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S19_GE19_scaffold_2259_prodigal-single.1__X__X__00535

Bact-Vir

S19_GE19_scaffold_2259_prodigal-single.1__X__X__00535

Identity

Kingdom:
phage

Quality

76.1 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 217-311
PDB
D2 medium residues 1-121_196-212
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02540.24 best NAD_synthase 98.3 5.40e-28 89.1% 45.0%
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2e18A00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.91 76.0 5.99e-01 89.9% 46.5%
1xngA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.90 74.0 5.90e-01 89.9% 47.4%
1kqpA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.88 77.0 5.98e-01 90.6% 46.9%
3n05A02 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.87 70.0 6.15e-01 82.6% 63.5%
3sdbA02 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.84 68.0 5.86e-01 84.1% 58.7%
4azsA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 38.0 3.31e-01 71.7% 83.6%
3obwA02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.51 33.0 3.59e-01 79.0% 75.4%
3ld9A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 39.0 3.57e-01 81.2% 86.6%
4u1qA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 36.0 3.29e-01 73.2% 74.9%
1suiA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 39.0 3.38e-01 82.6% 98.2%
3d8uB02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 35.0 3.44e-01 70.3% 98.0%
2gpyB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 39.0 3.57e-01 83.3% 95.8%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5034899 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.95 79.0 6.58e-01 89.9% 54.9%
None — 0.95 79.0 6.18e-01 87.7% 46.3%
4644409 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.93 78.0 6.08e-01 87.7% 45.2%
3964181 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.93 81.0 6.27e-01 89.1% 47.9%
4648784 2005.1.1.47 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase, tRNA_Me_trans 0.93 77.0 5.97e-01 89.9% 43.7%
133894 2005.1.1.47 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase, tRNA_Me_trans 0.93 77.0 6.21e-01 87.7% 49.6%
4263013 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.92 77.0 5.91e-01 89.9% 43.7%
4386055 2005.1.1.47 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase, tRNA_Me_trans 0.92 79.0 6.17e-01 89.9% 47.5%
4072992 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.92 78.0 5.95e-01 89.9% 43.6%
4675904 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.92 76.0 6.18e-01 89.9% 50.2%
None — 0.92 77.0 6.05e-01 89.9% 46.7%
None — 0.91 77.0 6.05e-01 89.9% 46.5%
3717378 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.91 77.0 5.84e-01 87.7% 44.7%
4432146 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.90 79.0 5.93e-01 89.9% 47.2%
4045263 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.90 77.0 6.09e-01 87.7% 49.6%
4253395 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.90 77.0 6.08e-01 87.7% 49.4%
4664976 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.90 75.0 5.97e-01 89.9% 48.2%
4070508 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.89 78.0 5.90e-01 90.6% 49.5%
None — 0.88 74.0 6.00e-01 87.7% 51.1%
5022630 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.88 74.0 5.73e-01 87.7% 44.5%
3951712 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.88 75.0 5.36e-01 88.4% 38.9%
4395650 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.88 74.0 5.91e-01 87.7% 49.4%
4060776 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.88 77.0 5.90e-01 90.6% 49.1%
4483631 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.87 75.0 5.68e-01 87.7% 55.4%
4262428 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.87 76.0 5.59e-01 89.9% 55.5%
4957756 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.87 76.0 5.53e-01 89.9% 50.8%
5021368 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.87 76.0 5.53e-01 89.9% 54.1%
2663304 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.87 68.0 5.88e-01 81.2% 55.7%
4052372 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.86 75.0 5.83e-01 89.9% 48.7%
4061833 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.85 75.0 5.65e-01 89.9% 57.2%
5071227 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.83 73.0 5.49e-01 91.3% 52.7%
4973517 2005.1.1.4 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Asn_synthase 0.79 64.0 5.89e-01 89.1% 66.9%
4368622 2003.1.5.8 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Ubie_methyltran 0.57 39.0 3.27e-01 70.3% 84.6%
4991834 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.56 45.0 3.71e-01 84.8% 98.0%
3967622 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.56 39.0 3.18e-01 71.0% 93.2%
4952995 7531.1.1.1 ↗ a/b three-layered sandwiches › Carbamate kinase-like › Carbamate kinase-like › Carbamate kinase-like › AA_kinase 0.53 37.0 3.30e-01 86.2% 51.6%
4447684 2003.1.5.55 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › PrmA 0.52 36.0 3.48e-01 71.0% 83.7%
4093975 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 36.0 3.88e-01 94.9% 81.7%
3973658 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.50 36.0 3.01e-01 73.9% 85.1%
D3 medium residues 122-177
