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BML_coassembly_scaffold_172_curated_closed_complete_prodigal-single.1__X__X__00178

Bact-Vir

BML_coassembly_scaffold_172_curated_closed_complete_prodigal-single.1__X__X__00178

Identity

Kingdom:
phage

Quality

92.8 mean pLDDT

3D Structure

Domains

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

D1 medium residues 1-140
PDB
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
8an5A01 3.30.460.40 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.79 62.0 5.56e-01 82.9% 65.1%
4wqkA00 3.30.460.40 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.72 56.0 5.22e-01 81.4% 69.7%
4wh5A00 3.30.460.40 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.68 54.0 5.23e-01 84.3% 81.6%
4o8sA01 3.10.450.620 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › JHP933, nucleotidyltransferase-like core domain 0.64 52.0 5.48e-01 85.7% 100.0%
3er9B03 3.30.460.60 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Poxvirus poly(A) polymerase, nucleotidyltransferase domain 0.62 48.0 4.95e-01 83.6% 86.5%
3h37A01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.59 51.0 5.05e-01 94.3% 89.7%
7qprA02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.58 41.0 4.16e-01 71.4% 91.1%
2be3B01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.57 41.0 4.23e-01 75.0% 100.0%
3ct8A00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.55 39.0 4.01e-01 71.4% 95.5%
4mtsA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.55 40.0 4.13e-01 73.6% 97.7%
3wfoA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.54 47.0 4.57e-01 94.3% 86.0%
3iuzA00 3.10.180.50 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 0.53 47.0 3.70e-01 100.0% 93.8%
1cjxA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 37.0 3.69e-01 73.6% 98.7%
1mpyA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 37.0 3.68e-01 73.6% 100.0%
4lqbA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 36.0 3.71e-01 70.0% 94.6%
2rffA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.52 39.0 4.29e-01 88.6% 99.1%
2nrkA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.51 43.0 4.09e-01 90.0% 96.4%
2pjsA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.51 36.0 4.22e-01 78.6% 100.0%
3oxhA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.50 35.0 3.58e-01 71.4% 89.1%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5040839 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.79 63.0 5.85e-01 96.4% 67.6%
4945608 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.79 60.0 5.52e-01 78.6% 68.0%
3059418 316.1.1.18 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › AbiEii 0.79 63.0 5.58e-01 83.6% 64.9%
4993673 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.76 61.0 5.55e-01 83.6% 66.3%
5069234 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.76 61.0 5.66e-01 97.9% 67.6%
4977130 316.1.1.41 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DUF6036 0.75 60.0 5.80e-01 83.6% 81.2%
4959743 316.1.1.39 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DUF2204 0.75 58.0 5.18e-01 80.7% 59.5%
3633420 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.73 60.0 5.06e-01 85.0% 61.8%
5058624 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.73 56.0 5.70e-01 80.7% 83.6%
3704072 316.1.1.14 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › LicD 0.72 68.0 5.87e-01 100.0% 80.5%
2092693 316.1.1.21 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Aminoglyc_resit 0.72 57.0 5.22e-01 82.1% 70.1%
3285469 316.1.1.21 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Aminoglyc_resit 0.72 56.0 5.02e-01 82.1% 69.4%
5021444 316.1.1.21 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Aminoglyc_resit 0.71 58.0 5.57e-01 85.7% 78.8%
3197794 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.69 51.0 4.61e-01 81.4% 56.3%
151131 316.1.1.21 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Aminoglyc_resit 0.68 55.0 5.28e-01 84.3% 81.6%
3726440 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.68 54.0 4.91e-01 93.6% 62.7%
3205500 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.68 59.0 4.99e-01 92.1% 60.4%
4969949 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.68 60.0 5.30e-01 93.6% 69.7%
5055016 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.68 59.0 5.17e-01 93.6% 69.3%
3281252 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.65 46.0 3.95e-01 82.1% 46.8%
3640051 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.63 55.0 4.65e-01 93.6% 66.7%
3197454 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.63 55.0 4.64e-01 93.6% 62.7%
5061454 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.62 46.0 4.53e-01 77.9% 79.9%
4278249 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.61 50.0 5.14e-01 88.6% 89.6%
1824581 316.1.1.1 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PolyA_pol 0.60 52.0 5.02e-01 94.3% 88.8%
4495995 316.1.1.1 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PolyA_pol 0.58 47.0 4.83e-01 92.9% 91.5%
