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LacPavin_0818_WC40_scaffold_193576_prodigal-single.1__X__X__00107

Bact-Vir

LacPavin_0818_WC40_scaffold_193576_prodigal-single.1__X__X__00107

Identity

Kingdom:
phage

Quality

94.4 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 1-78
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1aepA00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.60 52.0 4.21e-01 96.2% 100.0%
1st6A03 1.20.120.810 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vinculin, Vh2 four-helix bundle 0.60 51.0 3.70e-01 96.2% 38.4%
3h6pC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.59 39.0 4.48e-01 75.6% 94.6%
3bvoA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.59 40.0 3.88e-01 79.5% 64.0%
3mzvA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.58 46.0 3.15e-01 87.2% 79.6%
3qxyA02 3.90.1420.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 2 › Rubisco LSMT, substrate-binding domain 0.58 45.0 3.52e-01 83.3% 62.3%
4awyB00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.57 45.0 3.11e-01 84.6% 44.4%
2gmhA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.57 45.0 3.18e-01 87.2% 82.4%
2nr9A00 1.20.1540.10 Mainly Alpha › Up-down Bundle › Rhomboid-like fold › Rhomboid-like 0.57 44.0 3.38e-01 85.9% 37.5%
1yjsA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.57 50.0 3.53e-01 100.0% 87.6%
6wngA02 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.57 48.0 3.31e-01 94.9% 65.3%
2l1nA00 1.10.418.90 Mainly Alpha › Orthogonal Bundle › Actin-binding Protein, T-fimbrin; domain 1 › Protein of unknown function DUF1823 0.56 47.0 4.12e-01 93.6% 86.7%
3hwcA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.56 49.0 3.64e-01 100.0% 53.8%
1k32A03 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.55 42.0 4.39e-01 83.3% 94.4%
3bvxA02 1.20.1270.50 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain 0.55 48.0 4.30e-01 100.0% 79.3%
3djaA01 1.20.920.70 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.55 41.0 3.46e-01 83.3% 53.8%
2xq9A02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.55 41.0 3.53e-01 79.5% 53.7%
3rlbA00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.53 41.0 3.19e-01 83.3% 77.3%
3rkoG00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 40.0 3.73e-01 82.1% 81.0%
1y56B01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 42.0 3.04e-01 87.2% 65.5%
2hh6A00 1.10.1900.10 Mainly Alpha › Orthogonal Bundle › c-terminal domain of poly(a) binding protein › c-terminal domain of poly(a) binding protein 0.52 45.0 4.05e-01 98.7% 70.3%
8ab6B02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.52 38.0 2.88e-01 76.9% 50.3%
1auwA02 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.52 38.0 2.77e-01 78.2% 70.6%
6srbA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 35.0 3.13e-01 70.5% 56.0%
2j0wA02 1.20.120.1320 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartokinase, catalytic domain 0.51 41.0 3.93e-01 92.3% 100.0%
4jndA01 1.10.1740.220 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.51 37.0 3.23e-01 79.5% 54.6%
4o8sA02 1.20.58.1790 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › JHP933, helical tail domain 0.51 46.0 4.10e-01 98.7% 77.6%
2oerA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.50 40.0 3.08e-01 87.2% 69.8%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4951316 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.84 77.0 5.55e-01 100.0% 38.5%
4221251 1128.1.1.8 alpha bundles › LYR protein › LYR protein › LYR protein › PF29574 0.69 56.0 5.44e-01 87.2% 78.8%
3265419 1128.1.1.0 alpha bundles › LYR protein › LYR protein › LYR protein 0.66 54.0 5.37e-01 88.5% 86.3%
3944704 131.1.1.19 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › TraI_2 0.64 55.0 3.98e-01 96.2% 33.8%
3272278 3722.1.1.0 alpha bundles › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain 0.64 54.0 3.68e-01 98.7% 26.1%
3590515 4125.1.1.2 alpha superhelices › BH3980-like › BH3980-like › BH3980-like › HAAS 0.63 41.0 4.33e-01 76.9% 75.7%
3699448 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.62 44.0 3.38e-01 73.1% 41.8%
5074726 633.10.1.0 alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.62 48.0 4.68e-01 83.3% 75.3%
3182954 5050.1.1.0 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.62 55.0 4.05e-01 98.7% 71.7%
3206128 3567.1.1.139 a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › PF29055 0.61 45.0 3.92e-01 76.9% 88.7%
3242683 632.1.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.61 47.0 4.51e-01 83.3% 82.2%
3904595 611.2.1.0 alpha bundles › N-cbl like › N-terminal domain of cbl (N-cbl) › N-terminal domain of cbl (N-cbl) 0.60 54.0 4.74e-01 100.0% 76.5%
2634195 2008.1.1.49 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_SinI 0.60 44.0 3.17e-01 82.1% 26.0%
3236697 5057.1.1.0 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.59 47.0 3.83e-01 88.5% 83.9%
4030651 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 46.0 3.35e-01 83.3% 32.4%
3290402 3567.1.1.86 a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › DUF485 0.59 42.0 4.09e-01 79.5% 67.0%
3766780 5081.1.1.1 alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.58 52.0 4.24e-01 100.0% 94.5%
