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NC_055060.1__YP_010084095.1__KMD61_gp08__00035

Bact-Vir

NC_055060.1__YP_010084095.1__KMD61_gp08__00035

Identity

Accession:
NC_055060 ↗
Kingdom:
phage

Quality

86.5 mean pLDDT

Taxonomy

Bamfordvirae› Preplasmiviricota› Tectiliviricetes› Kalamavirales› Tectiviridae› Deltatectivirus› Streptomyces_phage_WheeHeim

TaxID: 2500797

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 13-65
PDB
Domain cluster: rep: PH2017_36_ELK_O_B_scaffold_2_prodigal-single.1__X__X__00144__D29-85
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1y3tA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.70 48.0 3.38e-01 71.7% 72.9%
1sq4A02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.68 50.0 3.86e-01 81.1% 58.7%
6nwmA01 2.60.120.280 Mainly Beta › Sandwich › Jelly Rolls › Regulatory protein AraC 0.65 52.0 3.80e-01 92.5% 73.5%
5ir2A00 3.50.30.40 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › Ribonuclease E inhibitor RraA/RraA-like 0.63 52.0 3.55e-01 98.1% 66.2%
4zfjD00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.63 43.0 2.89e-01 73.6% 24.2%
1sfnA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.63 51.0 3.42e-01 98.1% 69.8%
3rbtD01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.62 51.0 4.05e-01 100.0% 64.0%
1sefA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.62 43.0 3.45e-01 75.5% 60.5%
7afrX02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.61 38.0 3.68e-01 98.1% 53.3%
2c5qA00 3.50.30.40 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › Ribonuclease E inhibitor RraA/RraA-like 0.61 49.0 3.24e-01 90.6% 67.2%
1rc6A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.60 49.0 3.29e-01 98.1% 67.4%
4m0hA01 2.60.120.1440 Mainly Beta › Sandwich › Jelly Rolls › 0.60 43.0 3.28e-01 79.2% 30.9%
4damC00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 42.0 3.56e-01 81.1% 91.0%
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.57 41.0 2.84e-01 79.2% 24.0%
1bdp001 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 45.0 3.07e-01 98.1% 24.7%
2h4oA00 6.20.120.10 Special › Other non-globular › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.55 38.0 3.65e-01 88.7% 61.3%
3cewA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.55 46.0 3.74e-01 100.0% 58.2%
3o8oF01 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 46.0 3.04e-01 96.2% 28.9%
3kmhA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.55 45.0 2.96e-01 92.5% 27.1%
4d4iA01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.54 45.0 2.72e-01 96.2% 43.8%
6gfaA02 3.30.30.30 Alpha Beta › 2-Layer Sandwich › Defensin A-like › 0.54 35.0 3.46e-01 83.0% 58.9%
3daxB00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.54 48.0 2.79e-01 98.1% 26.6%
1ao0A01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.54 40.0 2.64e-01 90.6% 28.7%
3e7wA01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.53 44.0 2.71e-01 98.1% 29.0%
1u0mA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.53 35.0 2.60e-01 77.4% 25.3%
7syvx01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.52 37.0 2.84e-01 77.4% 82.5%
1t6sA01 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 35.0 3.11e-01 100.0% 45.3%
2fgtA02 3.10.450.310 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 39.0 3.49e-01 86.8% 73.2%
4oxiA01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.51 44.0 2.66e-01 100.0% 33.5%
1ylxA00 3.30.70.1480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GK1464-like 0.51 39.0 3.23e-01 92.5% 44.4%
1hdhA02 3.30.1120.10 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.51 35.0 3.20e-01 86.8% 50.6%
2k4nA00 3.30.720.70 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.50 41.0 3.31e-01 94.3% 55.9%
4ivkA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.50 40.0 2.42e-01 92.5% 82.2%
2h84A02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.50 34.0 2.55e-01 100.0% 26.4%
2wshA00 3.40.1440.40 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.50 34.0 2.68e-01 71.7% 85.1%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3251513 12.3.1.46 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › ComC_SSD 0.79 56.0 3.54e-01 75.5% 59.6%
3291419 10.12.1.61 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › HgmA_N 0.71 49.0 3.19e-01 73.6% 52.9%
1030918 10.12.1.39 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.71 50.0 3.57e-01 75.5% 45.9%
3692573 10.12.1.61 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › HgmA_N 0.71 48.0 3.01e-01 71.7% 42.6%
1279907 10.12.1.39 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.69 49.0 3.37e-01 73.6% 65.4%
3976988 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.69 57.0 4.11e-01 92.5% 76.8%
3967079 10.12.1.75 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding_2 0.68 56.0 3.85e-01 96.2% 63.4%
4996016 4237.1.1.1 ↗ beta barrels › FomD-like › FomD-like › FomD-like › DUF402 0.68 48.0 3.48e-01 77.4% 28.1%
3254382 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.68 50.0 3.95e-01 100.0% 37.4%
