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NC_019408.1__YP_006989318.1__D869_gp143__00289

Bact-Vir

NC_019408.1__YP_006989318.1__D869_gp143__00289

Identity

Accession:
NC_019408 ↗
Kingdom:
phage

Quality

84.5 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 medium residues 1-89
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1r6bX03 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.56 39.0 3.92e-01 71.9% 73.9%
3smtA02 3.90.1420.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 2 › Rubisco LSMT, substrate-binding domain 0.55 38.0 3.21e-01 74.2% 42.7%
3deeA01 1.10.150.690 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DUF2063 0.54 38.0 3.89e-01 79.8% 76.7%
2p6vA00 1.20.120.1110 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › TAFH/NHR1 domain 0.53 34.0 3.39e-01 71.9% 59.8%
4yt3A00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.50 37.0 2.49e-01 79.8% 28.6%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.50 32.0 3.38e-01 73.0% 71.6%
1zylA03 1.20.1270.170 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.50 34.0 3.36e-01 71.9% 84.5%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5070891 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.61 27.0 2.86e-01 92.1% 43.8%
3235811 601.19.1.0 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.52 40.0 3.25e-01 83.1% 61.7%
D2 medium residues 90-143
PDB
Domain cluster: representative
CATH (56)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2yxyA01 1.10.287.880 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Hypothetical protein YfhH domain 0.97 71.0 7.41e-01 75.9% 82.0%
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 0.95 69.0 7.10e-01 75.9% 78.8%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.94 78.0 8.06e-01 87.0% 92.2%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.93 75.0 8.10e-01 85.2% 100.0%
2katA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.92 70.0 5.29e-01 81.5% 37.4%
1zs3A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.92 80.0 5.42e-01 92.6% 29.2%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.92 76.0 6.16e-01 87.0% 51.1%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.92 73.0 6.43e-01 85.2% 60.5%
3agtA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.92 84.0 6.13e-01 100.0% 40.6%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.91 77.0 5.57e-01 90.7% 35.5%
1jgcA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.91 84.0 5.82e-01 100.0% 33.8%
2gs4A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.91 84.0 5.81e-01 100.0% 34.2%
2chpA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.91 76.0 5.41e-01 90.7% 33.1%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.91 72.0 6.38e-01 85.2% 61.3%
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 0.90 72.0 6.33e-01 85.2% 59.7%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.90 68.0 5.17e-01 79.6% 37.9%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.90 72.0 6.33e-01 85.2% 60.5%
3n71A03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.90 68.0 4.39e-01 79.6% 20.2%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.90 74.0 5.27e-01 90.7% 32.2%
3hiuD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.90 80.0 5.66e-01 98.1% 34.9%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.89 67.0 6.89e-01 83.3% 82.7%
4j8dD00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.89 61.0 4.24e-01 72.2% 24.1%
1nfvA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.89 81.0 5.55e-01 100.0% 32.0%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.88 80.0 6.38e-01 100.0% 56.3%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.88 79.0 5.89e-01 100.0% 42.7%
2wwxB00 1.20.1260.70 Mainly Alpha › Up-down Bundle › Ferritin › 0.87 70.0 4.59e-01 85.2% 23.5%
1tjoB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.87 75.0 5.14e-01 100.0% 29.1%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.87 70.0 6.01e-01 87.0% 57.3%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.86 66.0 5.87e-01 81.5% 59.5%
1vh6A01 6.10.140.1940 Special › Helix non-globular › Helix Hairpins › 0.86 79.0 6.37e-01 100.0% 55.7%
7e9uA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.86 77.0 4.42e-01 96.3% 15.3%
3tdvA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.86 65.0 4.29e-01 83.3% 21.4%
1s3qG00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.86 77.0 5.38e-01 100.0% 33.1%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.85 65.0 6.91e-01 79.6% 100.0%
3unoE00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.85 76.0 5.31e-01 100.0% 32.9%
3zc0D00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.85 75.0 4.98e-01 96.3% 27.3%
3kwoA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.85 74.0 5.30e-01 100.0% 34.9%
