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NC_054725.1__YP_010059366.1__KHQ85_gp116__00116

Bact-Vir

NC_054725.1__YP_010059366.1__KHQ85_gp116__00116

Identity

Accession:
NC_054725 ↗
Kingdom:
phage

Quality

90.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Skogvirus› Gordonia_phage_Skog

TaxID: 2704033

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 high residues 2-63
PDB
Domain cluster: rep: IMGVR_UViG_3300005099_000205-3300005099-Ga0072682_10918728__D21-82
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4b6dB00 3.30.60.20 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.80 53.0 5.50e-01 90.3% 73.7%
1uw0A01 3.30.1740.10 Alpha Beta › 2-Layer Sandwich › first zn-finger domain of poly(adp-ribose) polymerase-1 › Zinc finger, PARP-type 0.71 62.0 5.35e-01 96.8% 93.8%
2qkpD00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.62 40.0 3.14e-01 95.2% 31.3%
2hboA01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.60 46.0 3.64e-01 85.5% 66.2%
5e9aB03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.57 33.0 3.31e-01 75.8% 53.2%
3ooxA00 2.60.120.330 Mainly Beta › Sandwich › Jelly Rolls › B-lactam Antibiotic, Isopenicillin N Synthase; Chain 0.56 39.0 2.55e-01 74.2% 25.6%
1p97A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 38.0 3.13e-01 80.6% 37.7%
5jenA02 3.90.640.20 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › Heat-shock cognate protein, ATPase 0.56 39.0 3.39e-01 100.0% 46.5%
3h9wA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 39.0 3.22e-01 96.8% 41.3%
1l3aA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.56 50.0 3.64e-01 100.0% 80.1%
1f39A00 2.10.109.10 Mainly Beta › Ribbon › Umud Fragment, subunit A › Umud Fragment, subunit A 0.55 42.0 3.60e-01 82.3% 90.1%
1go3E01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 45.0 3.93e-01 91.9% 96.8%
1iv8A05 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 32.0 3.16e-01 75.8% 51.5%
3njaA02 2.10.70.100 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.54 35.0 3.85e-01 80.6% 89.1%
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.54 42.0 2.71e-01 83.9% 42.5%
4lxjA01 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.54 37.0 2.32e-01 72.6% 21.1%
2egcA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.54 40.0 3.75e-01 85.5% 65.3%
2kdyA01 2.60.40.1980 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 39.0 3.10e-01 80.6% 60.0%
3dsbA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 47.0 4.03e-01 100.0% 99.0%
1vkcA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 47.0 3.65e-01 100.0% 74.1%
3lodA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 47.0 3.60e-01 100.0% 57.9%
4pzaB00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.53 39.0 2.78e-01 82.3% 97.2%
3k8aB00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 41.0 3.51e-01 98.4% 51.5%
3c8iA00 2.40.410.10 Mainly Beta › Beta Barrel › putative membrane protein from Corynebacterium diphtheriae fold › putative membrane protein from Corynebacterium diphtheriae superfamily 0.51 42.0 3.48e-01 100.0% 75.6%
1bf5A04 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.51 43.0 3.59e-01 96.8% 70.8%
1rcqA01 2.40.37.10 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › Lyase, Ornithine Decarboxylase; Chain A, domain 1 0.51 42.0 3.33e-01 100.0% 92.7%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3513068 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.86 57.0 5.68e-01 91.9% 66.2%
3933161 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.85 57.0 6.03e-01 91.9% 78.2%
3889754 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.84 55.0 5.61e-01 90.3% 70.0%
3549345 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.83 55.0 5.58e-01 90.3% 70.0%
4929230 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.82 52.0 6.22e-01 83.9% 100.0%
3865409 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.82 55.0 5.60e-01 91.9% 71.7%
3487738 376.1.2.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain 0.82 55.0 5.99e-01 91.9% 86.0%
3990333 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.79 52.0 4.87e-01 90.3% 56.0%
