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SR-VP_0-2_scaffold_141_4953755_prodigal-single.1__X__X__00248

Bact-Vir

SR-VP_0-2_scaffold_141_4953755_prodigal-single.1__X__X__00248

Identity

Kingdom:
phage

Quality

72.5 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 5-52
PDB
Domain cluster: representative
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.88 75.0 7.01e-01 93.8% 84.5%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.87 76.0 6.63e-01 95.8% 70.0%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.87 77.0 5.96e-01 100.0% 69.6%
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 6.92e-01 95.8% 85.7%
2kwhA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.86 62.0 5.92e-01 100.0% 66.1%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.86 76.0 6.94e-01 100.0% 85.9%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.86 75.0 5.68e-01 97.9% 44.5%
3behB01 1.20.120.540 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels 0.85 75.0 5.64e-01 100.0% 41.0%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.85 73.0 4.88e-01 97.9% 25.3%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.85 69.0 6.12e-01 89.6% 63.2%
2itbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 72.0 4.69e-01 95.8% 26.8%
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.84 71.0 4.67e-01 100.0% 23.0%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.84 74.0 6.39e-01 100.0% 68.0%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 74.0 6.76e-01 100.0% 96.8%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.83 69.0 5.72e-01 100.0% 52.9%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.82 72.0 6.47e-01 100.0% 74.6%
7zmgL01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.82 71.0 6.01e-01 100.0% 58.7%
3okqA00 1.20.58.1540 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain 0.82 71.0 5.24e-01 100.0% 45.6%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 69.0 5.89e-01 93.8% 98.7%
2qf9A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.80 66.0 4.65e-01 95.8% 33.3%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 67.0 5.51e-01 100.0% 52.2%
4rg8A04 1.10.287.1240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 59.0 5.46e-01 83.3% 75.8%
3jcuZ00 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.77 67.0 6.23e-01 100.0% 83.6%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.77 67.0 5.79e-01 100.0% 66.7%
1kt1A03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.75 61.0 4.33e-01 95.8% 30.4%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.75 60.0 5.77e-01 97.9% 83.3%
5mlc900 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.75 65.0 5.00e-01 97.9% 85.0%
1f2eA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.75 62.0 4.91e-01 97.9% 45.3%
1jnrA03 1.20.58.100 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain 0.74 64.0 4.81e-01 100.0% 53.7%
1kmiZ02 1.10.287.500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 61.0 4.58e-01 100.0% 92.5%
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.74 63.0 4.53e-01 100.0% 35.4%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.73 63.0 5.43e-01 100.0% 82.1%
3u5nA02 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.73 63.0 4.74e-01 100.0% 40.8%
6gwuD00 3.40.1050.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-carbonic Anhydrase; Chain A › Carbonic anhydrase 0.73 56.0 3.59e-01 79.2% 19.8%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.72 63.0 5.41e-01 100.0% 66.7%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 59.0 5.72e-01 100.0% 82.8%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 53.0 5.01e-01 83.3% 65.6%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.71 59.0 5.21e-01 100.0% 63.6%
2y4tA02 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.70 54.0 5.31e-01 100.0% 82.7%
2cazC00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 58.0 5.38e-01 95.8% 71.9%
1ykhA00 6.10.140.200 Special › Helix non-globular › Helix Hairpins › 0.70 59.0 4.83e-01 100.0% 50.5%
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.69 54.0 4.85e-01 85.4% 65.7%
1xdxA01 3.30.1140.40 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › Tctex-1 0.67 47.0 3.71e-01 79.2% 36.0%
5jxxA02 1.20.1180.10 Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain 0.66 47.0 4.29e-01 77.1% 57.6%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 55.0 4.91e-01 100.0% 68.9%
2qsaA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.66 53.0 4.34e-01 97.9% 47.5%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.66 47.0 4.64e-01 93.8% 71.7%
4dyqA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.65 53.0 4.19e-01 91.7% 81.6%
3cbuA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 51.0 3.83e-01 97.9% 33.6%
3k2nA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.62 49.0 3.53e-01 100.0% 86.4%
2ckoA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.62 53.0 3.34e-01 100.0% 57.1%
2z16B01 1.20.91.10 Mainly Alpha › Up-down Bundle › Influenza Virus Matrix Protein; Chain A, domain 1 › Influenza matrix M1, N-terminal subdomain 1 0.59 42.0 3.64e-01 79.2% 47.4%
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 0.59 49.0 4.61e-01 100.0% 83.6%
1vzsA01 1.10.246.110 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › Mitochondrial ATP synthase-coupling factor 6 0.53 44.0 4.06e-01 95.8% 71.4%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3635635 3826.1.1.26 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › RRP36 0.93 86.0 5.90e-01 100.0% 33.3%
