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NC_054439.1__YP_010051221.1__KDW68_gp04__00004

Bact-Vir

NC_054439.1__YP_010051221.1__KDW68_gp04__00004

Identity

Accession:
NC_054439 ↗
Kingdom:
phage

Quality

65.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Liefievirus› Mycobacterium_phage_Paito

TaxID: 2315544

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 medium residues 1-139
PDB
Domain cluster: rep: NC_070897.1__YP_010663424.1__PP998_gp07__00007__D1-112
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25310.2 best VG15 61.9 1.40e-16 97.1% 60.9%
D2 medium residues 140-245
PDB
D3 medium residues 325-383
PDB
D4 medium residues 397-553
PDB
D5 medium residues 753-809
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3triA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.88 62.0 4.97e-01 73.7% 40.8%
1yqgA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.86 60.0 4.69e-01 73.7% 37.2%
2ahrA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.85 60.0 4.77e-01 73.7% 39.6%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.84 55.0 4.95e-01 70.2% 50.0%
2c5qA00 3.50.30.40 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › Ribonuclease E inhibitor RraA/RraA-like 0.83 56.0 3.62e-01 73.7% 17.2%
3ibyD02 1.10.287.1770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.83 57.0 4.85e-01 70.2% 81.0%
3l9wA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.82 58.0 4.07e-01 73.7% 36.2%
2whnA00 1.20.81.30 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › Type II secretion system (T2SS), domain F 0.78 53.0 4.17e-01 70.2% 38.2%
1tfeA02 1.10.286.20 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.75 51.0 5.56e-01 71.9% 88.9%
1ss3A00 1.10.287.720 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Pollen allergen ole e 6 0.74 51.0 5.42e-01 98.2% 84.0%
2ddmB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.72 51.0 3.20e-01 73.7% 73.4%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 49.0 5.17e-01 73.7% 80.4%
1rr7A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.70 43.0 4.76e-01 70.2% 78.3%
3kksB00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.69 51.0 3.77e-01 80.7% 36.2%
5hnmC00 3.30.1380.10 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › 0.69 54.0 3.79e-01 86.0% 88.8%
1vluA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.65 53.0 3.49e-01 93.0% 77.7%
7c5yA02 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.60 45.0 3.27e-01 78.9% 85.6%
1dcnA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.59 50.0 4.60e-01 89.5% 72.2%
4nb5B01 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 0.56 46.0 4.15e-01 96.5% 100.0%
2pjqA01 1.10.472.50 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › HD-domain/PDEase-like 0.53 44.0 3.94e-01 100.0% 73.0%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4932779 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.90 62.0 5.13e-01 77.2% 43.2%
3988376 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.89 63.0 5.26e-01 77.2% 46.7%
3286823 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.88 63.0 4.74e-01 73.7% 35.0%
4990523 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.88 64.0 5.25e-01 78.9% 45.3%
3808722 633.6.1.2 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX 0.88 58.0 4.05e-01 70.2% 24.4%
5032477 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.87 60.0 4.70e-01 73.7% 37.3%
3685821 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.86 60.0 4.67e-01 73.7% 36.5%
3255785 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.83 58.0 4.59e-01 73.7% 38.2%
3244718 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 0.80 56.0 4.89e-01 73.7% 49.4%
3643105 6026.1.1.1 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.79 55.0 3.98e-01 73.7% 27.1%
4502561 283.1.1.3 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › Creatinase/aminopeptidase › Creatinase/aminopeptidase › Pantoate_ligase 0.73 51.0 4.20e-01 73.7% 44.0%
5007440 5054.1.1.6 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TrkH 0.72 63.0 5.19e-01 100.0% 57.0%
4992636 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.72 50.0 4.08e-01 73.7% 40.0%
3228790 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.70 50.0 3.60e-01 75.4% 28.1%
5079848 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.66 44.0 4.37e-01 70.2% 85.0%
4991198 2.1.1.359 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › HupF_HypC 0.62 44.0 3.58e-01 78.9% 38.3%
4474302 195.1.1.1 ↗ alpha complex topology › NusB-like › NusB-like › NusB-like › NusB 0.61 48.0 3.57e-01 89.5% 32.9%
4028993 101.1.2.392 ↗ alpha arrays › HTH › HTH › winged helix domain › SNRNP200_wHTH 0.57 41.0 3.32e-01 77.2% 51.3%
D6 medium residues 810-937
PDB
Domain cluster: rep: NC_054446.1__YP_010051674.1__KDW76_gp04__00004__D543-637