Back to structures

RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00542

Bact-Vir

RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00542

Identity

Kingdom:
phage

Quality

88.0 mean pLDDT

3D Structure

Domains

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

D1 medium residues 1-65
PDB
Domain cluster: representative
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2yfqB01 1.10.8.1210 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.72 36.0 3.97e-01 90.8% 59.6%
3ermB00 1.10.10.710 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › PSPTO_1197 like 0.69 48.0 4.87e-01 84.6% 73.4%
6f7hA00 1.20.1080.10 Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. 0.69 58.0 3.89e-01 93.8% 63.7%
2ktmA00 1.10.790.10 Mainly Alpha › Orthogonal Bundle › Major Prion Protein › Prion/Doppel protein, beta-ribbon domain 0.67 53.0 5.31e-01 87.7% 83.8%
2hvrA03 1.10.10.1810 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › RNA ligase 0.67 51.0 4.67e-01 86.2% 62.1%
2nsaA00 1.10.3120.10 Mainly Alpha › Orthogonal Bundle › Trigger factor, domain 2 › Trigger factor, C-terminal domain 0.66 57.0 4.26e-01 96.9% 83.8%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 47.0 4.79e-01 73.8% 87.1%
1is8A01 1.10.286.10 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › GTP cyclohydrolase I, N-terminal domain 0.65 47.0 4.84e-01 87.7% 85.0%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.64 42.0 4.13e-01 70.8% 62.9%
1w9cA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.64 48.0 3.07e-01 81.5% 29.3%
6yz2A01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.62 45.0 3.68e-01 75.4% 64.2%
6xasW01 3.90.940.10 Alpha Beta › Alpha-Beta Complex › Eukaryotic RPB6 RNA polymerase subunit › RNA polymerase subunit, RPB6/omega 0.61 42.0 4.63e-01 72.3% 95.9%
2kbwA01 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.61 49.0 3.87e-01 93.8% 96.1%
1gcvB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 48.0 3.96e-01 93.8% 81.6%
2j3tD01 3.30.450.70 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.60 46.0 3.63e-01 81.5% 48.5%
3lmfA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.59 44.0 3.75e-01 80.0% 93.6%
3b5iA02 1.10.1200.220 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.59 45.0 4.03e-01 92.3% 57.9%
3iylB02 1.10.2050.10 Mainly Alpha › Orthogonal Bundle › Protein mu-1, chain B, domain 3 › Protein mu-1, chain B, domain 3 0.58 49.0 3.95e-01 96.9% 52.2%
1j3wC00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.58 44.0 3.55e-01 83.1% 51.1%
3l09A01 1.20.58.1460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 41.0 3.57e-01 73.8% 53.1%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.58 37.0 3.89e-01 75.4% 71.7%
5zjgA02 1.10.246.130 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain 0.57 46.0 3.95e-01 92.3% 62.5%
4q5qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 39.0 3.31e-01 75.4% 43.8%
1sg7A00 1.10.1740.70 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › ChaB 0.57 46.0 4.44e-01 90.8% 82.7%
1d2mA03 6.10.140.240 Special › Helix non-globular › Helix Hairpins › 0.57 48.0 4.84e-01 93.8% 100.0%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.57 42.0 4.47e-01 80.0% 89.5%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.55 42.0 3.51e-01 81.5% 50.9%
1lkvX02 1.10.220.30 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Flagellar motor switch protein FliG, alpha-alpha superhelical domain 0.55 45.0 3.63e-01 92.3% 72.0%
3uebF00 3.30.300.100 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like 0.55 47.0 4.06e-01 93.8% 74.0%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.55 42.0 4.11e-01 86.2% 98.6%
4oe8C00 1.10.8.1170 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.54 47.0 4.23e-01 93.8% 81.6%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.54 43.0 4.40e-01 84.6% 95.2%
1hwyA01 1.10.287.140 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 37.0 3.95e-01 76.9% 94.1%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.53 41.0 4.02e-01 83.1% 90.1%
3d85C00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.52 40.0 3.30e-01 89.2% 94.7%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.51 41.0 3.88e-01 84.6% 76.6%
1dkqA02 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.51 41.0 3.48e-01 96.9% 60.5%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3916145 148.1.1.5 alpha arrays › Histone-like › Histone-related › Histone › TFIID-18kDa 0.72 63.0 4.32e-01 100.0% 93.3%
5052725 3826.1.1.0 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.67 46.0 4.54e-01 70.8% 81.4%
4242465 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.65 54.0 4.78e-01 90.8% 78.9%
3808989 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.64 45.0 3.84e-01 72.3% 58.0%
4238922 589.1.2.1 alpha arrays › Triger factor/SurA peptide-binding domain-like › Triger factor/SurA peptide-binding domain-like › TF C-terminus (Pfam 05698) › Trigger_C 0.63 54.0 4.04e-01 96.9% 61.2%
3786619 103.4.1.2 alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › TFIIS_M 0.62 51.0 4.62e-01 96.9% 72.6%
2474689 192.13.1.1 alpha bundles › Long alpha-hairpin › ISY1 N-terminal domain-like › ISY1 N-terminal domain-like › Isy1 0.62 43.0 4.25e-01 73.8% 76.1%
3491163 864.1.1.2 a+b two layers › DLC › DLC › DLC › Tctex-1 0.62 48.0 3.96e-01 87.7% 50.0%
4890923 148.1.3.12 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_8 0.62 44.0 4.04e-01 75.4% 68.6%
4464903 109.4.1.19 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Vitellogenin_N 0.61 42.0 2.60e-01 70.8% 24.1%
