Back to structures

LacPavin_0818_WC40_scaffold_354720_prodigal-single.1__X__X__00368

Bact-Vir

LacPavin_0818_WC40_scaffold_354720_prodigal-single.1__X__X__00368

Identity

Kingdom:
phage

Quality

86.0 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 medium residues 1-66
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4f3lB02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.70 45.0 3.56e-01 71.2% 33.3%
4hz9B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.64 40.0 3.23e-01 86.4% 33.3%
3gwrB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 45.0 3.62e-01 87.9% 39.4%
4i4kA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 47.0 3.67e-01 87.9% 38.4%
6nhiA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.62 50.0 3.24e-01 92.4% 94.7%
2jq5A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 42.0 3.45e-01 87.9% 37.5%
3pcoB05 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.61 49.0 3.54e-01 92.4% 92.8%
6nrzA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.61 49.0 3.16e-01 92.4% 84.5%
3hriB01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.59 48.0 3.19e-01 92.4% 89.1%
4f3lA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.59 43.0 3.55e-01 78.8% 43.3%
2oztA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.58 40.0 3.35e-01 72.7% 43.2%
2daxA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.58 49.0 3.90e-01 97.0% 80.9%
4bboA00 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.58 47.0 3.95e-01 89.4% 65.5%
4qloA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 39.0 2.58e-01 72.7% 71.6%
4it1B01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.57 40.0 3.06e-01 74.2% 62.7%
3cskA02 3.30.540.30 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › 0.56 45.0 3.54e-01 95.5% 58.0%
3w1hA01 3.90.1150.110 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.55 41.0 3.02e-01 81.8% 41.8%
3ci0J01 3.10.610.10 Alpha Beta › Roll › Pili subunits › GSPII I/J protein-like 0.55 45.0 3.97e-01 93.9% 74.0%
1oygA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.55 44.0 2.75e-01 92.4% 72.8%
4q0yA00 2.60.40.4400 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 44.0 3.59e-01 90.9% 75.6%
2chrA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 38.0 3.16e-01 74.2% 41.7%
3loyA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 41.0 3.56e-01 86.4% 56.1%
2zadA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 37.0 3.18e-01 72.7% 82.5%
3tebB00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 44.0 3.08e-01 97.0% 41.7%
4ad8A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 35.0 2.39e-01 95.5% 15.5%
1shyB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 44.0 2.73e-01 95.5% 32.7%
3byqA00 3.30.1330.110 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › BB2672 0.53 43.0 3.19e-01 92.4% 59.2%
1t6eX01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.53 40.0 3.10e-01 87.9% 74.7%
2f86B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 45.0 3.63e-01 97.0% 92.2%
7qi3A01 3.30.2140.20 Alpha Beta › 2-Layer Sandwich › Arylamine N-acetyltransferase fold › 0.52 43.0 2.89e-01 100.0% 47.9%
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 45.0 2.99e-01 100.0% 75.8%
5e1qB01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.51 41.0 2.79e-01 92.4% 97.1%
1jpdX01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 35.0 3.15e-01 71.2% 85.9%
2y05A01 3.90.180.10 Alpha Beta › Alpha-Beta Complex › Quinone Oxidoreductase; Chain A, domain 1 › Medium-chain alcohol dehydrogenases, catalytic domain 0.51 40.0 3.15e-01 97.0% 38.7%
2cqaA01 2.40.50.360 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RuvBL1 DNA/RNA binding domain 0.51 29.0 2.84e-01 77.3% 47.3%
4dduA07 2.60.510.20 Mainly Beta › Sandwich › EV matrix protein fold › 0.51 35.0 3.02e-01 71.2% 52.3%
2rajA02 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.51 34.0 2.88e-01 71.2% 93.7%
2nyyA04 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.51 42.0 3.16e-01 100.0% 75.9%
6d92A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 43.0 3.00e-01 100.0% 63.9%
7tm7B01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.50 40.0 2.52e-01 93.9% 56.7%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3827143 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.63 52.0 4.25e-01 90.9% 88.8%
4937316 218.1.1.0 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.62 44.0 3.78e-01 74.2% 90.5%
4940297 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.62 50.0 3.23e-01 92.4% 90.1%
5058156 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.62 50.0 3.33e-01 92.4% 87.9%
3276546 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.62 50.0 3.21e-01 92.4% 96.0%
None 0.61 49.0 3.23e-01 92.4% 91.3%
4056328 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.61 48.0 3.20e-01 92.4% 90.2%