4809777 6004.1.1.2 extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.57 49.0 4.44e-01 100.0% 69.7%
4351705 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.57 40.0 3.97e-01 78.2% 70.0%
3328865 3788.1.1.0 alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) 0.56 45.0 4.69e-01 92.3% 100.0%
3932298 5057.1.1.0 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.56 46.0 3.67e-01 92.3% 86.7%
3591905 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.56 41.0 3.63e-01 78.2% 73.0%
3188398 4099.1.1.0 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.56 43.0 3.19e-01 84.6% 82.4%
3374865 104.1.1.4 alpha duplicates or obligate multimers › TFIIA, alpha-helical domain › TFIIA, alpha-helical domain › TFIIA, alpha-helical domain › DUF247 0.56 48.0 3.26e-01 100.0% 25.2%
3838117 622.4.1.32 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › YGGT 0.55 40.0 3.87e-01 78.2% 88.9%
5018474 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.55 46.0 4.18e-01 98.7% 69.1%
3778778 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 39.0 2.61e-01 75.6% 27.6%
3965610 3831.1.1.1 alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › LprI 0.55 42.0 4.14e-01 84.6% 89.4%
3414050 601.1.1.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.55 47.0 4.34e-01 98.7% 74.3%
4805048 5057.1.1.0 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.55 40.0 3.69e-01 78.2% 59.8%
3961066 603.1.1.96 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › EccD 0.55 47.0 4.20e-01 98.7% 78.3%
4003837 4970.1.1.0 alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.54 39.0 3.61e-01 78.2% 60.0%
5008618 241.1.1.5 a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › DUF2299 0.53 46.0 3.77e-01 96.2% 96.6%
3281498 604.24.1.1 alpha bundles › Spectrin repeat-like › Helical bundle domain in putative transcriptional regulator Jann_0659-related proteins › Helical bundle domain in putative transcriptional regulator Jann_0659-related proteins › PaaX_C 0.53 43.0 4.32e-01 93.6% 85.0%
3645906 2004.1.1.508 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD_C, UvrD_C_2 0.53 42.0 2.72e-01 88.5% 24.7%
5060948 4957.1.1.9 a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit › HAAS 0.51 39.0 4.01e-01 83.3% 90.7%
3382549 4156.1.1.0 alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like 0.51 39.0 3.52e-01 80.8% 62.9%
3644387 601.1.2.81 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Serinc 0.51 44.0 3.66e-01 100.0% 56.7%
3724806 221.4.1.1 a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.51 33.0 2.44e-01 80.8% 24.9%
3924866 170.1.1.0 alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C 0.51 39.0 3.65e-01 80.8% 85.3%
3626229 601.1.1.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.51 41.0 4.02e-01 91.0% 92.9%
3589151 829.1.1.2 a+b duplicates or obligate multimers › NinB › NinB › NinB › HNHc_6 0.51 40.0 3.54e-01 89.7% 56.0%
D2 medium residues 79-169
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4c0eA01 1.25.40.790 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.62 45.0 3.25e-01 98.9% 24.7%
3cxbA03 1.10.1740.30 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Secreted effector protein SifA helical domain 0.60 37.0 3.85e-01 79.1% 67.9%
3r2cA00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.55 48.0 4.17e-01 96.7% 96.4%
2oyoA02 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.54 47.0 4.32e-01 100.0% 90.4%
3hlzA02 1.20.120.1090 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 39.0 3.58e-01 83.5% 67.4%
3f6tA02 1.10.20.110 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › 0.51 41.0 3.60e-01 91.2% 84.4%
2f8lA01 1.10.150.470 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.51 41.0 4.30e-01 89.0% 98.8%
4hdrB02 3.40.50.10210 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain 0.50 39.0 2.87e-01 84.6% 83.1%
6o7uc01 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.50 31.0 2.48e-01 81.3% 28.9%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4385657 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.71 65.0 5.19e-01 100.0% 62.9%
5052475 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.70 61.0 5.37e-01 94.5% 69.2%
3590040 3226.1.1.2 alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › Sulfate_transp 0.57 40.0 2.70e-01 74.7% 54.6%
5051738 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.57 40.0 4.36e-01 97.8% 95.7%
4011767 3711.1.1.14 alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › Tim17 0.55 38.0 3.14e-01 71.4% 74.7%
4290562 7014.1.1.1 alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › BacA 0.54 45.0 4.28e-01 97.8% 78.2%
3637728 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.52 31.0 2.95e-01 74.7% 48.6%
2486840 604.39.1.5 alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters › ECF_trnsprt 0.52 44.0 3.74e-01 97.8% 73.6%
4996029 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 42.0 2.91e-01 91.2% 25.9%
4989157 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.51 36.0 3.57e-01 75.8% 68.0%
5039049 601.7.1.2 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.51 37.0 3.80e-01 79.1% 85.6%
4068275 5065.1.1.3 alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › BPD_transp_2 0.51 45.0 3.19e-01 100.0% 97.2%