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RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00130

Bact-Vir

RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00130

Identity

Kingdom:
phage

Quality

41.4 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 188-240
PDB
Domain cluster: representative
CATH (51)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2a2fX01 1.10.357.30 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Exocyst complex subunit Sec15 C-terminal domain, N-terminal subdomain 0.79 70.0 4.84e-01 98.1% 79.6%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.77 65.0 5.03e-01 94.3% 82.9%
3nf4A01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.75 65.0 5.05e-01 100.0% 62.2%
2jifA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.74 64.0 4.99e-01 100.0% 62.7%
1gw5A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.74 64.0 3.65e-01 100.0% 9.8%
2b1eA04 1.20.1280.170 Mainly Alpha › Up-down Bundle › Monooxygenase › Exocyst complex component Exo70 0.74 65.0 4.92e-01 100.0% 83.5%
8cdaC01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.72 60.0 4.80e-01 100.0% 62.4%
1bucA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.71 62.0 4.77e-01 100.0% 62.6%
4nv0A02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.71 48.0 4.25e-01 71.7% 47.6%
4hteA03 1.10.167.30 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › 0.70 52.0 4.57e-01 81.1% 65.0%
1x9bA00 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.70 53.0 5.31e-01 98.1% 84.9%
3d7iB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.69 54.0 4.48e-01 86.8% 54.1%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.68 48.0 4.28e-01 75.5% 51.9%
2guzB00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.68 56.0 5.28e-01 94.3% 87.7%
1zbpA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.67 49.0 4.34e-01 94.3% 51.8%
3uumA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 56.0 4.40e-01 98.1% 75.4%
3nb2A02 1.25.40.300 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Putative secreted effector protein 0.66 50.0 3.70e-01 90.6% 29.7%
4rfsS00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.65 55.0 3.89e-01 100.0% 79.7%
8b9zK01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 44.0 3.79e-01 71.7% 49.5%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.65 46.0 3.88e-01 75.5% 46.6%
1io1A01 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.64 49.0 3.55e-01 86.8% 53.3%
4qnsA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.64 53.0 4.27e-01 94.3% 75.5%
1orsC00 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.63 47.0 3.61e-01 83.0% 52.3%
5u56A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.63 54.0 4.32e-01 100.0% 70.5%
3urgA01 6.10.140.400 Special › Helix non-globular › Helix Hairpins › 0.63 51.0 4.99e-01 94.3% 85.0%
5jj6B01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.63 49.0 4.20e-01 98.1% 51.0%
2i9cA01 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.63 48.0 3.91e-01 100.0% 42.3%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.62 43.0 4.13e-01 75.5% 63.9%
4id0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.62 53.0 4.26e-01 100.0% 69.6%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.61 44.0 4.30e-01 77.4% 70.0%
4h0pB02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.61 51.0 3.43e-01 100.0% 32.7%
2kn6A02 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.61 44.0 3.84e-01 77.4% 84.1%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 49.0 4.14e-01 100.0% 74.5%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 47.0 3.99e-01 88.7% 83.7%
3vhlA02 1.20.58.740 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DOCK DHR2 domain, lobe C 0.60 46.0 3.75e-01 92.5% 67.5%
2e2eA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 48.0 3.57e-01 92.5% 33.1%
3m0fB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 45.0 3.47e-01 83.0% 82.9%
7zxkC01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.59 49.0 3.64e-01 98.1% 71.3%
4dwnA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.59 47.0 3.98e-01 98.1% 50.5%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.58 42.0 3.67e-01 75.5% 49.4%
1anxA04 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.58 46.0 4.39e-01 100.0% 83.3%
2if4A02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.58 47.0 3.71e-01 100.0% 60.2%
7vw6B01 1.10.10.1590 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › NADH-quinone oxidoreductase subunit E 0.58 46.0 4.34e-01 100.0% 74.6%
3smtA02 3.90.1420.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 2 › Rubisco LSMT, substrate-binding domain 0.57 46.0 3.41e-01 98.1% 73.8%
8thmA01 1.20.120.1310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain 0.57 42.0 3.70e-01 81.1% 81.2%
5vjhB03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 45.0 3.13e-01 100.0% 63.8%
1nklA00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.55 41.0 3.83e-01 90.6% 62.8%
5ce6A02 3.90.230.10 Alpha Beta › Alpha-Beta Complex › Creatine Amidinohydrolase › Creatinase/methionine aminopeptidase superfamily 0.54 44.0 2.86e-01 94.3% 54.2%
3qvmB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 40.0 2.65e-01 90.6% 58.9%
