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SR-VP_4-6_scaffold_141_2630357_prodigal-single.1__X__X__00408

Bact-Vir

SR-VP_4-6_scaffold_141_2630357_prodigal-single.1__X__X__00408

Identity

Kingdom:
phage

Quality

60.5 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 156-264
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.68 45.0 5.01e-01 99.1% 88.0%
3ezuA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.67 50.0 4.19e-01 77.1% 94.0%
2z1qB04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.67 53.0 4.94e-01 100.0% 67.6%
1foeA01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.66 48.0 3.99e-01 77.1% 74.5%
4hkrA00 1.20.140.140 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Calcium release-activated calcium channel protein Orai 0.66 50.0 4.37e-01 100.0% 53.3%
1gwcA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.65 42.0 3.89e-01 85.3% 51.1%
1rx0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.64 55.0 4.86e-01 100.0% 65.2%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.63 45.0 4.51e-01 98.2% 72.7%
3vadA01 1.20.140.20 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain 0.62 46.0 4.12e-01 78.0% 80.1%
3m9vA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.61 52.0 4.64e-01 99.1% 65.6%
4hfvA01 1.20.1440.330 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.58 40.0 3.97e-01 71.6% 84.6%
2b5uA02 1.10.287.620 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix Hairpins 0.57 39.0 3.44e-01 80.7% 47.2%
4n1yB00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.57 41.0 3.31e-01 77.1% 82.8%
4akgA02 1.20.140.100 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Dynein motor heavy chain, linker domain, N-terminal subdomain 0.56 50.0 4.40e-01 100.0% 81.5%
2yjkC00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.56 48.0 4.22e-01 90.8% 82.8%
3vkgA02 1.20.140.100 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Dynein motor heavy chain, linker domain, N-terminal subdomain 0.56 51.0 4.59e-01 100.0% 90.5%
8sbeA02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.54 40.0 3.41e-01 78.9% 71.1%
3bt5A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 49.0 4.36e-01 100.0% 93.4%
3r2kA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 48.0 4.20e-01 95.4% 85.1%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 43.0 3.91e-01 89.9% 94.8%
3rrkA02 1.20.1460.20 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › 0.53 45.0 4.01e-01 92.7% 73.5%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 39.0 3.84e-01 78.9% 94.9%
4etrB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 46.0 4.47e-01 100.0% 93.4%
6iknD01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.51 45.0 3.38e-01 96.3% 85.4%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3991109 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.75 55.0 5.05e-01 77.1% 87.1%
3277476 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.72 52.0 4.68e-01 100.0% 54.7%
3554292 611.2.1.1 ↗ alpha bundles › N-cbl like › N-terminal domain of cbl (N-cbl) › N-terminal domain of cbl (N-cbl) › Cbl_N 0.72 58.0 5.34e-01 100.0% 67.1%
3518474 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.70 51.0 4.80e-01 75.2% 81.5%
3998921 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.70 51.0 4.57e-01 75.2% 88.7%
3513364 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.69 51.0 4.60e-01 78.0% 72.7%
3719886 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.69 51.0 4.68e-01 77.1% 73.4%
3936715 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.68 51.0 4.70e-01 77.1% 79.0%
3217364 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.67 50.0 4.51e-01 78.0% 79.3%
3552608 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.67 49.0 4.39e-01 75.2% 77.3%
3873167 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.67 50.0 4.48e-01 78.0% 74.5%
3466334 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.66 48.0 4.54e-01 95.4% 63.1%
3625262 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.66 49.0 4.19e-01 77.1% 70.0%
3611462 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.66 49.0 4.51e-01 78.0% 75.7%
3929825 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.65 50.0 4.84e-01 99.1% 73.3%
4946483 133.2.1.1 ↗ alpha bundles › DH domain-like › Methenyltetrahydrofolate cyclohydrolase-like › Methenyltetrahydrofolate cyclohydrolase-like › FTCD_C 0.64 54.0 4.53e-01 98.2% 53.5%
4020167 633.26.1.0 ↗ alpha bundles › Bromodomain-like › SidC lipid-binding domain › SidC lipid-binding domain 0.64 49.0 4.74e-01 98.2% 73.3%
3231048 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.64 46.0 4.25e-01 75.2% 79.3%
3212520 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.64 51.0 4.52e-01 83.5% 74.0%
4013639 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.64 48.0 4.39e-01 78.0% 81.4%
4979245 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.64 44.0 4.17e-01 70.6% 93.1%
3459699 633.4.1.0 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor 0.64 47.0 4.17e-01 77.1% 69.0%
5060546 633.15.1.2 ↗ alpha bundles › Bromodomain-like › alpha-ketoacid dehydrogenase kinase-N › alpha-ketoacid dehydrogenase kinase-N › Alpha_Helical 0.63 46.0 4.50e-01 95.4% 69.2%
3334314 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.63 49.0 4.15e-01 80.7% 80.0%
