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MZ079855.1__QXN67551.1__X__00067

Bact-Vir

MZ079855.1__QXN67551.1__X__00067

Identity

Accession:
MZ079855 ↗
Kingdom:
phage

Quality

94.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Demerecviridae› Sugarlandvirus› Klebsiella_phage_vB_Kpn_3

TaxID: 2836075

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 20-138
PDB
Domain cluster: rep: term1_stool_scaffold_19_prodigal-single.1__X__X__00096__D449-569
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00476.27 best DNA_pol_A 63.3 2.90e-17 98.3% 22.6%
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6vddA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.92 81.0 8.26e-01 99.2% 93.9%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.87 47.0 6.06e-01 99.2% 90.1%
1bdp002 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.86 71.0 7.38e-01 98.3% 93.6%
2oduA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 43.0 4.59e-01 93.3% 66.7%
3c1yA02 1.20.1260.110 Mainly Alpha › Up-down Bundle › Ferritin › DNA integrity scanning linker region 0.70 41.0 3.79e-01 91.6% 46.6%
1sumB01 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 0.67 36.0 3.78e-01 95.8% 57.0%
1w9rA00 1.20.58.440 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › choline binding protein A 0.66 40.0 4.04e-01 99.2% 59.7%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.59 36.0 4.44e-01 95.0% 97.3%
1beoA00 1.10.239.10 Mainly Alpha › Orthogonal Bundle › Beta-cryptogein › Elicitin domain 0.59 35.0 3.87e-01 79.0% 71.4%
1f6fA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.55 47.0 4.08e-01 91.6% 61.7%
3snhA02 1.20.120.1240 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Dynamin, middle domain 0.54 31.0 2.59e-01 96.6% 30.1%
2vs0A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.53 35.0 4.15e-01 90.8% 97.6%
4jioA02 1.20.140.50 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › alix/aip1 like domains 0.53 41.0 3.89e-01 97.5% 68.5%
5y06A01 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 39.0 3.12e-01 95.0% 40.6%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3163747 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.92 82.0 5.20e-01 100.0% 22.4%
4072515 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.92 83.0 5.42e-01 100.0% 26.4%
4339694 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.92 81.0 5.21e-01 100.0% 23.4%
1391185 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.92 81.0 6.78e-01 100.0% 58.9%
57665 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.91 81.0 6.92e-01 100.0% 62.4%
3964115 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.90 78.0 7.54e-01 95.8% 82.3%
4061480 2484.1.1.58 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Taq-exonuc 0.90 81.0 5.67e-01 100.0% 33.9%
4995739 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.89 85.0 7.44e-01 100.0% 78.2%
4319500 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.89 80.0 5.12e-01 100.0% 23.3%
4848449 304.48.1.6 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_A 0.88 63.0 6.41e-01 85.7% 75.2%
3333792 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.87 81.0 6.96e-01 100.0% 66.3%
3595357 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.86 82.0 6.99e-01 100.0% 70.6%
3676005 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.86 80.0 5.33e-01 100.0% 29.0%
3274000 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.86 80.0 6.69e-01 98.3% 87.9%
3705119 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.85 81.0 6.59e-01 100.0% 80.0%
3272949 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.85 81.0 6.54e-01 100.0% 73.2%
3555725 2484.1.1.82 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_P_Exo 0.84 78.0 5.13e-01 100.0% 27.7%
4027632 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.84 69.0 6.89e-01 95.0% 84.2%
3505184 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.81 78.0 5.93e-01 100.0% 51.4%
3580212 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.81 62.0 6.89e-01 86.6% 100.0%
4975019 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.80 72.0 6.67e-01 100.0% 77.9%
3616267 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.80 76.0 6.59e-01 100.0% 70.0%
2970331 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.80 76.0 6.49e-01 100.0% 71.0%
3483300 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.79 75.0 5.97e-01 100.0% 67.7%
3211911 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.77 73.0 6.46e-01 100.0% 75.8%
3407160 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.74 68.0 6.19e-01 100.0% 76.0%
3424523 604.5.1.7 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ALMT 0.72 38.0 4.27e-01 95.0% 65.3%
5008391 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.68 40.0 3.87e-01 100.0% 51.9%
2526355 7094.1.1.2 ↗ alpha bundles › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › LIS_MGM1 0.66 50.0 5.33e-01 97.5% 88.6%
3659069 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.60 43.0 4.38e-01 95.0% 73.3%
4453411 5050.1.1.25 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › TLC 0.59 52.0 3.92e-01 92.4% 90.6%
4181065 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.59 51.0 4.56e-01 94.1% 95.8%
3784566 604.1.1.191 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF29057 0.57 33.0 3.52e-01 89.9% 64.0%
3606757 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.57 35.0 3.32e-01 95.0% 50.0%
3647237 611.3.1.0 ↗ alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.52 36.0 3.68e-01 72.3% 99.2%
D2 high residues 186-329
PDB
Domain cluster: rep: GOV_bin_1711_contig-70_0_prodigal-single.1__X__X__00411__D651-809
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00476.27 best DNA_pol_A 67.7 1.30e-18 100.0% 29.4%
D3 medium residues 1-19_330-380_410-425
PDB
Domain cluster: representative
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3594827 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.51 42.0 2.62e-01 96.5% 42.2%
D4 medium residues 139-184_381-409_426-467
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4x0qA03 3.30.70.370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.84 64.0 5.89e-01 77.8% 94.4%
1bgxT05 3.30.70.370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.81 62.0 6.11e-01 78.6% 97.5%
5eokA02 3.50.4.10 Alpha Beta › 3-Layer(bba) Sandwich › Hepatocyte Growth Factor › Hepatocyte Growth Factor 0.51 30.0 3.34e-01 78.6% 74.4%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2886666 807.1.1.1 ↗ a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.52 36.0 3.43e-01 71.8% 75.9%