Back to structures

js4906-29-5_S40_scaffold_13_prodigal-single.1__X__X__00004

Bact-Vir

js4906-29-5_S40_scaffold_13_prodigal-single.1__X__X__00004

Identity

Kingdom:
phage

Quality

78.0 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 6-179
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.69 31.0 4.36e-01 71.8% 85.9%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.69 30.0 3.69e-01 71.8% 62.7%
2qe7G01 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.66 29.0 3.81e-01 73.0% 73.2%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.63 30.0 3.74e-01 83.3% 70.9%
3ajwA00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 32.0 3.64e-01 72.4% 64.9%
1xwmA00 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 0.61 32.0 2.99e-01 77.6% 39.2%
8ek4A01 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.59 35.0 3.99e-01 79.9% 76.7%
3tulB00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.58 31.0 3.55e-01 72.4% 68.4%
2ptqA02 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.58 40.0 3.41e-01 70.1% 77.7%
5y06A01 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 32.0 2.90e-01 72.4% 41.5%
7c1iA01 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.57 32.0 4.21e-01 76.4% 98.0%
1sj7C00 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.56 39.0 4.04e-01 70.7% 85.5%
1hciA03 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 31.0 3.66e-01 77.6% 77.5%
4bwcA02 1.10.439.20 Mainly Alpha › Orthogonal Bundle › Penicillin Amidohydrolase; domain 1 › Phospholipase B-like, domain 2 0.55 31.0 3.77e-01 85.6% 82.1%
2rgnB01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.55 38.0 3.66e-01 70.7% 81.9%
1dofA01 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.54 39.0 3.48e-01 72.4% 81.6%
2gd5A00 6.10.140.1230 Special › Helix non-globular › Helix Hairpins › 0.54 38.0 4.24e-01 71.8% 91.5%
4gyvE00 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.54 38.0 3.51e-01 70.7% 81.9%
2rd0B00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 29.0 3.26e-01 73.0% 64.7%
2pfmA02 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.54 38.0 3.34e-01 70.7% 82.0%
2lsgA00 1.20.58.1280 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DNA repair protein Rev1, C-terminal domain 0.52 23.0 2.94e-01 85.1% 67.0%
1q5nA02 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.52 37.0 3.31e-01 70.7% 81.9%
7b00A01 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.52 47.0 3.44e-01 97.7% 46.6%
6wlvB01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.50 43.0 3.76e-01 92.5% 62.3%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3704098 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.61 30.0 3.11e-01 72.4% 47.6%
3450026 633.4.1.1 alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.57 44.0 4.61e-01 80.5% 91.4%
5050364 1075.1.2.1 alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.56 38.0 3.69e-01 93.1% 59.5%
3459699 633.4.1.0 alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor 0.55 45.0 4.76e-01 98.9% 96.1%
3574609 3755.4.1.0 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.54 32.0 3.09e-01 100.0% 50.5%
3360919 633.4.1.1 alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.54 41.0 4.49e-01 78.7% 95.8%
3263402 133.1.1.1 alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.54 38.0 3.58e-01 71.3% 83.8%
4964758 1079.1.1.0 alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA 0.53 40.0 3.81e-01 99.4% 65.9%
3940399 150.1.1.24 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Prominin 0.53 44.0 3.90e-01 88.5% 89.2%
3942760 1079.1.1.8 alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › LysE 0.52 39.0 3.71e-01 100.0% 65.4%
3523901 148.1.3.321 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › PF26346 0.52 32.0 3.29e-01 71.8% 64.8%
4979297 7064.1.1.1 alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › VIT1 0.51 36.0 3.56e-01 90.2% 67.8%
3624755 174.1.1.0 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.50 37.0 3.68e-01 97.1% 73.3%
3241030 4177.1.1.0 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.50 39.0 3.14e-01 100.0% 44.1%
D2 high residues 360-494
PDB
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1repC02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.69 46.0 5.44e-01 74.8% 100.0%
7xc2A02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.67 48.0 5.38e-01 96.3% 95.3%
5mmjh01 3.30.1370.30 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.65 35.0 4.50e-01 73.3% 93.3%
3qx3B03 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.65 34.0 3.89e-01 70.4% 68.0%
3keyA02 3.30.1370.230 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Stn1, C-terminal wHTH domain 0.64 40.0 4.85e-01 72.6% 96.6%
6kf9G01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.62 38.0 4.66e-01 77.8% 100.0%
4b09B02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.61 43.0 4.86e-01 81.5% 99.0%
1kyzA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 37.0 4.16e-01 77.0% 81.6%
3r0aA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 41.0 4.38e-01 80.0% 80.8%
4hqeA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 41.0 4.55e-01 97.0% 93.3%
1fpqA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 38.0 3.94e-01 80.0% 73.6%
2dchX01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.55 34.0 3.97e-01 82.2% 88.2%
3l9fA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 35.0 4.16e-01 90.4% 97.8%
1b24A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.53 37.0 4.22e-01 91.9% 100.0%