7s03A01 1.10.10.1450 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.51 37.0 3.84e-01 90.6% 90.0%
1mkyA03 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.51 43.0 3.66e-01 96.2% 70.0%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3176126 4015.1.1.1 ↗ alpha complex topology › alpha-helical domain in sec1/munc18-like (SM) proteins › alpha-helical domain in sec1/munc18-like (SM) proteins › alpha-helical domain in sec1/munc18-like (SM) proteins › Sec1 0.80 72.0 4.56e-01 100.0% 21.6%
3551630 109.4.1.1328 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF26034 0.78 67.0 5.22e-01 94.3% 48.2%
3223407 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.76 66.0 4.95e-01 100.0% 41.5%
4023249 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.75 65.0 5.32e-01 100.0% 58.0%
3407793 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.74 63.0 5.61e-01 100.0% 80.0%
3935195 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.74 65.0 4.58e-01 100.0% 46.1%
3993061 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.72 62.0 4.26e-01 100.0% 70.3%
3183312 109.4.1.957 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_TTI1_N 0.71 59.0 3.56e-01 100.0% 37.3%
4000262 192.5.1.1 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.71 56.0 4.79e-01 90.6% 91.1%
3295608 148.1.3.313 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Fes1 0.70 50.0 4.68e-01 83.0% 61.5%
3790121 603.1.1.114 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › HR1 0.69 55.0 4.57e-01 92.5% 83.0%
3864662 604.1.1.95 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › KIAA1755_C 0.68 55.0 4.73e-01 92.5% 81.1%
4181400 184.1.1.1 ↗ alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.67 56.0 5.35e-01 98.1% 86.2%
4933535 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.67 53.0 3.70e-01 90.6% 27.4%
4595970 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.67 54.0 5.23e-01 100.0% 81.7%
5072863 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.67 52.0 3.68e-01 90.6% 28.1%
4416633 604.11.1.1 ↗ alpha bundles › Spectrin repeat-like › XseB-like › XseB-like › Exonuc_VII_S 0.66 48.0 4.67e-01 77.4% 70.0%
3967403 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.66 47.0 4.41e-01 75.5% 61.5%
4031004 184.1.1.0 ↗ alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N 0.66 54.0 5.18e-01 98.1% 86.2%
5060248 4044.1.1.0 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins 0.65 45.0 4.16e-01 71.7% 55.7%
4300897 5094.1.1.1 ↗ a+b duplicates or obligate multimers › OmpH-like › OmpH-like › OmpH-like › OmpH 0.65 45.0 3.49e-01 75.5% 31.5%
3808540 376.1.6.9 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › IBR domain › PF26200 0.65 52.0 3.78e-01 88.7% 32.7%
3569141 632.22.1.28 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › JAKMIP_CC3 0.65 50.0 3.47e-01 84.9% 26.1%
3869122 4207.1.2.0 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region 0.65 49.0 3.58e-01 84.9% 30.3%
3291034 3271.1.1.1 ↗ alpha arrays › CdiA C-terminal nuclease domain › CdiA C-terminal nuclease domain › CdiA C-terminal nuclease domain › Ntox28 0.64 53.0 4.46e-01 96.2% 91.6%
3483644 109.4.1.1636 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › C12orf66_like 0.64 54.0 3.51e-01 100.0% 31.9%
3619662 192.12.1.3 ↗ alpha bundles › Long alpha-hairpin › Transcriptional repressor TraM › Transcriptional repressor TraM › DUF747 0.64 45.0 4.00e-01 75.5% 51.2%
3508392 604.6.1.32 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › Mito_morph_reg 0.64 49.0 3.93e-01 92.5% 79.0%
3251379 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.63 46.0 3.97e-01 79.2% 49.4%
4673890 109.4.1.264 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RMD1-3 0.62 51.0 3.33e-01 96.2% 25.4%
3170889 109.4.1.148 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › EST1_DNA_bind,EST1 0.62 51.0 2.94e-01 100.0% 23.6%
4536901 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.61 50.0 3.65e-01 98.1% 78.8%
3208235 109.4.1.146 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cohesin_load 0.61 48.0 3.11e-01 100.0% 17.2%
4426593 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.61 47.0 3.41e-01 92.5% 28.2%
165604 109.1.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C 0.60 49.0 3.95e-01 100.0% 60.3%
3261252 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.60 48.0 3.24e-01 92.5% 26.4%
2701721 628.1.1.1 ↗ alpha bundles › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › FCD 0.60 45.0 3.42e-01 84.9% 66.9%
3632017 109.4.1.404 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fes1 0.60 47.0 3.30e-01 100.0% 27.1%
4065523 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.59 49.0 3.81e-01 92.5% 41.7%
4224874 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.58 44.0 3.59e-01 88.7% 46.1%
4630325 509.1.1.10 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › HHD_RTEL1 0.58 48.0 4.41e-01 100.0% 74.7%
4317199 603.5.1.1 ↗ alpha bundles › STAT-like › FlgN-like › FlgN-like › FlgN 0.56 42.0 3.43e-01 92.5% 71.2%
5000506 2004.1.1.73 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.55 46.0 2.94e-01 96.2% 75.7%
3164806 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 43.0 4.39e-01 94.3% 100.0%
D2 medium residues 8-170
PDB