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NC_048751.1__YP_009843737.1__HWC07_gp056__00056

Bact-Vir

NC_048751.1__YP_009843737.1__HWC07_gp056__00056

Identity

Accession:
NC_048751 ↗
Kingdom:
phage

Quality

85.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Lietduovirus› Pantoea_phage_vB_PagM_LIET2

TaxID: 2508071

Cluster

View cluster (4 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 medium residues 1-57
PDB
Domain cluster: rep: OM971649.1__UQJ95609.1__ALHIDCOG_00221__00221__DFULL
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1iieA00 1.10.870.10 Mainly Alpha › Orthogonal Bundle › HLA-dr Antigens Associated Invariant Chain; Chain A › MHC class II-associated invariant chain, trimerisation domain 0.68 46.0 4.25e-01 71.9% 85.3%
6m4eA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.68 54.0 3.09e-01 86.0% 29.8%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4954771 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.64 48.0 3.43e-01 80.7% 27.1%
D2 medium residues 58-118
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2l37A00 6.10.250.890 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.73 37.0 4.36e-01 70.5% 69.8%
2uytA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.72 55.0 3.66e-01 83.6% 40.6%
8d7hD01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.71 53.0 3.74e-01 78.7% 62.4%
2k4jA00 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 45.0 3.76e-01 88.5% 41.9%
3fghA00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.63 43.0 4.20e-01 72.1% 86.6%
1u8vB03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.61 45.0 3.08e-01 78.7% 64.8%
3solA00 1.20.58.1630 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Chaperone lipoprotein PulS/OutS 0.60 43.0 3.81e-01 93.4% 51.6%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 49.0 4.12e-01 91.8% 55.1%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.59 37.0 3.61e-01 90.2% 56.7%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.59 44.0 3.82e-01 96.7% 50.5%
1yuzB01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.58 48.0 3.73e-01 91.8% 58.0%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.58 48.0 3.65e-01 91.8% 53.8%
2xdoD00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 47.0 2.96e-01 100.0% 97.3%
3k62A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.54 43.0 2.56e-01 88.5% 12.7%
1zarA01 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 0.50 33.0 3.02e-01 70.5% 50.6%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5060609 632.8.1.0 ↗ 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 0.72 52.0 4.83e-01 75.4% 61.3%
3386797 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.71 59.0 4.02e-01 93.4% 56.7%
2474881 397.7.1.0 ↗ few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 0.71 40.0 4.45e-01 82.0% 72.3%
4955657 5065.1.1.3 ↗ alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › BPD_transp_2 0.66 56.0 3.59e-01 93.4% 67.0%
2623804 7529.1.1.14 ↗ a/b three-layered sandwiches › Macro domain-like › Macro domain-like › Macro domain-like › PF29356 0.65 51.0 3.43e-01 91.8% 47.3%
4992271 5051.1.1.10 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › AA_permease_2 0.64 56.0 3.36e-01 98.4% 72.6%
5030545 101.1.2.21 ↗ alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repress 0.64 55.0 4.15e-01 93.4% 43.6%
3943344 183.1.1.0 ↗ alpha duplicates or obligate multimers › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain 0.64 55.0 4.14e-01 93.4% 42.9%
5084071 101.1.2.652 ↗ alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repr_C 0.64 55.0 4.14e-01 93.4% 42.1%
3602245 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.63 41.0 4.03e-01 86.9% 61.5%
4928573 183.1.1.5 ↗ alpha duplicates or obligate multimers › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Fe_dep_repress 0.63 55.0 4.38e-01 93.4% 52.2%
5042174 101.1.2.652 ↗ alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repr_C 0.63 54.0 4.12e-01 93.4% 43.7%
4963579 183.1.1.1 ↗ alpha duplicates or obligate multimers › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Fe_dep_repr_C 0.63 54.0 4.11e-01 93.4% 43.7%
3603679 183.1.1.0 ↗ alpha duplicates or obligate multimers › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain 0.63 54.0 4.26e-01 93.4% 50.8%
None — 0.62 54.0 4.01e-01 93.4% 42.1%
3953573 183.1.1.0 ↗ alpha duplicates or obligate multimers › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain 0.62 54.0 4.01e-01 93.4% 42.1%
4942421 101.1.2.21 ↗ alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repress 0.62 53.0 4.28e-01 93.4% 52.2%
4985324 101.1.2.652 ↗ alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repr_C 0.61 53.0 3.89e-01 93.4% 38.1%
4956886 101.1.2.652 ↗ alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repr_C 0.61 56.0 4.20e-01 100.0% 71.4%
5013300 101.1.2.652 ↗ alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repr_C 0.61 55.0 4.14e-01 100.0% 70.3%
3287685 4993.1.1.1 ↗ extended segments › Glu-tRNAGln amidotransferase C subunit › Glu-tRNAGln amidotransferase C subunit › Glu-tRNAGln amidotransferase C subunit › GatC 0.61 38.0 3.32e-01 96.7% 40.0%
3207747 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 50.0 3.40e-01 90.2% 30.5%
4060755 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 55.0 4.14e-01 100.0% 70.0%
4952217 101.1.2.652 ↗ alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repr_C 0.60 55.0 4.16e-01 100.0% 85.9%
3277186 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.59 46.0 3.78e-01 90.2% 74.4%
5053903 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 49.0 4.05e-01 98.4% 55.8%
4300466 4993.1.1.1 ↗ extended segments › Glu-tRNAGln amidotransferase C subunit › Glu-tRNAGln amidotransferase C subunit › Glu-tRNAGln amidotransferase C subunit › GatC 0.59 36.0 3.13e-01 96.7% 37.0%
1145703 604.5.1.3 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ArAE_1_C 0.58 46.0 3.97e-01 85.2% 100.0%
2075294 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 0.58 49.0 4.13e-01 95.1% 56.6%
3516806 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.58 51.0 3.28e-01 98.4% 22.9%
3711347 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.56 41.0 3.14e-01 78.7% 87.9%
4217329 4964.1.1.1 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › DNA_pol_A 0.55 41.0 3.31e-01 80.3% 94.2%
3483301 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.53 44.0 3.44e-01 98.4% 92.7%
5034272 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 33.0 2.97e-01 91.8% 45.9%
4441096 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.52 33.0 3.38e-01 88.5% 65.0%