←Back to structures

SR-VP_4-6_scaffold_141_3489769_prodigal-single.1__X__X__00267

Bact-Vir

SR-VP_4-6_scaffold_141_3489769_prodigal-single.1__X__X__00267

Identity

Kingdom:
phage

Quality

73.3 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 39-167
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2o7gA00 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.74 46.0 5.49e-01 81.4% 90.9%
1or7B01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.74 50.0 5.77e-01 76.7% 93.6%
4nqwA01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.74 47.0 5.76e-01 82.2% 98.8%
1h3lB00 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.74 45.0 5.68e-01 75.2% 100.0%
4cxfA01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.73 46.0 5.55e-01 83.7% 95.4%
2i53A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.72 37.0 3.94e-01 80.6% 56.8%
1tj7A03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.70 31.0 4.08e-01 79.1% 74.6%
1dcnA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.66 31.0 3.98e-01 80.6% 76.4%
3whkA02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.63 36.0 4.61e-01 82.2% 100.0%
3pfyA02 6.10.20.180 Special › Helix non-globular › Arc Repressor Mutant, subunit A › 0.61 30.0 4.04e-01 86.8% 100.0%
1gq2A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 49.0 3.79e-01 92.2% 86.0%
6cnzF00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.58 46.0 4.29e-01 88.4% 67.7%
1bgvA03 1.10.285.10 Mainly Alpha › Orthogonal Bundle › Glutamate Dehydrogenase; Chain A, domain 3 › Glutamate Dehydrogenase, chain A, domain 3 0.56 33.0 4.09e-01 95.3% 97.4%
4iu9B02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.52 37.0 3.21e-01 72.9% 92.1%
4h3tA02 1.10.132.100 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.51 39.0 3.80e-01 79.1% 78.7%
6cfcA01 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.51 42.0 3.97e-01 99.2% 71.4%
2wglA00 1.10.4190.10 Mainly Alpha › Orthogonal Bundle › Urease accessory protein UreF › Urease accessory protein UreF 0.50 37.0 3.22e-01 77.5% 94.7%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4216342 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.82 47.0 6.11e-01 82.2% 98.7%
4287311 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.81 48.0 5.39e-01 90.7% 76.0%
3974456 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.79 46.0 5.96e-01 84.5% 100.0%
4162124 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.79 47.0 5.58e-01 87.6% 85.6%
2492244 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.79 46.0 5.96e-01 79.1% 100.0%
3284058 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.77 49.0 5.92e-01 86.0% 96.5%
3283530 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.77 54.0 6.05e-01 88.4% 92.0%
4196260 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.77 52.0 5.82e-01 88.4% 89.0%
2492230 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.76 49.0 5.30e-01 84.5% 76.4%
3282226 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.75 51.0 5.58e-01 85.3% 83.8%
3163617 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.72 47.0 5.52e-01 90.7% 94.4%
None — 0.72 49.0 5.42e-01 77.5% 85.7%
3587541 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.72 45.0 5.32e-01 86.0% 91.1%
4623581 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.71 48.0 5.26e-01 88.4% 84.8%
4498700 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.71 50.0 5.53e-01 78.3% 92.0%
3953375 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.70 50.0 5.38e-01 89.1% 86.4%
3277846 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.69 47.0 5.21e-01 87.6% 89.0%
3959877 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.68 49.0 5.30e-01 79.1% 88.2%
3969653 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.66 41.0 4.94e-01 90.7% 98.8%
3498294 148.1.3.40 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › ORC5_lid 0.65 43.0 4.70e-01 93.8% 82.9%
3290535 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.64 49.0 5.11e-01 79.8% 86.7%
3940544 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.64 46.0 5.04e-01 95.3% 90.5%
3713493 148.1.3.113 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_TRIP13_C 0.60 51.0 5.18e-01 98.4% 95.9%
4298559 5065.1.1.1 ↗ alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › ABC-3 0.60 43.0 3.21e-01 72.9% 100.0%
4895331 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.60 39.0 4.50e-01 82.2% 94.4%
3284192 3563.1.1.1 ↗ alpha bundles › Twin arginine protein translocation system component TatC › Twin arginine protein translocation system component TatC › Twin arginine protein translocation system component TatC › TatC 0.58 52.0 4.21e-01 100.0% 60.4%
5014208 192.29.1.302 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF998 0.56 33.0 2.96e-01 71.3% 41.1%
3481350 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.54 39.0 3.19e-01 75.2% 73.9%
