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LSDeep1_scaffold_41_prodigal-single.1__X__X__00028

Bact-Vir

LSDeep1_scaffold_41_prodigal-single.1__X__X__00028

Identity

Kingdom:
phage

Quality

85.8 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 3-77
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06056.19 best Terminase_5 20.7 4.40e-04 44.0% 44.8%
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1j1vA00 1.10.1750.10 Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain 0.87 80.0 7.34e-01 100.0% 78.7%
1l8qA03 1.10.1750.10 Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain 0.85 79.0 6.88e-01 100.0% 72.9%
5f64A02 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 0.84 50.0 5.03e-01 84.0% 60.0%
3vfzB00 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 0.82 50.0 5.49e-01 85.3% 74.6%
2x48A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.82 53.0 6.18e-01 92.0% 92.6%
3ulqB00 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 0.80 47.0 5.31e-01 84.0% 75.9%
4gvpA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.80 48.0 3.39e-01 84.0% 21.8%
1r71A01 1.10.10.730 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › KorB DNA-binding domain 0.79 56.0 6.38e-01 93.3% 100.0%
4krdB00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.67 58.0 4.30e-01 96.0% 76.3%
4nb5B01 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 50.0 4.85e-01 97.3% 75.3%
2pmiB00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.62 55.0 3.95e-01 98.7% 39.0%
1jhgA00 1.10.1270.10 Mainly Alpha › Orthogonal Bundle › Trp Operon Repressor; Chain A › TrpR-like 0.62 48.0 4.29e-01 82.7% 60.4%
5jbrA01 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 0.62 48.0 4.66e-01 100.0% 74.4%
2xseA00 1.20.120.1440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › JBP1, DNA-binding domain 0.61 54.0 4.27e-01 100.0% 84.3%
4nvsA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.61 46.0 3.60e-01 80.0% 51.6%
2ijeS00 1.10.840.10 Mainly Alpha › Orthogonal Bundle › Son of Sevenless (SoS) protein; Chain S, domain 2 › Ras guanine-nucleotide exchange factors catalytic domain 0.60 42.0 3.01e-01 74.7% 89.9%
1aa6A03 3.40.228.10 Alpha Beta › 3-Layer(aba) Sandwich › Dimethylsulfoxide Reductase; domain 2 › Dimethylsulfoxide Reductase, domain 2 0.60 49.0 3.65e-01 90.7% 90.3%
3iwfB00 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 43.0 4.08e-01 86.7% 64.0%
8e9gJ01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.59 44.0 3.39e-01 100.0% 35.9%
1orjD00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.57 44.0 3.72e-01 84.0% 59.2%
4ivnA01 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 41.0 4.09e-01 88.0% 75.0%
8aigA01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.56 40.0 3.99e-01 78.7% 72.7%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.55 46.0 4.64e-01 93.3% 92.0%
2f2cA02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.55 48.0 4.35e-01 100.0% 82.1%
3rkoF01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.55 41.0 3.22e-01 98.7% 37.5%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 46.0 3.65e-01 93.3% 72.1%
2k9lA00 1.10.10.1330 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › RNA polymerase sigma-54 factor, core-binding domain 0.54 42.0 4.20e-01 90.7% 81.6%
3owaA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.54 45.0 3.76e-01 94.7% 76.8%
8hk0A01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.54 43.0 3.85e-01 93.3% 90.8%
4yibA01 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.54 38.0 3.02e-01 73.3% 89.9%
4qhpA05 1.25.50.10 Mainly Alpha › Alpha Horseshoe › Zincin-like fold › Peptidase M1, alanyl aminopeptidase, C-terminal domain 0.53 46.0 3.03e-01 97.3% 31.5%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.53 44.0 4.13e-01 93.3% 84.9%
2b6cA01 1.20.1660.10 Mainly Alpha › Up-down Bundle › ARM repeat fold › Hypothetical protein (EF3068) 0.53 40.0 3.55e-01 92.0% 54.3%
1z72A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.52 42.0 3.12e-01 92.0% 82.9%
3a04A01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 45.0 3.20e-01 100.0% 52.6%
4s3mB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.52 47.0 4.16e-01 100.0% 84.9%
8e9gK01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 41.0 3.89e-01 98.7% 71.4%
6humG01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.52 40.0 3.13e-01 100.0% 38.7%
2mf4A01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.51 37.0 3.64e-01 78.7% 73.2%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4106860 101.1.6.4 alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.90 82.0 7.49e-01 100.0% 76.8%
4197050 101.1.6.4 alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.89 81.0 7.15e-01 100.0% 69.5%
4449691 101.1.6.4 alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.88 62.0 6.79e-01 76.0% 87.3%
3512259 101.1.6.0 alpha arrays › HTH › HTH › TrpR 0.88 82.0 7.21e-01 100.0% 81.0%
4529157 101.1.6.4 alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.87 78.0 7.29e-01 98.7% 80.0%
4604979 101.1.6.4 alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.84 77.0 6.86e-01 100.0% 72.1%
4347676 101.1.6.4 alpha arrays › HTH › HTH › TrpR › Bac_DnaA_C 0.82 74.0 6.98e-01 98.7% 88.9%
3977374 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.78 55.0 6.32e-01 90.7% 100.0%
3278077 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.78 58.0 6.48e-01 100.0% 98.3%
