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NC_021532.1__YP_008125999.1__M610_gp028__00028

Bact-Vir

NC_021532.1__YP_008125999.1__M610_gp028__00028

Identity

Accession:
NC_021532 ↗
Kingdom:
phage

Quality

77.0 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 182-227
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5h9cA00 1.10.287.210 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 49.0 4.04e-01 80.4% 42.3%
3f1iH00 1.20.5.1940 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.69 49.0 3.86e-01 82.6% 35.7%
3ngxA02 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.67 58.0 4.72e-01 95.7% 71.4%
1w36C06 1.10.10.990 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.67 50.0 4.37e-01 91.3% 52.8%
1is8A01 1.10.286.10 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › GTP cyclohydrolase I, N-terminal domain 0.65 50.0 4.63e-01 87.0% 66.7%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.63 48.0 4.21e-01 93.5% 54.7%
6aqgA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.61 46.0 3.26e-01 80.4% 97.9%
4rrfA01 3.50.80.10 Alpha Beta › 3-Layer(bba) Sandwich › D-tyrosyl-trna(Tyr) Deacylase; Chain: A; › D-tyrosyl-tRNA(Tyr) deacylase 0.61 47.0 3.36e-01 84.8% 47.8%
3djcB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 45.0 3.63e-01 80.4% 61.4%
2mvtA00 1.10.60.50 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › 0.58 45.0 4.56e-01 91.3% 83.0%
3vtfA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 47.0 3.15e-01 97.8% 48.6%
5o6aD00 1.10.8.970 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Flavivirus envelope glycoprotein M-like 0.54 40.0 3.68e-01 91.3% 60.6%
2bsnA00 3.30.420.180 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › CobE/GbiG C-terminal domain 0.54 44.0 3.20e-01 100.0% 31.7%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4238922 589.1.2.1 alpha arrays › Triger factor/SurA peptide-binding domain-like › Triger factor/SurA peptide-binding domain-like › TF C-terminus (Pfam 05698) › Trigger_C 0.74 57.0 3.85e-01 87.0% 23.6%
3400028 3843.1.1.30 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › DUF4781 0.68 50.0 4.14e-01 80.4% 44.7%
4947232 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.68 56.0 4.78e-01 97.8% 63.7%
3433557 7516.1.1.114 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › PF28143 0.66 56.0 3.40e-01 97.8% 46.5%
3599779 253.1.1.1 a+b complex topology › Argininosuccinate synthetase-C › Argininosuccinate synthetase-C › Argininosuccinate synthetase-C › Arginosuc_syn_C 0.58 44.0 2.80e-01 84.8% 42.4%
D2 medium residues 1-72
PDB
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ujpA02 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.61 44.0 3.84e-01 77.8% 55.7%
6xehA01 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.60 38.0 3.33e-01 76.4% 42.3%
3k40A02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.59 49.0 3.37e-01 94.4% 57.5%
7e7gA01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.59 51.0 3.53e-01 97.2% 63.6%
2f5xA02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.59 51.0 4.35e-01 100.0% 73.4%
6xy9A01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 48.0 3.22e-01 93.1% 82.3%
2wjwA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 44.0 3.46e-01 83.3% 54.6%
4wnyA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.58 42.0 3.52e-01 79.2% 96.2%
2dgmA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.58 50.0 3.36e-01 98.6% 51.0%
1vchD00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 42.0 3.31e-01 80.6% 53.2%
1xfdA02 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 44.0 3.11e-01 88.9% 32.4%
6yuqA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 42.0 3.10e-01 88.9% 48.1%
1riiB00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.55 45.0 3.32e-01 100.0% 82.7%
1fuyB01 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 46.0 3.67e-01 100.0% 70.1%
6ouvA03 3.40.50.920 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 44.0 3.71e-01 93.1% 56.8%
1fztA00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.54 45.0 3.39e-01 100.0% 83.4%
6jimB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 36.0 2.97e-01 87.5% 35.0%
1y97A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 44.0 3.39e-01 100.0% 81.0%
4gu5B01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 37.0 3.11e-01 75.0% 71.5%
2yzkA00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 45.0 3.48e-01 98.6% 93.2%
8c9vA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 45.0 3.46e-01 100.0% 84.0%
7kl6A01 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 44.0 3.61e-01 98.6% 75.7%
3hjgA00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.52 44.0 3.30e-01 100.0% 82.2%
4q6bA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 43.0 3.68e-01 100.0% 89.6%
5cxxB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 41.0 2.89e-01 93.1% 27.0%
3gdwB00 3.40.50.510 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component 0.52 38.0 3.07e-01 100.0% 40.6%
5vogA00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 42.0 3.31e-01 98.6% 78.4%
