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js4906-25-2-S21_Prophage_curated_prodigal-single.1__X__X__00052

Bact-Vir

js4906-25-2-S21_Prophage_curated_prodigal-single.1__X__X__00052

Identity

Kingdom:
phage

Quality

95.6 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 4-83
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24692.2 best DUF7659 58.3 1.20e-15 100.0% 53.3%
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2fwrA01 3.40.1170.30 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › 0.72 32.0 3.78e-01 81.2% 57.9%
5zyrA02 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 0.60 53.0 4.36e-01 100.0% 80.1%
5y9sC01 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 42.0 4.17e-01 73.8% 100.0%
2rdpA00 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 49.0 4.10e-01 93.8% 68.6%
5fo5A00 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 44.0 4.32e-01 82.5% 97.7%
7dvrA01 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 0.57 49.0 4.14e-01 97.5% 77.3%
1lnwF01 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 0.57 47.0 4.12e-01 93.8% 82.3%
3cdhA00 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 0.56 48.0 4.12e-01 97.5% 79.1%
3spdA00 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.55 46.0 3.49e-01 92.5% 79.5%
2m8cA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.55 45.0 3.75e-01 88.7% 65.7%
3d68A01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.55 36.0 3.51e-01 93.8% 59.8%
1hi9A01 3.40.50.10780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dipeptide transport protein 0.54 32.0 2.42e-01 92.5% 22.2%
1kwmA01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.54 37.0 3.59e-01 93.8% 63.6%
4jndA01 1.10.1740.220 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.54 33.0 2.91e-01 88.7% 37.7%
3kzgA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.54 43.0 3.74e-01 88.7% 69.8%
1bjaA00 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 0.53 42.0 4.05e-01 87.5% 96.8%
2nyiA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 42.0 4.03e-01 100.0% 74.4%
2qwwC00 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 0.53 46.0 3.92e-01 98.8% 72.5%
3q23A02 3.30.70.2440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 42.0 3.55e-01 90.0% 91.3%
2fxaA00 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 0.53 44.0 3.59e-01 92.5% 60.9%
2fbhA00 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 0.53 43.0 3.72e-01 93.8% 74.5%
4i2oA02 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 0.52 28.0 2.87e-01 100.0% 50.0%
4yifF00 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 0.52 43.0 3.80e-01 97.5% 78.5%
2ckwA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.52 35.0 3.15e-01 71.2% 81.9%
2q88A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 41.0 3.54e-01 88.7% 66.9%
6a80A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 42.0 3.69e-01 90.0% 67.8%
7wu7501 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 44.0 3.85e-01 100.0% 94.4%
4c0rA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 41.0 3.59e-01 88.7% 68.9%
3pvlA04 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 39.0 3.68e-01 83.7% 99.0%
4b8xA00 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 0.51 42.0 3.56e-01 93.8% 70.7%
3tqlA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.50 41.0 3.61e-01 92.5% 70.6%
2ieeA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.50 40.0 3.48e-01 90.0% 62.9%
4jcmA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.50 42.0 2.78e-01 97.5% 83.9%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4990094 304.56.1.0 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like 0.64 36.0 3.82e-01 97.5% 62.9%
5030717 304.11.1.0 a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase 0.62 40.0 4.07e-01 93.8% 66.3%
2496734 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.60 53.0 4.33e-01 100.0% 80.1%
None 0.60 35.0 2.59e-01 70.0% 22.5%
5020161 601.1.2.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.60 47.0 3.75e-01 100.0% 42.1%
3213800 5001.1.1.153 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srd, 7TM_GPCR_Str 0.59 47.0 3.12e-01 100.0% 20.3%
3971354 2003.1.5.16 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › CheR 0.59 34.0 2.53e-01 70.0% 22.0%
4667119 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.58 51.0 4.34e-01 98.8% 72.6%
3902090 377.1.1.0 few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.58 33.0 3.80e-01 81.2% 84.0%
3989440 101.1.2.1 alpha arrays › HTH › HTH › winged helix domain › HTH_1 0.56 42.0 4.09e-01 81.2% 97.8%
3199320 4099.1.1.0 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.55 36.0 3.26e-01 98.8% 47.8%
4026000 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 37.0 3.87e-01 72.5% 88.0%
5051539 101.1.2.14 alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.54 42.0 3.76e-01 83.7% 92.2%
3282607 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 47.0 4.12e-01 98.8% 80.0%
3609011 5050.1.1.28 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › BT1 0.54 46.0 3.18e-01 100.0% 75.9%
3514596 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 40.0 3.94e-01 78.8% 83.5%
3801856 3755.4.1.75 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › PF28572 0.54 48.0 3.63e-01 100.0% 50.3%
5006819 101.1.2.14 alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.54 39.0 3.76e-01 78.8% 88.4%
4140340 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.53 48.0 3.90e-01 100.0% 88.7%
3781291 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.53 47.0 4.35e-01 98.8% 100.0%
4945461 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.52 39.0 3.74e-01 81.2% 91.6%
5010818 101.1.2.150 alpha arrays › HTH › HTH › winged helix domain › HTH_45 0.52 41.0 3.78e-01 88.7% 86.4%
