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SR-VP_4-6_scaffold_141_3113143_prodigal-single.1__X__X__00217

Bact-Vir

SR-VP_4-6_scaffold_141_3113143_prodigal-single.1__X__X__00217

Identity

Kingdom:
phage

Quality

59.1 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 medium residues 166-219
PDB
Domain cluster: representative
CATH (65)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4i1aA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.95 69.0 4.21e-01 79.6% 15.0%
2rklF00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.94 70.0 7.14e-01 77.8% 80.8%
1iipA02 1.10.150.160 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.92 85.0 7.15e-01 100.0% 64.7%
2yxyA01 1.10.287.880 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Hypothetical protein YfhH domain 0.91 67.0 6.97e-01 79.6% 84.0%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.90 71.0 6.29e-01 85.2% 60.5%
7c1iA01 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.89 67.0 5.35e-01 79.6% 43.0%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.88 71.0 6.26e-01 87.0% 61.8%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.88 66.0 7.05e-01 79.6% 100.0%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.87 77.0 5.81e-01 98.1% 94.4%
2hr2A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.87 66.0 4.66e-01 87.0% 28.2%
3zc0D00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.87 72.0 4.84e-01 92.6% 25.7%
3ro3A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.87 63.0 4.36e-01 79.6% 25.8%
3e6sA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.87 78.0 5.42e-01 98.1% 34.0%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.86 69.0 5.73e-01 87.0% 51.1%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.86 68.0 6.03e-01 85.2% 59.7%
4fymF00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.86 68.0 4.51e-01 87.0% 22.5%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.86 72.0 5.48e-01 94.4% 41.3%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.86 64.0 6.54e-01 79.6% 82.7%
1s3qG00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.85 78.0 5.41e-01 100.0% 33.1%
1vh6A01 6.10.140.1940 Special › Helix non-globular › Helix Hairpins › 0.85 76.0 6.23e-01 100.0% 55.7%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.85 68.0 7.25e-01 85.2% 100.0%
2katA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.84 63.0 4.87e-01 81.5% 37.4%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.84 74.0 5.32e-01 100.0% 35.1%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 75.0 5.44e-01 100.0% 40.0%
3pwfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 70.0 5.24e-01 92.6% 38.9%
3qhbA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 75.0 5.12e-01 100.0% 31.3%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.84 66.0 5.95e-01 87.0% 62.7%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.84 75.0 6.02e-01 100.0% 53.4%
4gyoA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.83 64.0 4.18e-01 83.3% 100.0%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.83 70.0 5.13e-01 92.6% 37.0%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.83 63.0 5.64e-01 81.5% 59.5%
1j30A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.83 74.0 5.41e-01 100.0% 46.1%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.81 70.0 5.49e-01 92.6% 48.6%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.81 65.0 5.44e-01 87.0% 62.6%
1jgcA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.81 71.0 5.07e-01 100.0% 35.0%
3hiuD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.80 71.0 5.10e-01 100.0% 36.8%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.80 57.0 5.44e-01 79.6% 64.1%
2lf0A01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.80 67.0 6.50e-01 92.6% 86.7%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 72.0 6.53e-01 100.0% 83.1%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.80 65.0 4.97e-01 96.3% 40.3%
3craB01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.80 66.0 5.69e-01 94.4% 59.3%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.79 62.0 5.43e-01 87.0% 57.3%
3r2kA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.79 70.0 5.02e-01 100.0% 35.7%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.79 62.0 5.31e-01 87.0% 54.0%
1tjoB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.79 72.0 4.94e-01 100.0% 30.9%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.79 61.0 5.11e-01 87.0% 49.5%
4fm3A00 1.20.1270.390 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.79 69.0 5.73e-01 100.0% 56.8%
2oh3A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.78 67.0 4.93e-01 98.1% 36.1%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.78 64.0 6.55e-01 94.4% 96.1%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.77 63.0 5.00e-01 92.6% 45.1%
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.77 65.0 4.86e-01 100.0% 42.9%
