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SRR1747027_scaffold_2_prodigal-single.1__X__X__00219

Bact-Vir

SRR1747027_scaffold_2_prodigal-single.1__X__X__00219

Identity

Kingdom:
phage

Quality

82.4 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 1-227_337-361
PDB
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1xo1A02 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.74 47.0 5.92e-01 76.2% 100.0%
3tnjA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.68 34.0 4.81e-01 70.6% 100.0%
6hcdD00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.66 33.0 4.44e-01 82.5% 88.1%
3pieC01 3.40.50.12390 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.63 51.0 5.06e-01 92.1% 79.3%
1kjnA00 3.40.50.10160 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › MTH777-like 0.60 32.0 3.96e-01 73.4% 82.9%
3gemD00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 36.0 3.89e-01 89.3% 70.1%
4hjhB01 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.57 32.0 4.07e-01 88.1% 91.9%
2j5bB01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.56 41.0 4.58e-01 78.2% 95.9%
6oibA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 30.0 3.71e-01 71.4% 85.4%
5ul3A01 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.54 32.0 4.02e-01 91.7% 93.6%
3hdtA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 29.0 3.45e-01 70.2% 74.4%
1xngA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 35.0 3.60e-01 87.3% 66.8%
3mdqA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 27.0 3.78e-01 73.4% 100.0%
1jphA00 3.20.20.210 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.53 40.0 3.55e-01 76.2% 82.9%
2f8lA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 41.0 4.26e-01 86.5% 84.6%
1oaaA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 38.0 3.82e-01 89.3% 71.8%
2zw9B01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 45.0 4.06e-01 90.1% 88.4%
3sp1A01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 40.0 3.95e-01 78.6% 97.4%
2derB01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.51 35.0 3.82e-01 81.3% 83.7%
7vc6A02 3.40.50.1700 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycoside hydrolase family 3 C-terminal domain 0.51 33.0 3.64e-01 88.9% 77.8%
1pzxB01 3.40.50.10440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dihydroxyacetone kinase; domain 1 0.51 26.0 3.54e-01 77.4% 97.5%
3rdkB00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.50 38.0 3.49e-01 77.4% 80.8%
3c8zA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.50 41.0 3.80e-01 84.5% 83.9%
2iw1A02 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.50 31.0 3.61e-01 73.8% 83.3%
2gdzA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 39.0 3.84e-01 90.9% 74.8%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4125023 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.77 50.0 6.01e-01 73.4% 95.3%
4029535 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.76 52.0 6.10e-01 74.6% 95.6%
3387660 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.75 48.0 5.74e-01 73.4% 93.5%
3964138 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.73 51.0 6.03e-01 76.6% 100.0%
4299585 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.72 52.0 6.08e-01 79.0% 100.0%
3913336 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.70 45.0 5.17e-01 81.0% 85.9%
3612297 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.67 55.0 5.62e-01 87.3% 88.7%
3300817 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.64 55.0 4.95e-01 90.1% 80.9%
3203047 2006.1.4.29 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN-like_DDX60 0.63 49.0 5.30e-01 90.5% 94.3%
4943545 4143.1.1.11 a+b two layers › THUMP domain-like › THUMP domain-like › THUMP domain-like › UPF0020 0.63 29.0 4.31e-01 86.1% 98.2%
4628515 2006.1.4.5 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.63 54.0 5.30e-01 90.1% 90.9%
3400646 2006.1.4.5 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.63 54.0 5.00e-01 90.1% 90.5%
3605878 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.63 43.0 4.91e-01 73.4% 91.6%
3294273 2006.1.4.5 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.63 54.0 5.28e-01 90.1% 83.7%
4443696 2006.1.4.5 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N 0.63 54.0 4.87e-01 90.1% 81.2%
None 0.63 54.0 5.06e-01 89.7% 91.7%
3283061 2006.1.4.3 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › NYN 0.62 40.0 4.75e-01 73.8% 92.0%
5072240 2006.1.4.25 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_I 0.61 45.0 4.98e-01 79.4% 93.0%
3333830 2003.1.5.30 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_7 0.61 32.0 3.95e-01 82.1% 79.2%
4024047 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.61 48.0 5.01e-01 81.0% 87.8%
3599611 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.60 49.0 4.69e-01 83.3% 89.1%
3470605 2005.1.1.0 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.60 34.0 4.36e-01 82.1% 93.3%
4582905 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.58 36.0 4.18e-01 88.1% 83.8%
3194567 7514.1.1.1 a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › NAD_binding_1 0.58 35.0 4.41e-01 89.3% 97.4%
3335892 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.57 49.0 4.73e-01 89.3% 94.6%
3471700 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.56 45.0 4.68e-01 82.9% 90.2%