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cf7B00 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 0.64 47.0 4.27e-01 82.1% 97.6%
3lfuA02 1.10.10.160 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.62 49.0 4.67e-01 91.1% 90.0%
1lujB01 1.10.10.490 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Beta-catenin-interacting ICAT 0.61 47.0 4.86e-01 85.7% 92.5%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.61 43.0 3.94e-01 76.8% 73.1%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 46.0 3.70e-01 89.3% 94.0%
2q8kA02 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 0.58 42.0 4.16e-01 80.4% 73.3%
4u2vA02 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.57 42.0 3.88e-01 83.9% 80.0%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.56 39.0 3.61e-01 71.4% 64.8%
4od8D00 6.10.140.1880 Special › Helix non-globular › Helix Hairpins › 0.56 43.0 4.46e-01 83.9% 94.1%
4fbcA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.55 47.0 3.39e-01 98.2% 60.9%
1ykhA00 6.10.140.200 Special › Helix non-globular › Helix Hairpins › 0.54 39.0 3.31e-01 76.8% 48.4%
3f1iS00 1.20.5.1940 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.54 41.0 3.71e-01 83.9% 61.0%
7smtA02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.53 43.0 3.06e-01 89.3% 42.0%
2qgaB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.53 36.0 2.99e-01 73.2% 50.0%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 38.0 3.45e-01 83.9% 56.8%
1ze0A02 1.10.4070.10 Mainly Alpha › Orthogonal Bundle › putative redox-enzyme maturation protein fold › putative redox-enzyme maturation protein domain 0.53 38.0 3.47e-01 76.8% 85.9%
7nc3F01 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.53 41.0 3.43e-01 92.9% 54.4%
2pjwH00 1.20.5.1940 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.52 42.0 3.65e-01 91.1% 58.0%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 44.0 4.02e-01 92.9% 91.8%
5dkoA02 1.10.3900.10 Mainly Alpha › Orthogonal Bundle › YacF-like › YacF-like 0.51 41.0 2.99e-01 89.3% 99.4%
4arvA02 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.51 39.0 3.13e-01 89.3% 83.3%
1id3G00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.51 39.0 3.10e-01 82.1% 67.6%
3l1nA01 6.10.140.790 Special › Helix non-globular › Helix Hairpins › 0.50 37.0 3.85e-01 89.3% 84.3%
1bhaA00 1.10.287.170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.50 36.0 3.48e-01 78.6% 73.1%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.50 37.0 3.12e-01 83.9% 87.3%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.50 38.0 3.77e-01 91.1% 76.7%
4qmgC01 2.40.50.90 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.50 44.0 3.19e-01 98.2% 50.3%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.50 39.0 3.52e-01 87.5% 61.0%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 40.0 3.43e-01 94.6% 94.2%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3742018 7094.1.1.2 ↗ alpha bundles › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › LIS_MGM1 0.70 55.0 4.69e-01 87.5% 54.7%
3438527 219.1.1.23 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › MINDY_DUB 0.68 57.0 3.70e-01 92.9% 33.6%
4374802 639.2.1.2 ↗ alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) › DUF2767 0.67 50.0 4.75e-01 80.4% 98.5%
3997708 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.66 47.0 3.53e-01 75.0% 63.7%
3245655 101.1.2.552 ↗ alpha arrays › HTH › HTH › winged helix domain › eIF-3c_N 0.66 47.0 3.72e-01 76.8% 75.0%
4483631 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.64 52.0 3.40e-01 98.2% 19.3%
3433575 101.1.1.138 ↗ alpha arrays › HTH › HTH › Three-helical HTH › GeBP-like_DBD 0.62 47.0 4.02e-01 83.9% 88.4%
4942997 2005.1.1.7 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d 0.61 48.0 3.14e-01 89.3% 26.2%
3181110 5086.1.1.110 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HisKA 0.61 39.0 3.28e-01 71.4% 37.9%
4825675 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.60 48.0 3.23e-01 94.6% 43.3%
3282208 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.59 37.0 3.19e-01 71.4% 40.0%
3988710 2004.1.1.23 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SNF2-rel_dom 0.59 41.0 2.71e-01 75.0% 97.6%
3594748 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.59 44.0 3.58e-01 85.7% 40.0%
4011501 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.56 46.0 3.58e-01 100.0% 44.1%
3746144 192.29.1.273 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › NICE-3 0.56 40.0 3.84e-01 75.0% 64.6%
3740241 219.1.1.23 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › MINDY_DUB 0.55 42.0 2.75e-01 85.7% 19.3%
3247930 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.54 38.0 3.14e-01 73.2% 65.7%
3513291 131.1.1.12 ↗ alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD_4 0.54 43.0 3.09e-01 94.6% 55.0%
2857735 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.53 43.0 3.61e-01 89.3% 76.3%
3514794 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.52 43.0 3.36e-01 91.1% 65.0%
4940281 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.51 39.0 3.72e-01 91.1% 70.8%
1145707 650.1.1.3 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › HsbA 0.50 36.0 3.36e-01 78.6% 60.0%