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rifcsphigho2-12_scaffold_combined_curated_prodigal-single.1__X__X__00333

Bact-Vir

rifcsphigho2-12_scaffold_combined_curated_prodigal-single.1__X__X__00333

Identity

Kingdom:
phage

Quality

81.9 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 11-74
PDB
Domain cluster: representative
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ff4A01 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 0.78 57.0 4.90e-01 81.2% 50.5%
3e3vA01 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 0.68 50.0 5.40e-01 85.9% 92.5%
3dewA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.68 49.0 5.33e-01 85.9% 96.2%
2iaiA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.67 47.0 4.75e-01 81.2% 73.8%
4ye6A02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.65 51.0 5.28e-01 85.9% 100.0%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.64 46.0 4.31e-01 85.9% 61.5%
4jykA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.63 50.0 5.19e-01 93.8% 96.6%
4irfB00 1.10.1780.10 Mainly Alpha › Orthogonal Bundle › Double Clp-N motif › Clp, N-terminal domain 0.62 43.0 3.41e-01 75.0% 75.7%
4hh5A00 1.10.1780.10 Mainly Alpha › Orthogonal Bundle › Double Clp-N motif › Clp, N-terminal domain 0.61 43.0 3.21e-01 73.4% 70.6%
3fdqA01 1.20.120.1030 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Motility repressor MogR, DNA-binding domain 0.61 49.0 4.02e-01 89.1% 46.7%
1lfuP00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.61 46.0 4.32e-01 98.4% 64.6%
3e1sA01 1.10.10.2220 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.60 47.0 4.20e-01 87.5% 60.0%
4eqqA02 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 0.59 40.0 4.41e-01 84.4% 95.8%
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.58 48.0 4.48e-01 98.4% 90.5%
2vk9A03 1.10.3730.30 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › 0.56 41.0 3.60e-01 78.1% 84.7%
1tzzB01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.55 45.0 3.87e-01 100.0% 88.2%
1urvA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.55 47.0 3.65e-01 100.0% 59.1%
1sxjE03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.55 41.0 3.60e-01 84.4% 53.6%
3k1rA01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.54 42.0 3.97e-01 100.0% 70.4%
2b4lA02 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.53 46.0 3.48e-01 98.4% 79.6%
2j4jF00 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.51 42.0 3.00e-01 95.3% 78.3%
3ibyD02 1.10.287.1770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 42.0 3.88e-01 92.2% 86.9%
1jt6A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 38.0 3.12e-01 85.9% 56.2%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3952565 101.1.2.8 ↗ alpha arrays › HTH › HTH › winged helix domain › Trans_reg_C 0.78 57.0 4.92e-01 81.2% 50.0%
1699723 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.75 58.0 5.25e-01 82.8% 66.7%
3700443 101.1.1.176 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DEK_C 0.72 54.0 5.43e-01 82.8% 78.5%
3593415 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.72 55.0 5.17e-01 85.9% 67.5%
3705896 101.1.2.365 ↗ alpha arrays › HTH › HTH › winged helix domain › DEK_C 0.71 55.0 5.33e-01 85.9% 75.7%
5012836 247.1.1.1 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B 0.71 63.0 4.10e-01 98.4% 49.5%
3177431 101.1.1.94 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Reb1_MybAD 0.70 57.0 5.52e-01 87.5% 97.1%
3450177 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.69 50.0 5.49e-01 87.5% 98.0%
4983508 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.69 48.0 4.68e-01 81.2% 67.1%
3694221 101.1.1.36 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeobox_KN 0.66 48.0 4.98e-01 85.9% 83.3%
3806070 101.1.17.0 ↗ alpha arrays › HTH › HTH › FF domain 0.66 48.0 5.20e-01 79.7% 100.0%
4586835 101.1.1.36 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeobox_KN 0.63 46.0 4.64e-01 98.4% 78.5%
3528634 101.1.1.36 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeobox_KN 0.63 48.0 4.46e-01 93.8% 63.5%
4683204 101.35.1.5 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH1 0.63 48.0 4.14e-01 87.5% 50.5%
4258338 101.35.1.5 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH1 0.62 48.0 4.07e-01 87.5% 49.1%
3470203 101.1.1.36 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeobox_KN 0.62 48.0 5.05e-01 98.4% 98.2%
3213449 509.1.1.0 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain 0.61 48.0 4.75e-01 100.0% 81.4%
3520270 101.35.1.5 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH1 0.61 45.0 3.94e-01 87.5% 50.5%
4996181 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.61 45.0 4.73e-01 93.8% 94.5%
3991909 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.61 48.0 5.07e-01 92.2% 100.0%
4927335 5069.1.3.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.60 47.0 3.59e-01 85.9% 74.7%
3603105 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.60 43.0 4.18e-01 100.0% 68.0%
4213222 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.60 47.0 4.70e-01 98.4% 85.9%
4683153 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.59 47.0 4.12e-01 95.3% 56.0%
3236669 101.1.1.36 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeobox_KN 0.59 46.0 4.38e-01 93.8% 72.0%
5039374 2006.1.4.2 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.59 43.0 3.55e-01 78.1% 61.7%
3623357 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.59 41.0 4.26e-01 84.4% 87.3%
3767171 101.1.1.36 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeobox_KN 0.58 47.0 4.21e-01 93.8% 61.1%
4982234 5060.2.1.1 ↗ alpha bundles › V-type ATP synthase subunit C › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › Toxin coregulated pilus biosynthesis protein E cytoplasmic domain › T2SSF 0.58 44.0 3.55e-01 85.9% 70.4%
