0 5.15e-01 87.3% 48.0%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 66.0 6.32e-01 98.4% 78.1%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.78 72.0 6.34e-01 100.0% 78.4%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.78 69.0 6.21e-01 98.4% 72.1%
2e87A01 1.20.120.1190 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.77 67.0 5.05e-01 100.0% 40.0%
3rx6A00 1.20.58.1090 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phage polarity suppression protein monomer 0.77 68.0 4.76e-01 96.8% 97.3%
4iloA00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.77 70.0 4.65e-01 100.0% 70.8%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.76 67.0 6.27e-01 98.4% 84.4%
4mh6A00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 68.0 5.04e-01 100.0% 70.4%
3r6nA02 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 67.0 4.89e-01 95.2% 48.4%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.75 68.0 5.60e-01 100.0% 57.3%
2pmsC00 6.10.140.920 Special › Helix non-globular › Helix Hairpins › 0.75 69.0 5.63e-01 100.0% 60.6%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.75 62.0 6.11e-01 93.7% 88.2%
1twcA01 4.10.860.120 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › RNA polymerase II, clamp domain 0.75 51.0 4.02e-01 73.0% 34.1%
3cazB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.74 63.0 4.41e-01 100.0% 29.0%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 58.0 5.99e-01 95.2% 88.1%
6xkyA01 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.74 62.0 4.55e-01 100.0% 33.7%
3l1nA02 1.20.1280.140 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.73 57.0 5.18e-01 85.7% 64.4%
3g3oA00 3.20.100.30 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › VTC, catalytic tunnel domain 0.73 52.0 3.35e-01 76.2% 16.7%
3uumA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 58.0 4.73e-01 92.1% 46.7%
4ip8A00 1.10.132.110 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein 0.72 54.0 4.57e-01 81.0% 85.7%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.72 65.0 5.32e-01 100.0% 59.8%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 62.0 5.11e-01 100.0% 52.5%
1p49A02 1.10.287.550 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 55.0 5.72e-01 85.7% 89.8%
3zgxA02 6.10.140.1720 Special › Helix non-globular › Helix Hairpins › 0.70 61.0 5.45e-01 100.0% 76.9%
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 48.0 4.45e-01 73.0% 57.0%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.68 59.0 5.54e-01 100.0% 83.3%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.68 57.0 5.43e-01 100.0% 81.3%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 52.0 5.12e-01 82.5% 76.5%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.67 58.0 5.44e-01 100.0% 79.7%
5c8aA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.67 47.0 4.48e-01 81.0% 61.5%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.65 51.0 5.21e-01 92.1% 90.0%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.65 56.0 5.33e-01 100.0% 84.4%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 48.0 4.60e-01 84.1% 68.4%
4ehsA00 1.10.860.10 Mainly Alpha › Orthogonal Bundle › DNAb Helicase; Chain A › DNAb Helicase; Chain A 0.64 48.0 3.92e-01 82.5% 42.7%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.63 46.0 4.66e-01 81.0% 85.2%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.62 46.0 4.75e-01 82.5% 91.4%
5mmjn01 1.10.287.1480 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 44.0 4.03e-01 88.9% 53.9%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 48.0 4.29e-01 92.1% 57.1%
1b04A03 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.62 46.0 4.65e-01 81.0% 80.6%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.61 45.0 4.33e-01 81.0% 68.9%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.60 51.0 4.67e-01 96.8% 71.8%
4rg8A04 1.10.287.1240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 47.0 4.77e-01 96.8% 96.8%
5dikA00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.52 37.0 3.17e-01 77.8% 96.4%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5030596 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.91 77.0 7.69e-01 90.5% 87.7%
3735933 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.85 76.0 5.75e-01 100.0% 43.4%
3838026 5058.1.1.2 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st 0.84 74.0 6.59e-01 98.4% 68.9%
3696717 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.83 74.0 5.24e-01 100.0% 33.2%
