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LacPavin_0818_WC55_scaffold_113784_prodigal-single.1__X__X__00385

Bact-Vir

LacPavin_0818_WC55_scaffold_113784_prodigal-single.1__X__X__00385

Identity

Kingdom:
phage

Quality

79.8 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 high residues 355-449
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qw4B02 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.63 54.0 4.37e-01 96.8% 85.9%
1t8hA00 3.60.140.10 Alpha Beta › 4-Layer Sandwich › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases 0.59 51.0 3.74e-01 97.9% 90.1%
2xzlA05 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 48.0 3.80e-01 100.0% 78.8%
2kd0A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 36.0 4.07e-01 94.7% 88.7%
6jzqD01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 41.0 3.62e-01 85.3% 95.8%
1vq8X00 3.10.440.10 Alpha Beta › Roll › Ribosomal Protein L31e; Chain: W; › Ribosomal protein L31 0.52 39.0 4.16e-01 78.9% 100.0%
2i76A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 35.0 3.11e-01 70.5% 62.9%
1wd5A01 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 42.0 3.68e-01 92.6% 77.4%
7febA03 3.40.50.12790 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › FHIPEP family, domain 4 0.50 38.0 3.86e-01 97.9% 82.6%
5agaA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 43.0 3.50e-01 100.0% 75.2%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3284957 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.57 43.0 3.78e-01 82.1% 76.7%
4296076 288.1.1.1 a+b four layers › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › Cu-oxidase_4 0.56 49.0 3.64e-01 100.0% 95.3%
4023026 288.1.1.1 a+b four layers › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › Cu-oxidase_4 0.55 49.0 3.52e-01 98.9% 94.3%
5036060 259.1.1.2 a+b two layers › Ribosomal protein L31e-like › Ribosomal protein L31e/gp120 outer domain › Ribosomal protein L31e/gp120 outer domain › Ribosomal_L31e 0.54 40.0 4.40e-01 77.9% 100.0%
4586546 259.1.1.2 a+b two layers › Ribosomal protein L31e-like › Ribosomal protein L31e/gp120 outer domain › Ribosomal protein L31e/gp120 outer domain › Ribosomal_L31e 0.53 40.0 4.13e-01 80.0% 94.4%
3708082 2004.1.1.23 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SNF2-rel_dom 0.53 44.0 3.25e-01 93.7% 74.3%
4627017 2004.1.1.606 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › PF30321 0.52 46.0 3.75e-01 100.0% 63.7%
4965542 259.1.1.2 a+b two layers › Ribosomal protein L31e-like › Ribosomal protein L31e/gp120 outer domain › Ribosomal protein L31e/gp120 outer domain › Ribosomal_L31e 0.52 39.0 4.09e-01 80.0% 95.6%
3830234 2004.1.1.153 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_2 0.51 43.0 3.39e-01 94.7% 92.4%
3419412 2004.1.1.56 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NB-ARC 0.51 43.0 3.52e-01 98.9% 63.0%
3172253 2004.1.1.212 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Microtub_bd 0.51 40.0 2.77e-01 89.5% 58.4%
4995573 259.1.1.2 a+b two layers › Ribosomal protein L31e-like › Ribosomal protein L31e/gp120 outer domain › Ribosomal protein L31e/gp120 outer domain › Ribosomal_L31e 0.50 41.0 3.89e-01 86.3% 81.8%
D2 medium residues 98-166
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1lycA02 1.10.420.10 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 2 › Peroxidase, domain 2 0.55 45.0 3.46e-01 92.8% 65.6%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5024302 101.1.2.404 alpha arrays › HTH › HTH › winged helix domain › DUF505 0.52 36.0 2.29e-01 94.2% 13.5%
D3 medium residues 167-354
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF17338.9 best GP88 102.5 4.70e-29 91.5% 73.2%
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3u61C01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.67 38.0 4.10e-01 86.7% 63.0%
3ndoA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.63 43.0 4.03e-01 95.2% 56.9%
3ciwA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.62 45.0 3.65e-01 84.6% 40.1%
1eucB03 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.61 42.0 4.67e-01 87.2% 87.7%
3b0pA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.60 45.0 4.19e-01 92.6% 61.6%
7jt8I02 3.90.190.20 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Mur ligase, C-terminal domain 0.59 35.0 3.97e-01 83.5% 75.7%
5nusA00 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.59 46.0 4.43e-01 80.3% 95.3%
2a4aA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.58 44.0 3.96e-01 93.1% 57.6%
2n9uA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 34.0 4.04e-01 79.3% 82.9%
1a49A01 3.40.1380.20 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › Pyruvate kinase, C-terminal domain 0.58 31.0 3.23e-01 78.2% 54.5%
2o7sA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.58 41.0 3.78e-01 93.6% 56.7%
2nx2A00 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 36.0 3.72e-01 81.4% 64.6%
4ff5A00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.57 42.0 3.98e-01 91.5% 62.6%
1jeyB01 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.57 43.0 4.10e-01 78.7% 94.3%
1bqcA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.57 45.0 3.87e-01 96.3% 52.0%
7u7hA01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.56 42.0 3.97e-01 88.8% 64.1%
5c54G00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.56 43.0 3.66e-01 93.6% 49.2%
4f1jA00 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.56 44.0 4.36e-01 83.0% 90.5%
2jbmA02 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 37.0 4.16e-01 89.4% 87.0%
6xigA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 45.0 3.81e-01 85.6% 61.7%
4evsA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 42.0 4.38e-01 87.8% 86.0%
5fi9A01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.54 45.0 3.51e-01 88.3% 79.7%
4ohxA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 42.0 3.97e-01 84.6% 67.1%
