Back to structures

SR-VP_2-4_scaffold_141_2952615_prodigal-single.1__X__X__00293

Bact-Vir

SR-VP_2-4_scaffold_141_2952615_prodigal-single.1__X__X__00293

Identity

Kingdom:
phage

Quality

86.9 mean pLDDT

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 27-123
PDB
Domain cluster: representative
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1nkgA01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.72 55.0 3.97e-01 79.4% 91.6%
4h0aA00 3.40.33.10 Alpha Beta › 3-Layer(aba) Sandwich › Pathogenesis-related Protein p14a › CAP 0.66 46.0 3.23e-01 70.1% 44.9%
3bdrA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.66 51.0 4.40e-01 83.5% 98.1%
2jkgA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.66 45.0 3.79e-01 70.1% 83.6%
8ew8A01 3.50.70.10 Alpha Beta › 3-Layer(bba) Sandwich › Chalcone isomerase › 0.66 55.0 4.07e-01 88.7% 81.0%
5gv0A00 2.40.160.110 Mainly Beta › Beta Barrel › Porin › 0.66 56.0 4.72e-01 92.8% 77.8%
4hbrA00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 47.0 4.19e-01 76.3% 65.7%
1p32B00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.63 52.0 4.28e-01 88.7% 63.2%
3u1wA01 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 45.0 3.72e-01 77.3% 70.5%
7snsB01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.62 47.0 3.95e-01 80.4% 100.0%
1ospO02 3.90.930.1 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.62 55.0 4.82e-01 99.0% 97.3%
3iujA02 2.130.10.120 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain 0.61 45.0 3.13e-01 78.4% 59.1%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.61 43.0 4.02e-01 87.6% 59.2%
2w4yA00 2.40.160.220 Mainly Beta › Beta Barrel › Porin › 0.60 46.0 4.30e-01 82.5% 91.0%
7ne4A01 2.130.10.120 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain 0.60 43.0 3.01e-01 75.3% 66.9%
6zhhA01 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.59 43.0 3.58e-01 77.3% 71.7%
3s27B01 3.10.450.330 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 43.0 3.89e-01 77.3% 63.9%
4eqaC00 2.40.128.650 Mainly Beta › Beta Barrel › Lipocalin › 0.59 44.0 3.78e-01 78.4% 94.7%
4fr9A00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 46.0 4.10e-01 86.6% 68.8%
4rs6A01 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.58 49.0 4.65e-01 94.8% 92.4%
1a87A01 3.30.1120.60 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Colicin 0.57 43.0 4.34e-01 78.4% 83.5%
1sgoA01 3.30.2280.10 Alpha Beta › 2-Layer Sandwich › copper amine oxidase-like fold › Hypothetical protein (hspc210) 0.57 47.0 4.55e-01 92.8% 81.5%
7mhuA01 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.56 41.0 2.75e-01 76.3% 38.8%
4rbnA01 3.10.450.330 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 41.0 3.74e-01 77.3% 63.6%
3e1eC00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.55 42.0 3.79e-01 84.5% 99.3%
1iucA00 2.120.10.70 Mainly Beta › 6 Propeller › Neuraminidase › Fucose-specific lectin 0.54 45.0 3.22e-01 92.8% 92.9%
1mhmA00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.54 44.0 3.30e-01 89.7% 43.9%
1vr8A00 3.40.1000.20 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › TM1622-like 0.54 45.0 4.00e-01 89.7% 86.7%
1t6lA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.54 48.0 3.57e-01 99.0% 98.4%
5tvfD00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.53 44.0 3.23e-01 89.7% 44.4%
2greA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.53 46.0 3.57e-01 100.0% 91.5%
2qyvA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.53 46.0 3.47e-01 99.0% 89.8%
1wthA02 3.10.450.190 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 36.0 3.63e-01 71.1% 85.3%
3ge2A00 2.40.128.50 Mainly Beta › Beta Barrel › Lipocalin › 0.52 41.0 4.24e-01 94.8% 89.9%
1t82A00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.52 40.0 3.59e-01 83.5% 99.3%
4pxcA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 46.0 3.30e-01 100.0% 88.2%
4q7aA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 46.0 3.46e-01 100.0% 88.1%
3n5fA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 46.0 3.32e-01 100.0% 90.4%
5k8pD01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 45.0 3.22e-01 96.9% 86.1%
2bs6A01 2.40.128.190 Mainly Beta › Beta Barrel › Lipocalin › 0.51 39.0 4.17e-01 97.9% 92.9%
1r3nG01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.51 44.0 3.15e-01 99.0% 84.4%
1z2lA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.50 45.0 3.20e-01 100.0% 88.9%
1tluA00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.50 42.0 4.03e-01 93.8% 82.1%
6z46V01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.50 44.0 3.56e-01 95.9% 87.4%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4975637 241.2.1.0 a+b two layers › Type III secretory system chaperone-like › Frataxin-like › Frataxin-like 0.74 56.0 6.10e-01 93.8% 98.8%
3704328 292.2.1.0 a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.70 47.0 5.01e-01 74.2% 79.5%
3168452 331.10.2.3 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase › Med1 0.70 59.0 5.76e-01 91.8% 98.1%
4122018 4099.1.1.10 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med1 0.69 58.0 5.76e-01 90.7% 96.0%
4225063 3840.1.1.2 a+b two layers › Bacterial conjugation factor PsiB › Bacterial conjugation factor PsiB › Bacterial conjugation factor PsiB › PerB 0.69 61.0 5.88e-01 99.0% 86.4%