3594128 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.52 38.0 3.81e-01 80.0% 75.3%
5015873 7523.1.1.4 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_3 0.52 42.0 3.59e-01 88.7% 63.8%
5010794 101.1.2.728 alpha arrays › HTH › HTH › winged helix domain › PF31122 0.52 42.0 4.03e-01 91.3% 98.9%
3476838 7523.1.1.20 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Lig_chan-Glu_bd 0.51 42.0 3.47e-01 92.5% 66.0%
5039516 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.51 37.0 3.65e-01 76.2% 92.9%
4935618 101.1.2.141 alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.50 40.0 3.87e-01 90.0% 94.7%
D2 high residues 88-149
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24692.2 best DUF7659 66.7 3.00e-18 91.9% 40.7%
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ldjA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.69 61.0 4.98e-01 100.0% 67.8%
2k85A00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.66 57.0 5.64e-01 100.0% 93.8%
1on2A01 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 0.66 56.0 5.32e-01 93.5% 91.7%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.65 57.0 4.76e-01 100.0% 69.1%
3cdlA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.63 50.0 5.25e-01 98.4% 100.0%
6e6qA00 1.10.10.1100 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › BFD-like [2Fe-2S]-binding domain 0.63 51.0 5.36e-01 91.9% 100.0%
2iaiA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.63 44.0 4.43e-01 83.9% 73.8%
1ltmA02 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.62 54.0 3.96e-01 100.0% 96.5%
3h20A04 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.61 49.0 4.40e-01 95.2% 62.9%
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.60 48.0 4.77e-01 91.9% 100.0%
3hugA00 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 0.60 41.0 3.84e-01 85.5% 56.2%
3c07B00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.59 51.0 3.54e-01 100.0% 46.3%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.59 48.0 4.55e-01 96.8% 98.7%
2p6rA03 1.10.3380.30 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › 0.59 46.0 3.28e-01 91.9% 59.2%
3fr3B02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 46.0 3.82e-01 90.3% 52.2%
1zk8A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.57 39.0 4.18e-01 83.9% 97.8%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.57 40.0 3.24e-01 74.2% 38.7%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.56 40.0 3.98e-01 74.2% 96.9%
3dewA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.55 41.0 4.32e-01 93.5% 100.0%
3t9oB00 1.20.120.30 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartate receptor, ligand-binding domain 0.55 43.0 3.62e-01 90.3% 63.3%
3zh9B03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.55 45.0 3.73e-01 98.4% 69.0%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 39.0 3.75e-01 77.4% 76.7%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.54 41.0 3.91e-01 83.9% 81.3%
4nsmA00 6.10.250.2770 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.54 38.0 3.65e-01 80.6% 64.8%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.53 36.0 3.06e-01 91.9% 39.3%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 46.0 4.34e-01 100.0% 96.2%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.52 36.0 3.13e-01 74.2% 45.6%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.52 36.0 3.52e-01 74.2% 64.8%
1sw6A00 1.25.40.20 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ankyrin repeat-containing domain 0.51 42.0 2.91e-01 100.0% 24.0%
2xmzA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 40.0 2.74e-01 91.9% 62.0%
2wauA02 1.20.58.830 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 42.0 3.47e-01 96.8% 73.8%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3928846 7022.1.1.0 alpha bundles › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein 0.64 40.0 3.09e-01 74.2% 28.6%
3279034 101.1.1.5 alpha arrays › HTH › HTH › Three-helical HTH › TetR_N 0.64 55.0 5.05e-01 100.0% 75.0%
4950966 192.30.1.0 alpha bundles › Long alpha-hairpin › SepCysE N-terminal domain › SepCysE N-terminal domain 0.63 39.0 4.01e-01 80.6% 65.0%
3282096 101.1.1.5 alpha arrays › HTH › HTH › Three-helical HTH › TetR_N 0.62 53.0 5.05e-01 98.4% 84.0%
5040698 7000.1.1.0 alpha arrays › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS 0.61 49.0 4.96e-01 90.3% 93.3%
4187216 101.1.1.5 alpha arrays › HTH › HTH › Three-helical HTH › TetR_N 0.60 52.0 4.95e-01 98.4% 84.0%
3489866 210.1.2.0 a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain 0.59 51.0 5.11e-01 100.0% 100.0%
3281341 101.1.1.5 alpha arrays › HTH › HTH › Three-helical HTH › TetR_N 0.58 50.0 4.69e-01 98.4% 78.8%
4507542 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.58 41.0 3.59e-01 74.2% 64.4%
3386552 650.1.1.1 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.57 49.0 4.74e-01 93.5% 98.6%
3485769 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.56 46.0 3.34e-01 95.2% 55.9%
5012670 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.56 48.0 3.46e-01 100.0% 38.4%
3278248 150.5.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.55 39.0 3.58e-01 74.2% 98.8%
3226377 7022.1.1.1 alpha bundles › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › MBOAT 0.54 37.0 2.63e-01 82.3% 23.1%
3802176 604.16.1.3 alpha bundles › Spectrin repeat-like › Hypothetical membrane protein Ta0354, soluble domain › Hypothetical membrane protein Ta0354, soluble domain › Vwaint 0.53 45.0 3.87e-01 98.4% 87.6%
2572867 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.52 36.0 3.05e-01 74.2% 42.3%
3894027 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.51 44.0 3.11e-01 100.0% 45.5%