3u37A02 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.54 41.0 3.79e-01 80.3% 85.5%
4v2xA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 48.0 3.93e-01 96.8% 59.0%
3r79A00 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.53 38.0 3.59e-01 86.2% 60.4%
2dskA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 45.0 3.87e-01 94.7% 57.3%
4c0hA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 41.0 3.85e-01 83.5% 72.8%
5l3qA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 40.0 3.93e-01 89.4% 73.8%
1gjwA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.52 46.0 3.29e-01 96.8% 54.2%
3i6sA03 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.52 34.0 4.00e-01 87.2% 94.6%
2w5fA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 46.0 3.72e-01 97.3% 53.2%
3u62A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 33.0 3.85e-01 80.3% 93.0%
1e8cB03 3.90.190.20 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Mur ligase, C-terminal domain 0.51 36.0 4.05e-01 86.2% 94.4%
5l3sB02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 39.0 3.80e-01 90.4% 71.9%
2gb3A02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.50 34.0 3.21e-01 95.2% 54.7%
6p4xA03 3.40.367.20 Alpha Beta › 3-Layer(aba) Sandwich › Hexokinase; domain 1 › 0.50 36.0 3.17e-01 73.4% 94.7%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4991251 2002.1.1.453 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › GP88 0.76 73.0 6.20e-01 100.0% 83.5%
4421220 2495.1.1.0 a/b three-layered sandwiches › Cell-division inhibitor MinC, N-terminal domain › Cell-division inhibitor MinC, N-terminal domain › Cell-division inhibitor MinC, N-terminal domain 0.66 32.0 4.32e-01 79.3% 88.4%
3937233 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.66 39.0 4.22e-01 84.0% 66.9%
4977028 2002.1.1.29 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DHDPS 0.66 43.0 3.85e-01 92.6% 46.2%
4994618 7542.1.2.3 a/b three-layered sandwiches › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain II › AcnX_2nd 0.62 27.0 3.66e-01 75.0% 80.0%
139515 2002.1.1.55 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_25 0.61 40.0 4.01e-01 92.6% 64.6%
4173857 7563.1.1.4 a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related › YpsA 0.59 37.0 3.76e-01 81.4% 61.7%
3299538 2006.1.6.12 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › VWA_2 0.58 45.0 4.45e-01 79.8% 88.5%
4927931 2007.3.1.0 a/b three-layered sandwiches › Flavodoxin-like › Succinyl-CoA synthetase domains › Succinyl-CoA synthetase domains 0.58 36.0 4.16e-01 77.1% 84.1%
4971612 2002.1.1.120 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.58 51.0 4.43e-01 93.1% 69.3%
4935184 2002.1.1.120 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.58 48.0 4.34e-01 87.2% 73.5%
1066802 2002.1.1.55 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_25 0.57 42.0 3.98e-01 91.5% 62.6%
3835138 2002.1.1.66 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DHquinase_I 0.57 40.0 3.65e-01 93.6% 53.2%
5069122 2002.1.1.120 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.57 48.0 4.03e-01 89.9% 69.8%
5076479 2004.1.1.211 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CLP1_P 0.57 42.0 4.20e-01 84.0% 72.5%
5055473 2002.1.1.120 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.57 47.0 4.11e-01 87.2% 65.5%
3988527 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 29.0 3.84e-01 86.2% 93.7%
4988241 2002.1.1.120 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.56 47.0 4.13e-01 87.8% 65.5%
3278814 2007.3.1.0 a/b three-layered sandwiches › Flavodoxin-like › Succinyl-CoA synthetase domains › Succinyl-CoA synthetase domains 0.56 38.0 4.27e-01 78.2% 87.6%
1842690 2002.1.1.29 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DHDPS 0.56 43.0 3.64e-01 93.6% 48.7%
3233285 2006.1.6.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › VWA 0.56 44.0 4.36e-01 80.9% 91.3%
3934215 2004.1.1.211 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CLP1_P 0.56 44.0 4.10e-01 84.6% 66.5%
3245690 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.55 43.0 4.24e-01 81.9% 82.9%
5044064 2002.1.1.83 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_1 0.55 42.0 3.27e-01 84.6% 36.8%
4990332 2004.1.1.211 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CLP1_P 0.54 41.0 4.04e-01 84.6% 72.2%
3930395 2004.1.1.211 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CLP1_P 0.53 42.0 3.98e-01 85.1% 67.4%
4256623 7570.1.1.1 a/b three-layered sandwiches › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › Mur_ligase_C 0.53 38.0 4.14e-01 86.7% 88.2%
4420367 2007.1.3.2 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › UPF0004 0.53 32.0 3.85e-01 85.6% 88.8%
1501391 2002.1.1.8 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Cellulase 0.53 48.0 3.94e-01 96.8% 59.2%
4456392 2002.1.1.176 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PEP_mutase 0.53 45.0 3.86e-01 89.9% 59.0%
3602816 2006.1.6.12 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › VWA_2 0.52 42.0 3.92e-01 83.0% 75.1%
2594905 2484.1.1.42 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hexokinase_2 0.52 37.0 3.24e-01 72.9% 95.0%
4100507 2003.1.6.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like 0.51 43.0 3.52e-01 90.4% 83.9%
4257987 7577.1.1.1 a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Aminotran_1_2 0.51 42.0 3.74e-01 87.2% 64.8%
3927700 2007.9.1.0 a/b three-layered sandwiches › Flavodoxin-like › Toll/Interleukin receptor TIR domain › Toll/Interleukin receptor TIR domain 0.51 31.0 3.64e-01 84.0% 88.0%
None 0.51 43.0 3.74e-01 90.4% 68.6%
3723072 2004.1.1.43 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SRP54 0.51 42.0 3.73e-01 88.3% 74.4%
3808715 2002.1.1.106 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › GDPD 0.50 43.0 3.68e-01 90.4% 66.8%