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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00244

Bact-Vir

SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00244

Identity

Kingdom:
phage

Quality

82.3 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 2-57
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2yuxA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.73 57.0 4.62e-01 100.0% 44.4%
3pyfA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.73 63.0 4.66e-01 94.6% 92.0%
1lxnA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.72 64.0 5.31e-01 100.0% 90.8%
6rpxA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.72 56.0 4.93e-01 100.0% 56.5%
8gk4C02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.72 55.0 4.66e-01 83.9% 100.0%
3pvlA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.71 58.0 4.87e-01 100.0% 53.1%
1lxjA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 61.0 5.04e-01 100.0% 86.4%
1y6kR01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.70 57.0 4.74e-01 100.0% 51.0%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.69 57.0 4.78e-01 89.3% 89.1%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.68 52.0 5.41e-01 100.0% 100.0%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.67 52.0 5.00e-01 98.2% 74.2%
4ncbA01 3.30.530.60 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.67 56.0 4.14e-01 92.9% 96.6%
3ce8A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 56.0 4.96e-01 100.0% 94.4%
7u7nA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 55.0 4.66e-01 100.0% 54.6%
3egrA00 3.10.20.520 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phenylacetic acid degradation B 0.66 56.0 5.46e-01 100.0% 87.3%
2a2lC00 3.30.450.150 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Haem-degrading domain 0.65 45.0 3.38e-01 73.2% 29.4%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.64 55.0 3.88e-01 94.6% 89.2%
2ed8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 46.0 4.14e-01 100.0% 53.5%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.63 53.0 4.47e-01 92.9% 89.4%
3au4A02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.63 48.0 4.13e-01 100.0% 51.1%
3kg0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 54.0 4.56e-01 100.0% 96.9%
1s55A00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.62 52.0 3.81e-01 94.6% 36.5%
1n26A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 50.0 4.20e-01 96.4% 49.5%
3weeA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.62 50.0 3.56e-01 91.1% 50.8%
1es6A02 2.60.510.10 Mainly Beta › Sandwich › EV matrix protein fold › EV matrix protein 0.61 51.0 4.37e-01 98.2% 99.0%
2wdtC02 3.30.1490.420 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Ubiquitin carboxyl-terminal hydrolase, domain 2 0.61 49.0 4.22e-01 96.4% 79.2%
2z5bA00 3.30.230.100 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.61 51.0 3.98e-01 94.6% 68.5%
1sq2N00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 53.0 4.28e-01 100.0% 52.7%
5x6vF00 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.61 43.0 3.45e-01 76.8% 38.1%
7neaA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.60 50.0 3.94e-01 92.9% 98.3%
3q8pB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.60 47.0 4.03e-01 96.4% 62.0%
2z5bB01 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.60 43.0 3.38e-01 75.0% 47.9%
1wkyA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.60 48.0 3.72e-01 98.2% 37.5%
3r7wC02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.59 40.0 3.38e-01 75.0% 38.3%
3bpnC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 49.0 4.13e-01 100.0% 59.4%
4cvuA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.58 45.0 3.19e-01 100.0% 25.6%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.58 44.0 4.55e-01 94.6% 98.0%
2o3iA01 3.40.1610.10 Alpha Beta › 3-Layer(aba) Sandwich › CV3147-like fold › CV3147-like domain 0.57 45.0 3.07e-01 92.9% 25.0%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.56 45.0 4.26e-01 98.2% 75.0%
1darA05 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 46.0 4.10e-01 100.0% 86.2%
2re9A01 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.55 44.0 3.30e-01 92.9% 67.5%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.55 42.0 3.58e-01 92.9% 57.8%
1rfeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 43.0 3.39e-01 96.4% 39.7%
3am2A02 2.60.120.1050 Mainly Beta › Sandwich › Jelly Rolls › 0.54 44.0 3.56e-01 96.4% 61.5%
3r5xD02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 42.0 3.05e-01 85.7% 64.5%
6xzqA01 3.40.91.90 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain 0.52 43.0 3.19e-01 96.4% 74.7%
2pjyC00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.51 41.0 3.81e-01 96.4% 91.1%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4654177 1119.1.1.1 ↗ a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.76 67.0 4.33e-01 100.0% 96.3%
4344924 868.1.1.3 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › Med20 0.74 65.0 4.42e-01 100.0% 94.3%
5049019 304.26.1.1 ↗ a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › Thiamine_BP 0.73 64.0 5.28e-01 100.0% 86.4%
4147528 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.73 60.0 5.57e-01 91.1% 100.0%
3712597 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.73 59.0 5.08e-01 89.3% 85.6%
5069565 304.26.1.0 ↗ a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like 0.73 64.0 5.41e-01 100.0% 93.7%
4040528 304.24.1.16 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › PrmA 0.73 64.0 5.50e-01 100.0% 92.2%
3760983 3335.1.1.3 ↗ beta barrels › Handle domain in transferrin-binding protein B › Handle domain in transferrin-binding protein B › Handle domain in transferrin-binding protein B › KCTD18_C 0.73 63.0 5.14e-01 94.6% 100.0%