4025205 601.19.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.83 74.0 5.57e-01 100.0% 44.7%
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 0.83 74.0 6.43e-01 100.0% 67.4%
4806319 3755.1.1.2 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › YscO-like 0.82 73.0 6.69e-01 100.0% 83.1%
3168993 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.82 73.0 6.74e-01 100.0% 78.8%
5035207 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 0.82 73.0 6.13e-01 100.0% 61.0%
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 0.82 73.0 5.98e-01 100.0% 57.4%
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 0.81 74.0 6.27e-01 98.4% 65.7%
3978264 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 0.81 73.0 5.48e-01 100.0% 44.0%
3805780 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.81 72.0 4.85e-01 100.0% 49.1%
3972992 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 0.80 62.0 6.22e-01 85.7% 83.1%
3973899 5086.1.1.92 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_AprE 0.80 71.0 5.43e-01 100.0% 46.2%
3697355 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 0.80 67.0 5.06e-01 100.0% 38.7%
3449084 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.79 72.0 6.04e-01 100.0% 62.9%
3733140 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.79 67.0 5.03e-01 100.0% 38.7%
4013859 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.79 62.0 4.02e-01 88.9% 19.0%
4543996 3600.1.1.1 ↗ alpha bundles › uncharacterized protein SYNW0670 › uncharacterized protein SYNW0670 › uncharacterized protein SYNW0670 › YlqD 0.78 70.0 5.82e-01 98.4% 58.1%
3947741 5086.1.1.84 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_MFP_RND 0.78 71.0 5.69e-01 100.0% 57.5%
3701046 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.78 61.0 5.40e-01 87.3% 58.9%
4570960 605.1.1.137 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › RRP36 0.78 65.0 4.75e-01 95.2% 35.6%
4174593 3922.1.1.248 ↗ 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 › PF25876 0.77 68.0 6.36e-01 93.7% 86.7%
4297853 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.77 67.0 5.29e-01 100.0% 47.4%
3814372 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 68.0 5.75e-01 100.0% 94.3%
3605626 192.12.1.0 ↗ alpha bundles › Long alpha-hairpin › Transcriptional repressor TraM › Transcriptional repressor TraM 0.77 68.0 5.71e-01 98.4% 58.1%
3594586 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.77 67.0 5.73e-01 100.0% 62.1%
3386973 5086.1.1.84 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_MFP_RND 0.77 69.0 6.11e-01 100.0% 81.1%
5063778 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 0.76 66.0 3.90e-01 93.7% 13.6%
3408277 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.76 70.0 5.65e-01 100.0% 63.5%
3317016 150.5.1.102 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › PF28483 0.76 64.0 6.27e-01 95.2% 86.8%
3976486 3826.1.1.1 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.76 63.0 5.62e-01 92.1% 64.4%
3410128 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.75 57.0 5.70e-01 87.3% 81.5%
3641196 5041.1.1.27 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › PRA1 0.75 58.0 4.76e-01 84.1% 47.8%
337179 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.74 63.0 4.41e-01 100.0% 29.0%
3989298 601.19.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.74 63.0 4.77e-01 100.0% 40.6%
3611289 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.73 66.0 5.01e-01 100.0% 74.5%
3928077 3636.1.1.0 ↗ a+b two layers › XPD arch domain › XPD arch domain › XPD arch domain 0.73 64.0 4.86e-01 96.8% 77.2%
3390311 604.7.1.0 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A 0.73 64.0 5.35e-01 100.0% 56.4%
3962991 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.71 64.0 4.53e-01 100.0% 33.3%
4463865 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 0.71 62.0 4.01e-01 100.0% 22.4%
3515350 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.70 64.0 5.43e-01 100.0% 68.0%
3282043 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.70 58.0 5.38e-01 100.0% 71.8%
5004498 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.68 50.0 4.39e-01 82.5% 52.0%
3407923 192.24.1.1 ↗ alpha bundles › Long alpha-hairpin › RPC62 helical hairpin domain › RPC62 helical hairpin domain › RPC3_helical 0.66 59.0 5.09e-01 100.0% 84.0%
3309441 547.1.1.0 ↗ alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain 0.65 53.0 4.73e-01 90.5% 85.6%