2kpoA00 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 37.0 3.35e-01 93.1% 53.6%
3lkdA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 42.0 2.93e-01 100.0% 70.9%
4xymC03 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.50 39.0 3.07e-01 87.5% 81.7%
1di0A00 3.40.50.960 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Lumazine/riboflavin synthase 0.50 37.0 3.06e-01 83.3% 67.6%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5052297 876.1.1.0 a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin 0.89 75.0 7.08e-01 91.7% 75.3%
5071270 876.1.1.1 a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParBc 0.86 73.0 6.93e-01 93.1% 80.0%
3943767 876.1.1.1 a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParBc 0.84 71.0 6.71e-01 91.7% 80.0%
4940273 876.1.1.0 a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin 0.80 65.0 6.44e-01 86.1% 82.7%
3961649 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.64 45.0 3.95e-01 73.6% 56.2%
5051165 7512.1.1.3 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 0.59 42.0 3.03e-01 75.0% 59.5%
4485296 7523.1.1.14 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › TctC 0.58 51.0 4.26e-01 100.0% 70.0%
None 0.58 50.0 3.71e-01 100.0% 85.4%
3604199 2007.1.3.38 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › 2-thiour_desulf_put 0.58 42.0 3.40e-01 79.2% 60.0%
4277518 7563.1.1.4 a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related › YpsA 0.58 50.0 3.80e-01 100.0% 84.7%
4333564 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.57 45.0 4.13e-01 87.5% 92.6%
3969228 7523.1.1.26 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_6 0.56 47.0 3.09e-01 97.2% 73.4%
3948330 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.56 40.0 3.49e-01 75.0% 52.7%
3562229 197.1.1.1 alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › FERM_M 0.56 48.0 3.97e-01 100.0% 78.5%
151025 2003.1.6.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like 0.56 45.0 3.40e-01 90.3% 43.6%
5058560 7584.1.1.1 a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › AMP-binding 0.55 47.0 3.86e-01 97.2% 94.3%
4594511 2007.1.5.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like 0.55 40.0 3.84e-01 79.2% 82.4%
4958427 7525.1.1.1 a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_1 0.54 47.0 3.53e-01 100.0% 84.7%
3929297 2003.4.1.1 a/b three-layered sandwiches › Rossmann-like › Tryptophan synthase beta subunit-like PLP-dependent enzymes › Tryptophan synthase beta subunit-like PLP-dependent enzymes › PALP 0.54 42.0 3.45e-01 97.2% 92.4%
4956540 7597.1.1.0 a/b three-layered sandwiches › Endolysin C-terminal domain › Endolysin C-terminal domain › Endolysin C-terminal domain 0.53 40.0 3.91e-01 88.9% 71.8%
4941532 246.2.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.53 45.0 3.32e-01 100.0% 85.1%
4491503 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.53 38.0 3.40e-01 77.8% 56.4%
3290355 7516.1.1.1 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › NTP_transferase 0.53 42.0 2.88e-01 87.5% 86.8%
4971343 2002.1.1.0 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.53 46.0 3.05e-01 100.0% 56.3%
5082791 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.53 44.0 3.42e-01 97.2% 61.1%
4244672 7573.1.1.1 a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like › Pribosyltran 0.53 46.0 3.45e-01 100.0% 77.4%
4948839 7573.1.1.1 a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like › Pribosyltran 0.51 43.0 3.45e-01 98.6% 93.7%
4074012 2484.1.1.174 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.51 44.0 3.76e-01 100.0% 81.6%
4146261 2007.1.5.1 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like › Asp_Glu_race 0.51 43.0 3.62e-01 97.2% 83.8%
5073142 2484.1.1.94 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HypF_C_2 0.51 39.0 2.64e-01 86.1% 21.9%
4927269 2007.1.14.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like 0.51 38.0 3.14e-01 84.7% 56.7%
3557377 2007.1.2.4 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.50 42.0 3.38e-01 100.0% 81.2%
3291388 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.50 43.0 3.62e-01 97.2% 65.6%
D3 medium residues 73-176
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.66 38.0 4.29e-01 73.1% 74.4%
1qdmA03 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.61 41.0 4.62e-01 76.9% 90.9%
2kkcA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.59 39.0 3.99e-01 76.0% 70.0%
6hxlB01 1.10.230.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450-Terp; domain 2 › Cytochrome P450-Terp, domain 2 0.52 36.0 3.48e-01 72.1% 100.0%
2j6lA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.52 37.0 2.77e-01 76.9% 81.3%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5006645 101.1.1.63 alpha arrays › HTH › HTH › Three-helical HTH › HTH_28 0.69 37.0 4.63e-01 72.1% 90.0%
5050695 3352.1.1.15 alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › GT87 0.60 48.0 3.29e-01 87.5% 35.2%
2562506 7524.1.1.1 a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Aldedh 0.53 38.0 2.93e-01 76.0% 90.4%