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SR-VP_0-2_scaffold_141_2510002_prodigal-single.1__X__X__00225

Bact-Vir

SR-VP_0-2_scaffold_141_2510002_prodigal-single.1__X__X__00225

Identity

Kingdom:
phage

Quality

72.0 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 3-60
PDB
Domain cluster: representative
CATH (51)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3iylU02 1.10.287.1520 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.86 62.0 6.51e-01 75.9% 83.0%
2icwG01 1.20.120.390 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1 0.84 68.0 5.22e-01 87.9% 43.5%
2o5iN07 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.83 75.0 5.92e-01 100.0% 90.5%
3fblA00 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 63.0 5.64e-01 91.4% 58.5%
4jleA00 6.10.280.180 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Plasmodium RESA, N-terminal helical domain 0.82 66.0 4.84e-01 87.9% 34.2%
1vq8P03 1.10.1200.60 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.82 59.0 6.08e-01 77.6% 80.0%
5uh5D02 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.82 72.0 5.41e-01 98.3% 73.9%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.81 69.0 6.31e-01 94.8% 73.0%
3v9rB00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.79 55.0 5.07e-01 72.4% 62.5%
4dvyP01 1.10.357.130 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.76 67.0 4.59e-01 100.0% 58.4%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.76 57.0 4.67e-01 84.5% 44.8%
4k08A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.74 67.0 4.96e-01 100.0% 93.1%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.74 62.0 5.19e-01 96.6% 55.1%
3u3iA02 1.20.58.1110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 57.0 4.65e-01 86.2% 47.2%
4cb8A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.72 59.0 3.49e-01 100.0% 11.1%
1zv1A00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.72 49.0 4.89e-01 70.7% 72.9%
5hxgB00 1.10.4000.10 Mainly Alpha › Orthogonal Bundle › Flagellar transcriptional activator fold › Flagellar transcriptional activator FlhD 0.71 52.0 5.04e-01 77.6% 92.3%
4hiaA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.70 52.0 3.66e-01 84.5% 26.1%
3h3mA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.69 55.0 4.80e-01 100.0% 57.3%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.69 51.0 4.93e-01 91.4% 72.3%
5dn6J00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.68 58.0 5.41e-01 100.0% 77.0%
3u4qA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 58.0 3.85e-01 94.8% 29.8%
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 0.68 53.0 5.28e-01 89.7% 85.0%
3e3vA03 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.67 49.0 5.00e-01 77.6% 80.4%
2i7uA00 6.10.250.1010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.67 55.0 5.46e-01 94.8% 96.8%
2ewfA02 1.20.1270.310 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.67 54.0 4.94e-01 96.6% 65.4%
3c24A02 1.10.3640.10 Mainly Alpha › Orthogonal Bundle › putative oxidoreductase fold › Semialdehyde dehydrogenase-like, C-terminal 0.67 51.0 4.33e-01 84.5% 49.0%
1gvnA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.67 53.0 4.67e-01 87.9% 66.7%
1hr5A00 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 0.66 51.0 5.55e-01 98.3% 100.0%
2l35A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.66 55.0 5.40e-01 94.8% 88.9%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.65 58.0 4.86e-01 100.0% 64.9%
1vx7301 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 52.0 4.83e-01 100.0% 70.3%
1l5jA03 3.40.1060.10 Alpha Beta › 3-Layer(aba) Sandwich › Aconitase; Domain 2 › Aconitase, Domain 2 0.64 49.0 3.56e-01 86.2% 43.4%
2itbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.63 53.0 3.73e-01 96.6% 57.1%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.63 55.0 5.12e-01 100.0% 79.5%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 54.0 5.05e-01 96.6% 100.0%
3bemB00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.62 55.0 3.79e-01 100.0% 78.5%
3of4A00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.62 54.0 3.72e-01 100.0% 79.7%
1rsoB00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.61 45.0 4.62e-01 84.5% 85.7%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 50.0 4.62e-01 100.0% 70.5%
5ux1D00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.61 54.0 3.70e-01 98.3% 31.5%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 51.0 4.79e-01 100.0% 75.3%
4ex8A00 3.40.1790.10 Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain 0.61 52.0 3.32e-01 100.0% 19.9%
3g2bA00 1.10.10.1150 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Coenzyme PQQ synthesis protein D (PqqD) 0.60 41.0 3.59e-01 75.9% 45.6%
8a0rA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 50.0 4.00e-01 100.0% 45.4%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.60 48.0 4.64e-01 87.9% 81.5%
1b48A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 50.0 4.16e-01 100.0% 91.7%
4hwhE00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.59 50.0 4.43e-01 98.3% 68.2%
