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pre1_saliva_scaffold_4_prodigal-single.1__X__X__00021

Bact-Vir

pre1_saliva_scaffold_4_prodigal-single.1__X__X__00021

Identity

Kingdom:
phage

Quality

62.7 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 175-325
PDB
D2 high residues 413-441_760-903
PDB
D3 medium residues 107-174_337-368
PDB
D4 medium residues 443-622_642-657
PDB
Domain cluster: representative
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gowA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.67 63.0 4.64e-01 100.0% 64.0%
1eswA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.63 58.0 4.28e-01 99.0% 71.0%
1ps9A01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.61 56.0 4.56e-01 100.0% 64.9%
3l5aA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.61 56.0 4.50e-01 100.0% 66.8%
3wnkA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.61 55.0 4.58e-01 98.5% 67.8%
3vmnA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.60 55.0 4.40e-01 98.5% 61.6%
4n0rA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.60 56.0 4.77e-01 99.5% 62.9%
2f2hA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.60 55.0 4.43e-01 99.5% 57.1%
1jndA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.60 55.0 4.70e-01 98.5% 63.7%
3rr1B02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.59 42.0 3.97e-01 91.8% 60.3%
3gycA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.58 54.0 4.31e-01 100.0% 66.4%
1c3fA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.58 51.0 4.60e-01 100.0% 69.8%
1peqA02 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.57 50.0 3.78e-01 94.9% 66.1%
4h41B00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.56 51.0 4.27e-01 98.0% 71.7%
4wiwD01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.55 50.0 4.45e-01 98.5% 78.2%
4g56A01 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.55 48.0 4.25e-01 100.0% 65.8%
6ysiH01 3.100.10.10 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › 0.54 23.0 3.50e-01 86.7% 100.0%
1knwA02 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.54 46.0 4.24e-01 92.9% 71.4%
1xp3A00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.54 47.0 4.08e-01 97.4% 61.6%
3vnyA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 46.0 3.83e-01 89.8% 60.3%
5z1aA03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 45.0 3.92e-01 90.8% 99.0%
7plsA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 50.0 4.16e-01 99.5% 68.9%
3kp1A01 3.20.20.440 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › D-Lysine 5,6-aminomutase alpha subunit 0.53 49.0 3.82e-01 99.0% 79.4%
3n12A00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 48.0 4.05e-01 99.5% 90.7%
3cz8A01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.52 48.0 4.48e-01 100.0% 88.6%
2pcqA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 43.0 3.81e-01 98.5% 61.3%
8d88A01 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.51 45.0 4.09e-01 97.4% 72.0%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2710014 2002.1.1.179 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydr_30_2 0.64 58.0 4.87e-01 98.5% 67.6%
4950147 2002.1.1.93 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_77 0.63 57.0 4.26e-01 99.5% 71.9%
4933505 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.63 57.0 4.68e-01 98.5% 62.5%
4382024 2002.1.1.8 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Cellulase 0.62 58.0 4.62e-01 100.0% 76.5%
2722736 2002.1.1.93 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_77 0.62 57.0 4.20e-01 99.0% 71.7%
2775457 2002.1.1.4 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Alpha-amylase 0.61 56.0 4.31e-01 99.5% 68.8%
3721023 2002.1.1.45 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_31_2nd 0.60 55.0 4.56e-01 99.0% 60.0%
4024620 2485.1.1.45 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_8 0.60 26.0 3.08e-01 93.9% 55.7%
5036421 2002.1.1.45 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_31_2nd 0.58 53.0 4.39e-01 99.0% 59.1%
3962111 2002.1.1.83 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_1 0.56 45.0 4.28e-01 100.0% 72.0%
3498109 2496.1.1.1 ↗ a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › CRAL_TRIO 0.56 39.0 3.91e-01 90.3% 68.5%
3931610 300.1.1.9 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › MIT_C 0.56 38.0 3.90e-01 88.8% 72.4%
3934317 2002.1.1.30 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.53 48.0 4.09e-01 98.0% 95.8%
3987755 2002.1.1.101 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Orn_Arg_deC_N 0.52 45.0 4.07e-01 92.3% 68.3%
5069122 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.51 47.0 4.00e-01 99.5% 64.4%
D5 medium residues 623-641_658-757
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5f1yA02 3.50.30.60 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › LD-carboxypeptidase A C-terminal domain-like 0.60 42.0 3.74e-01 85.7% 48.9%
2h9aA01 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.59 44.0 3.48e-01 93.3% 36.6%
3cgbA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.59 33.0 3.07e-01 70.6% 41.6%
5bwiA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.58 49.0 3.66e-01 91.6% 51.6%
1xrsA00 3.20.20.440 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › D-Lysine 5,6-aminomutase alpha subunit 0.58 50.0 3.30e-01 95.0% 52.7%
3ii1A02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.57 49.0 3.47e-01 98.3% 35.1%
4m8kA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.56 48.0 3.94e-01 92.4% 83.1%
3up8A00 3.20.20.100 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › NADP-dependent oxidoreductase domain 0.55 46.0 3.52e-01 91.6% 47.7%