3iq1B00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.85 77.0 5.39e-01 100.0% 34.0%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.84 75.0 7.16e-01 100.0% 87.1%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.83 71.0 6.43e-01 98.1% 70.4%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 73.0 6.77e-01 100.0% 81.2%
1e52A00 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.83 64.0 6.37e-01 88.9% 80.4%
3t9jA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.82 73.0 5.30e-01 100.0% 37.5%
2lf0A01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.81 71.0 6.91e-01 100.0% 86.7%
6umqA01 1.20.930.60 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.80 70.0 5.33e-01 94.4% 73.0%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.79 70.0 5.70e-01 100.0% 55.9%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.79 65.0 5.04e-01 92.6% 41.3%
1d2mA03 6.10.140.240 Special › Helix non-globular › Helix Hairpins › 0.79 61.0 5.70e-01 83.3% 68.2%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 69.0 6.33e-01 100.0% 84.5%
3nrxA00 1.20.58.1520 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 67.0 5.21e-01 100.0% 51.2%
3kflA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.78 69.0 4.78e-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 0.77 66.0 5.48e-01 100.0% 54.8%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.76 66.0 5.35e-01 100.0% 52.8%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.74 66.0 5.08e-01 100.0% 51.3%
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 0.73 54.0 5.63e-01 85.2% 93.8%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.71 62.0 5.84e-01 100.0% 81.2%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4432094 192.11.1.1 alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 1.00 73.0 7.78e-01 75.9% 85.4%
4469597 192.17.1.11 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › UVR 0.97 73.0 7.27e-01 77.8% 76.4%
5050536 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.96 72.0 6.47e-01 77.8% 60.0%
4489484 2002.1.1.30 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.95 88.0 5.04e-01 98.1% 12.3%
None 0.95 77.0 4.31e-01 85.2% 8.9%
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 0.95 78.0 8.14e-01 87.0% 94.0%
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 0.95 81.0 8.09e-01 90.7% 89.1%
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 0.95 77.0 7.37e-01 85.2% 76.7%
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 0.95 89.0 7.43e-01 100.0% 65.9%
3262528 138.1.1.0 alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.94 74.0 6.26e-01 90.7% 55.0%
5028028 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.94 88.0 6.33e-01 100.0% 41.5%
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 0.93 85.0 7.50e-01 98.1% 72.0%
3240245 192.17.1.1 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › Rbsn 0.93 76.0 7.89e-01 85.2% 92.0%
4966900 605.1.1.0 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.93 75.0 7.01e-01 85.2% 70.8%
3753240 3291.1.1.54 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › CC2D1A-B_DM14 0.93 83.0 5.63e-01 96.3% 30.6%
3560750 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.92 83.0 7.49e-01 96.3% 74.3%
3774145 192.17.1.6 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.92 77.0 5.55e-01 88.9% 35.6%
4930709 3877.1.1.0 alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.92 82.0 5.40e-01 100.0% 26.7%
3186698 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.92 84.0 7.28e-01 100.0% 70.0%
165192 150.1.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.91 77.0 5.55e-01 90.7% 35.3%
3230314 192.17.1.6 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.91 76.0 6.86e-01 88.9% 68.6%
3336677 605.1.1.132 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF641 0.91 81.0 7.16e-01 96.3% 69.3%
3738041 192.5.1.1 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.91 83.0 7.03e-01 100.0% 63.5%
5025189 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.90 82.0 8.19e-01 98.1% 98.2%
5079107 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.90 83.0 6.11e-01 100.0% 43.1%
3781506 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 0.90 82.0 5.76e-01 100.0% 63.2%
3434261 148.1.3.26 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_9 0.90 83.0 5.83e-01 100.0% 38.7%
5054157 632.11.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › DUF357 0.89 71.0 6.30e-01 85.2% 61.3%
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 0.88 79.0 5.89e-01 100.0% 42.7%
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 0.87 79.0 6.56e-01 100.0% 58.9%
4514051 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.87 78.0 6.03e-01 100.0% 47.0%
5035275 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.86 78.0 6.18e-01 100.0% 53.3%
4267546 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 0.84 75.0 6.32e-01 100.0% 60.0%
3882466 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.78 68.0 5.33e-01 100.0% 47.8%