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rifoxya1_full_scaffold_1_prodigal-single.1__X__X__00174

Bact-Vir

rifoxya1_full_scaffold_1_prodigal-single.1__X__X__00174

Identity

Kingdom:
phage

Quality

87.9 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 5-60
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ch5B02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.63 53.0 3.70e-01 96.4% 76.5%
2ed8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 40.0 3.59e-01 100.0% 44.2%
4hscX04 2.60.40.1430 Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 0.60 50.0 4.08e-01 100.0% 48.2%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.60 45.0 4.16e-01 100.0% 61.8%
1s3rA04 2.60.40.1430 Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 0.59 50.0 4.01e-01 100.0% 47.7%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 45.0 3.85e-01 100.0% 49.0%
3rj2X00 2.60.120.1150 Mainly Beta › Sandwich › Jelly Rolls › 0.59 43.0 3.40e-01 100.0% 34.6%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 44.0 3.96e-01 100.0% 57.5%
6hj2A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.59 51.0 3.31e-01 100.0% 43.8%
1uyvA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.58 50.0 3.28e-01 100.0% 43.9%
2iqgA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.58 50.0 3.35e-01 100.0% 35.4%
2pstX00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.58 35.0 3.49e-01 98.2% 55.7%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.56 46.0 4.00e-01 100.0% 57.3%
7eehA01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.56 42.0 2.87e-01 87.5% 91.6%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.56 48.0 3.86e-01 100.0% 54.6%
4avaA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 41.0 3.09e-01 100.0% 31.2%
2v0uA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 43.0 3.22e-01 85.7% 91.1%
2f1eA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.56 46.0 3.72e-01 100.0% 46.6%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 46.0 4.00e-01 100.0% 96.9%
1kfiA04 3.30.310.50 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain 0.55 44.0 3.64e-01 100.0% 100.0%
3g9kF01 3.60.20.40 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Gamma-glutamyltranspeptidase, small (S) subunit 0.55 35.0 2.61e-01 82.1% 21.5%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.55 46.0 3.85e-01 100.0% 55.0%
2z3gB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.55 44.0 3.50e-01 100.0% 40.9%
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.55 47.0 3.72e-01 100.0% 76.7%
1xe0C00 2.60.120.340 Mainly Beta › Sandwich › Jelly Rolls › Nucleoplasmin core domain 0.55 43.0 3.64e-01 100.0% 50.5%
3ujzA03 2.60.20.40 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › 0.54 35.0 2.98e-01 100.0% 36.0%
6z9cA01 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.54 46.0 3.64e-01 100.0% 45.1%
4jn3A01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.54 42.0 2.87e-01 87.5% 61.8%
3ihlB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 45.0 3.05e-01 100.0% 57.6%
2z04B03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.54 38.0 2.74e-01 78.6% 34.4%
4iauA01 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.53 34.0 3.11e-01 100.0% 46.2%
3doaA03 3.40.970.40 Alpha Beta › 3-Layer(aba) Sandwich › Ribonuclease HI; Chain A › fibrinogen binding protein from staphylococcus aureus domain like 0.53 32.0 3.55e-01 100.0% 74.4%
3b8fB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.53 43.0 3.33e-01 100.0% 37.3%
7c2fB01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.53 40.0 3.60e-01 98.2% 55.8%
1wkyA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 44.0 3.40e-01 100.0% 56.2%
1wmdA02 2.60.120.380 Mainly Beta › Sandwich › Jelly Rolls › 0.53 46.0 3.66e-01 100.0% 75.2%
2j3wC00 3.30.450.70 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.53 44.0 3.34e-01 92.9% 77.8%
1i7dA03 2.70.20.10 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Topoisomerase I, domain 3 0.53 44.0 3.40e-01 100.0% 92.2%
1jx4A04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.52 43.0 3.72e-01 100.0% 57.1%
7pzaA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 41.0 3.27e-01 89.3% 74.6%
2mv2A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.52 40.0 3.11e-01 92.9% 79.1%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.51 44.0 3.39e-01 100.0% 41.6%
2xhkB01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 42.0 3.39e-01 100.0% 50.4%
4ecnA02 2.60.40.3540 Mainly Beta › Sandwich › Immunoglobulin-like › Domain of unknown function DUF4458 0.51 41.0 3.25e-01 100.0% 42.6%
1rfeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.50 40.0 3.11e-01 98.2% 37.5%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3959955 304.163.1.3 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › PF31118 0.62 45.0 4.81e-01 100.0% 100.0%
4472559 2005.1.1.30 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › BshC 0.62 53.0 3.34e-01 100.0% 21.5%