4186957 192.29.1.164 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › RRP36 0.93 86.0 6.28e-01 100.0% 41.7%
3195418 192.8.1.376 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › RRP36 0.92 85.0 6.60e-01 100.0% 65.3%
4600185 3602.1.1.15 ↗ alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › DUF444 0.90 82.0 6.93e-01 100.0% 65.3%
4142309 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.89 80.0 5.43e-01 100.0% 30.0%
3394875 109.4.1.102 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › WAPL 0.89 79.0 4.44e-01 100.0% 9.0%
4089826 622.1.1.33 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › T3SS_needle_F 0.88 79.0 6.47e-01 100.0% 56.5%
4203104 3560.1.1.7 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 8 › Mediator of RNA polymerase II transcription subunit 8 › Mediator of RNA polymerase II transcription subunit 8 › Med10 0.87 78.0 5.42e-01 100.0% 33.1%
3199446 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.86 77.0 6.02e-01 100.0% 48.0%
4574972 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.86 77.0 7.18e-01 100.0% 80.0%
2914508 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 0.86 72.0 4.36e-01 95.8% 15.5%
3267437 101.1.1.196 ↗ alpha arrays › HTH › HTH › Three-helical HTH › RWP-RK 0.86 64.0 5.10e-01 100.0% 42.2%
3906467 1008.1.1.106 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › CSN5_C 0.86 76.0 6.18e-01 100.0% 56.7%
4034201 192.7.1.1 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › FemAB 0.86 77.0 7.16e-01 100.0% 80.0%
3896686 192.8.1.36 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › M_domain 0.86 76.0 5.95e-01 100.0% 48.0%
3761938 4207.1.2.0 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region 0.85 74.0 5.21e-01 100.0% 32.0%
3637046 192.8.1.327 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › PigL_N 0.85 74.0 5.68e-01 100.0% 43.6%
3888162 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 73.0 5.47e-01 100.0% 40.0%
3581757 11.12.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD,Neur_chan_memb 0.84 70.0 4.48e-01 100.0% 20.0%
4039238 192.6.1.1 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › ATP-synt_DE 0.84 72.0 6.91e-01 97.9% 85.5%
3470751 3755.3.1.297 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › KIF9 0.83 72.0 4.98e-01 100.0% 30.0%
5057198 1073.1.1.0 ↗ alpha arrays › Mitochondrial calcium uniporter (MCU) › Mitochondrial calcium uniporter (MCU) › Mitochondrial calcium uniporter (MCU) 0.83 71.0 5.19e-01 100.0% 36.2%
3600361 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 0.82 73.0 5.80e-01 100.0% 50.5%
3607086 4992.1.1.0 ↗ extended segments › RelB-like › RelB-like › RelB-like 0.82 71.0 6.04e-01 100.0% 60.0%
3175197 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 72.0 5.24e-01 100.0% 36.9%
5060383 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.82 65.0 5.64e-01 89.6% 57.3%
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 0.81 71.0 5.88e-01 100.0% 56.5%
4959083 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.81 70.0 4.79e-01 100.0% 28.2%
3171363 605.8.1.2 ↗ alpha duplicates or obligate multimers › ROP-like › BAS1536-like › BAS1536-like › PF27894 0.81 71.0 6.80e-01 100.0% 89.1%
2055367 650.1.1.3 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › HsbA 0.81 69.0 6.20e-01 100.0% 68.6%
3741928 109.4.1.1483 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_M, HAT_Syf1_CNRKL1_C 0.80 71.0 4.09e-01 100.0% 15.1%
3594129 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.79 67.0 4.39e-01 100.0% 22.3%
3229793 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.79 63.0 5.10e-01 85.4% 49.4%
3256299 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.79 68.0 4.99e-01 100.0% 40.8%
5030987 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 66.0 5.68e-01 100.0% 60.0%
3648998 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.78 68.0 5.49e-01 100.0% 52.2%
3410365 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 0.78 66.0 3.91e-01 100.0% 12.6%
4947533 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.77 66.0 5.14e-01 100.0% 44.5%
3973208 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 0.76 61.0 5.16e-01 85.4% 60.0%
3969538 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 0.76 64.0 6.23e-01 100.0% 87.3%
3679408 5076.2.1.9 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › Choline_transpo 0.75 62.0 3.78e-01 97.9% 19.4%
4042007 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.75 64.0 5.00e-01 100.0% 49.1%
3650275 3602.1.1.0 ↗ alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain 0.75 61.0 5.28e-01 100.0% 58.7%
3456370 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.75 66.0 4.62e-01 100.0% 41.9%
3817103 630.1.1.1 ↗ a+b complex topology › RuBisCo LSMT C-terminal, substrate-binding domain › RuBisCo LSMT C-terminal, substrate-binding domain › RuBisCo LSMT C-terminal, substrate-binding domain › Rubis-subs-bind 0.75 64.0 4.42e-01 100.0% 34.1%
3934503 614.1.1.1 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain › L27 0.74 57.0 5.69e-01 85.4% 82.0%
3810882 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.73 59.0 3.60e-01 87.5% 44.0%
3858340 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.68 56.0 4.16e-01 100.0% 38.6%
3513381 4082.1.1.0 ↗ alpha duplicates or obligate multimers › Hairy Orange domain › Hairy Orange domain › Hairy Orange domain 0.67 54.0 5.03e-01 89.6% 75.0%
3707613 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.66 53.0 3.42e-01 93.8% 18.4%
4218603 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 0.65 53.0 3.92e-01 100.0% 32.0%