3411079 3369.1.1.1 beta meanders › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › Lamp2-like_luminal 0.68 57.0 4.64e-01 89.7% 78.9%
3929502 274.1.1.0 a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.67 49.0 5.00e-01 77.3% 77.7%
3519601 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.67 58.0 5.41e-01 94.8% 90.0%
5047554 241.1.1.5 a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › DUF2299 0.66 57.0 4.91e-01 93.8% 89.3%
4199183 9.1.1.0 beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.65 52.0 4.50e-01 84.5% 95.9%
2458379 12.1.1.13 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Suc_Porlyase_C 0.64 44.0 5.03e-01 77.3% 95.8%
5042381 2004.1.1.198 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.64 45.0 3.00e-01 74.2% 32.8%
3519579 295.1.1.20 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › Intu_longin_3 0.63 39.0 4.28e-01 84.5% 75.0%
4978331 331.10.2.0 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.62 40.0 4.70e-01 82.5% 92.9%
3585414 292.2.1.0 a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.61 53.0 5.09e-01 95.9% 91.8%
3260117 331.10.1.1 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › S-adenosylmethionine decarboxylase › SAM_decarbox 0.61 45.0 3.12e-01 78.4% 76.7%
3305495 331.10.1.1 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › S-adenosylmethionine decarboxylase › SAM_decarbox 0.61 44.0 2.99e-01 75.3% 80.3%
3402152 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.60 51.0 4.84e-01 96.9% 100.0%
3686499 298.1.1.25 a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › ox_reductase_C 0.60 48.0 3.58e-01 88.7% 70.9%
4975535 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.60 41.0 4.37e-01 96.9% 85.0%
5074419 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.60 37.0 4.33e-01 86.6% 92.3%
4297071 512.1.1.0 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.59 42.0 4.68e-01 100.0% 96.0%
4974181 331.3.1.74 a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PF27226 0.59 43.0 4.31e-01 93.8% 73.7%
3440815 5.1.11.35 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed › Beta-prop_AT5G49610-like 0.58 42.0 2.94e-01 76.3% 42.9%
4973139 511.1.1.0 beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.58 47.0 4.00e-01 85.6% 75.5%
4970968 331.10.2.0 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.58 49.0 4.66e-01 89.7% 77.9%
3685200 109.3.1.1 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank 0.58 43.0 3.34e-01 90.7% 36.2%
3372166 632.7.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.58 46.0 2.95e-01 84.5% 25.9%
3546306 292.2.1.1 a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › POLO_box 0.58 44.0 4.53e-01 100.0% 83.2%
4276439 2004.1.1.429 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_15 0.57 42.0 2.81e-01 77.3% 79.7%
4015579 632.7.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.57 46.0 3.02e-01 86.6% 27.7%
4956106 512.1.1.0 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.57 34.0 3.94e-01 87.6% 82.9%
3438520 511.1.1.1 beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › HSP70 0.56 46.0 3.14e-01 87.6% 34.6%
3964888 10.12.1.0 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.56 48.0 3.71e-01 93.8% 56.7%
4956103 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.56 36.0 3.96e-01 92.8% 85.3%
3242312 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.55 40.0 2.90e-01 76.3% 44.1%
5074323 331.10.2.0 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.55 43.0 4.13e-01 84.5% 87.0%
5028231 4312.1.1.0 a+b two layers › RelE-like › RelE-like › RelE-like 0.54 37.0 3.59e-01 70.1% 100.0%
5044087 3504.3.1.1 beta barrels › MutM N-terminal domain-like › Fibrinogen binding protein N-terminal domain › Fibrinogen binding protein N-terminal domain › NFACT_N 0.54 46.0 3.95e-01 90.7% 94.0%
3822070 331.10.2.8 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase › SAM_decarbox 0.54 43.0 4.13e-01 86.6% 83.5%
5004871 331.4.1.0 a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.54 40.0 4.10e-01 86.6% 83.3%
5060264 7579.1.1.0 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.54 46.0 3.30e-01 96.9% 80.9%
4768813 331.10.1.1 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › S-adenosylmethionine decarboxylase › SAM_decarbox 0.54 44.0 3.44e-01 89.7% 45.2%
4062329 331.10.2.1 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase › AdoMet_dc 0.53 42.0 4.15e-01 86.6% 86.7%
3353407 331.10.1.1 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › S-adenosylmethionine decarboxylase › SAM_decarbox 0.53 44.0 3.03e-01 89.7% 33.0%
4976589 331.10.2.0 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.52 39.0 4.03e-01 85.6% 83.2%
5061484 331.10.2.1 a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase › AdoMet_dc 0.52 42.0 4.06e-01 89.7% 81.6%
1554358 3146.1.1.1 a+b complex topology › gH main domain › gH main domain › gH main domain › Herpes_glycop_H 0.51 46.0 2.82e-01 100.0% 48.2%
3164643 2011.1.1.20 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M20, Peptidase_M28 0.51 45.0 3.26e-01 100.0% 90.2%
4185386 7515.1.1.5 a/b three-layered sandwiches › Alkaline phosphatase-like › Alkaline phosphatase-like › Alkaline phosphatase-like › Sulfatase,SGSH_C 0.51 42.0 2.84e-01 94.8% 74.5%
3815390 5.3.1.1 beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II › S_locus_glycop 0.50 37.0 3.32e-01 79.4% 93.1%