4945201 218.1.1.11 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_C 0.61 42.0 3.51e-01 72.7% 44.2%
3598220 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 47.0 3.74e-01 86.4% 59.3%
4573447 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.60 48.0 3.11e-01 92.4% 89.2%
4932527 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.60 49.0 3.17e-01 92.4% 87.1%
None 0.59 48.0 3.15e-01 92.4% 87.4%
4673719 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.59 47.0 3.13e-01 92.4% 87.7%
3309559 5.1.4.16 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A 0.59 40.0 2.69e-01 77.3% 17.0%
3702616 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 47.0 3.78e-01 84.8% 52.8%
4087500 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.59 47.0 4.33e-01 92.4% 80.0%
3643457 219.1.1.71 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › PDDEXK_6 0.59 49.0 3.70e-01 100.0% 54.1%
3718419 330.1.1.22 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF26536 0.59 40.0 2.98e-01 72.7% 64.1%
5072764 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 39.0 4.33e-01 71.2% 94.0%
4035814 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.58 46.0 3.07e-01 92.4% 90.6%
3627567 883.1.1.15 a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › LBP_BPI_CETP+LBP_BPI_CETP_C 0.57 47.0 2.95e-01 93.9% 26.7%
4986251 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.57 44.0 4.04e-01 93.9% 62.2%
3344712 10.1.1.0 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.57 47.0 3.61e-01 92.4% 41.3%
3702239 220.1.1.1 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.57 41.0 3.38e-01 80.3% 43.0%
4000111 2004.1.1.87 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.56 43.0 3.07e-01 89.4% 25.3%
4020435 7579.1.1.37 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › DUF1749 0.56 41.0 2.68e-01 80.3% 30.5%
4957500 283.2.1.0 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like 0.56 49.0 4.38e-01 100.0% 77.9%
5011023 512.1.1.0 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.56 45.0 4.24e-01 89.4% 80.0%
1174546 218.1.1.0 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.56 38.0 3.05e-01 72.7% 64.3%
4482719 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.56 44.0 3.88e-01 90.9% 75.0%
4444614 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 40.0 3.86e-01 80.3% 68.8%
3720662 883.1.1.23 a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › HAM1_C, HAM1_N 0.55 46.0 3.30e-01 92.4% 66.5%
None 0.55 39.0 2.49e-01 95.5% 12.6%
3415330 223.1.1.2 a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.55 39.0 2.97e-01 75.8% 34.8%
4029165 2004.1.1.198 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.55 43.0 2.70e-01 89.4% 38.6%
4489834 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.54 42.0 3.77e-01 90.9% 74.3%
4300310 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.54 38.0 3.39e-01 77.3% 68.3%
4256472 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.54 41.0 3.71e-01 90.9% 66.7%
3460645 4177.1.1.0 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.53 36.0 2.31e-01 71.2% 14.2%
3668884 331.3.1.43 a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PDF2_C 0.53 42.0 2.84e-01 87.9% 74.3%
3164849 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.53 43.0 3.78e-01 92.4% 79.0%
3201176 243.5.1.0 a+b two layers › Cystatin-like › Amine oxidase N-terminal region › Amine oxidase N-terminal region 0.53 44.0 3.57e-01 95.5% 72.6%
3771653 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.53 39.0 3.44e-01 84.8% 51.4%
3619214 295.1.1.0 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.53 34.0 3.66e-01 71.2% 78.2%
3607207 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 41.0 2.72e-01 90.9% 86.1%
3509244 11.1.1.41 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.52 44.0 3.29e-01 92.4% 64.8%
3481288 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 39.0 3.30e-01 92.4% 47.8%
3797649 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 40.0 3.55e-01 93.9% 55.5%
4534145 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.51 41.0 3.57e-01 92.4% 73.6%
4336680 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.51 39.0 3.40e-01 92.4% 60.8%
4460812 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.50 40.0 3.48e-01 90.9% 74.5%
4335178 3016.1.1.0 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.50 40.0 3.52e-01 92.4% 74.5%
4160518 3016.1.1.11 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › SelA 0.50 41.0 3.63e-01 93.9% 67.0%
D2 medium residues 67-118
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hl8A03 1.20.1280.70 Mainly Alpha › Up-down Bundle › Monooxygenase › Exonuclease ExoI, domain 3 0.71 54.0 5.19e-01 84.6% 72.6%
2zj8A04 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.53 37.0 3.68e-01 76.9% 80.7%