5048540 1075.5.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter 0.54 46.0 3.57e-01 93.8% 67.2%
4369316 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.54 39.0 3.39e-01 76.0% 81.5%
4962406 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.53 40.0 3.43e-01 92.2% 50.0%
3216944 5050.1.1.11 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › UNC-93 0.53 45.0 3.77e-01 90.7% 85.5%
4885751 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.53 45.0 3.84e-01 92.2% 89.3%
5028383 1075.5.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE 0.53 45.0 3.83e-01 93.0% 89.3%
3970628 5050.1.1.60 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_3 0.52 37.0 3.26e-01 72.9% 83.6%
3191002 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.52 44.0 3.66e-01 93.0% 80.8%
5065994 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.52 39.0 3.46e-01 79.8% 91.0%
3612025 5050.1.1.28 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › BT1 0.52 41.0 3.08e-01 92.2% 34.1%
3759765 5050.1.1.11 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › UNC-93 0.52 43.0 3.61e-01 89.1% 79.5%
3228706 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.52 44.0 3.56e-01 93.0% 78.8%
3670753 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 0.51 33.0 2.74e-01 96.9% 36.0%
4936746 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.51 37.0 3.25e-01 74.4% 84.1%
4603378 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.51 37.0 3.20e-01 76.0% 76.7%
4949390 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.51 42.0 3.73e-01 88.4% 90.8%
3693315 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.51 43.0 3.57e-01 92.2% 82.2%
4984025 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.51 37.0 3.35e-01 75.2% 93.7%
3188177 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.50 43.0 3.59e-01 92.2% 83.1%
3697359 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.50 42.0 3.44e-01 93.0% 74.9%
3740287 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.50 42.0 3.58e-01 92.2% 85.5%
D2 high residues 189-278
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hugA00 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 0.72 51.0 5.35e-01 98.9% 82.5%
3vfzB00 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 0.72 47.0 5.41e-01 96.7% 96.8%
2o8xA00 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 0.70 46.0 5.29e-01 91.1% 98.4%
2dr1A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.61 43.0 3.78e-01 100.0% 48.9%
2bdeA03 1.20.58.1160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 36.0 3.90e-01 88.9% 70.1%
1ae9A00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.60 51.0 4.24e-01 97.8% 72.5%
4lwsA00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.57 39.0 3.78e-01 100.0% 62.0%
3kbbA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.57 41.0 4.52e-01 96.7% 100.0%
5m0nA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.54 45.0 2.96e-01 94.4% 68.3%
4gouA01 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.54 47.0 4.05e-01 100.0% 76.4%
3ezhA00 1.20.120.960 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase NarX, sensor domain 0.52 43.0 4.03e-01 93.3% 97.4%
3w6bB00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.52 44.0 3.74e-01 95.6% 84.3%
3rrkA02 1.20.1460.20 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › 0.52 45.0 3.84e-01 100.0% 71.0%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5081618 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 0.63 40.0 3.71e-01 93.3% 48.3%
5058465 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.58 49.0 4.45e-01 94.4% 88.8%
3971272 7579.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.56 49.0 3.24e-01 100.0% 80.7%
4961944 192.15.1.225 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › DUF4212 0.55 38.0 3.82e-01 100.0% 68.4%
3907051 131.1.1.32 ↗ alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › Pecanex_C 0.55 46.0 3.55e-01 93.3% 62.4%
3785619 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.53 42.0 3.90e-01 96.7% 67.0%
3716174 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.53 41.0 3.93e-01 97.8% 70.0%
3727312 192.2.1.6 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_3 0.53 45.0 4.31e-01 97.8% 87.3%
3741919 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.53 41.0 4.01e-01 97.8% 77.0%
3687292 4177.2.1.7 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › Inhibitor of kappaB kinase beta dimerization domain › Inhibitor of kappaB kinase beta dimerization domain › DUF7603 0.52 39.0 2.76e-01 100.0% 24.3%
3514746 5064.1.1.6 ↗ alpha bundles › Photosystem I reaction center subunit XI, PsaL › Photosystem I reaction center subunit XI, PsaL › Photosystem I reaction center subunit XI, PsaL › DUF2238 0.52 40.0 3.56e-01 83.3% 84.6%
5044090 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.51 43.0 3.58e-01 94.4% 65.6%
3482686 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.50 39.0 3.91e-01 82.2% 88.9%