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NC_029074.1__YP_009223949.1__AXJ10_gp41__00041

Bact-Vir

NC_029074.1__YP_009223949.1__AXJ10_gp41__00041

Identity

Accession:
NC_029074 ↗
Kingdom:
phage

Quality

61.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Gordtnkvirus› Gordonia_phage_GordTnk2

TaxID: 1622192

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 55-118
PDB
Domain cluster: rep: OR159659.1__WKW85462.1__SEA_REYNAULD_9__00009__D21-74
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4g59C02 3.30.500.30 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.74 56.0 4.19e-01 81.2% 43.7%
1xexB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.74 54.0 4.00e-01 78.1% 34.2%
4bq2D02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.65 45.0 2.68e-01 73.4% 26.8%
3rpjA00 3.30.310.230 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Sigma factor-binding protein Crl monomer 0.65 50.0 4.03e-01 84.4% 50.0%
1hdhA02 3.30.1120.10 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.63 48.0 4.58e-01 84.4% 100.0%
1aisA02 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.63 42.0 3.83e-01 70.3% 70.1%
1f02T00 4.10.820.10 Few Secondary Structures › Irregular › Translocated Intimin Receptor; Chain T › Translocated intimin receptor, central domain 0.62 42.0 4.22e-01 70.3% 92.4%
2d9uA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.60 42.0 4.09e-01 75.0% 71.6%
1ej6B00 3.90.1830.10 Alpha Beta › Alpha-Beta Complex › Inner capsid protein lambda-1 › Inner capsid protein lambda-1 0.59 41.0 2.25e-01 71.9% 5.1%
1yw5A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.59 42.0 4.23e-01 76.6% 77.8%
2m2lA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 39.0 3.89e-01 70.3% 77.6%
2j8gA02 2.10.270.10 Mainly Beta › Ribbon › left handed beta-beta-3-solenoid › Cholin Binding 0.58 40.0 3.72e-01 73.4% 61.0%
2dk7A00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.58 45.0 4.41e-01 89.1% 94.5%
2n88A00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 39.0 4.08e-01 76.6% 87.9%
1b44D00 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 43.0 3.63e-01 85.9% 63.2%
1qnaA01 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.54 37.0 3.35e-01 73.4% 62.4%
2wtzA02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.54 38.0 2.58e-01 75.0% 86.8%
5xpyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 43.0 3.63e-01 89.1% 76.9%
1goiB03 2.10.10.20 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › Carbohydrate-binding module superfamily 5/12 0.52 34.0 3.62e-01 93.8% 84.3%
1oe4A00 3.40.470.10 Alpha Beta › 3-Layer(aba) Sandwich › Uracil-DNA Glycosylase, subunit E › Uracil-DNA glycosylase-like domain 0.52 44.0 3.07e-01 100.0% 46.5%
3ga8A00 3.10.20.860 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.52 42.0 4.16e-01 89.1% 88.1%
7d27A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.51 36.0 2.47e-01 75.0% 87.4%
3g7nB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 40.0 2.78e-01 90.6% 49.8%
6y48D01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 44.0 2.88e-01 98.4% 44.0%
1bakA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 45.0 3.68e-01 100.0% 75.6%
2x8nA01 3.30.2020.40 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › Uncharacterised protein PF10387, DUF2442 0.50 33.0 2.98e-01 75.0% 44.3%
1ileA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.50 43.0 3.16e-01 100.0% 86.4%
7szeB01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.50 35.0 3.02e-01 75.0% 56.1%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4396994 3755.3.1.305 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Rad50_zn_hook 0.74 54.0 3.02e-01 78.1% 7.1%
3619159 292.2.1.5 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › Polo_box_3 0.73 55.0 4.80e-01 81.2% 70.5%
4032017 2004.1.1.301 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_27 0.72 54.0 3.10e-01 81.2% 8.4%
4112414 2004.1.1.301 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_27 0.72 55.0 3.41e-01 81.2% 15.8%
4018649 4.8.1.1 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo 0.67 50.0 4.86e-01 79.7% 84.3%
4231809 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.66 48.0 2.88e-01 78.1% 11.6%
3391894 4.8.1.1 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo 0.64 47.0 4.63e-01 79.7% 88.6%
4386701 310.2.1.35 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › PF28954 0.63 48.0 3.65e-01 81.2% 81.4%
4230575 3355.1.1.16 ↗ alpha complex topology › dicarboxylate/sodium symporter › dicarboxylate/sodium symporter › dicarboxylate/sodium symporter › DcuC 0.63 53.0 3.19e-01 93.8% 82.8%
3930845 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.62 45.0 4.46e-01 79.7% 80.0%
4618205 604.1.1.150 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF28954 0.61 47.0 3.85e-01 82.8% 90.8%
3176989 601.19.1.40 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › PF28954 0.61 47.0 3.51e-01 82.8% 71.2%
3289119 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.61 44.0 2.77e-01 79.7% 13.5%
3774120 4320.1.1.1 ↗ alpha superhelices › Taf5 N-terminal domain-like › Taf5 N-terminal domain-like › Taf5 N-terminal domain-like › TFIID_NTD2 0.60 39.0 2.65e-01 73.4% 18.3%
5001324 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 44.0 3.71e-01 81.2% 80.0%
3931602 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.58 42.0 4.11e-01 79.7% 77.1%
3670347 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.58 43.0 4.03e-01 81.2% 82.3%
4023242 220.1.1.187 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › VPS13_C 0.57 44.0 3.54e-01 82.8% 82.4%
3294614 2002.1.1.192 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › AMP_deaminase 0.57 44.0 2.72e-01 100.0% 14.2%
4467333 331.1.1.1 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › TBP 0.56 42.0 3.68e-01 93.8% 53.7%
3672390 331.1.1.1 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › TBP 0.56 39.0 3.34e-01 75.0% 56.4%
3390232 384.1.1.0 ↗ few secondary structure elements › BPTI-like › BPTI-like › BPTI-like 0.54 34.0 3.75e-01 79.7% 84.0%
3244769 4099.1.1.28 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › PF29108 0.53 35.0 3.21e-01 73.4% 48.9%
4934744 2004.1.1.308 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_21 0.52 45.0 2.83e-01 95.3% 66.5%
4955635 375.1.1.63 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › LysW-like_globular 0.52 39.0 3.92e-01 79.7% 82.8%
3683580 2003.1.2.16 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3,NAD_binding_8 0.52 42.0 2.84e-01 90.6% 24.5%
5002278 2484.1.1.71 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RACo_C_ter 0.51 45.0 2.98e-01 100.0% 35.1%
3510576 331.1.1.1 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › TBP 0.51 33.0 3.21e-01 78.1% 53.8%
4927153 375.1.1.63 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › LysW-like_globular 0.51 36.0 3.88e-01 79.7% 89.1%
3655242 220.1.1.13 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DCP1 0.51 45.0 3.38e-01 100.0% 73.8%
3164822 309.1.1.4 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16_C 0.51 43.0 2.93e-01 95.3% 46.7%
3395458 7569.1.1.1 ↗ a/b three-layered sandwiches › Uracil-DNA glycosylase-like › Uracil-DNA glycosylase-like › Uracil-DNA glycosylase-like › UDG 0.50 42.0 2.96e-01 100.0% 46.5%
3912274 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.50 40.0 3.97e-01 89.1% 98.6%