Back to structures

JGI24723J26617_10000007_prodigal-single.1__X__X__00499

Bact-Vir

JGI24723J26617_10000007_prodigal-single.1__X__X__00499

Identity

Kingdom:
phage

Quality

94.2 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 1-52
PDB
Domain cluster: representative
CATH (55)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.98 83.0 8.64e-01 94.2% 95.8%
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 0.98 82.0 8.29e-01 88.5% 88.5%
1jgcA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.97 92.0 6.21e-01 100.0% 32.5%
3ggyA00 1.20.1260.60 Mainly Alpha › Up-down Bundle › Ferritin › Vacuolar protein sorting-associated protein Ist1 0.96 90.0 5.91e-01 100.0% 28.0%
3pwfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.96 90.0 6.42e-01 100.0% 39.7%
2gd5A00 6.10.140.1230 Special › Helix non-globular › Helix Hairpins › 0.96 89.0 6.27e-01 100.0% 36.6%
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 0.95 82.0 6.97e-01 90.4% 61.0%
1j30A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.95 89.0 6.25e-01 100.0% 36.9%
2vxxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.95 89.0 5.94e-01 100.0% 30.2%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.95 88.0 6.15e-01 100.0% 35.9%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.94 82.0 7.79e-01 100.0% 81.4%
3t9jA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.94 88.0 6.16e-01 100.0% 36.1%
2hr2A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.94 77.0 5.28e-01 92.3% 28.8%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.93 77.0 8.17e-01 88.5% 100.0%
1nt2B02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.93 86.0 7.84e-01 100.0% 98.5%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.93 82.0 7.11e-01 98.1% 65.3%
3iq1B00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.93 86.0 5.87e-01 100.0% 33.3%
2ieqA00 1.20.5.300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.93 85.0 7.00e-01 100.0% 98.9%
2rd0B00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.92 84.0 6.02e-01 100.0% 52.5%
3c18A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.92 84.0 6.28e-01 100.0% 44.9%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.91 82.0 7.08e-01 96.2% 65.8%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.91 76.0 7.67e-01 90.4% 90.4%
3zc0D00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.90 83.0 5.48e-01 100.0% 27.8%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.90 82.0 7.39e-01 100.0% 75.4%
1yw0A00 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.90 82.0 5.14e-01 100.0% 21.4%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.89 81.0 7.61e-01 100.0% 85.5%
1e2aA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.88 80.0 6.29e-01 100.0% 52.0%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.88 80.0 8.07e-01 98.1% 100.0%
1fpoC02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.87 78.0 6.44e-01 100.0% 57.1%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.87 77.0 6.09e-01 100.0% 62.3%
4gzrB00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.87 80.0 6.92e-01 100.0% 90.9%
3p42A02 6.10.250.2280 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.87 66.0 5.98e-01 94.2% 61.4%
1wfdA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.85 66.0 5.41e-01 86.5% 47.3%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.85 74.0 6.08e-01 100.0% 54.8%
3nkzA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.85 74.0 6.06e-01 100.0% 53.6%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.84 73.0 6.67e-01 94.2% 98.5%
1pd3A00 1.10.287.230 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.81 72.0 7.17e-01 100.0% 96.3%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 63.0 5.09e-01 90.4% 60.4%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.77 65.0 5.92e-01 96.2% 100.0%
2ke4A00 6.10.140.470 Special › Helix non-globular › Helix Hairpins › 0.77 67.0 5.46e-01 100.0% 54.1%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.77 66.0 4.74e-01 98.1% 35.8%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.76 65.0 5.94e-01 100.0% 90.1%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.76 66.0 6.21e-01 100.0% 84.4%
1dd3A01 1.20.5.710 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Single helix bin 0.76 56.0 5.47e-01 80.8% 78.9%
4bx8A03 3.90.830.10 Alpha Beta › Alpha-Beta Complex › Syntaxin Binding Protein 1; Chain A, domain 2 › Sec1/Munc18 (SM) protein, domain 3a 0.76 64.0 5.15e-01 100.0% 48.1%
6h9xA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.75 63.0 5.16e-01 100.0% 50.0%
4ijjB00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.75 62.0 4.68e-01 96.2% 61.5%
2o5vA02 1.20.1050.90 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › RecF/RecN/SMC, N-terminal domain 0.74 62.0 4.33e-01 96.2% 29.0%
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 0.74 60.0 6.13e-01 94.2% 100.0%
1b3qA01 1.10.287.560 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Histidine kinase CheA-like, homodimeric domain 0.74 61.0 5.89e-01 100.0% 83.9%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 60.0 5.42e-01 100.0% 70.5%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.72 59.0 4.25e-01 100.0% 30.3%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.70 58.0 5.09e-01 100.0% 65.9%
2bdeA03 1.20.58.1160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 57.0 5.18e-01 100.0% 67.5%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.69 62.0 5.47e-01 100.0% 73.0%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4209183 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.98 93.0 6.86e-01 100.0% 45.2%