4497102 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.67 56.0 3.94e-01 98.1% 67.8%
4264722 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.67 53.0 3.78e-01 90.6% 71.8%
3969365 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.66 53.0 3.85e-01 92.5% 70.3%
3588800 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.66 52.0 3.56e-01 90.6% 65.4%
4007792 10.12.1.115 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › PF30437 0.66 53.0 3.99e-01 90.6% 85.2%
1030915 10.12.1.27 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_3 0.66 48.0 3.59e-01 81.1% 51.1%
3277683 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.65 55.0 3.97e-01 98.1% 68.5%
4299999 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.65 52.0 3.72e-01 90.6% 73.3%
4225307 10.12.1.104 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding, Cupin_2 0.65 52.0 3.73e-01 90.6% 73.9%
3941961 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.65 48.0 3.89e-01 79.2% 74.0%
4378922 10.12.1.104 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding, Cupin_2 0.64 50.0 3.61e-01 88.7% 71.9%
3387563 10.12.1.64 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › ExsA_N 0.64 51.0 3.61e-01 92.5% 67.2%
3947214 10.12.1.104 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding, Cupin_2 0.64 51.0 3.67e-01 92.5% 71.8%
3968985 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.64 54.0 3.90e-01 98.1% 70.6%
4558923 865.1.1.2 ↗ beta complex topology › PheT/TilS domain › PheT/TilS domain › PheT/TilS domain › TilS_C 0.64 46.0 3.71e-01 77.4% 90.5%
3966549 10.12.1.64 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › ExsA_N 0.63 50.0 3.66e-01 92.5% 71.5%
3784922 229.1.1.1 ↗ a+b two layers › Cdc48 domain 2-like › Cdc48 domain 2-like › Cdc48 domain 2-like › CDC48_2 0.63 37.0 2.93e-01 100.0% 28.2%
3942603 10.12.1.39 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.63 50.0 3.65e-01 90.6% 71.6%
4585394 10.12.1.121 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › HgmA_C, HgmA_N 0.62 51.0 3.08e-01 98.1% 34.3%
3968004 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.62 51.0 3.76e-01 98.1% 70.3%
3602759 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.62 43.0 4.15e-01 98.1% 65.0%
4010514 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.61 48.0 3.46e-01 92.5% 68.6%
3975454 10.12.1.138 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_3, Cupin_2 0.61 51.0 3.35e-01 100.0% 42.7%
4534746 10.12.1.39 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.60 50.0 3.43e-01 100.0% 82.0%
3743745 229.1.1.1 ↗ a+b two layers › Cdc48 domain 2-like › Cdc48 domain 2-like › Cdc48 domain 2-like › CDC48_2 0.59 36.0 2.83e-01 98.1% 29.1%
2723972 1143.1.1.1 ↗ beta sandwiches › beta sandwich domain in acetophenone carboxylase (Apc) alpha subunit › beta sandwich domain in acetophenone carboxylase (Apc) alpha subunit › beta sandwich domain in acetophenone carboxylase (Apc) alpha subunit › Hydant_A_C 0.59 41.0 3.65e-01 79.2% 48.1%
4479523 837.1.1.1 ↗ a+b two layers › Ribosomal protein S16 › Ribosomal protein S16 › Ribosomal protein S16 › Ribosomal_S16 0.59 34.0 2.50e-01 98.1% 21.4%
3943625 10.12.1.8 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › AraC_binding 0.58 46.0 3.64e-01 98.1% 74.1%
3837975 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.58 44.0 3.15e-01 94.3% 27.3%
3394203 5.1.4.223 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_RIC1_2nd 0.55 45.0 2.91e-01 96.2% 77.6%
4933961 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.55 41.0 2.53e-01 86.8% 30.5%
2834373 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.54 39.0 3.20e-01 77.4% 78.1%
3218749 295.1.1.4 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › COMM_domain 0.53 44.0 4.27e-01 100.0% 90.0%
3989031 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.53 41.0 2.62e-01 84.9% 69.6%
3462061 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.52 43.0 2.97e-01 98.1% 73.5%
4928381 4.7.1.1 ↗ beta barrels › SH3 › RNase P subunit p29 › RNase P subunit p29 › RNase_P-MRP_p29 0.51 43.0 3.86e-01 92.5% 91.8%
3247669 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.51 36.0 2.41e-01 100.0% 16.2%
4928223 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.51 40.0 3.67e-01 98.1% 100.0%
5018729 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.51 40.0 3.24e-01 98.1% 42.7%
3961853 210.1.3.3 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_4 0.51 39.0 2.79e-01 98.1% 99.1%
5030079 2002.1.1.60 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › AP_endonuc_2 0.50 43.0 2.52e-01 98.1% 39.2%
D2 medium residues 76-108
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4bvxA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 43.0 3.29e-01 100.0% 51.4%
1v4aA01 1.10.4050.10 Mainly Alpha › Orthogonal Bundle › Nucleotidyltransferase substrate binding subunit/domain fold › Glutamine synthase adenylyltransferase GlnE 0.55 47.0 3.36e-01 100.0% 42.2%