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NC_041962.1__YP_009604238.1__FDH87_gp017__00108

Bact-Vir

NC_041962.1__YP_009604238.1__FDH87_gp017__00108

Identity

Accession:
NC_041962 ↗
Kingdom:
phage

Quality

88.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Tinduovirus› Tsukamurella_phage_TIN4

TaxID: 1636547

Cluster

Singleton — not in a non-trivial cluster

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 58-110
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2zetC00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.83 57.0 4.09e-01 71.7% 29.8%
1y02A01 1.10.720.140 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.82 56.0 4.88e-01 79.2% 48.7%
3goxA02 3.30.60.130 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.79 63.0 6.28e-01 84.9% 98.1%
1w36B03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.73 39.0 2.41e-01 79.2% 9.4%
1ul4A01 4.10.1100.10 Few Secondary Structures › Irregular › DNA-binding domain of squamosa promoter binding protein-like 12 (lacking the second zinc- binding site) › Transcription factor, SBP-box domain 0.67 47.0 4.46e-01 75.5% 75.4%
4x0qA04 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.58 40.0 2.93e-01 73.6% 29.2%
2iqcA00 1.25.40.490 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.57 51.0 3.55e-01 100.0% 46.2%
5y6iA01 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 0.55 37.0 3.35e-01 71.7% 86.3%
2miqA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.54 43.0 3.55e-01 86.8% 57.4%
4tmaJ00 3.30.50.10 Alpha Beta › 2-Layer Sandwich › Erythroid Transcription Factor GATA-1; Chain A › Erythroid Transcription Factor GATA-1, subunit A 0.54 38.0 3.80e-01 88.7% 71.9%
4fx5A03 1.20.120.1690 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.54 37.0 2.97e-01 71.7% 59.0%
8be0A01 3.40.91.90 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain 0.53 46.0 3.16e-01 98.1% 36.6%
7l9pK01 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.51 35.0 2.74e-01 71.7% 100.0%
7vbnL01 3.30.160.190 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › atu1810 like domain 0.51 36.0 3.04e-01 75.5% 66.3%
4bmjA00 6.20.250.40 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.51 35.0 3.39e-01 81.1% 64.5%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3684391 376.1.1.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4 0.85 61.0 5.05e-01 75.5% 48.9%
3720327 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.84 59.0 4.70e-01 73.6% 43.0%
3554759 376.1.3.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › FYVE_CARP1-2 0.80 55.0 5.29e-01 71.7% 66.7%
5067930 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.77 58.0 5.03e-01 81.1% 55.0%
4983870 376.1.3.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger 0.74 63.0 5.14e-01 92.5% 96.8%
3932949 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.70 51.0 4.43e-01 77.4% 53.8%
4998314 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.68 49.0 4.73e-01 77.4% 73.3%
4942517 4018.1.1.2 ↗ a+b two layers › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › Inositol_P 0.67 38.0 2.73e-01 88.7% 19.3%
5016552 378.1.1.10 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH_4 0.67 52.0 4.08e-01 84.9% 49.1%
4938236 377.1.1.2 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › Ribosomal_S14 0.65 47.0 4.22e-01 77.4% 56.8%
4445903 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.57 42.0 2.74e-01 83.0% 18.5%
4930554 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 35.0 3.36e-01 75.5% 55.0%
3638055 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 0.56 42.0 2.87e-01 83.0% 67.2%
3770678 386.1.1.143 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › Znf_XAF1_N 0.55 41.0 4.06e-01 81.1% 94.5%
3866157 389.1.1.36 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin › Ldl_recept_a 0.54 37.0 3.95e-01 75.5% 84.4%
3921366 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.54 41.0 3.75e-01 86.8% 73.3%
3322382 376.1.6.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › IBR domain › IBR 0.53 38.0 3.77e-01 75.5% 92.7%
3928397 389.3.1.1 ↗ few secondary structure elements › EGF-like › LDL receptor-like module › LDL receptor-like module › Ldl_recept_a 0.53 38.0 3.50e-01 81.1% 64.0%
3469416 101.19.1.1 ↗ alpha arrays › HTH › C-terminal subdomain in oxygen-independent coproporphyrinogen III oxidase HemN › C-terminal subdomain in oxygen-independent coproporphyrinogen III oxidase HemN › HemN_C 0.50 41.0 3.35e-01 92.5% 67.6%
D2 medium residues 113-189
PDB
Domain cluster: rep: OK283618.1__UCR92177.1__LPLM1_00042__00042__D87-159
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02945.22 best Endonuclease_7 56.2 3.50e-15 92.2% 87.8%