Back to structures

LacPavin_0818_WC40_scaffold_75050_prodigal-single.1__X__X__00050

Bact-Vir

LacPavin_0818_WC40_scaffold_75050_prodigal-single.1__X__X__00050

Identity

Kingdom:
phage

Quality

63.0 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 74-120
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2jwkA00 3.30.420.270 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.81 60.0 5.17e-01 80.9% 52.7%
1zc3B00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.73 54.0 4.15e-01 80.9% 39.4%
1k0eB00 3.60.120.10 Alpha Beta › 4-Layer Sandwich › Anthranilate synthase › Anthranilate synthase 0.73 52.0 3.06e-01 78.7% 9.2%
3d1cA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.72 45.0 2.81e-01 76.6% 11.9%
17gsA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.69 49.0 3.84e-01 76.6% 76.8%
5vmzA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.68 49.0 5.18e-01 78.7% 100.0%
3rbtD01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.66 48.0 3.58e-01 78.7% 64.0%
5teqA01 3.30.470.110 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › 0.66 49.0 3.15e-01 97.9% 17.1%
4bndA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.65 49.0 3.38e-01 80.9% 96.2%
3h5aD01 3.90.930.70 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.63 54.0 4.48e-01 100.0% 79.5%
3mfqA01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.61 41.0 2.91e-01 70.2% 87.9%
3p54A02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.61 50.0 4.45e-01 95.7% 77.5%
1vx7H01 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.61 46.0 3.92e-01 87.2% 83.5%
1dq3A02 3.30.160.90 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.61 45.0 3.91e-01 83.0% 57.9%
3k6qA02 3.30.160.620 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.60 48.0 3.97e-01 100.0% 48.3%
7lgjA01 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.60 50.0 3.29e-01 100.0% 25.5%
3igfA02 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 43.0 3.66e-01 76.6% 55.4%
2p6rA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 43.0 2.85e-01 78.7% 87.8%
2onfA01 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.59 45.0 3.33e-01 85.1% 38.1%
2z86D02 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.59 47.0 3.05e-01 95.7% 86.9%
2m3xC02 2.40.10.360 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.59 40.0 3.55e-01 97.9% 49.3%
3d6wB01 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 40.0 3.57e-01 74.5% 51.4%
4o2zA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.58 49.0 3.46e-01 100.0% 36.6%
2c60A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.57 42.0 3.66e-01 83.0% 81.0%
2yzsA01 3.100.10.20 Alpha Beta › Ribosomal Protein L15; Chain: K; domain 2 › Ribosomal Protein L15; Chain: K; domain 2 › CRISPR-associated endonuclease Cas1, N-terminal domain 0.57 40.0 3.45e-01 76.6% 68.8%
4d0yA00 3.30.1380.10 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › 0.56 38.0 2.68e-01 74.5% 95.1%
4otpA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.56 45.0 3.41e-01 100.0% 83.2%
2pi2D00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 40.0 3.11e-01 83.0% 90.2%
5iz3A01 3.30.540.10 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › Fructose-1,6-Bisphosphatase, subunit A, domain 1 0.55 43.0 2.95e-01 87.2% 33.9%
1fs7A01 1.10.1130.10 Mainly Alpha › Orthogonal Bundle › Flavocytochrome C3; Chain A, domain 2 › Flavocytochrome C3; Chain A 0.55 42.0 2.57e-01 83.0% 76.8%
1iv8A02 3.30.1590.10 Alpha Beta › 2-Layer Sandwich › Maltooligosyl trehalose synthase, domain 2 › Maltooligosyl trehalose synthase, domain 2 0.55 44.0 3.49e-01 100.0% 48.3%
2yyzA02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.55 39.0 3.69e-01 76.6% 74.1%
4akgA12 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 37.0 2.91e-01 78.7% 29.1%
5zx8A00 3.40.50.1470 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidyl-tRNA hydrolase 0.54 44.0 3.07e-01 100.0% 73.7%
4mbsA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.53 43.0 2.68e-01 97.9% 45.7%
7d4rB01 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.53 39.0 2.62e-01 80.9% 65.1%
5a35A00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.53 40.0 3.29e-01 95.7% 50.0%
3oymA01 1.10.340.70 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › 0.52 35.0 2.95e-01 72.3% 62.4%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 40.0 3.07e-01 83.0% 44.0%
2pvpA01 3.40.50.20 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 43.0 3.33e-01 97.9% 49.6%
2ckwA04 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.52 38.0 3.16e-01 89.4% 98.1%
1b8pA02 3.90.110.10 Alpha Beta › Alpha-Beta Complex › L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 › Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal 0.52 40.0 2.75e-01 83.0% 32.6%
1o22A00 3.90.1000.10 Alpha Beta › Alpha-Beta Complex › Orphan Protein Tm0875; Chain: A; › Hypothetical protein TM0875 0.52 40.0 2.88e-01 85.1% 62.4%
3bs1A00 2.40.50.1020 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › LytTr DNA-binding domain 0.51 35.0 2.98e-01 80.9% 48.5%
2jugA01 1.10.10.1830 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Non-ribosomal peptide synthase, adenylation domain 0.51 34.0 3.38e-01 74.5% 67.3%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5022340 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.86 62.0 5.36e-01 76.6% 60.0%
3468148 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.83 58.0 3.76e-01 76.6% 17.9%
3542422 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.79 55.0 5.80e-01 74.5% 90.0%
3723017 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.78 54.0 4.90e-01 74.5% 53.8%
