Back to structures

Ig7659_scaffold_8_prodigal-single.1__X__X__00036

Bact-Vir

Ig7659_scaffold_8_prodigal-single.1__X__X__00036

Identity

Kingdom:
phage

Quality

71.8 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 220-374
PDB
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1n4kA02 1.25.10.30 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › IP3 receptor type 1 binding core, RIH domain 0.59 33.0 3.43e-01 83.9% 56.1%
2khvA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.58 33.0 4.20e-01 98.7% 100.0%
2pusA04 6.10.140.300 Special › Helix non-globular › Helix Hairpins › 0.57 33.0 3.83e-01 96.8% 79.6%
6yttA01 1.10.8.190 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 0.54 26.0 3.13e-01 85.8% 67.0%
2wv2A00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.53 49.0 3.51e-01 100.0% 61.2%
1c17M00 1.20.120.220 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ATP synthase, F0 complex, subunit A 0.53 30.0 3.21e-01 89.0% 61.3%
3ctwB00 1.10.8.930 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Protein of unknown function DUF1465 0.52 29.0 3.25e-01 94.2% 70.0%
3hdeC00 1.10.530.40 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.50 30.0 2.96e-01 87.7% 53.0%
6o0aA01 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.50 34.0 3.46e-01 100.0% 70.5%
8b2sA01 1.10.530.40 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.50 31.0 3.20e-01 92.3% 61.7%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3510049 2004.1.1.286 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TraG-D_C 0.92 77.0 5.13e-01 100.0% 26.7%
4996239 601.7.1.2 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.63 37.0 3.92e-01 89.7% 62.9%
3277781 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.63 37.0 4.13e-01 85.8% 74.2%
5077650 601.7.1.2 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.61 37.0 4.00e-01 87.1% 70.0%
3203655 601.16.1.0 alpha bundles › Four-helical up-and-down bundle › FAT domain of focal adhesion kinase › FAT domain of focal adhesion kinase 0.55 27.0 2.86e-01 84.5% 47.9%
3278871 2006.1.1.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.51 40.0 3.46e-01 83.2% 87.7%
D2 medium residues 1-87
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1sumB02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.75 52.0 4.64e-01 71.3% 80.5%
1fioA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 42.0 3.30e-01 70.1% 61.1%
3piwA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.60 41.0 3.43e-01 71.3% 42.9%
1xlyA00 1.20.200.20 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › She2 domain 0.60 44.0 3.32e-01 79.3% 81.7%
4dkcB00 1.20.1250.80 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Interleukin-34 0.59 39.0 3.26e-01 72.4% 36.9%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.59 41.0 4.49e-01 74.7% 88.7%
1kf6C00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.56 46.0 4.11e-01 92.0% 77.7%
4a25B01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 40.0 3.33e-01 77.0% 77.6%
5ejrA01 1.25.40.530 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › MyTH4 domain 0.55 40.0 3.10e-01 77.0% 78.1%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.55 40.0 3.75e-01 77.0% 89.6%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.54 41.0 4.24e-01 81.6% 86.4%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.54 35.0 4.02e-01 71.3% 95.1%
2fzfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 41.0 3.42e-01 81.6% 81.3%
3p9aF00 1.10.132.80 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.52 36.0 3.15e-01 71.3% 81.3%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4531422 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.69 50.0 4.69e-01 75.9% 70.5%
3262123 331.1.1.12 a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › DUF155 0.67 48.0 3.60e-01 74.7% 69.5%
3488077 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.63 45.0 4.39e-01 74.7% 93.7%
5066829 5081.1.1.1 alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.63 44.0 3.32e-01 72.4% 85.7%
4422429 2004.1.1.238 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C,ResIII 0.61 49.0 2.97e-01 85.1% 58.1%
4977048 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.60 41.0 3.93e-01 75.9% 59.2%
4328699 150.3.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › Hormone_1 0.60 41.0 3.13e-01 72.4% 31.6%
3594932 6158.1.1.0 alpha bundles › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region 0.58 41.0 4.18e-01 73.6% 84.7%
3713379 109.4.1.22 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N 0.57 44.0 2.97e-01 81.6% 62.5%
4944733 7523.1.1.0 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.56 44.0 3.32e-01 83.9% 60.5%
4077176 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.53 37.0 3.74e-01 74.7% 83.3%
D3 medium residues 127-162_486-581
PDB
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1e9rD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.79 75.0 5.58e-01 100.0% 78.7%
5e3iA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.56 36.0 4.05e-01 100.0% 84.8%
1g5hB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.55 36.0 3.94e-01 100.0% 80.4%
3ialA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.52 37.0 3.93e-01 100.0% 81.5%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3510049 2004.1.1.286 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TraG-D_C 0.91 87.0 5.65e-01 100.0% 88.5%
3942256 2004.1.1.552 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T4SS-DNA_transf, TraG-D_C 0.84 80.0 5.11e-01 100.0% 86.4%
4408828 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.81 70.0 4.96e-01 92.4% 82.6%
3942393 2004.1.1.173 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TrwB_AAD_bind 0.80 76.0 5.11e-01 100.0% 80.9%