4394681 862.1.1.4 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › RepB_primase 0.62 51.0 3.52e-01 100.0% 25.9%
4992171 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 45.0 4.35e-01 100.0% 69.2%
3287357 3115.3.1.0 ↗ a+b two layers › GP2-like › P56 › P56 0.61 50.0 4.93e-01 100.0% 91.5%
2559791 4187.2.1.1 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 › NAGPA 0.60 49.0 4.20e-01 100.0% 54.7%
3320228 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.60 49.0 2.87e-01 98.2% 15.6%
5053329 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.59 47.0 3.75e-01 89.3% 55.0%
3647077 2487.1.1.7 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › PA 0.59 49.0 3.30e-01 94.6% 97.8%
3615394 11.1.4.80 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › C2_ITFG1 0.59 47.0 3.75e-01 100.0% 42.5%
3443843 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.59 50.0 2.90e-01 100.0% 16.1%
3735244 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.59 41.0 2.88e-01 100.0% 21.0%
3028533 188.1.1.0 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain 0.58 51.0 3.26e-01 100.0% 42.4%
3839866 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.58 50.0 4.34e-01 100.0% 96.7%
3593981 302.1.1.0 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.57 47.0 4.00e-01 100.0% 53.3%
3874464 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.57 49.0 3.03e-01 100.0% 55.8%
4241460 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.57 41.0 3.15e-01 100.0% 32.6%
4883268 304.139.2.1 ↗ a+b two layers › Alpha-beta plaits › Cas7-related › CRISPR-associated protein Cas7f/Csy3 › Cas_Csy3 0.57 48.0 2.97e-01 100.0% 15.6%
3379402 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.56 42.0 2.44e-01 96.4% 7.5%
3335071 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.56 46.0 2.74e-01 100.0% 17.2%
4647537 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.56 44.0 3.67e-01 100.0% 46.4%
5054307 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.56 41.0 4.43e-01 98.2% 100.0%
3966922 102.1.3.28 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain › PF27805 0.56 44.0 3.36e-01 87.5% 60.2%
3645596 109.4.1.1476 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, DYW_deaminase, E_motif 0.55 42.0 2.45e-01 82.1% 10.0%
3573883 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.55 46.0 3.69e-01 100.0% 48.0%
4946583 302.1.1.0 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.55 45.0 3.74e-01 100.0% 50.4%
3739303 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.54 47.0 3.72e-01 100.0% 48.3%
3420651 109.4.1.1521 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase, Eplus_motif, E_motif 0.54 44.0 2.80e-01 100.0% 26.8%
3816405 109.4.1.1383 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.54 44.0 2.56e-01 100.0% 15.0%
3278973 375.1.1.185 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_8 0.54 36.0 4.04e-01 91.1% 100.0%
4996589 3662.1.1.4 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC_bac 0.54 44.0 3.56e-01 96.4% 58.3%
3357050 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.54 45.0 2.63e-01 100.0% 20.5%
3442726 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.53 44.0 2.52e-01 100.0% 15.8%
4928783 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.53 40.0 3.87e-01 80.4% 79.4%
4443054 3115.1.1.9 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › YjeJ 0.53 45.0 3.61e-01 100.0% 48.3%
4648475 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.53 43.0 4.24e-01 100.0% 88.3%
3832603 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.53 43.0 2.47e-01 100.0% 16.3%
4463006 3115.2.1.0 ↗ a+b two layers › GP2-like › GP2 › GP2 0.53 37.0 3.92e-01 96.4% 95.6%
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 0.52 40.0 4.21e-01 94.6% 98.0%
3236126 10.10.1.1 ↗ beta sandwiches › jelly-roll › Lipase/lipooxygenase domain (PLAT/LH2 domain) › Lipase/lipooxygenase domain (PLAT/LH2 domain) › PLAT 0.51 44.0 3.47e-01 100.0% 48.8%
3600531 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.51 41.0 4.23e-01 100.0% 98.1%
3698363 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.51 44.0 3.14e-01 100.0% 41.7%
4169665 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.51 41.0 2.52e-01 89.3% 25.3%
3623319 292.2.1.0 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.51 41.0 3.63e-01 87.5% 72.5%
3632352 10.1.1.11 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Glyco_hydro_16 0.51 35.0 2.51e-01 92.9% 21.0%
3719429 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.51 44.0 4.32e-01 100.0% 96.7%
4936454 375.1.1.58 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › MCM_OB 0.51 39.0 4.01e-01 100.0% 89.1%
5016177 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.50 38.0 3.99e-01 100.0% 96.0%
1683816 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.50 42.0 4.27e-01 100.0% 98.2%
3646564 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.50 42.0 2.41e-01 91.1% 50.7%