4259375 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.98 92.0 6.94e-01 100.0% 47.3%
3799151 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.97 92.0 5.82e-01 100.0% 24.2%
3497845 109.4.1.1474 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_6, TPR_16 0.97 92.0 5.36e-01 100.0% 14.9%
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 0.97 89.0 9.06e-01 96.2% 100.0%
3703892 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.97 92.0 5.97e-01 100.0% 27.5%
3598711 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.97 92.0 4.98e-01 100.0% 7.2%
4477580 5086.1.1.118 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › BBS2_hp 0.97 91.0 7.51e-01 100.0% 61.2%
3623892 150.1.1.109 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › LUC7 0.97 91.0 6.23e-01 100.0% 33.5%
4674043 632.11.1.12 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › UVR 0.96 90.0 7.30e-01 100.0% 57.8%
3944931 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.96 90.0 7.29e-01 100.0% 57.8%
3790037 109.4.1.1946 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_2, TPR_8, TPR_12 0.96 90.0 5.31e-01 100.0% 16.0%
3484742 3922.1.1.197 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › BBS2_hp 0.96 90.0 7.40e-01 100.0% 61.2%
3256134 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 0.96 89.0 6.58e-01 100.0% 43.3%
3677185 4992.1.1.27 extended segments › RelB-like › RelB-like › RelB-like › Ist1 0.95 89.0 7.18e-01 100.0% 57.8%
2800296 150.1.1.3 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.95 88.0 6.17e-01 100.0% 35.6%
3378334 604.12.1.65 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT_ATG1 0.95 88.0 6.29e-01 100.0% 38.5%
3738041 192.5.1.1 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.95 88.0 7.31e-01 100.0% 61.2%
4993041 150.1.1.3 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.94 88.0 7.44e-01 100.0% 65.0%
5005597 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 0.94 88.0 6.25e-01 100.0% 39.3%
3626769 192.5.1.14 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.94 87.0 7.09e-01 100.0% 73.3%
3440791 604.12.1.65 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT_ATG1 0.94 87.0 6.37e-01 100.0% 41.6%
4974154 150.1.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.94 86.0 5.82e-01 100.0% 30.6%
3732610 3291.1.1.3 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Ist1 0.94 87.0 5.59e-01 100.0% 25.4%
3816612 3291.1.1.3 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Ist1 0.94 87.0 5.75e-01 100.0% 28.9%
4399468 150.1.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.94 86.0 5.87e-01 100.0% 32.7%
3213526 192.5.1.14 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.94 87.0 6.69e-01 100.0% 62.9%
3246163 109.4.1.1286 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_12 0.93 87.0 5.12e-01 100.0% 15.5%
3166880 906.1.1.0 few secondary structure elements › CCCH zinc finger › CCCH zinc finger › CCCH zinc finger 0.93 86.0 7.68e-01 100.0% 74.3%
3175368 376.1.3.81 few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › Rbsn 0.93 86.0 7.49e-01 100.0% 69.3%
3999236 622.1.1.1 alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › HSCB_C 0.93 85.0 6.60e-01 100.0% 49.5%
4930198 605.1.1.2 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › H-kinase_dim 0.93 83.0 7.94e-01 98.1% 85.0%
3451986 3291.1.1.79 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › DUF1771 0.93 85.0 6.42e-01 100.0% 45.2%
5030918 632.11.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › DUF357 0.92 85.0 7.17e-01 98.1% 65.0%
3525292 906.1.1.3 few secondary structure elements › CCCH zinc finger › CCCH zinc finger › CCCH zinc finger › LUC7 0.92 84.0 8.04e-01 100.0% 86.7%
3907712 5086.1.1.150 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › LUC7 0.92 84.0 7.38e-01 100.0% 69.3%
4873190 3291.1.1.3 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Ist1 0.92 85.0 5.61e-01 100.0% 28.3%
3748986 3755.3.1.322 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › LUC7 0.92 84.0 5.67e-01 100.0% 29.7%
4015620 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 0.91 83.0 5.55e-01 100.0% 28.9%
3567670 192.5.1.14 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.91 83.0 6.82e-01 100.0% 73.3%
4023890 622.1.1.1 alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › HSCB_C 0.90 82.0 7.05e-01 100.0% 65.8%
3784740 3712.1.1.1 a+b complex topology › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Med11 0.90 82.0 7.17e-01 100.0% 69.3%
3925617 192.5.1.14 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1_TOCA 0.90 83.0 6.91e-01 100.0% 61.2%
3569669 4177.1.1.2 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.90 81.0 5.34e-01 100.0% 26.7%
3516214 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.90 81.0 6.68e-01 100.0% 57.8%
3527434 6006.1.1.6 extended segments › Voltage gated calcium channel IQ domain › Voltage gated calcium channel IQ domain › Voltage gated calcium channel IQ domain › PF27661 0.89 80.0 5.61e-01 100.0% 33.5%
4955275 632.11.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.89 80.0 6.60e-01 100.0% 57.8%
3356408 103.1.1.0 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.86 77.0 5.81e-01 100.0% 43.3%
4784166 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.73 61.0 5.70e-01 100.0% 75.7%