3624992 2496.1.1.1 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › CRAL_TRIO 0.56 41.0 4.51e-01 89.3% 92.7%
5041206 2007.1.14.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like 0.56 39.0 4.41e-01 82.1% 91.8%
None 0.55 42.0 4.59e-01 89.7% 95.6%
3503431 2496.1.1.1 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › CRAL_TRIO 0.55 41.0 4.40e-01 87.7% 89.3%
3302232 2003.1.5.30 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_7 0.54 45.0 3.93e-01 86.5% 92.8%
3508968 2496.1.1.1 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › CRAL_TRIO 0.54 40.0 4.39e-01 87.7% 91.9%
1546466 2496.1.1.1 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › CRAL_TRIO 0.54 39.0 4.30e-01 85.7% 92.0%
4266161 2003.1.1.85 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › SpnB_Rossmann 0.54 36.0 3.76e-01 89.3% 71.7%
3574194 2496.1.1.1 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › CRAL_TRIO 0.53 39.0 4.23e-01 88.5% 91.0%
3683595 2003.1.5.30 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_7 0.53 44.0 3.82e-01 86.5% 94.8%
3999525 2496.1.1.1 a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like › CRAL_TRIO 0.52 40.0 4.32e-01 88.1% 93.5%
5053129 2004.1.1.70 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › dNK 0.52 34.0 3.64e-01 78.2% 73.8%
4958939 7601.1.1.2 a/b three-layered sandwiches › Lactate racemase N-terminal domain › Lactate racemase N-terminal domain › Lactate racemase N-terminal domain › DUF362 0.51 43.0 3.83e-01 89.7% 88.0%
5053026 2500.1.1.5 a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › NRDD 0.51 43.0 3.43e-01 90.1% 75.3%
D2 high residues 240-327
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5hmlA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.61 50.0 5.21e-01 98.9% 98.8%
1ngnA00 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.60 51.0 4.38e-01 100.0% 58.3%
1miwA04 1.10.246.80 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.60 38.0 4.39e-01 79.5% 89.1%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.58 32.0 3.57e-01 79.5% 68.7%
5z7cA01 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.56 48.0 3.91e-01 98.9% 80.1%
3tahA02 1.10.287.1770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 36.0 3.63e-01 88.6% 65.9%
1f4qA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.55 46.0 3.83e-01 94.3% 99.4%
2kdoA02 1.10.10.900 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › SBDS protein C-terminal domain, subdomain 1 0.54 37.0 4.02e-01 73.9% 90.4%
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.53 34.0 3.58e-01 70.5% 72.2%
2f5jB00 1.10.274.30 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › MRG domain 0.53 42.0 3.52e-01 87.5% 72.3%
3l9vC00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 44.0 3.59e-01 95.5% 58.6%
2imfA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 43.0 3.44e-01 95.5% 70.4%
4nxiA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 44.0 3.48e-01 94.3% 60.1%
2p0tA02 1.10.60.30 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › PSPTO4464-like domains 0.51 31.0 3.35e-01 78.4% 73.6%
6ll8A01 3.90.1640.10 Alpha Beta › Alpha-Beta Complex › inorganic pyrophosphatase (n-terminal core) › inorganic pyrophosphatase (n-terminal core) 0.50 41.0 3.34e-01 94.3% 78.5%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4940107 102.3.1.1 alpha arrays › HhH/H2TH › eIF2alpha middle domain › eIF2alpha middle domain › EIF_2_alpha 0.66 50.0 5.13e-01 88.6% 85.9%
4343577 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.65 53.0 3.74e-01 85.2% 30.6%
4030601 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.65 55.0 4.97e-01 89.8% 68.7%
4995753 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.64 55.0 4.94e-01 94.3% 68.1%
3898674 102.1.1.77 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › TNK-like_SAM 0.64 48.0 4.96e-01 94.3% 87.5%
3329195 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.62 55.0 4.83e-01 95.5% 70.4%
3610816 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.57 41.0 4.19e-01 88.6% 77.6%
5045366 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.57 45.0 4.65e-01 89.8% 90.6%
4319405 235.1.1.5 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Transgly 0.56 47.0 3.65e-01 98.9% 80.0%
4021753 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.54 38.0 3.86e-01 71.6% 89.4%
3722072 3924.1.1.1 alpha complex topology › Sterol uptake control protein 2 › Sterol uptake control protein 2 › Sterol uptake control protein 2 › Fungal_trans_2 0.53 41.0 3.21e-01 85.2% 60.0%
4944587 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.52 43.0 4.12e-01 92.0% 78.1%
5073287 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.52 45.0 3.68e-01 98.9% 78.9%
3286645 2485.1.1.58 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Rv2466c-like 0.52 44.0 3.42e-01 96.6% 60.0%
4959578 186.1.1.0 alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.52 41.0 4.10e-01 89.8% 92.6%
3254469 101.1.10.9 alpha arrays › HTH › HTH › Cyclin-like › Cyclin 0.52 43.0 3.50e-01 94.3% 87.8%
3534849 101.1.10.7 alpha arrays › HTH › HTH › Cyclin-like › Cyclin_C 0.51 41.0 3.81e-01 88.6% 72.2%
3987246 235.1.1.5 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Transgly 0.51 44.0 3.18e-01 100.0% 73.1%
4294975 563.1.1.1 alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.50 38.0 3.10e-01 81.8% 47.8%
3498081 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.50 43.0 3.46e-01 98.9% 54.1%