6zb8A01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.55 47.0 3.37e-01 94.1% 35.8%
1yh0A02 3.40.50.1370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase 0.55 35.0 3.19e-01 76.5% 44.4%
6cmzA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 33.0 3.32e-01 84.0% 58.0%
1mzhA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 45.0 3.72e-01 90.8% 52.9%
1tzzA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.54 45.0 3.50e-01 89.1% 43.4%
7dz9A01 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.54 48.0 3.78e-01 99.2% 46.9%
4o1eB00 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.54 44.0 3.49e-01 90.8% 50.6%
2nv9D02 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.54 43.0 3.54e-01 86.6% 50.2%
3pnuA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.54 42.0 3.10e-01 100.0% 29.9%
7zs9401 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.54 42.0 3.46e-01 84.9% 90.6%
1lwjA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 48.0 3.52e-01 100.0% 36.8%
2pljA02 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.52 42.0 3.40e-01 87.4% 47.6%
1ivnA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.51 47.0 4.09e-01 100.0% 73.6%
3bofA02 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.51 46.0 3.56e-01 100.0% 88.8%
3zs7A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.50 41.0 3.12e-01 87.4% 61.0%
2qagB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 42.0 3.38e-01 92.4% 65.9%
1yd9B00 3.40.220.10 Alpha Beta › 3-Layer(aba) Sandwich › Leucine Aminopeptidase, subunit E; domain 1 › Leucine Aminopeptidase, subunit E, domain 1 0.50 40.0 3.45e-01 85.7% 84.5%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3179687 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.59 48.0 3.49e-01 89.1% 48.9%
1698195 2002.1.1.168 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_44 0.59 49.0 3.61e-01 91.6% 48.6%
1721882 2487.1.1.18 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › Peptidase_S66C 0.58 43.0 3.77e-01 86.6% 50.5%
4157810 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.58 36.0 3.56e-01 73.9% 56.8%
3642369 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.58 32.0 3.48e-01 77.3% 63.0%
4957359 2002.1.1.60 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › AP_endonuc_2 0.57 51.0 3.98e-01 100.0% 45.2%
4977545 2002.1.1.113 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › CdhD 0.57 44.0 3.37e-01 90.8% 34.9%
4956962 2002.1.1.60 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › AP_endonuc_2 0.57 50.0 3.89e-01 100.0% 45.1%
4378044 2004.1.1.138 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DNA_pol3_delta 0.56 42.0 4.01e-01 86.6% 67.9%
3003998 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.56 44.0 3.59e-01 85.7% 50.0%
5076558 2004.1.1.791 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GvpD_bR2 0.55 46.0 3.64e-01 90.8% 79.6%
4024569 2006.1.1.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.55 44.0 3.67e-01 86.6% 53.5%
3987704 7542.1.1.4 ↗ a/b three-layered sandwiches › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain › Peptidase_S66C 0.55 44.0 3.80e-01 86.6% 55.1%
145698 2002.1.1.13 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Aldo_ket_red 0.55 44.0 3.40e-01 87.4% 46.5%
3336027 207.1.1.77 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FBD 0.54 43.0 4.29e-01 84.9% 92.8%
4999753 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.54 44.0 3.21e-01 87.4% 44.9%
5066313 2002.1.1.94 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_42 0.54 47.0 3.44e-01 100.0% 67.8%
4971884 2002.1.1.90 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › MTHFR 0.54 44.0 3.38e-01 90.8% 53.6%
4974696 2002.1.1.79 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DUF72 0.54 44.0 3.59e-01 91.6% 55.8%
5000049 2004.1.1.196 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_22 0.53 42.0 3.59e-01 86.6% 55.6%
3410655 2004.1.1.222 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › RhoGAP_pG1_pG2 0.53 39.0 3.55e-01 76.5% 63.1%
3672327 2007.1.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like 0.53 43.0 4.02e-01 87.4% 77.3%
4473494 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 42.0 3.19e-01 85.7% 74.0%
3957157 2002.1.1.13 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Aldo_ket_red 0.52 44.0 3.38e-01 92.4% 58.2%
5000083 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.52 42.0 3.42e-01 87.4% 44.3%
3784324 7529.1.1.1 ↗ a/b three-layered sandwiches › Macro domain-like › Macro domain-like › Macro domain-like › Macro 0.52 41.0 3.20e-01 85.7% 62.2%
3198938 2003.1.5.79 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_23 0.52 43.0 3.24e-01 89.1% 69.3%
3373788 207.1.1.77 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FBD 0.52 41.0 3.21e-01 84.9% 46.9%
3392242 2002.1.1.101 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Orn_Arg_deC_N 0.52 41.0 3.28e-01 84.9% 58.7%
4993147 2002.1.1.134 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_2 0.51 42.0 3.41e-01 90.8% 51.0%
5058373 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.51 45.0 3.52e-01 96.6% 53.8%
4613567 2003.1.1.120 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NAD-bd_HRPKS_sdrA 0.51 41.0 3.63e-01 87.4% 69.7%
5048942 2484.1.1.39 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Fumble 0.51 38.0 3.36e-01 79.8% 87.7%
4946571 2008.1.1.85 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_TdeIII 0.50 34.0 2.93e-01 73.1% 41.0%
3738964 2002.1.1.13 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Aldo_ket_red 0.50 42.0 3.31e-01 95.0% 46.5%
3569469 7529.1.1.10 ↗ a/b three-layered sandwiches › Macro domain-like › Macro domain-like › Macro domain-like › AKAP_110 0.50 40.0 3.30e-01 86.6% 68.0%