3225668 207.1.1.81 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.77 57.0 3.59e-01 83.0% 16.1%
4936221 2003.1.7.13 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NagB/RpiA/CoA transferase-like › NAD_kinase_C 0.75 55.0 3.83e-01 80.9% 35.0%
3787709 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.74 52.0 5.51e-01 74.5% 95.0%
4992470 896.1.1.0 a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.73 54.0 5.01e-01 80.9% 63.3%
81577 880.1.1.1 a+b duplicates or obligate multimers › ADC synthase › ADC synthase › ADC synthase › Chorismate_bind 0.72 52.0 3.01e-01 78.7% 8.7%
3493703 386.1.1.20 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-met 0.72 53.0 5.48e-01 80.9% 88.9%
4995140 2484.1.1.124 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.71 52.0 3.79e-01 83.0% 58.6%
4990102 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.70 50.0 5.09e-01 76.6% 86.7%
3289942 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.69 50.0 4.14e-01 78.7% 87.1%
3928014 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.69 48.0 5.33e-01 74.5% 100.0%
5077089 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.68 48.0 4.21e-01 74.5% 78.6%
4928066 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.68 51.0 3.51e-01 83.0% 46.1%
3566388 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.68 46.0 4.79e-01 72.3% 81.4%
3613640 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.68 49.0 3.04e-01 78.7% 28.4%
3394477 377.9.1.0 few secondary structure elements › Glucocorticoid receptor-like › HIT/MYND zinc finger-like › HIT/MYND zinc finger-like 0.67 50.0 4.65e-01 80.9% 85.0%
3601402 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.67 48.0 2.92e-01 78.7% 24.5%
3658440 386.1.1.26 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_6 0.66 50.0 4.76e-01 85.1% 70.9%
4934385 2484.1.1.302 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.66 46.0 3.13e-01 76.6% 64.2%
4262261 4.8.1.5 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.65 44.0 4.19e-01 74.5% 60.0%
4454944 101.1.2.468 alpha arrays › HTH › HTH › winged helix domain › McbB 0.65 49.0 4.15e-01 83.0% 88.7%
3869223 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.65 50.0 4.26e-01 87.2% 65.0%
4964626 101.1.2.931 alpha arrays › HTH › HTH › winged helix domain › DUF7528 0.63 52.0 3.88e-01 97.9% 43.1%
4214812 4.8.1.26 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › bPH_8 0.62 47.0 3.93e-01 85.1% 63.6%
5028765 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.60 45.0 3.23e-01 83.0% 88.7%
4351809 4.8.1.5 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.60 40.0 3.78e-01 74.5% 55.0%
5022798 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.60 52.0 2.95e-01 97.9% 10.2%
3616888 207.1.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.60 44.0 2.73e-01 83.0% 13.2%
4307219 4.8.1.5 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.60 42.0 4.00e-01 74.5% 65.5%
3960493 1001.1.1.0 a+b two layers › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 0.60 39.0 2.91e-01 72.3% 25.6%
3922598 4120.1.1.43 few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP › TSTD2_N 0.60 44.0 4.03e-01 80.9% 63.1%
3714703 1021.1.1.0 a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.59 44.0 3.54e-01 83.0% 47.0%
4276957 4.8.1.5 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.59 40.0 3.88e-01 74.5% 61.8%
1413813 4.8.1.5 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.58 39.0 3.77e-01 74.5% 60.0%
3740384 1021.1.1.0 a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.58 48.0 4.35e-01 93.6% 93.8%
5059406 220.1.1.291 beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_4 0.58 43.0 3.80e-01 83.0% 61.3%
4995731 502.1.1.0 a+b two layers › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain 0.57 41.0 3.84e-01 78.7% 100.0%
5054192 802.1.1.0 a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 0.56 49.0 3.89e-01 100.0% 100.0%
5015831 2008.1.1.107 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.56 47.0 3.45e-01 97.9% 88.9%
4810374 3740.1.1.1 alpha arrays › F420-reducing hydrogenase subunit beta › F420-reducing hydrogenase subunit beta › F420-reducing hydrogenase subunit beta › FrhB_FdhB_N,FrhB_FdhB_C 0.56 43.0 2.74e-01 85.1% 98.0%
5016928 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.55 45.0 2.94e-01 93.6% 58.6%
4061485 4967.1.1.0 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.54 41.0 2.71e-01 80.9% 25.1%
3622481 604.29.1.1 alpha bundles › Spectrin repeat-like › Trehalose-6-phosphate phosphatase N-terminal helical bundle › Trehalose-6-phosphate phosphatase N-terminal helical bundle › T6PP_N 0.54 43.0 3.29e-01 89.4% 77.4%
4033493 4.8.1.5 beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.53 37.0 3.63e-01 74.5% 63.6%
1569147 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.53 40.0 3.31e-01 95.7% 50.9%
3209881 109.4.1.207 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_2 0.53 38.0 2.16e-01 78.7% 9.2%
1841610 4018.1.1.1 a+b two layers › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › FBPase 0.52 44.0 3.02e-01 97.9% 89.2%
5005237 4967.1.1.11 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › GIIM 0.52 40.0 2.72e-01 83.0% 27.5%
3385884 2003.1.15.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Glycosyltransferase Maf N-terminal domain › Maf_flag10_N 0.51 40.0 2.84e-01 95.7% 72.6%
1147677 4967.1.1.2 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › RdRP_1 0.51 38.0 3.35e-01 93.6% 98.9%
1571442 4967.1.1.2 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › RdRP_1 0.50 38.0 3.23e-01 83.0% 50.0%