3588825 2004.1.1.552 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T4SS-DNA_transf, TraG-D_C 0.79 74.0 4.87e-01 100.0% 83.1%
3512583 2004.1.1.173 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TrwB_AAD_bind 0.79 75.0 4.96e-01 100.0% 80.0%
3280179 2004.1.1.552 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T4SS-DNA_transf, TraG-D_C 0.78 73.0 4.87e-01 100.0% 82.9%
4313221 2004.1.1.552 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T4SS-DNA_transf, TraG-D_C 0.78 73.0 4.80e-01 100.0% 80.0%
4065107 2004.1.1.552 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T4SS-DNA_transf, TraG-D_C 0.75 70.0 4.47e-01 100.0% 68.8%
3291254 2004.1.1.286 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TraG-D_C 0.74 69.0 4.50e-01 100.0% 68.7%
3286563 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.57 35.0 3.66e-01 97.7% 65.6%
3314214 7502.1.1.7 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon2 0.55 35.0 3.76e-01 100.0% 74.5%
5011457 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.55 34.0 3.87e-01 100.0% 85.3%
4335045 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.53 33.0 3.68e-01 100.0% 78.1%
4671615 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.53 33.0 3.60e-01 100.0% 76.2%
4932715 7502.1.1.1 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.51 34.0 3.37e-01 100.0% 63.7%
5056023 3110.1.1.0 a/b three-layered sandwiches › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain 0.51 34.0 3.73e-01 97.0% 84.8%
3222006 7502.1.1.0 a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.50 31.0 3.44e-01 100.0% 79.0%
D4 medium residues 163-214_380-485
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qaiB00 3.40.50.10580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ATPase, V1 complex, subunit F 0.68 33.0 4.23e-01 98.7% 79.1%
1yb5A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.61 44.0 4.36e-01 98.7% 69.6%
6h0cA02 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.59 42.0 4.32e-01 99.4% 75.7%
2j6pA00 3.40.250.10 Alpha Beta › 3-Layer(aba) Sandwich › Oxidized Rhodanese; domain 1 › Rhodanese-like domain 0.59 39.0 4.06e-01 82.9% 71.7%
4j1qA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 51.0 3.78e-01 98.7% 56.6%
3e9qA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 50.0 4.29e-01 97.5% 89.8%
1b1aA00 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.54 37.0 3.99e-01 98.7% 80.3%
2orwB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 40.0 4.37e-01 98.7% 94.5%
4g4sO01 3.40.50.12120 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › POC1 chaperone 0.53 41.0 3.79e-01 99.4% 64.0%
3czpB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 44.0 3.99e-01 98.7% 67.6%
3b1fA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 46.0 4.50e-01 100.0% 93.1%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3510049 2004.1.1.286 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TraG-D_C 0.89 86.0 5.81e-01 100.0% 61.2%
3942256 2004.1.1.552 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T4SS-DNA_transf, TraG-D_C 0.77 74.0 4.93e-01 100.0% 59.6%
4928996 2004.1.1.173 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TrwB_AAD_bind 0.72 68.0 4.85e-01 100.0% 60.2%
4984219 2004.1.1.76 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.69 55.0 3.97e-01 100.0% 31.2%
5024736 2004.1.1.173 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TrwB_AAD_bind 0.65 61.0 4.49e-01 100.0% 64.7%
4408828 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.63 60.0 4.38e-01 100.0% 50.4%
4954697 2004.1.1.343 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_14 0.62 47.0 3.88e-01 99.4% 45.6%
5070648 2004.1.1.343 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_14 0.61 46.0 4.86e-01 99.4% 87.1%
4954700 2004.1.1.343 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_14 0.61 46.0 3.91e-01 99.4% 48.2%
5022193 2004.1.1.343 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_14 0.60 45.0 3.89e-01 99.4% 51.5%
5014344 2004.1.1.343 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_14 0.59 43.0 3.80e-01 99.4% 51.5%
4037283 7514.1.1.3 a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › NAD_binding_6 0.57 39.0 4.30e-01 98.1% 88.0%
None 0.55 39.0 3.92e-01 99.4% 70.6%
3252783 2004.1.1.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA 0.55 40.0 3.85e-01 98.7% 65.6%
3738034 2004.1.1.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA 0.54 37.0 3.45e-01 98.7% 54.9%
4985426 3110.1.1.0 a/b three-layered sandwiches › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain 0.54 31.0 3.78e-01 83.5% 90.5%
4392500 2004.1.1.233 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Cas3-like_C_2 0.54 44.0 3.99e-01 100.0% 64.3%
3565119 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 47.0 2.71e-01 96.8% 20.5%
4965519 2004.1.1.194 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C_2 0.52 46.0 4.19e-01 96.8% 87.1%
3349317 7589.1.1.1 a/b three-layered sandwiches › YgbK-like › YgbK-like › YgbK-like › SBD_N 0.52 41.0 3.29e-01 88.0% 44.1%
5037094 2004.1.1.194 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C_2 0.51 45.0 4.06e-01 98.1% 86.7%
3695548 2004.1.1.425 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA, DUF815 0.51 39.0 3.82e-01 99.4% 72.2%
3608352 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.51 45.0 3.71e-01 100.0% 88.1%
5066333 2004.1.1.196 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_22 0.50 41.0 3.59e-01 99.4% 57.1%
3953468 2002.1.1.16 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Bac_luciferase 0.50 44.0 3.35e-01 96.8% 51.9%
D5 medium residues 784-803_882-944
PDB