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BML_coassembly_scaffold_25_prodigal-single.1__X__X__00321

Bact-Vir

BML_coassembly_scaffold_25_prodigal-single.1__X__X__00321

Identity

Kingdom:
phage

Quality

90.0 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 320-455
PDB
Domain cluster: representative
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5078492 2006.1.2.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases 0.54 45.0 4.14e-01 92.6% 87.6%
D2 medium residues 26-122_466-520
PDB
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4kq9A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.68 39.0 4.72e-01 100.0% 86.7%
3l49A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.63 40.0 4.15e-01 100.0% 65.3%
1gkuB05 3.40.50.140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 37.0 4.13e-01 100.0% 81.0%
8b0qA01 3.30.420.340 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › UvrC, RNAse H endonuclease domain 0.56 36.0 3.44e-01 100.0% 55.1%
8oqxA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 32.0 3.61e-01 100.0% 78.9%
1jkmA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 42.0 3.23e-01 86.8% 38.5%
2vgnA02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.51 33.0 3.59e-01 100.0% 78.0%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4067862 2484.1.1.174 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.62 38.0 4.23e-01 100.0% 77.4%
4954915 2003.1.1.386 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Sacchrp_dh_C 0.57 38.0 2.79e-01 100.0% 26.4%
4494257 2484.1.1.55 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH_dom 0.54 38.0 3.60e-01 100.0% 61.1%
5051475 2006.1.6.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › VWA 0.51 40.0 3.58e-01 100.0% 57.8%
4201001 2007.1.19.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › FabD/lysophospholipase-like › SAT 0.51 46.0 3.76e-01 100.0% 93.1%
D3 medium residues 131-307
PDB
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vkwA01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.58 31.0 3.69e-01 95.5% 75.2%
1v6zA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.56 22.0 3.63e-01 83.6% 100.0%
2egvA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.51 21.0 3.28e-01 75.7% 100.0%
3vseA01 2.30.130.10 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › PUA domain 0.50 21.0 3.35e-01 85.3% 100.0%
D4 medium residues 523-533_563-701
PDB
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vwxg01 6.20.370.70 Special › Other non-globular › Rhinovirus 14, subunit 4 › 0.55 15.0 2.75e-01 74.7% 81.1%
3ce2A02 1.10.287.830 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › putative peptidase helix hairpin domain like 0.52 16.0 3.00e-01 86.7% 91.5%
3afgA02 3.40.50.200 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain 0.51 37.0 2.95e-01 76.0% 45.8%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4995822 2499.2.1.1 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › Phage_sheath_1 0.86 68.0 5.48e-01 80.7% 49.8%
4888782 2499.2.1.2 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › Phage_sheath_1,Gp18_domIII_N 0.85 79.0 6.25e-01 96.7% 57.9%
4882286 2499.2.1.1 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › Phage_sheath_1 0.84 62.0 6.23e-01 80.7% 75.5%
5004680 2499.2.1.1 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › Phage_sheath_1 0.82 62.0 4.91e-01 79.3% 42.2%
4889792 2499.2.1.0 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 0.80 60.0 5.15e-01 81.3% 52.5%
3978226 2499.2.1.1 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › Phage_sheath_1 0.79 61.0 4.82e-01 79.3% 45.4%
2141717 2499.2.1.5 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › VipB 0.77 60.0 4.46e-01 80.0% 52.7%
2391375 2499.2.1.1 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › Phage_sheath_1 0.77 50.0 4.24e-01 82.0% 43.0%
3947382 2499.2.1.5 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › VipB 0.76 59.0 4.42e-01 79.3% 53.0%
5060661 2499.2.1.1 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › Phage_sheath_1 0.76 52.0 4.30e-01 84.7% 42.0%
1515363 2499.2.1.5 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 › VipB 0.75 57.0 4.46e-01 79.3% 59.5%
2832219 2499.2.1.0 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 0.74 59.0 4.33e-01 83.3% 48.6%
3164915 3019.1.1.11 beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › Phage_sheath_1 0.71 49.0 4.19e-01 78.7% 46.7%
4988098 2499.2.1.0 a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 0.62 50.0 4.17e-01 84.0% 52.3%
D5 medium residues 702-778
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF17482.8 best Phage_sheath_1C 29.3 1.00e-06 92.2% 63.5%
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3kg0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.71 44.0 4.11e-01 76.6% 49.5%
6fgjA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.70 52.0 4.14e-01 77.9% 54.7%
5is2A01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.69 40.0 3.79e-01 77.9% 48.4%
2fb0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 43.0 4.08e-01 77.9% 52.1%
2pgcC01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 44.0 4.11e-01 77.9% 53.6%
3e8oB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 42.0 3.92e-01 77.9% 49.0%
2z67A00 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.67 38.0 2.38e-01 76.6% 9.9%
6s2vC02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.66 50.0 4.07e-01 80.5% 49.0%
3fgvA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 41.0 3.91e-01 77.9% 51.6%
4hl9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 40.0 3.79e-01 77.9% 51.1%
