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LacPavin_0818_WC40_scaffold_269347_prodigal-single.1__X__X__00251

Bact-Vir

LacPavin_0818_WC40_scaffold_269347_prodigal-single.1__X__X__00251

Identity

Kingdom:
phage

Quality

82.3 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 3-44_171-233
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF26809.1 best Phage_T4_gp13 38.4 1.50e-09 95.2% 25.1%
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fp4A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.71 64.0 4.86e-01 98.1% 70.4%
1kqfC00 1.20.950.20 Mainly Alpha › Up-down Bundle › Fumarate Reductase Cytochrome B subunit › Transmembrane di-heme cytochromes, Chain C 0.71 51.0 3.94e-01 74.3% 50.0%
1xioA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.70 52.0 4.06e-01 79.0% 37.3%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.70 49.0 4.97e-01 73.3% 72.8%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.69 48.0 4.62e-01 75.2% 63.0%
2uxwA04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.69 48.0 4.50e-01 72.4% 66.2%
1zvzA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.68 50.0 4.75e-01 76.2% 70.2%
3n3dB00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.68 61.0 4.34e-01 99.0% 53.7%
3q2qA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.66 59.0 4.19e-01 98.1% 53.8%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.63 43.0 4.28e-01 71.4% 92.0%
8ex5A02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.61 51.0 4.00e-01 90.5% 88.7%
2v5cA03 1.20.58.460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hyaluronidase post-catalytic domain-like 0.61 44.0 4.12e-01 93.3% 60.8%
8b70A01 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.61 54.0 3.62e-01 98.1% 91.9%
4fjqA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.59 53.0 3.64e-01 98.1% 34.6%
3rrkA02 1.20.1460.20 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › 0.58 40.0 3.57e-01 71.4% 76.8%
2vzbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.58 51.0 4.35e-01 96.2% 79.6%
1st6A03 1.20.120.810 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vinculin, Vh2 four-helix bundle 0.58 42.0 3.30e-01 76.2% 36.2%
6i9kA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.58 42.0 3.06e-01 78.1% 27.7%
4ib4A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.57 42.0 3.13e-01 79.0% 32.3%
4rngC00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.57 39.0 4.36e-01 81.9% 89.2%
2jexA01 1.10.287.30 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › E2 (early) protein, N terminal domain, subdomain 1 0.57 41.0 4.33e-01 80.0% 83.3%
4mhlA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.56 47.0 4.09e-01 90.5% 59.6%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 36.0 4.26e-01 82.9% 95.9%
6k6iA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.55 48.0 3.89e-01 100.0% 49.3%
1tjoB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 48.0 4.10e-01 97.1% 77.1%
2clbA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 47.0 4.13e-01 93.3% 84.3%
1nafA02 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 42.0 4.64e-01 82.9% 98.8%
1sumB01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.53 43.0 4.33e-01 85.7% 89.7%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.53 45.0 4.39e-01 96.2% 83.0%
1dd5A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.53 42.0 4.17e-01 85.7% 96.3%
1dtoA01 1.10.287.30 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › E2 (early) protein, N terminal domain, subdomain 1 0.52 40.0 4.04e-01 81.9% 82.4%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3785454 4006.1.1.0 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain 0.68 51.0 5.16e-01 78.1% 96.2%
3471420 3843.1.1.0 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.67 50.0 5.18e-01 79.0% 81.0%
3689704 601.1.3.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › A middle domain of Talin 1 0.64 49.0 4.20e-01 80.0% 97.5%
3449357 150.1.1.110 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › DUF7358 0.63 47.0 3.97e-01 77.1% 65.9%
5077194 191.1.1.0 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.63 49.0 4.73e-01 82.9% 79.0%
3594375 601.1.2.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.62 44.0 3.78e-01 75.2% 46.1%
4982132 5069.1.3.135 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DUF5985 0.62 44.0 4.66e-01 79.0% 83.0%
3218065 3684.1.1.0 alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.62 44.0 3.98e-01 73.3% 60.0%
3412891 150.1.1.31 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Tweety 0.61 43.0 3.20e-01 73.3% 38.5%
3239921 3684.1.1.0 alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.60 44.0 3.76e-01 76.2% 56.4%
5051764 622.4.1.0 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.60 50.0 4.32e-01 88.6% 91.0%
5029785 633.22.1.1 alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) › VKOR 0.59 43.0 3.94e-01 76.2% 67.9%
4941521 5069.1.3.0 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.59 45.0 4.71e-01 80.0% 90.5%
4058767 7015.1.1.0 alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.58 50.0 4.53e-01 92.4% 84.3%
4935971 150.1.1.3 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.57 50.0 4.43e-01 97.1% 91.6%
3962012 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.55 42.0 4.38e-01 91.4% 87.4%
3408710 149.1.1.1 alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.55 44.0 2.86e-01 86.7% 73.0%