3406232 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.63 47.0 4.36e-01 78.9% 78.4%
3592583 633.10.1.0 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.62 43.0 4.30e-01 100.0% 67.8%
3217241 633.10.1.0 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.62 47.0 4.05e-01 85.3% 52.1%
3219995 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.61 48.0 4.36e-01 82.6% 70.3%
3652633 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.60 44.0 4.20e-01 78.0% 76.2%
3546062 376.1.2.39 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › RHG29_45_N 0.59 43.0 4.35e-01 76.1% 100.0%
3614754 5.1.4.301 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_1, Kelch_KLHDC2_KLHL20_DRC7 0.59 48.0 3.07e-01 97.2% 18.1%
4943286 633.10.1.0 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.59 44.0 4.02e-01 98.2% 58.1%
3644752 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.58 47.0 4.14e-01 87.2% 61.9%
3427223 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.58 47.0 4.19e-01 87.2% 61.9%
3916065 633.21.1.23 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CD20 0.58 50.0 4.42e-01 100.0% 65.0%
4029410 633.4.1.0 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor 0.58 43.0 3.93e-01 100.0% 58.0%
4294309 133.2.1.1 ↗ alpha bundles › DH domain-like › Methenyltetrahydrofolate cyclohydrolase-like › Methenyltetrahydrofolate cyclohydrolase-like › FTCD_C 0.57 49.0 4.23e-01 98.2% 85.9%
3259879 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.56 50.0 4.37e-01 96.3% 75.0%
3925519 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.56 51.0 4.16e-01 99.1% 62.6%
5002054 4323.1.1.0 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C 0.53 46.0 4.09e-01 92.7% 80.7%
D2 high residues 268-434
PDB
D3 high residues 474-536
PDB
D4 medium residues 24-76
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4y6cA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.76 68.0 4.44e-01 98.1% 29.2%
3deeA01 1.10.150.690 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DUF2063 0.72 58.0 5.09e-01 94.3% 65.1%
4leuA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.70 58.0 3.91e-01 88.7% 50.0%
6fhpD00 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.69 54.0 5.17e-01 88.7% 87.1%
1bqbA02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.69 53.0 3.99e-01 88.7% 34.0%
1re0B02 1.10.1000.11 Mainly Alpha › Orthogonal Bundle › Arf Nucleotide-binding Site Opener; domain 2 › Arf Nucleotide-binding Site Opener,domain 2 0.66 52.0 4.12e-01 88.7% 60.9%
1dmhA00 2.60.130.10 Mainly Beta › Sandwich › Protocatechuate 3,4-Dioxygenase, subunit A › Aromatic compound dioxygenase 0.66 45.0 2.79e-01 71.7% 12.3%
3mpiA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.66 55.0 4.27e-01 96.2% 79.3%
3vsmA01 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.61 50.0 3.11e-01 96.2% 36.0%
2pkeA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.59 48.0 4.36e-01 98.1% 76.9%
5y5nA01 3.40.50.1220 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › TPP-binding domain 0.59 49.0 3.45e-01 98.1% 80.2%
5efrA02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.58 41.0 3.83e-01 79.2% 60.3%
4oo0B00 3.90.950.10 Alpha Beta › Alpha-Beta Complex › Maf protein › 0.57 49.0 3.36e-01 100.0% 71.1%
6cgvM01 1.20.120.1500 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pre-hexon-linking protein IIIa 0.51 43.0 3.23e-01 92.5% 79.1%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3605533 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.74 62.0 3.92e-01 92.5% 33.5%
3817621 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.74 58.0 3.41e-01 84.9% 15.9%
3441897 109.4.1.1336 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2, PPR_3 0.71 59.0 3.69e-01 88.7% 20.4%
3346105 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.71 56.0 4.24e-01 84.9% 46.7%
3328095 109.4.1.1273 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3 0.71 56.0 4.20e-01 84.9% 46.7%
3432371 109.4.1.1308 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_3, TPR_24 0.70 56.0 3.57e-01 86.8% 40.0%
3833310 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.70 55.0 4.40e-01 84.9% 56.0%
3832904 109.4.1.1293 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1 0.69 60.0 3.58e-01 96.2% 24.8%
3717237 109.4.1.3255 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_19, ARM_TT21_2nd 0.69 57.0 4.15e-01 88.7% 36.3%
3826294 109.4.1.1262 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_long 0.68 59.0 4.24e-01 94.3% 36.4%
3311468 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.68 55.0 3.79e-01 88.7% 29.4%
3814023 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.68 56.0 4.00e-01 90.6% 38.0%
3832025 109.4.1.189 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2 0.68 58.0 4.11e-01 92.5% 64.1%
3445102 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.67 55.0 4.04e-01 90.6% 42.2%
3315059 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.66 56.0 4.51e-01 92.5% 83.0%
3327863 109.4.1.184 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1 0.66 55.0 4.27e-01 90.6% 60.9%
3315061 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.65 55.0 4.36e-01 92.5% 80.0%
3812661 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.65 54.0 4.45e-01 92.5% 87.4%
3669292 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.65 55.0 3.88e-01 98.1% 76.0%