3bguA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 42.0 3.92e-01 77.9% 53.1%
1ylxA00 3.30.70.1480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GK1464-like 0.64 40.0 3.76e-01 75.3% 49.5%
4k15A00 2.60.40.3860 Mainly Beta › Sandwich › Immunoglobulin-like › 0.64 35.0 2.93e-01 76.6% 29.7%
7qprA02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.64 47.0 3.93e-01 77.9% 51.9%
3dfeA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 34.0 3.36e-01 74.0% 47.6%
1gpmA03 3.30.300.10 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.62 43.0 3.84e-01 71.4% 67.6%
2jdjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 43.0 3.89e-01 77.9% 52.9%
4djbA00 3.30.70.2870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Mastadenovirus E4 ORF3 0.62 42.0 3.71e-01 76.6% 46.6%
3mgjA00 3.30.70.2690 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › LOR/SDH bifunctional enzyme, conserved domain 0.62 39.0 3.64e-01 72.7% 50.0%
2nvmA00 3.30.310.110 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › XisI-like 0.61 40.0 3.63e-01 80.5% 49.0%
4zrlA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.60 43.0 3.82e-01 77.9% 54.7%
1u8sA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.59 34.0 3.36e-01 72.7% 50.0%
2od6C00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 40.0 3.63e-01 77.9% 52.3%
4bzaA03 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.58 42.0 4.17e-01 76.6% 97.5%
4pxdA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 42.0 3.74e-01 80.5% 60.0%
3bb5A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 36.0 3.36e-01 75.3% 49.5%
5xzqF00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 39.0 3.60e-01 77.9% 56.3%
2oh1C00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 40.0 3.13e-01 77.9% 75.6%
2vfrA04 3.30.70.2520 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 38.0 3.55e-01 71.4% 62.8%
1vkvA01 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.54 38.0 3.00e-01 75.3% 36.1%
1s7iA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.53 40.0 3.48e-01 81.8% 83.1%
1tr0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 38.0 3.44e-01 77.9% 54.7%
1thgA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 40.0 2.47e-01 85.7% 48.6%
2iiiA00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.52 41.0 3.60e-01 88.3% 86.7%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4995823 283.2.1.2 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › Phage_sheath_1C 0.96 71.0 6.16e-01 76.6% 59.1%
4957559 283.2.1.2 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › Phage_sheath_1C 0.92 79.0 7.06e-01 88.3% 73.0%
4883050 283.2.1.2 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › Phage_sheath_1C 0.87 70.0 6.72e-01 87.0% 75.6%
4888785 283.2.1.2 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › Phage_sheath_1C 0.87 80.0 7.72e-01 100.0% 93.0%
3980756 283.2.1.2 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › Phage_sheath_1C 0.85 74.0 6.59e-01 97.4% 68.6%
3949098 283.2.1.2 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › Phage_sheath_1C 0.84 75.0 6.57e-01 100.0% 67.3%
1518918 283.2.1.2 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › Phage_sheath_1C 0.83 72.0 6.33e-01 96.1% 65.2%
3945698 283.2.1.10 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › PF29514 0.78 68.0 6.08e-01 97.4% 69.2%
1312370 304.28.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › ACR_tran 0.71 51.0 4.41e-01 80.5% 50.0%
4086504 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.70 44.0 3.98e-01 76.6% 46.7%
3244701 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.69 50.0 3.76e-01 77.9% 32.8%
3787214 312.1.1.6 a+b three layers › HIT-like › HIT-related › HIT-related › CwfJ_C_2,CwfJ_C_1 0.64 45.0 3.18e-01 75.3% 23.8%
4970138 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.63 44.0 3.98e-01 72.7% 56.2%
3292735 306.7.1.1 a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.62 48.0 4.07e-01 85.7% 78.5%
3605708 1189.1.1.0 alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor 0.62 45.0 2.94e-01 79.2% 66.4%
3181971 304.4.1.11 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › EthD 0.61 44.0 3.64e-01 77.9% 46.2%
3966499 304.28.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › ACR_tran 0.60 43.0 3.88e-01 76.6% 55.5%
3735506 206.1.1.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.59 43.0 3.07e-01 77.9% 89.6%
4028322 304.51.1.0 a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related 0.59 41.0 3.42e-01 74.0% 80.7%
3838614 3747.1.1.1 a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bb_rod 0.58 43.0 3.90e-01 79.2% 61.9%
4021691 4010.1.1.2 a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1,RNA_pol_Rpb2_3 0.57 42.0 2.76e-01 79.2% 34.2%
3706941 312.1.1.0 a+b three layers › HIT-like › HIT-related › HIT-related 0.56 42.0 3.43e-01 81.8% 41.3%
5006107 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.55 38.0 3.54e-01 77.9% 56.0%
5004549 304.5.1.2 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF190 0.54 37.0 3.35e-01 71.4% 59.3%
3508551 304.114.1.0 a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.53 36.0 3.10e-01 76.6% 44.2%
1288930 304.114.1.0 a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.53 35.0 3.26e-01 71.4% 52.5%
3736643 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.52 37.0 3.35e-01 79.2% 52.7%
3759055 304.114.1.0 a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.52 35.0 3.00e-01 71.4% 42.4%
3200673 616.1.1.0 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.51 37.0 3.51e-01 77.9% 88.4%
4267116 323.1.1.5 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.50 36.0 2.52e-01 76.6% 78.1%