Back to structures

LSDeep1_scaffold_42_prodigal-single.1__X__X__00065

Bact-Vir

LSDeep1_scaffold_42_prodigal-single.1__X__X__00065

Identity

Kingdom:
phage

Quality

74.4 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 high residues 7-101
PDB
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vsrA00 3.40.960.10 Alpha Beta › 3-Layer(aba) Sandwich › Endonuclease; Chain A › VSR Endonuclease 0.77 71.0 6.24e-01 100.0% 85.1%
3rpjA00 3.30.310.230 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Sigma factor-binding protein Crl monomer 0.64 47.0 4.26e-01 75.8% 92.9%
5karA01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.64 56.0 3.72e-01 98.9% 85.1%
5fc1A01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.64 56.0 3.71e-01 98.9% 84.1%
1x5eA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.61 36.0 3.51e-01 86.3% 51.4%
1nj1A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.60 38.0 3.76e-01 72.6% 59.6%
5awhA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.59 53.0 4.34e-01 100.0% 70.4%
4fdaA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 51.0 3.84e-01 98.9% 93.0%
1lw7A01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.58 48.0 4.07e-01 93.7% 62.1%
5v1qB01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.58 44.0 3.17e-01 82.1% 43.7%
4lizA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.57 48.0 4.25e-01 92.6% 83.3%
4g6uA02 3.40.1350.110 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.57 44.0 3.98e-01 85.3% 83.3%
4o5aA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 42.0 3.71e-01 86.3% 53.2%
3wqlA01 3.40.1180.10 Alpha Beta › 3-Layer(aba) Sandwich › Undecaprenyl pyrophosphate synthetase › Decaprenyl diphosphate synthase-like 0.57 45.0 3.32e-01 84.2% 72.1%
8hi4A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 48.0 3.63e-01 96.8% 99.2%
5xilA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.57 39.0 3.56e-01 72.6% 53.1%
4u63A01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.56 48.0 3.99e-01 95.8% 78.7%
1ad1A00 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.56 46.0 3.40e-01 91.6% 90.5%
4a8jA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 46.0 3.36e-01 91.6% 79.4%
7o0aD01 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.56 47.0 3.65e-01 94.7% 61.1%
3a4lB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 47.0 3.92e-01 97.9% 81.5%
4q34A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.55 47.0 3.34e-01 97.9% 85.0%
1pyoC00 3.40.50.1460 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 42.0 3.60e-01 83.2% 91.3%
7c2fB01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.54 42.0 4.40e-01 84.2% 95.3%
4gp6A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 43.0 3.68e-01 91.6% 97.1%
2qxyA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 48.0 4.47e-01 100.0% 84.9%
3d3qA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 47.0 4.05e-01 98.9% 89.0%
7nn3B01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 46.0 3.23e-01 98.9% 78.7%
4p02A02 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 0.53 45.0 3.40e-01 93.7% 39.7%
1j1uA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 43.0 3.44e-01 89.5% 77.0%
2o3rA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 41.0 3.77e-01 83.2% 93.5%
6nuiA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 45.0 3.68e-01 97.9% 86.1%
7whfC02 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.52 38.0 3.82e-01 77.9% 89.0%
6c6bB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 47.0 3.69e-01 98.9% 76.9%
5da9A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 42.0 2.96e-01 91.6% 86.7%
2d00A01 3.40.50.10580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ATPase, V1 complex, subunit F 0.52 26.0 2.98e-01 70.5% 62.7%
3a32A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.52 40.0 2.78e-01 83.2% 34.3%
3ttyA02 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.52 44.0 3.48e-01 100.0% 79.1%
4wi1A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.51 37.0 3.42e-01 75.8% 87.8%
3bblA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 45.0 4.04e-01 100.0% 71.7%
6wctD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 42.0 3.79e-01 97.9% 67.3%
2yv4A00 3.40.50.11030 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Threonylcarbamoyl-AMP synthase, C-terminal domain 0.51 37.0 3.64e-01 100.0% 71.6%
4wnyA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.51 42.0 3.80e-01 92.6% 72.7%
6qelJ01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 45.0 3.69e-01 100.0% 86.0%
3qk7A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 45.0 3.98e-01 100.0% 68.8%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5048618 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.81 74.0 6.55e-01 100.0% 94.1%
5080733 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.79 74.0 6.56e-01 100.0% 77.7%
4940595 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.78 65.0 6.45e-01 97.9% 85.0%
5022187 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.77 71.0 5.96e-01 100.0% 75.5%
3979018 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.77 71.0 6.01e-01 100.0% 76.0%
3964563 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.76 70.0 6.07e-01 100.0% 78.6%
5053107 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.76 68.0 6.09e-01 96.8% 77.5%
4995722 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.76 68.0 6.76e-01 100.0% 93.0%
3281852 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.75 69.0 5.97e-01 100.0% 72.4%