5057036 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.58 48.0 4.74e-01 88.6% 82.0%
3952545 211.1.1.0 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.58 33.0 4.19e-01 80.7% 97.5%
1179385 316.1.1.7 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Pox_polyA_pol 0.57 50.0 4.65e-01 95.0% 83.2%
4388749 316.1.1.48 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MdcG 0.56 42.0 4.50e-01 78.6% 94.2%
3784617 211.1.1.0 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.53 29.0 3.85e-01 82.9% 96.2%
3944466 211.1.1.10 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase_5 0.52 36.0 3.60e-01 71.4% 100.0%
5034252 211.1.1.0 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.51 39.0 4.05e-01 78.6% 95.4%
3294949 7579.1.1.5 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S10 0.51 44.0 3.19e-01 98.6% 70.0%
3617433 7579.1.1.5 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S10 0.51 44.0 3.16e-01 97.9% 75.5%
3997898 101.1.2.407 alpha arrays › HTH › HTH › winged helix domain › WHD_ORC2 0.51 34.0 3.71e-01 88.6% 83.5%
5009407 211.1.1.1 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase 0.50 44.0 3.41e-01 95.7% 97.7%
D2 medium residues 141-201
PDB
Domain cluster: representative
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4rv1F00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.65 57.0 3.46e-01 100.0% 26.0%
2iaiA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.63 54.0 4.25e-01 100.0% 77.2%
3g2eB00 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.61 47.0 3.39e-01 85.2% 91.4%
2vixA02 1.10.150.630 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.61 47.0 4.19e-01 85.2% 80.9%
4cs9B02 1.20.120.1350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pneumovirus matrix protein 2 (M2), zinc-binding domain 0.59 43.0 3.62e-01 78.7% 51.4%
3kbtA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 46.0 3.03e-01 88.5% 22.9%
1l5jA01 1.25.40.310 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Aconitate B, HEAT-like domain 0.58 46.0 3.61e-01 100.0% 36.6%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 47.0 3.70e-01 95.1% 65.4%
1h7cA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 46.0 3.94e-01 95.1% 97.1%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.55 48.0 4.49e-01 98.4% 81.3%
4nnaA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 46.0 2.93e-01 98.4% 27.4%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 45.0 4.01e-01 96.7% 93.5%
3tp3A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 43.0 3.45e-01 100.0% 79.1%
1gwiA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.53 43.0 2.70e-01 93.4% 55.7%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.51 40.0 3.56e-01 91.8% 84.5%
4ga0A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.50 44.0 3.39e-01 100.0% 47.6%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5058173 316.1.1.39 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DUF2204 0.77 68.0 4.65e-01 98.4% 32.4%
4998411 4995.1.1.1 alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.71 62.0 5.81e-01 100.0% 100.0%
3421725 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 62.0 4.12e-01 100.0% 52.8%
3310140 109.4.1.273 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PI4KB-PIK1_PIK 0.70 59.0 4.85e-01 100.0% 55.8%
5004518 4995.1.1.1 alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.69 58.0 5.52e-01 98.4% 98.7%
3231402 109.27.1.0 alpha superhelices › Repetitive alpha hairpins › BACK domain › BACK domain 0.67 57.0 5.74e-01 98.4% 100.0%
3804487 109.27.1.0 alpha superhelices › Repetitive alpha hairpins › BACK domain › BACK domain 0.66 56.0 5.30e-01 100.0% 81.3%
3254975 603.2.1.2 alpha bundles › STAT-like › STAT › STAT › Dict-STAT-coil 0.61 49.0 4.04e-01 90.2% 74.8%
3391962 226.1.1.1 a+b two layers › POZ domain › POZ domain › POZ domain › BTB 0.60 51.0 3.68e-01 100.0% 31.3%
3494126 4156.1.1.2 alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › HA2_N,HA2_C 0.60 47.0 3.30e-01 88.5% 27.4%
5011123 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 46.0 3.98e-01 96.7% 69.5%
1144608 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.56 45.0 3.72e-01 90.2% 81.6%
3836512 592.1.1.2 alpha arrays › PWI domain-like › PWI domain › PWI domain › Helicase_PWI 0.56 44.0 3.61e-01 86.9% 76.5%
3413751 109.4.1.471 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › GCFC 0.56 45.0 2.92e-01 100.0% 24.7%
3741735 101.1.1.69 alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-bind_7 0.55 39.0 3.54e-01 75.4% 67.1%
4352992 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 45.0 3.28e-01 98.4% 73.0%
3363326 310.2.1.29 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › TMEM128 0.52 39.0 3.17e-01 88.5% 62.9%
3219246 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.52 40.0 4.07e-01 91.8% 96.7%
3592632 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.51 44.0 3.89e-01 100.0% 74.7%
3259816 592.6.1.2 alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain › PF26582 0.51 39.0 3.34e-01 86.9% 59.1%