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NC_028882.1__YP_009206052.1__AVT15_gp114__00087

Bact-Vir

NC_028882.1__YP_009206052.1__AVT15_gp114__00087

Identity

Accession:
NC_028882 ↗
Kingdom:
phage

Quality

66.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vandenendeviridae› Nankokuvirus› Pseudomonas_phage_vB_PaeM_PS24

TaxID: 1542092

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 9-70
PDB
Domain cluster: representative
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2fe1A00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.83 55.0 4.26e-01 72.6% 33.1%
1vq8P03 1.10.1200.60 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.80 55.0 5.75e-01 72.6% 80.0%
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.80 56.0 4.98e-01 74.2% 53.6%
3dfzA02 1.10.8.610 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › SirC, precorrin-2 dehydrogenase, C-terminal helical domain-like 0.79 58.0 5.47e-01 87.1% 64.9%
4bpxD00 1.20.930.80 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.78 60.0 4.05e-01 82.3% 31.5%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.77 59.0 5.03e-01 82.3% 58.6%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.77 68.0 5.49e-01 100.0% 54.7%
3qnmA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.76 53.0 4.67e-01 75.8% 50.0%
4aq4A02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.75 55.0 3.77e-01 80.6% 22.2%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.75 68.0 6.40e-01 100.0% 85.1%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.74 58.0 5.02e-01 82.3% 60.4%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.74 64.0 5.41e-01 100.0% 58.7%
3fblA00 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 50.0 4.55e-01 77.4% 53.7%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 56.0 4.63e-01 82.3% 69.2%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.72 54.0 5.15e-01 82.3% 68.5%
2wglA00 1.10.4190.10 Mainly Alpha › Orthogonal Bundle › Urease accessory protein UreF › Urease accessory protein UreF 0.72 62.0 4.36e-01 100.0% 65.6%
2l35A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.70 51.0 5.09e-01 82.3% 76.2%
4k08A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.70 55.0 4.27e-01 91.9% 38.2%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.69 53.0 4.55e-01 80.6% 55.2%
1op1A00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.69 52.0 4.78e-01 82.3% 62.2%
5xnyA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.69 59.0 4.98e-01 96.8% 66.4%
6ig5A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.69 55.0 4.23e-01 88.7% 39.1%
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 46.0 4.14e-01 74.2% 51.2%
4y9jA01 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.69 60.0 4.57e-01 100.0% 91.3%
2d2sA02 1.20.58.1220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, C-terminal helical domain 0.68 58.0 4.97e-01 100.0% 59.4%
6dv2G02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.68 56.0 4.01e-01 91.9% 40.2%
3c8tA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.68 56.0 4.85e-01 91.9% 58.8%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.68 53.0 4.34e-01 87.1% 46.4%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.67 51.0 4.56e-01 98.4% 57.1%
2mpnA00 6.10.140.1340 Special › Helix non-globular › Helix Hairpins › 0.66 56.0 5.46e-01 93.5% 88.2%
4zqeA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.66 48.0 4.21e-01 79.0% 50.0%
5dn6J00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.66 52.0 4.99e-01 88.7% 78.4%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.66 46.0 4.32e-01 75.8% 58.2%
1wpbG01 1.10.287.680 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.66 45.0 4.73e-01 71.0% 87.0%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.66 54.0 5.07e-01 91.9% 73.1%
3gfaA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.65 52.0 3.60e-01 85.5% 29.1%
4hwhE00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.65 48.0 4.41e-01 87.1% 59.1%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.64 50.0 5.00e-01 88.7% 86.2%
1jalA03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.64 52.0 4.79e-01 91.9% 96.3%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 43.0 4.42e-01 74.2% 78.9%
3q18A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.62 46.0 3.85e-01 83.9% 44.0%
3zxsC02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.58 48.0 3.64e-01 93.5% 93.5%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.56 51.0 4.49e-01 100.0% 71.1%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.55 41.0 4.12e-01 85.5% 82.0%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3798302 103.4.1.0 ↗ alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein 0.87 71.0 6.81e-01 87.1% 80.0%
5066143 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.84 74.0 6.93e-01 98.4% 81.3%
3446460 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.83 75.0 4.56e-01 100.0% 17.2%
3735607 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.82 64.0 5.81e-01 82.3% 66.3%
4024271 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.82 73.0 5.62e-01 100.0% 46.7%
3740910 1008.1.1.0 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain 0.81 66.0 6.90e-01 88.7% 100.0%
5055977 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.81 72.0 6.15e-01 100.0% 67.0%
5039692 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 0.80 70.0 6.15e-01 100.0% 66.3%
3988447 5043.1.1.0 ↗ extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like 0.80 64.0 6.68e-01 88.7% 100.0%
5028558 5058.1.1.2 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st 0.79 69.0 5.95e-01 100.0% 63.0%
3486312 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.79 61.0 4.83e-01 82.3% 44.5%
3410594 4177.1.1.6 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3_WASP_bdg 0.78 60.0 4.08e-01 82.3% 24.9%
3953860 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.78 64.0 5.99e-01 88.7% 76.0%
3742303 310.2.1.1 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.77 69.0 4.82e-01 100.0% 33.0%
5055969 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.76 66.0 5.81e-01 100.0% 66.3%
3189978 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 0.76 65.0 5.41e-01 100.0% 54.8%
4996722 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.76 65.0 5.72e-01 100.0% 66.3%
4937236 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.76 65.0 5.65e-01 100.0% 64.0%
3770290 4177.1.1.41 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › EVC2_like 0.75 64.0 4.53e-01 100.0% 31.3%
3941435 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.74 66.0 4.98e-01 100.0% 80.0%
4478129 166.1.1.1 ↗ alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.74 53.0 4.71e-01 82.3% 52.2%
5001019 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.73 65.0 4.65e-01 96.8% 75.3%
3842812 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.73 66.0 4.50e-01 100.0% 29.8%
3468553 328.7.1.0 ↗ a+b two layers › IF3-like › Smr domain › Smr domain 0.72 56.0 4.12e-01 85.5% 33.3%
4983736 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.71 56.0 4.83e-01 83.9% 57.9%
5043880 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.71 62.0 5.62e-01 100.0% 71.8%
3412555 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.70 54.0 4.51e-01 85.5% 47.3%
4384067 632.7.1.37 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › LETM1_RBD 0.70 59.0 4.83e-01 91.9% 63.6%
5058780 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.70 61.0 5.14e-01 100.0% 58.1%
3363051 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.69 62.0 5.40e-01 96.8% 83.3%
3455580 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.66 58.0 3.86e-01 100.0% 27.3%