5056125 2008.1.1.14 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr 0.75 70.0 6.21e-01 100.0% 81.5%
4467650 2008.1.1.167 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Vsr, DUF559 0.73 67.0 5.92e-01 100.0% 79.3%
4954232 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.73 57.0 6.09e-01 82.1% 97.5%
4985335 2006.1.6.15 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › DUF58 0.71 65.0 4.83e-01 100.0% 77.4%
4025795 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.71 66.0 5.92e-01 100.0% 84.6%
3673147 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.71 64.0 6.01e-01 98.9% 80.0%
3808239 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.71 64.0 6.36e-01 100.0% 93.0%
4027358 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.71 63.0 5.72e-01 97.9% 72.8%
4027159 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.70 64.0 6.02e-01 100.0% 87.0%
3262617 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.69 54.0 5.17e-01 83.2% 90.9%
4271425 2008.1.1.81 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF2726 0.69 63.0 5.27e-01 100.0% 67.5%
3427403 2008.1.1.151 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF28664 0.64 56.0 4.69e-01 98.9% 80.6%
5059310 2006.1.6.15 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › DUF58 0.63 56.0 4.38e-01 98.9% 75.6%
3967787 2008.1.1.88 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Tox-REase-5 0.63 52.0 4.60e-01 88.4% 84.4%
5034672 2485.1.1.0 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.62 36.0 3.69e-01 87.4% 58.5%
4281154 2004.1.1.191 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 0.61 53.0 4.40e-01 100.0% 86.5%
2330444 292.2.1.15 a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › PF29923 0.59 46.0 4.18e-01 84.2% 83.8%
5064865 2004.1.1.146 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase 0.58 48.0 3.59e-01 90.5% 83.4%
4978476 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.58 43.0 3.92e-01 78.9% 76.2%
5078948 2005.1.1.29 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1g 0.58 40.0 3.03e-01 71.6% 97.8%
1175828 2007.6.1.3 a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain › PGI 0.57 48.0 3.69e-01 94.7% 55.6%
4315678 2007.6.1.0 a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain 0.57 48.0 3.93e-01 93.7% 55.7%
1836756 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.57 37.0 3.63e-01 70.5% 59.6%
3862376 2004.1.1.122 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › IIGP 0.57 48.0 3.24e-01 94.7% 46.1%
3741630 2005.1.1.0 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.57 44.0 3.65e-01 83.2% 86.5%
1318473 224.1.1.1 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.57 46.0 4.18e-01 90.5% 83.6%
4040968 2004.1.1.71 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › IPPT 0.57 51.0 3.86e-01 100.0% 91.3%
4014215 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.56 43.0 3.38e-01 83.2% 63.7%
4091867 314.1.1.2 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.56 41.0 2.69e-01 74.7% 23.2%
4982951 2004.1.1.162 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Rad51 0.56 48.0 3.58e-01 94.7% 67.8%
4278210 2007.6.1.0 a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain 0.56 47.0 3.89e-01 93.7% 58.3%
3343894 2007.6.1.3 a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain › PGI 0.56 47.0 3.77e-01 93.7% 62.1%
4981516 2005.1.1.0 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.56 47.0 4.06e-01 93.7% 76.7%
5025002 2004.1.1.162 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Rad51 0.56 49.0 3.74e-01 98.9% 72.5%
3340982 2007.6.1.3 a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain › PGI 0.56 47.0 3.41e-01 94.7% 43.5%
2771816 2007.6.1.3 a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain › PGI 0.55 46.0 3.62e-01 93.7% 61.1%
3510951 2007.2.5.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase › Rhodanese 0.55 44.0 3.86e-01 86.3% 92.1%
4681347 7579.1.1.0 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.55 47.0 3.53e-01 100.0% 80.4%
3164628 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 0.54 47.0 4.12e-01 94.7% 72.1%
3405320 2004.1.1.16 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Arf 0.53 47.0 3.66e-01 100.0% 68.6%
3226005 2004.1.1.163 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › KTI12 0.53 46.0 3.88e-01 98.9% 85.3%
3175231 2003.1.6.6 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like › Misat_Tub_SegII+Tubulin_3 0.53 45.0 3.30e-01 97.9% 90.7%
5055197 2005.1.1.13 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.52 44.0 3.82e-01 93.7% 71.3%
4996845 2004.1.1.146 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase 0.52 46.0 3.56e-01 100.0% 72.7%
5071262 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 45.0 3.07e-01 100.0% 80.3%
3255447 224.1.1.2 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.52 42.0 3.87e-01 86.3% 72.5%
4324598 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.52 43.0 3.56e-01 94.7% 93.5%
3930511 2007.2.3.10 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › DSPn 0.51 40.0 3.90e-01 83.2% 80.0%
5022511 2004.1.2.3 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › PEP carboxykinase catalytic C-terminal domain › Hpr_kinase_C 0.51 44.0 3.78e-01 100.0% 78.8%
3728118 2003.1.1.3 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.51 38.0 3.45e-01 81.1% 79.3%
2624530 2004.1.1.103 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Sua5_C 0.51 37.0 3.57e-01 100.0% 67.0%
4989618 2004.1.1.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA 0.50 42.0 3.39e-01 95.8% 76.6%