5h20A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 37.0 4.11e-01 91.1% 95.1%
4hlyA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 37.0 4.08e-01 74.1% 100.0%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4192947 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.68 55.0 5.08e-01 84.4% 99.4%
3638163 101.1.2.154 alpha arrays › HTH › HTH › winged helix domain › CDT1_C 0.66 39.0 4.37e-01 72.6% 73.8%
3588764 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.66 53.0 5.62e-01 85.2% 99.2%
3168448 101.1.2.154 alpha arrays › HTH › HTH › winged helix domain › CDT1_C 0.65 39.0 3.98e-01 72.6% 61.2%
1145702 101.1.2.134 alpha arrays › HTH › HTH › winged helix domain › Stn1_C 0.64 41.0 4.84e-01 72.6% 96.6%
4487383 101.1.2.101 alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.60 44.0 4.84e-01 94.1% 93.6%
2427478 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.58 42.0 3.61e-01 73.3% 53.4%
4027206 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.58 39.0 3.91e-01 76.3% 65.0%
4373647 101.1.2.101 alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.58 44.0 4.66e-01 97.8% 90.0%
4933997 101.1.2.101 alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.57 43.0 4.55e-01 97.8% 89.2%
3972517 101.1.2.8 alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.57 42.0 4.58e-01 76.3% 96.3%
3702324 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.57 39.0 4.45e-01 71.1% 97.0%
4635715 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.57 45.0 4.23e-01 83.0% 71.9%
5035027 101.1.2.30 alpha arrays › HTH › HTH › winged helix domain › TrmB 0.57 39.0 4.14e-01 80.0% 79.8%
4979490 101.1.2.101 alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.56 42.0 4.47e-01 98.5% 89.2%
5049515 101.1.2.101 alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.55 44.0 4.75e-01 98.5% 100.0%
3710667 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.53 46.0 3.72e-01 94.1% 51.5%
4503351 101.1.2.101 alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.53 39.0 4.29e-01 98.5% 97.1%
5076707 101.1.2.48 alpha arrays › HTH › HTH › winged helix domain › PadR 0.53 37.0 4.12e-01 96.3% 93.3%
3744355 101.1.2.148 alpha arrays › HTH › HTH › winged helix domain › ORC5_C 0.53 43.0 4.44e-01 96.3% 93.6%
D3 medium residues 188-347
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1hkqA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.76 48.0 5.40e-01 93.8% 80.8%
2nraC01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.66 45.0 4.66e-01 93.8% 73.3%
4h0eA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.65 31.0 4.36e-01 90.0% 100.0%
4j3cA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.55 25.0 3.62e-01 81.9% 100.0%
1wg1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 22.0 3.08e-01 87.5% 74.6%
2cpjA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.53 20.0 2.52e-01 82.5% 49.5%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3588764 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.79 50.0 5.77e-01 94.4% 85.0%
2618 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.76 48.0 5.40e-01 93.8% 80.8%
3590646 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.73 48.0 5.38e-01 93.8% 84.8%
4218945 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.72 46.0 5.17e-01 94.4% 82.4%
3508541 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.70 45.0 4.99e-01 94.4% 80.0%
3992233 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.69 38.0 4.76e-01 93.1% 86.0%
4192947 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.68 60.0 5.97e-01 94.4% 89.7%
4437876 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.68 59.0 5.92e-01 94.4% 90.6%
3986771 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.68 45.0 4.98e-01 93.8% 81.5%
4606139 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.66 35.0 4.73e-01 87.5% 100.0%
3946400 101.1.2.16 alpha arrays › HTH › HTH › winged helix domain › Rep3_N 0.66 59.0 5.72e-01 94.4% 89.7%
2061059 101.1.2.131 alpha arrays › HTH › HTH › winged helix domain › RctB_central 0.66 59.0 5.67e-01 95.0% 89.4%
3786023 101.1.2.154 alpha arrays › HTH › HTH › winged helix domain › CDT1_C 0.65 39.0 3.40e-01 83.7% 39.2%
5017359 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.65 34.0 4.68e-01 90.0% 97.6%
3274016 101.1.2.393 alpha arrays › HTH › HTH › winged helix domain › WH_MCM2 0.65 34.0 4.61e-01 88.7% 100.0%
3700540 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.65 33.0 4.52e-01 87.5% 97.5%
4991791 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.65 34.0 4.33e-01 91.3% 85.3%
3187002 101.1.2.635 alpha arrays › HTH › HTH › winged helix domain › CDT1_C, PF26121 0.63 38.0 3.09e-01 83.7% 32.4%
4976018 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.63 32.0 4.02e-01 100.0% 81.1%
4028677 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.62 33.0 3.98e-01 91.3% 78.1%
1944496 101.1.2.131 alpha arrays › HTH › HTH › winged helix domain › RctB_central 0.62 38.0 4.56e-01 93.8% 90.8%
3264579 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.58 25.0 2.96e-01 88.1% 53.9%
3932917 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.57 31.0 3.92e-01 90.0% 91.1%
3716735 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.56 31.0 3.62e-01 90.0% 73.9%
3613894 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.53 35.0 2.92e-01 89.4% 39.2%
3487323 214.1.1.1 a+b two layers › SH2 › SH2 › SH2 › SH2 0.50 26.0 3.25e-01 90.6% 85.9%