3810942 4030.1.1.10 alpha bundles › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › PPR 0.61 37.0 3.72e-01 81.5% 61.5%
5078867 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.61 43.0 3.91e-01 75.4% 70.0%
5055517 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.61 49.0 3.94e-01 93.8% 77.9%
4988487 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.60 48.0 4.52e-01 87.7% 92.4%
1878710 4970.1.1.1 alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.57 35.0 3.79e-01 92.3% 73.2%
3250474 109.1.1.7 alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C_3 0.56 40.0 2.98e-01 76.9% 34.1%
None 0.56 44.0 2.84e-01 90.8% 18.3%
3897328 2003.1.5.111 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Rsm22 0.56 46.0 2.98e-01 96.9% 74.6%
3496813 304.110.1.7 a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like › TEX47 0.55 46.0 3.22e-01 90.8% 85.9%
5018187 192.4.1.0 alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.54 39.0 3.97e-01 75.4% 83.1%
3767943 304.6.1.1 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › FAD-oxidase_C 0.53 36.0 2.69e-01 73.8% 46.7%
3838710 7014.1.1.2 alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › TauE 0.53 42.0 3.44e-01 90.8% 77.7%
4927356 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.52 41.0 3.54e-01 86.2% 78.1%
3371667 7516.1.1.47 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Cellulose_synt 0.51 44.0 2.55e-01 100.0% 46.1%
3783731 2004.1.1.505 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, AAA_30 0.51 38.0 2.39e-01 83.1% 84.0%
4307602 4070.1.1.0 alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like 0.51 39.0 3.03e-01 89.2% 37.1%
D2 medium residues 66-150
PDB
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1eyuA00 3.40.210.10 Alpha Beta › 3-Layer(aba) Sandwich › PvuII Endonuclease; Chain A › PVUII Endonuclease, subunit A 0.66 59.0 4.83e-01 100.0% 67.9%
1tx3D00 3.40.600.10 Alpha Beta › 3-Layer(aba) Sandwich › ECO RV Endonuclease; Chain A › DNA mismatch repair MutH/Restriction endonuclease, type II 0.64 54.0 3.98e-01 96.5% 73.4%
2kcqA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.60 50.0 4.14e-01 100.0% 51.0%
2ar1A00 3.10.590.10 Alpha Beta › Roll › ph1033 like fold › ph1033 like domains 0.59 47.0 3.90e-01 87.1% 66.2%
2og4A01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.59 51.0 3.76e-01 100.0% 48.1%
3m6wA03 2.30.130.60 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › 0.59 40.0 4.46e-01 85.9% 91.0%
4oxiA01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.56 47.0 3.02e-01 94.1% 42.1%
3iuwA00 2.30.130.30 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › Hypothetical protein. 0.55 44.0 4.51e-01 89.4% 97.5%
3thxB01 3.40.1170.10 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › DNA repair protein MutS, domain I 0.53 39.0 3.37e-01 76.5% 88.5%
5gjnA01 2.40.37.10 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › Lyase, Ornithine Decarboxylase; Chain A, domain 1 0.51 40.0 3.38e-01 84.7% 51.7%
2nvaA01 2.40.37.10 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › Lyase, Ornithine Decarboxylase; Chain A, domain 1 0.51 39.0 3.47e-01 84.7% 60.9%
1w07A02 2.40.110.10 Mainly Beta › Beta Barrel › Butyryl-CoA Dehydrogenase, subunit A; domain 2 › Butyryl-CoA Dehydrogenase, subunit A, domain 2 0.50 41.0 3.65e-01 96.5% 86.9%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5057963 2492.1.1.1 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.69 48.0 4.00e-01 71.8% 69.0%
5005296 2008.1.1.232 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF25941 0.68 59.0 5.28e-01 97.6% 83.3%
3733515 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.67 56.0 4.47e-01 92.9% 62.9%
3721927 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.67 56.0 4.47e-01 94.1% 80.0%
3696080 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.67 54.0 3.99e-01 89.4% 57.8%
3730987 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.66 58.0 4.65e-01 100.0% 85.1%
4284098 2008.1.1.198 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF6998 0.66 57.0 4.99e-01 97.6% 65.4%
4928024 1.1.9.0 beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.59 46.0 4.12e-01 87.1% 98.4%
4934245 1.1.9.0 beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.57 48.0 3.95e-01 92.9% 98.1%
4330983 1.1.9.11 beta barrels › cradle loop barrel › RIFT-related › PUA domain › TruB-C_2 0.56 39.0 4.29e-01 85.9% 95.4%
3289010 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.56 48.0 4.21e-01 97.6% 94.0%
3222968 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.56 42.0 3.13e-01 80.0% 86.0%
3219878 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.55 43.0 2.94e-01 83.5% 58.7%
5080764 7518.1.1.0 a/b three-layered sandwiches › PK C-terminal domain-like › PK C-terminal domain-like › PK C-terminal domain-like 0.55 40.0 3.60e-01 76.5% 91.7%
4939916 5104.1.1.0 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.52 41.0 4.08e-01 96.5% 80.0%
4025299 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.52 39.0 2.91e-01 82.4% 91.7%
5023622 1.1.9.6 beta barrels › cradle loop barrel › RIFT-related › PUA domain › UPF0113 0.51 38.0 4.05e-01 83.5% 98.6%
5053674 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.50 37.0 2.98e-01 80.0% 95.7%
3784215 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.50 32.0 3.06e-01 78.8% 53.3%
3960499 4052.1.1.0 beta complex topology › Acyl-CoA dehydrogenase middle domain-like › Acyl-CoA dehydrogenase middle domain-like › Acyl-CoA dehydrogenase middle domain-like 0.50 38.0 3.94e-01 87.1% 94.7%