1ailA00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.58 45.0 4.27e-01 89.7% 70.0%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.56 42.0 4.11e-01 84.5% 100.0%
4griA04 1.10.8.70 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 0.50 33.0 3.44e-01 79.3% 73.6%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.96 80.0 6.58e-01 87.9% 53.7%
3265542 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.93 66.0 7.61e-01 77.6% 100.0%
4024271 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.92 76.0 5.62e-01 87.9% 37.8%
4025379 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.90 74.0 5.32e-01 87.9% 34.0%
4028068 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.90 76.0 5.53e-01 89.7% 38.6%
3740910 1008.1.1.0 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain 0.90 74.0 7.61e-01 87.9% 92.7%
4030224 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.90 73.0 5.45e-01 87.9% 37.8%
4027571 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.90 73.0 5.29e-01 87.9% 34.2%
None — 0.86 65.0 3.62e-01 84.5% 6.8%
3236179 708.1.2.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like 0.86 70.0 4.92e-01 86.2% 32.5%
4027695 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.86 75.0 5.10e-01 94.8% 30.0%
None — 0.85 63.0 3.73e-01 79.3% 11.2%
3686609 6026.1.1.0 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.83 67.0 5.84e-01 93.1% 57.8%
5028558 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 0.83 67.0 5.56e-01 87.9% 59.0%
3589830 5043.2.1.8 ↗ extended segments › Sensor proteins transmembrane domains › NarQ transmembrane domain › NarQ transmembrane domain › DUF5592 0.82 65.0 6.09e-01 84.5% 84.3%
1288509 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.82 65.0 4.72e-01 87.9% 32.1%
3786677 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.81 64.0 6.57e-01 86.2% 100.0%
3466340 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.81 59.0 3.87e-01 77.6% 21.3%
4620052 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 0.80 64.0 3.90e-01 87.9% 14.8%
3353220 4207.1.1.0 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) 0.79 61.0 5.02e-01 87.9% 46.7%
3412555 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.79 67.0 5.40e-01 94.8% 64.5%
4346136 605.1.1.108 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › GrpE 0.78 64.0 6.19e-01 91.4% 86.2%
3392260 6026.1.1.0 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.78 61.0 5.83e-01 87.9% 74.3%
4026417 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.77 64.0 5.93e-01 94.8% 72.0%
3597506 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.77 64.0 5.92e-01 94.8% 72.0%
4032782 4125.1.1.0 ↗ alpha superhelices › BH3980-like › BH3980-like › BH3980-like 0.76 55.0 5.33e-01 81.0% 69.2%
3621479 6026.1.1.1 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.76 55.0 4.85e-01 77.6% 57.6%
3326759 284.1.3.1 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.76 55.0 5.07e-01 81.0% 60.0%
3385053 5076.2.1.10 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › PF29520 0.76 66.0 4.26e-01 100.0% 49.3%
4276514 3826.1.1.88 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › CC_BshC 0.74 63.0 5.94e-01 94.8% 80.0%
3539738 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.74 59.0 3.91e-01 96.6% 22.2%
3699443 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.73 65.0 5.13e-01 100.0% 49.6%
3616157 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.73 63.0 5.39e-01 100.0% 68.4%
4318142 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.72 50.0 3.74e-01 72.4% 30.7%
3218140 188.1.1.1 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.71 56.0 3.57e-01 86.2% 60.7%
3643105 6026.1.1.1 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.71 55.0 4.09e-01 86.2% 32.3%
4149728 547.1.1.1 ↗ alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.71 55.0 5.06e-01 87.9% 70.0%
3400382 3877.1.1.1 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC › 60KD_IMP 0.69 60.0 3.87e-01 100.0% 72.9%
3552520 241.15.1.3 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › SPC25 0.68 58.0 5.62e-01 96.6% 90.8%
5043641 205.1.1.16 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_7 0.68 54.0 3.75e-01 87.9% 59.5%
3232510 3075.1.1.1 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › PFU 0.67 47.0 4.37e-01 79.3% 57.3%
4952348 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.66 51.0 3.58e-01 86.2% 37.3%
3700089 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 0.64 55.0 5.29e-01 98.3% 87.7%
4025064 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.63 50.0 4.92e-01 96.6% 81.5%
149872 3291.1.1.1 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.62 55.0 4.97e-01 100.0% 74.7%
3459951 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.62 55.0 4.46e-01 100.0% 52.7%
4978688 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.60 51.0 4.42e-01 100.0% 62.1%
3182497 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 0.57 46.0 2.82e-01 100.0% 12.6%
3928221 4.1.1.310 ↗ beta barrels › SH3 › SH3 › SH3 › PF26050 0.52 44.0 3.38e-01 96.6% 41.4%