2628065 247.1.1.1 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B 0.58 49.0 3.22e-01 100.0% 43.0%
3692760 864.1.1.9 ↗ a+b two layers › DLC › DLC › DLC › DUF7888 0.57 43.0 3.52e-01 84.4% 64.2%
3459794 101.1.2.386 ↗ alpha arrays › HTH › HTH › winged helix domain › WH_DRP 0.57 49.0 4.29e-01 98.4% 63.0%
4994323 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.56 47.0 3.52e-01 100.0% 35.9%
4979555 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.56 42.0 4.31e-01 87.5% 90.0%
4971151 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.55 47.0 3.42e-01 100.0% 33.0%
4929245 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.55 44.0 4.32e-01 92.2% 81.4%
3948212 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 43.0 3.25e-01 98.4% 32.1%
4982522 2004.1.3.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.53 45.0 3.31e-01 100.0% 33.5%
3344894 129.1.1.4 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › IlvC 0.53 39.0 3.20e-01 79.7% 89.2%
None — 0.53 42.0 3.91e-01 100.0% 68.2%
3665049 101.1.1.36 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeobox_KN 0.53 43.0 3.88e-01 93.8% 62.1%
4065783 150.1.2.5 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Heme oxygenase/Ribonucleotide reductase › TENA_THI-4 0.53 43.0 2.99e-01 92.2% 63.8%
3671293 509.1.1.12 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PF25972 0.52 45.0 4.41e-01 98.4% 97.1%
D2 high residues 94-147
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u78A02 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 0.78 57.0 6.19e-01 87.0% 93.3%
6qpqB00 1.10.10.580 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Structural maintenance of chromosome 1. Chain E 0.68 58.0 5.12e-01 100.0% 90.1%
1pd3A00 1.10.287.230 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 41.0 4.20e-01 85.2% 68.5%
1iufA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.62 48.0 4.34e-01 87.0% 63.6%
2w9yA00 1.20.120.1100 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.60 47.0 3.52e-01 94.4% 34.6%
4xzjA01 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.56 48.0 3.25e-01 98.1% 64.9%
4g84A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 47.0 2.96e-01 100.0% 32.7%
2xvtC00 1.10.150.510 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Receptor activity modifying family 0.55 43.0 3.92e-01 90.7% 83.5%
1wgfA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.54 40.0 4.02e-01 81.5% 83.0%
2lbfB01 1.10.10.1410 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.54 41.0 3.87e-01 87.0% 68.1%
3bjdA01 1.10.1240.20 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Lytic transglycosylase, superhelical linker domain 0.54 45.0 3.92e-01 100.0% 76.1%
3dwlG00 1.25.40.190 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Actin-related protein 2/3 complex subunit 5 0.54 42.0 3.44e-01 100.0% 43.9%
3oxfA05 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 43.0 3.93e-01 94.4% 69.3%
3n3wA00 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.53 42.0 3.17e-01 90.7% 65.3%
5cwkA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 44.0 3.18e-01 98.1% 35.7%
2gz4A00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.52 43.0 3.04e-01 98.1% 90.5%
2rekA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.52 44.0 3.18e-01 100.0% 50.6%
3rm5B02 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.51 41.0 2.77e-01 92.6% 71.0%
4dlqA02 1.25.40.610 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.50 41.0 3.56e-01 100.0% 64.2%
3mg2B01 1.10.2090.10 Mainly Alpha › Orthogonal Bundle › orange carotenoid protein, domain 2 › Orange carotenoid-binding protein, N-terminal domain 0.50 40.0 3.10e-01 98.1% 39.5%
5d91A02 1.20.120.1760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain 0.50 40.0 2.81e-01 90.7% 65.7%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4942265 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.74 65.0 5.63e-01 100.0% 82.4%
3354221 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.71 59.0 5.50e-01 88.9% 75.4%
3402809 101.1.2.160 ↗ alpha arrays › HTH › HTH › winged helix domain › BLACT_WH 0.71 62.0 5.35e-01 100.0% 83.5%
3893171 101.1.1.12 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_Tc3_2 0.70 58.0 5.62e-01 96.3% 81.7%
3933926 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.69 57.0 5.37e-01 96.3% 75.4%
4964486 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 58.0 5.10e-01 100.0% 88.2%
5070167 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.66 54.0 5.40e-01 94.4% 85.5%
4246456 3455.1.1.0 ↗ alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors 0.59 43.0 3.86e-01 81.5% 55.0%
3285819 101.1.2.92 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_11 0.55 46.0 3.63e-01 100.0% 54.6%
3373319 5059.1.1.8 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › Mg_trans_NIPA 0.55 46.0 3.28e-01 98.1% 65.0%
5073329 109.2.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid 0.55 48.0 3.01e-01 100.0% 20.7%
4955397 2007.2.3.11 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › PTP-SAK 0.55 44.0 3.31e-01 92.6% 53.1%
1227109 7579.1.1.44 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_6 0.52 39.0 2.63e-01 87.0% 23.5%
3838117 622.4.1.32 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › YGGT 0.52 40.0 3.52e-01 100.0% 53.3%
3662616 605.1.1.204 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › YGGT 0.52 44.0 3.80e-01 100.0% 64.4%
1311351 150.1.2.5 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Heme oxygenase/Ribonucleotide reductase › TENA_THI-4 0.51 41.0 2.74e-01 92.6% 66.0%
3472785 4030.1.1.0 ↗ 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 0.51 42.0 4.09e-01 94.4% 83.3%
4513194 7579.1.1.6 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.51 41.0 2.61e-01 90.7% 36.6%
D3 medium residues 335-379
PDB
Domain cluster: representative