3541586 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.78 52.0 4.90e-01 91.9% 57.3%
4936660 376.1.2.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain 0.76 63.0 6.63e-01 93.5% 98.2%
5034811 376.1.2.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain 0.76 62.0 6.38e-01 93.5% 90.0%
4961820 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.76 55.0 5.65e-01 80.6% 80.0%
3271441 376.1.2.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain 0.74 59.0 6.16e-01 100.0% 96.4%
3237220 220.1.1.84 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_15 0.72 43.0 3.47e-01 93.5% 32.2%
8200 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.72 62.0 5.03e-01 96.8% 76.9%
158834 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.70 62.0 4.86e-01 100.0% 62.7%
4028826 377.1.2.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger 0.67 61.0 4.84e-01 100.0% 74.2%
2673846 3167.1.1.1 ↗ a+b two layers › 40S ribosomal protein rpS21 (S21e) › 40S ribosomal protein rpS21 (S21e) › 40S ribosomal protein rpS21 (S21e) › Ribosomal_S21e 0.67 49.0 4.48e-01 79.0% 65.1%
3700246 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.66 60.0 4.86e-01 100.0% 70.4%
3597430 377.1.2.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger 0.66 58.0 5.07e-01 98.4% 95.7%
3260561 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.66 57.0 4.87e-01 96.8% 92.0%
3250863 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.65 59.0 5.32e-01 100.0% 94.1%
3351761 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.65 58.0 5.05e-01 100.0% 83.2%
4654276 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.65 58.0 4.85e-01 100.0% 75.2%
3662203 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.64 57.0 5.10e-01 100.0% 92.9%
3923898 377.1.2.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger 0.63 56.0 5.13e-01 98.4% 91.3%
4965857 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.60 49.0 4.80e-01 91.9% 87.0%
3195099 220.1.1.9 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Voldacs 0.60 46.0 3.57e-01 100.0% 38.1%
2855565 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.59 42.0 3.69e-01 95.2% 51.1%
3712376 2.1.1.225 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF30388 0.59 43.0 3.51e-01 95.2% 40.8%
3460699 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.59 46.0 4.18e-01 100.0% 63.5%
3788285 395.1.1.4 ↗ few secondary structure elements › Midkine-related › Midkine-related › Midkine-related › Flocculin_t3 0.57 41.0 4.46e-01 82.3% 94.0%
3592295 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.56 43.0 3.17e-01 90.3% 31.9%
4014737 222.1.1.0 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.56 43.0 3.74e-01 85.5% 93.0%
3713555 12.1.1.50 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Glyco_hydro_31_3rd 0.56 39.0 3.50e-01 75.8% 53.7%
4645680 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.55 32.0 3.14e-01 75.8% 47.1%
5050686 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.55 40.0 3.62e-01 90.3% 56.5%
3979778 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.54 39.0 3.03e-01 96.8% 35.6%
4929903 2.1.1.7 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › S1 0.54 44.0 3.72e-01 91.9% 93.3%
3274454 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.54 39.0 2.26e-01 95.2% 8.5%
3476122 284.1.1.0 ↗ a+b two layers › FKBP-like › FKBP-like › FKBP-like 0.53 37.0 2.92e-01 74.2% 54.8%
3701898 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.53 36.0 2.44e-01 71.0% 74.6%
4974435 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.53 43.0 3.75e-01 100.0% 58.9%
4004354 10.12.1.115 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › PF30437 0.52 44.0 3.51e-01 98.4% 94.1%
5045422 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.52 37.0 2.97e-01 100.0% 36.3%
3743499 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.50 43.0 2.75e-01 100.0% 20.6%
3235864 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 44.0 4.11e-01 96.8% 100.0%
5009490 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 37.0 3.15e-01 85.5% 77.5%
D2 medium residues 66-137
PDB
Domain cluster: rep: NC_055792.1__YP_010101721.1__KNU50_gp71__00071__D91-151