3944370 101.1.1.318 alpha arrays › HTH › HTH › Three-helical HTH › PF30335 0.76 57.0 5.96e-01 96.0% 84.3%
4964802 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.76 51.0 5.64e-01 84.0% 86.7%
5003692 101.1.6.12 alpha arrays › HTH › HTH › TrpR › HTH_23 0.74 51.0 5.46e-01 90.7% 83.1%
2628410 101.1.1.86 alpha arrays › HTH › HTH › Three-helical HTH › Raf1_HTH 0.74 56.0 5.95e-01 100.0% 90.9%
5004314 101.1.1.60 alpha arrays › HTH › HTH › Three-helical HTH › HTH_23 0.73 50.0 5.08e-01 90.7% 72.0%
5012580 101.1.10.76 alpha arrays › HTH › HTH › Cyclin-like › HTH_23 0.68 63.0 5.39e-01 100.0% 73.9%
5079108 101.1.1.60 alpha arrays › HTH › HTH › Three-helical HTH › HTH_23 0.68 62.0 5.73e-01 100.0% 89.5%
4954922 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.67 62.0 5.50e-01 100.0% 81.0%
4994271 101.1.1.60 alpha arrays › HTH › HTH › Three-helical HTH › HTH_23 0.67 61.0 5.35e-01 100.0% 92.7%
3254469 101.1.10.9 alpha arrays › HTH › HTH › Cyclin-like › Cyclin 0.67 56.0 4.20e-01 92.0% 80.0%
5053358 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.65 54.0 4.57e-01 90.7% 85.6%
4422641 2004.1.1.363 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD-helicase+UvrD_C 0.65 51.0 2.98e-01 84.0% 12.5%
3253586 101.1.10.9 alpha arrays › HTH › HTH › Cyclin-like › Cyclin 0.63 57.0 4.57e-01 100.0% 55.2%
3391523 4156.1.1.5 alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › POLQ_helical 0.63 54.0 4.15e-01 97.3% 58.9%
4472469 613.1.1.1 alpha complex topology › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › tRNA-synt_2c 0.63 56.0 4.18e-01 100.0% 77.4%
4970998 101.1.6.0 alpha arrays › HTH › HTH › TrpR 0.63 52.0 4.73e-01 89.3% 80.0%
4938723 101.1.2.141 alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.62 46.0 3.91e-01 92.0% 46.2%
3968886 101.1.1.77 alpha arrays › HTH › HTH › Three-helical HTH › HTH_50 0.62 42.0 4.46e-01 80.0% 80.0%
4314061 101.1.3.1 alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.62 54.0 5.03e-01 100.0% 76.3%
3718570 101.1.10.9 alpha arrays › HTH › HTH › Cyclin-like › Cyclin 0.62 56.0 4.70e-01 100.0% 64.8%
4029192 101.1.2.236 alpha arrays › HTH › HTH › winged helix domain › POLR3C_WHD 0.62 47.0 3.04e-01 96.0% 16.5%
4260337 101.1.3.1 alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.62 55.0 5.07e-01 100.0% 76.8%
3519938 4156.1.1.5 alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › POLQ_helical 0.60 53.0 4.07e-01 98.7% 52.6%
5058443 2004.1.1.191 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.59 49.0 3.64e-01 90.7% 39.0%
4666988 132.1.1.0 alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) 0.59 42.0 3.97e-01 78.7% 62.2%
4060271 132.1.1.1 alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.59 42.0 4.06e-01 78.7% 65.9%
4948103 613.1.1.1 alpha complex topology › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › tRNA-synt_2c 0.59 52.0 3.72e-01 100.0% 79.1%
5071227 2005.1.1.18 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.59 53.0 3.51e-01 100.0% 98.0%
3728888 109.3.1.2 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank,Ank_2 0.59 43.0 3.14e-01 94.7% 26.1%
3681611 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.57 51.0 4.04e-01 100.0% 58.1%
4471337 132.1.1.1 alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.57 41.0 4.24e-01 78.7% 80.0%
4927066 186.1.1.0 alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.57 47.0 3.91e-01 90.7% 61.5%
5042406 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.57 50.0 4.63e-01 98.7% 91.6%
5005153 4156.1.1.6 alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Helicase_dom4_arc 0.56 50.0 3.75e-01 97.3% 41.7%
4060877 132.1.1.1 alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.56 41.0 3.90e-01 78.7% 64.4%
3927372 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.56 49.0 4.84e-01 100.0% 98.8%
5002248 101.1.2.136 alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.56 45.0 3.93e-01 90.7% 57.5%
3204144 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.56 49.0 4.11e-01 100.0% 63.1%
3414131 108.2.1.1 alpha arrays › EF-hand › Insect pheromone/odorant-binding proteins › Insect pheromone/odorant-binding proteins › PBP_GOBP 0.55 48.0 4.53e-01 97.3% 83.3%
4373693 132.1.1.1 alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.55 42.0 3.96e-01 81.3% 67.8%
3424337 101.1.2.31 alpha arrays › HTH › HTH › winged helix domain › TFIIE_alpha 0.55 46.0 4.55e-01 94.7% 92.5%
3432556 632.1.1.13 alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Rx_N 0.54 38.0 3.58e-01 73.3% 64.2%
4668975 132.1.1.0 alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) 0.54 42.0 4.02e-01 81.3% 71.8%
3278820 191.1.1.48 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_46 0.54 40.0 3.42e-01 78.7% 60.8%
143220 603.1.1.8 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Spectrin_2 0.54 40.0 3.99e-01 80.0% 86.3%
5040184 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 45.0 4.45e-01 96.0% 96.2%
3908884 109.4.1.926 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › FH3_FHOD1-3 0.53 42.0 2.98e-01 88.0% 51.0%
4224903 132.1.1.1 alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.51 39.0 3.76e-01 81.3% 71.8%
3804601 140.1.1.11 alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DALR_1 0.51 40.0 3.61e-01 88.0% 70.0%
4093622 132.1.1.1 alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.51 38.0 3.63e-01 81.3% 76.7%