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KR153873.1__AKG94476.1__X__00013

Bact-Vir

KR153873.1__AKG94476.1__X__00013

Identity

Accession:
KR153873 ↗
Kingdom:
phage

Quality

64.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Autographivirales› Autotranscriptaviridae› Piedvirus› Delftia_phage_IME-DE1

TaxID: 1647385

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 3-60
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1svdM00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.72 63.0 5.18e-01 100.0% 61.1%
2lvhA00 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.67 44.0 4.89e-01 91.4% 86.7%
2fhzA00 3.30.190.30 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › 0.65 52.0 4.36e-01 91.4% 58.5%
2ckaA01 3.40.5.120 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.65 47.0 5.02e-01 100.0% 91.8%
1gh9A00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.62 43.0 4.02e-01 72.4% 80.3%
1kk1A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.60 45.0 3.19e-01 82.8% 41.8%
3gidB02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.60 40.0 3.69e-01 89.7% 49.4%
4j3cB02 3.40.1280.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha/beta knot › SPOUT methyltransferase, trefoil knot domain 0.60 44.0 3.27e-01 81.0% 47.3%
1jx4A04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.59 47.0 4.02e-01 89.7% 55.1%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.59 48.0 4.27e-01 91.4% 95.2%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.58 45.0 3.76e-01 87.9% 65.1%
3holA03 2.40.128.240 Mainly Beta › Beta Barrel › Lipocalin › 0.57 46.0 4.04e-01 89.7% 100.0%
2xy1A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 49.0 4.18e-01 100.0% 62.9%
1ghpA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.55 41.0 2.80e-01 86.2% 44.7%
3cjmA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.55 46.0 3.11e-01 100.0% 64.3%
2g5gX01 3.40.50.11550 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 40.0 2.91e-01 82.8% 82.1%
1vrmA01 3.10.520.10 Alpha Beta › Roll › T-fold › ApbE-like domains 0.54 45.0 3.20e-01 100.0% 32.7%
1rniA01 3.30.720.160 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Bifunctional DNA primase/polymerase, N-terminal 0.53 41.0 3.99e-01 100.0% 75.7%
2k2dA00 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.53 34.0 3.68e-01 93.1% 80.9%
2zuoA08 2.30.30.620 Mainly Beta › Roll › SH3 type barrels. › 0.53 41.0 4.19e-01 98.3% 86.2%
5faaA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 43.0 3.51e-01 100.0% 69.9%
7eehA01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.51 45.0 2.97e-01 100.0% 69.9%
1u5tB01 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 37.0 3.41e-01 84.5% 95.3%
3bc9A01 2.60.40.1220 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 41.0 3.66e-01 100.0% 62.4%
2qyzA01 3.30.1490.160 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ctc02137 like domains 0.50 39.0 4.09e-01 87.9% 94.3%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3991455 822.2.1.1 ↗ a+b two layers › GYF/BRK domain-like › BRK domain-like › BRK domain-like › BRK 0.71 47.0 4.86e-01 98.3% 72.7%
3705025 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.69 61.0 4.66e-01 100.0% 43.7%
3404684 10.12.1.84 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › VKGC_lumenal_dom 0.68 57.0 3.97e-01 98.3% 38.1%
5057576 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.66 58.0 5.05e-01 96.6% 89.4%
5031069 327.3.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GMP synthetase C-terminal dimerisation domain › GMP synthetase C-terminal dimerisation domain › GMP_synt_C 0.65 48.0 3.42e-01 82.8% 74.4%
5035801 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.64 56.0 4.98e-01 100.0% 89.4%
5058499 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.63 56.0 4.95e-01 100.0% 95.3%
5030867 304.160.1.1 ↗ a+b two layers › Alpha-beta plaits › Gas vesicle protein GvpF › Gas vesicle protein GvpF › GvpL_GvpF 0.63 52.0 4.32e-01 93.1% 82.9%
3839311 304.28.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › ACR_tran 0.62 52.0 4.29e-01 96.6% 91.8%
3739712 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.61 38.0 2.93e-01 100.0% 27.7%
3822338 223.1.1.77 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › Intu_longin_3 0.61 41.0 3.28e-01 70.7% 87.0%
3282957 384.1.1.0 ↗ few secondary structure elements › BPTI-like › BPTI-like › BPTI-like 0.58 39.0 4.37e-01 70.7% 91.1%
4928827 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.58 41.0 3.22e-01 75.9% 41.5%
3526555 2002.1.1.106 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › GDPD 0.58 45.0 2.96e-01 87.9% 56.5%
3968712 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.58 48.0 4.32e-01 100.0% 67.5%
3962625 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.57 48.0 4.27e-01 100.0% 64.4%
5081712 7572.1.1.1 ↗ a/b three-layered sandwiches › Phosphofructokinase C-terminal domain › Phosphofructokinase C-terminal domain › Phosphofructokinase C-terminal domain › PFK 0.56 47.0 3.54e-01 93.1% 73.1%
4026823 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.56 39.0 4.26e-01 94.8% 97.7%
3353704 11.10.1.5 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › MATH_2 0.56 44.0 3.43e-01 91.4% 44.8%
3607227 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.56 41.0 4.28e-01 86.2% 96.0%
3486643 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.56 43.0 3.66e-01 91.4% 94.5%
4558763 223.2.1.20 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_1 0.56 39.0 3.14e-01 77.6% 88.9%
3193904 221.1.1.93 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › DUF2420 0.55 46.0 3.65e-01 98.3% 53.1%
4588442 7591.1.1.1 ↗ a/b three-layered sandwiches › Tetraacyldisaccharide 4'-kinase C-terminal domain › Tetraacyldisaccharide 4'-kinase C-terminal domain › Tetraacyldisaccharide 4'-kinase C-terminal domain › LpxK 0.54 44.0 3.51e-01 91.4% 100.0%
5031168 10.1.2.190 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) › GH114_assoc 0.54 43.0 3.33e-01 93.1% 40.0%
3402688 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.54 45.0 3.19e-01 100.0% 39.3%
3469808 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 43.0 4.31e-01 89.7% 98.3%
4024044 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 38.0 3.22e-01 77.6% 44.4%
5049438 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 37.0 2.83e-01 77.6% 30.0%
3409245 223.2.1.36 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Intu_longin_3 0.53 36.0 3.08e-01 70.7% 42.0%
4944404 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 38.0 2.99e-01 75.9% 91.5%
3698817 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.53 36.0 2.94e-01 70.7% 92.7%
2640865 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 41.0 4.26e-01 89.7% 98.2%
3892842 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.52 41.0 4.03e-01 89.7% 81.5%
4673301 2484.1.1.72 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › YqgF 0.52 40.0 2.93e-01 89.7% 82.6%
3698553 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.52 38.0 3.89e-01 86.2% 92.7%
5071730 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 35.0 2.69e-01 75.9% 70.6%
D2 high residues 64-120
PDB