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SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00304

Bact-Vir

SR-VP_2-4_scaffold_141_1208361_prodigal-single.1__X__X__00304

Identity

Kingdom:
phage

Quality

91.0 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 15-92
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3voqA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.79 52.0 4.46e-01 79.5% 44.8%
3ulbA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.70 48.0 4.74e-01 80.8% 66.3%
3fehA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 51.0 4.29e-01 78.2% 52.4%
2giaA00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.67 47.0 3.78e-01 74.4% 40.3%
2lnjA00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.65 47.0 3.70e-01 76.9% 40.6%
2kt4B01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.64 53.0 4.37e-01 91.0% 99.3%
2z6oA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.63 49.0 3.88e-01 85.9% 79.5%
2xrnA02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.62 45.0 3.50e-01 78.2% 40.7%
6i0iA00 3.30.350.10 Alpha Beta › 2-Layer Sandwich › Subtilisin Inhibitor › Subtilisin inhibitor-like 0.61 42.0 3.78e-01 71.8% 95.4%
4hwxA00 3.30.350.10 Alpha Beta › 2-Layer Sandwich › Subtilisin Inhibitor › Subtilisin inhibitor-like 0.61 42.0 3.72e-01 71.8% 93.0%
3bjnA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.60 42.0 3.37e-01 74.4% 38.9%
4oddA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.58 49.0 4.05e-01 96.2% 94.6%
4wfvA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 49.0 4.04e-01 98.7% 94.1%
4ghbA00 2.40.160.190 Mainly Beta › Beta Barrel › Porin › 0.57 49.0 3.42e-01 94.9% 95.7%
1e5pA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 48.0 3.97e-01 96.2% 96.0%
1kyfA01 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.56 46.0 3.86e-01 89.7% 82.8%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.56 45.0 4.48e-01 85.9% 97.5%
1na8B00 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.56 39.0 3.27e-01 74.4% 80.0%
1dzkA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 48.0 3.98e-01 98.7% 95.9%
8b4hA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 42.0 3.34e-01 80.8% 61.1%
3mnmA00 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.55 41.0 3.68e-01 79.5% 92.0%
4c92C00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.55 44.0 4.39e-01 88.5% 84.8%
1zc3B00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 43.0 3.83e-01 83.3% 77.1%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.54 44.0 3.87e-01 92.3% 65.6%
3htyA00 2.40.128.280 Mainly Beta › Beta Barrel › Lipocalin › 0.54 39.0 3.76e-01 78.2% 94.7%
7wa9A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 44.0 3.69e-01 92.3% 83.0%
2ywqA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.53 40.0 3.90e-01 82.1% 85.2%
3tqmA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.53 40.0 3.90e-01 83.3% 85.6%
1gyvA00 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.53 39.0 3.42e-01 79.5% 94.2%
1t17A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 42.0 3.51e-01 93.6% 81.1%
3fynA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 40.0 3.27e-01 84.6% 84.9%
2r5rA00 3.10.270.10 Alpha Beta › Roll › Urate Oxidase › Urate Oxidase; 0.52 43.0 3.18e-01 100.0% 69.5%
1zxqA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 36.0 3.54e-01 73.1% 88.2%
3fn9C04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 35.0 3.37e-01 71.8% 82.6%
2xzhA00 2.130.10.110 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Clathrin heavy-chain terminal domain 0.51 42.0 2.75e-01 91.0% 38.5%
3ecrB03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.51 42.0 3.92e-01 94.9% 98.0%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 35.0 3.63e-01 73.1% 89.2%
1f2uA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 42.0 3.49e-01 97.4% 53.7%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3235213 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.74 52.0 4.30e-01 71.8% 53.1%
3686517 220.1.1.112 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_10 0.73 51.0 3.94e-01 82.1% 34.5%
3707991 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.72 49.0 3.95e-01 70.5% 48.7%
4959998 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.72 52.0 4.74e-01 76.9% 61.9%
4945347 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.68 44.0 3.68e-01 70.5% 39.2%
4025081 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.67 50.0 4.05e-01 79.5% 52.0%
4117578 223.1.1.5 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › HrcA 0.65 45.0 3.63e-01 73.1% 37.4%
5004057 300.1.1.0 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease 0.65 45.0 3.50e-01 71.8% 72.7%
5052185 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.64 44.0 3.72e-01 71.8% 44.6%
3968288 7520.1.1.1 ↗ a/b three-layered sandwiches › CinA-like › CinA-like › CinA-like › CinA 0.63 47.0 3.64e-01 78.2% 79.4%
3565552 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.63 46.0 3.91e-01 82.1% 47.2%