1e2aA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.76 69.0 5.55e-01 100.0% 55.9%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.75 60.0 4.85e-01 90.7% 46.4%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.75 67.0 5.42e-01 100.0% 55.9%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.75 63.0 4.48e-01 100.0% 36.6%
1rv2D04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.75 62.0 5.78e-01 100.0% 74.3%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.75 55.0 5.22e-01 79.6% 70.3%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 63.0 5.90e-01 100.0% 95.7%
2zueA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.73 60.0 4.69e-01 92.6% 42.9%
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.71 53.0 5.54e-01 87.0% 95.8%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.69 57.0 5.33e-01 98.1% 81.7%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.68 56.0 4.93e-01 100.0% 83.3%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.68 54.0 5.09e-01 100.0% 73.3%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.68 52.0 4.67e-01 88.9% 59.5%
4cc9B00 1.20.5.4730 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.64 47.0 3.88e-01 79.6% 49.0%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5035450 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.98 75.0 5.99e-01 79.6% 45.3%
4419795 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.95 68.0 7.79e-01 74.1% 100.0%
4228771 506.2.1.0 ↗ beta meanders › Colicin E3 ribonuclease domain-like › UvrB interaction domain › UvrB interaction domain 0.95 73.0 5.03e-01 81.5% 27.5%
4033601 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.94 83.0 6.69e-01 94.4% 53.7%
4266946 192.17.1.11 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › UVR 0.93 76.0 5.70e-01 90.7% 39.2%
3616031 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.92 83.0 6.68e-01 98.1% 54.7%
4618805 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.92 79.0 7.91e-01 92.6% 90.9%
5073700 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.91 67.0 4.48e-01 77.8% 22.7%
4472442 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.91 64.0 7.29e-01 74.1% 100.0%
5007277 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.90 73.0 6.20e-01 87.0% 55.3%
4347101 5086.1.1.119 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › RRG1_C 0.90 82.0 6.81e-01 100.0% 60.0%
5030918 632.11.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › DUF357 0.90 72.0 6.27e-01 87.0% 58.7%
4942399 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.89 75.0 6.22e-01 90.7% 54.4%
None — 0.89 73.0 4.11e-01 87.0% 9.1%
5044025 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.89 77.0 6.53e-01 94.4% 60.0%
3409452 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.89 79.0 6.73e-01 98.1% 62.4%
4324075 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.88 71.0 7.48e-01 85.2% 95.8%
4530141 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.87 72.0 7.52e-01 90.7% 96.0%
3965106 605.1.1.4 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.87 79.0 7.02e-01 100.0% 73.3%
5025189 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.87 77.0 7.67e-01 98.1% 98.2%
140767 632.8.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › DUF6853 0.87 77.0 5.81e-01 98.1% 94.4%
3799142 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.87 72.0 6.56e-01 90.7% 71.4%
3560590 3755.3.1.142 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › FAM186A-B_C 0.86 77.0 5.53e-01 100.0% 36.7%
3560750 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.86 75.0 6.88e-01 98.1% 75.7%
3961063 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.85 76.0 4.69e-01 98.1% 18.6%
3576866 3291.1.1.1 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.85 77.0 5.19e-01 100.0% 30.3%
55853 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.84 71.0 5.12e-01 92.6% 34.9%
4955275 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.84 73.0 6.16e-01 100.0% 58.9%
4993041 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.84 71.0 6.19e-01 92.6% 62.5%
4085606 632.22.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.83 73.0 5.79e-01 100.0% 50.9%
3419469 3444.2.1.0 ↗ alpha arrays › DP domain › XPC-binding domain and DDI helical domain › XPC-binding domain 0.83 68.0 6.77e-01 90.7% 89.1%
5027310 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.82 73.0 5.98e-01 100.0% 55.8%
4930709 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.81 71.0 4.84e-01 100.0% 28.2%
3687822 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.80 63.0 3.86e-01 87.0% 14.2%
4386662 3291.1.1.158 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Seryl_tRNA_N 0.80 72.0 5.53e-01 98.1% 47.8%
3425296 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.80 72.0 5.29e-01 100.0% 63.7%
2389382 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.79 70.0 4.97e-01 100.0% 34.6%
4514051 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.79 71.0 5.46e-01 98.1% 47.8%