4957771 5069.1.3.137 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DUF7521 0.55 41.0 4.43e-01 80.0% 96.7%
5050590 3352.1.1.0 alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.53 46.0 3.26e-01 96.2% 55.8%
4609203 5069.1.3.10 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › ATP-synt_I 0.53 41.0 4.05e-01 83.8% 77.4%
3875883 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.52 41.0 2.87e-01 85.7% 33.3%
3701383 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.50 45.0 3.68e-01 98.1% 56.4%
3470680 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.50 41.0 2.69e-01 86.7% 48.4%
D2 medium residues 48-169
PDB
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1rgxA02 2.60.40.4230 Mainly Beta › Sandwich › Immunoglobulin-like › Resistin head domain 0.67 34.0 4.33e-01 100.0% 89.1%
2osxA01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.63 35.0 3.87e-01 96.7% 66.7%
4wz9A01 2.60.40.1730 Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain 0.62 41.0 3.39e-01 100.0% 37.9%
5nn3A05 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.60 35.0 3.41e-01 93.4% 53.8%
3l4yA05 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.59 37.0 3.53e-01 94.3% 55.8%
5i0dA05 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.58 38.0 3.62e-01 99.2% 57.6%
2xmjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 29.0 3.98e-01 82.0% 95.2%
4nzfD02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.57 32.0 3.63e-01 96.7% 73.3%
4b6zA01 2.60.40.3120 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 35.0 3.68e-01 96.7% 66.4%
7kbrC01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.56 33.0 3.27e-01 91.0% 54.5%
4d6gA03 2.60.220.10 Mainly Beta › Sandwich › Chondroitinase Ac; Chain A, domain 3 › Polysaccharide lyase family 8-like, C-terminal 0.55 34.0 3.39e-01 98.4% 56.9%
1o7dC02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 34.0 3.85e-01 99.2% 83.1%
4e9jA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.54 29.0 3.77e-01 82.0% 92.8%
3amkA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 35.0 3.84e-01 97.5% 80.0%
1r17A02 2.60.40.1290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 41.0 3.75e-01 100.0% 62.0%
3irpX02 2.60.40.1290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 40.0 3.78e-01 100.0% 64.9%
4ba0A04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 35.0 3.33e-01 95.9% 57.0%
2d73A03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 33.0 3.49e-01 100.0% 70.8%
5axgA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 38.0 3.81e-01 99.2% 75.4%
4a0tA03 2.60.320.30 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › 0.50 36.0 4.04e-01 100.0% 98.9%
3wnkA04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.50 36.0 3.59e-01 96.7% 71.2%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2841577 10.2.1.0 beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.65 42.0 5.10e-01 98.4% 100.0%
4163669 12.1.1.0 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.64 37.0 3.64e-01 97.5% 52.3%
3572172 4178.1.1.0 beta sandwiches › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain 0.61 38.0 3.65e-01 93.4% 55.4%
3877348 4178.1.1.0 beta sandwiches › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain 0.61 38.0 3.64e-01 93.4% 55.8%
1588492 4178.1.1.0 beta sandwiches › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain 0.59 36.0 3.51e-01 94.3% 55.1%
4061251 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 30.0 3.57e-01 90.2% 78.8%
3452049 12.1.1.3 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Alpha-amylase_C 0.54 36.0 3.89e-01 98.4% 79.0%
3178085 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 31.0 2.99e-01 91.0% 50.4%
2133129 327.16.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif II in type III secretion system › Ring-building motif II in type III secretion system › Secretin_N 0.54 29.0 3.74e-01 85.2% 91.5%
3553689 101.1.2.22 alpha arrays › HTH › HTH › winged helix domain › PCI 0.53 30.0 3.68e-01 89.3% 88.0%
3296862 101.1.2.22 alpha arrays › HTH › HTH › winged helix domain › PCI 0.53 30.0 3.75e-01 90.2% 90.7%
3785105 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.53 33.0 3.69e-01 91.0% 80.0%
4385498 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.53 30.0 3.04e-01 91.0% 54.4%
3602011 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.53 32.0 2.94e-01 90.2% 44.8%
3967140 327.16.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif II in type III secretion system › Ring-building motif II in type III secretion system › Secretin_N 0.53 29.0 3.79e-01 85.2% 100.0%
3972739 327.16.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif II in type III secretion system › Ring-building motif II in type III secretion system › Secretin_N 0.53 30.0 3.84e-01 85.2% 98.6%
4025539 101.1.2.22 alpha arrays › HTH › HTH › winged helix domain › PCI 0.52 31.0 3.72e-01 89.3% 93.3%
3493997 101.1.2.22 alpha arrays › HTH › HTH › winged helix domain › PCI 0.52 29.0 3.63e-01 90.2% 89.3%
3514901 101.1.2.22 alpha arrays › HTH › HTH › winged helix domain › PCI 0.52 29.0 3.60e-01 89.3% 89.3%
3936571 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.52 29.0 3.57e-01 89.3% 89.3%
1713377 12.1.1.21 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Glyco_hydro_66 0.51 38.0 3.80e-01 99.2% 74.8%
4443872 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.51 31.0 3.00e-01 91.0% 54.1%
3267853 4081.1.1.2 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.50 39.0 3.22e-01 100.0% 45.9%