5062817 300.1.1.0 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease 0.63 44.0 3.67e-01 71.8% 78.2%
3255028 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.62 44.0 3.44e-01 79.5% 34.7%
1684916 9.1.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Lipocalin 0.57 49.0 4.04e-01 98.7% 94.1%
4359254 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.57 45.0 4.62e-01 84.6% 93.3%
5027613 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) 0.56 44.0 3.15e-01 87.2% 72.9%
2792228 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.56 47.0 3.80e-01 96.2% 92.0%
4646686 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.55 43.0 4.51e-01 84.6% 98.6%
4497181 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.55 40.0 3.13e-01 75.6% 95.2%
4930094 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.55 42.0 3.81e-01 80.8% 78.1%
3603056 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.55 43.0 4.37e-01 84.6% 98.7%
3716829 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.55 42.0 3.91e-01 85.9% 86.7%
5065881 331.3.1.18 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › DAPG_hydrolase 0.55 46.0 3.64e-01 96.2% 75.4%
3533330 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 39.0 3.70e-01 75.6% 86.3%
3588355 330.2.1.1 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › Ribosomal_S30AE 0.55 39.0 3.64e-01 75.6% 76.0%
3409717 633.33.1.1 ↗ alpha bundles › Bromodomain-like › Rogdi › Rogdi › Rogdi_lz 0.55 44.0 3.16e-01 91.0% 70.4%
3280054 331.3.1.11 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc2 0.55 44.0 3.65e-01 92.3% 84.3%
5023443 330.4.1.0 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain 0.55 42.0 4.47e-01 83.3% 100.0%
184719 3514.1.1.1 ↗ a+b two layers › uncharacterized protein PA1076 › uncharacterized protein PA1076 › uncharacterized protein PA1076 › DUF5064 0.54 44.0 3.87e-01 92.3% 65.6%
5013768 330.2.1.5 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.54 37.0 3.50e-01 70.5% 86.3%
5024241 330.2.1.5 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.54 40.0 3.83e-01 80.8% 86.3%
3608102 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 42.0 4.43e-01 85.9% 98.6%
4040973 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.54 42.0 4.40e-01 83.3% 92.9%
3604391 512.1.1.2 ↗ 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_2nd 0.54 42.0 3.92e-01 85.9% 90.0%
4135153 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.54 42.0 4.33e-01 85.9% 96.0%
5028953 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.54 41.0 3.94e-01 83.3% 91.1%
3171541 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.54 45.0 3.90e-01 97.4% 94.6%
4026643 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 43.0 4.17e-01 87.2% 85.9%
3798506 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.53 39.0 2.62e-01 79.5% 40.9%
4026008 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 45.0 4.37e-01 93.6% 90.6%
3329783 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.52 45.0 4.29e-01 100.0% 85.3%
4927872 330.2.1.5 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.52 39.0 3.43e-01 80.8% 67.5%
3603448 3291.1.1.49 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › NFACT_N 0.52 39.0 3.12e-01 80.8% 40.0%
2409339 11.1.1.14 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Glyco_hydro_2 0.52 36.0 3.39e-01 71.8% 90.5%
3476559 5.1.13.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › Propeller domain of DCAF15 › DCAF15_WD40 0.52 44.0 2.86e-01 92.3% 47.0%
4932637 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.52 39.0 3.76e-01 82.1% 90.0%
4978348 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) 0.52 40.0 3.93e-01 85.9% 98.8%
5080980 330.2.1.1 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › Ribosomal_S30AE 0.52 39.0 3.47e-01 79.5% 74.5%
4937410 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.52 37.0 3.54e-01 75.6% 88.4%
3497120 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 44.0 4.19e-01 100.0% 88.4%
5011024 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) 0.51 39.0 3.60e-01 85.9% 79.1%
4941364 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.51 38.0 3.54e-01 82.1% 73.3%
4304505 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.51 38.0 3.31e-01 83.3% 90.0%
3436093 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 40.0 4.15e-01 89.7% 96.0%
3212053 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.51 43.0 2.95e-01 98.7% 77.2%
4983377 330.2.1.5 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.51 39.0 3.58e-01 83.3% 78.1%
4939419 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 0.51 38.0 3.77e-01 84.6% 96.5%
3655368 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.50 40.0 4.10e-01 89.7% 96.0%
5029238 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.50 37.0 3.49e-01 82.1% 86.0%
5071146 330.2.1.5 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.50 37.0 3.50e-01 82.1% 85.0%