5065393 304.5.1.1 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › P-II 0.72 63.0 5.19e-01 100.0% 77.7%
5007807 304.26.1.1 ↗ a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › Thiamine_BP 0.72 63.0 5.35e-01 100.0% 89.5%
3964448 304.44.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 › PriA_C 0.72 56.0 4.84e-01 85.7% 100.0%
3898409 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.71 58.0 4.81e-01 100.0% 51.0%
4930471 304.4.1.79 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › MCR_D 0.71 61.0 5.12e-01 100.0% 89.0%
5035636 304.26.1.1 ↗ a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › Thiamine_BP 0.71 62.0 5.16e-01 100.0% 87.0%
5073020 304.26.1.0 ↗ a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like 0.70 60.0 5.05e-01 100.0% 92.9%
3733460 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.68 57.0 3.69e-01 100.0% 35.6%
3839805 304.28.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › ACR_tran 0.68 51.0 4.15e-01 82.1% 55.2%
3934346 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 57.0 4.56e-01 96.4% 48.2%
5053336 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.67 55.0 4.69e-01 96.4% 89.0%
3575366 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.66 51.0 4.34e-01 98.2% 50.5%
3271532 223.3.1.8 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Beta-lactamase2 0.66 47.0 3.36e-01 76.8% 33.7%
3628286 223.2.1.33 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_3 0.66 45.0 3.42e-01 71.4% 76.2%
4491515 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.66 55.0 3.64e-01 100.0% 34.7%
5073903 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.66 52.0 3.97e-01 89.3% 100.0%
3210904 12.6.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycoside hydrolase family 127 middle domain-related › Glycoside hydrolase family 127 middle domain-related 0.65 55.0 4.29e-01 100.0% 73.3%
4613363 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.65 54.0 3.58e-01 100.0% 35.2%
3404684 10.12.1.84 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › VKGC_lumenal_dom 0.65 56.0 3.85e-01 100.0% 62.4%
5053097 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.64 51.0 4.46e-01 96.4% 92.6%
3969578 3268.1.1.0 ↗ a+b two layers › N-terminal domain in xanthine dehydrogenase › N-terminal domain in xanthine dehydrogenase › N-terminal domain in xanthine dehydrogenase 0.63 42.0 4.28e-01 92.9% 70.9%
5047755 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.63 51.0 3.94e-01 94.6% 50.7%
3484794 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.63 52.0 4.75e-01 100.0% 97.5%
4990094 304.56.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like 0.62 50.0 4.74e-01 91.1% 100.0%
4029586 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.62 52.0 3.85e-01 94.6% 74.7%
3911249 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.62 47.0 4.07e-01 98.2% 50.5%
3512390 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.62 49.0 4.47e-01 96.4% 100.0%
3831785 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.61 49.0 4.19e-01 94.6% 77.0%
3699329 70.3.1.1 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like › SET 0.61 49.0 3.07e-01 100.0% 14.9%
4252321 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 50.0 4.17e-01 96.4% 55.2%
4161260 7056.1.1.3 ↗ few secondary structure elements › Zinc binding domain of metalloprotease Spartan › Zinc binding domain of metalloprotease Spartan › Zinc binding domain of metalloprotease Spartan › Zn_ribbon_SprT 0.60 43.0 4.53e-01 98.2% 95.6%
3730751 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.60 51.0 4.03e-01 100.0% 82.3%
3482279 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 50.0 3.42e-01 94.6% 53.0%
3932578 304.24.1.7 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › V_ATPase_I 0.59 48.0 4.18e-01 100.0% 84.0%
3929391 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.59 50.0 4.15e-01 100.0% 80.9%
3398459 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.59 50.0 4.25e-01 100.0% 99.0%
3411631 304.5.1.0 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.59 47.0 4.15e-01 94.6% 100.0%
3414928 382.1.1.6 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › QVR 0.59 50.0 4.38e-01 98.2% 62.5%
3535929 386.1.1.248 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_ZNF592 0.58 46.0 3.30e-01 98.2% 28.6%
3695272 221.1.1.93 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › DUF2420 0.57 46.0 3.60e-01 98.2% 39.3%
3897820 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 48.0 4.38e-01 92.9% 98.7%
3603767 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.56 46.0 3.85e-01 96.4% 54.3%
3620456 221.1.1.64 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Formin_GBD_N 0.56 43.0 3.60e-01 100.0% 46.4%
3315515 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.56 48.0 3.77e-01 98.2% 45.8%
3501768 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.55 45.0 4.27e-01 98.2% 80.0%
3595016 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 38.0 3.17e-01 94.6% 39.1%
4465843 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.53 43.0 3.85e-01 100.0% 93.3%
3998576 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.53 42.0 3.12e-01 100.0% 29.7%
3312666 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 41.0 3.96e-01 96.4% 72.9%
3549361 11.1.1.794 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › LIFR_D4 0.53 42.0 3.51e-01 94.6% 48.6%
3622256 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.53 43.0 3.25e-01 96.4% 34.8%
4990489 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 40.0 4.15e-01 92.9% 100.0%
3710611 2007.2.3.2 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › DSPc 0.51 42.0 2.77e-01 96.4% 33.6%