←Back to structures

S2_005_003_R2_scaffold_7_prodigal-single.1__X__X__00684

Bact-Vir

S2_005_003_R2_scaffold_7_prodigal-single.1__X__X__00684

Identity

Kingdom:
phage

Quality

82.6 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 8-107
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2jiwA01 3.30.379.10 Alpha Beta › 2-Layer Sandwich › Chitobiase; domain 2 › Chitobiase/beta-hexosaminidase domain 2-like 0.56 44.0 4.18e-01 86.0% 79.3%
2yptA02 3.30.2010.10 Alpha Beta › 2-Layer Sandwich › Zincin-like › "Metalloproteases (""zincins""), catalytic domain" 0.53 39.0 4.22e-01 86.0% 96.3%
3bhnA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.52 40.0 3.19e-01 84.0% 92.0%
4xllA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.51 36.0 3.02e-01 72.0% 92.9%
3cyfA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.51 36.0 2.97e-01 72.0% 93.0%
2b5dX01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.50 38.0 2.60e-01 81.0% 95.5%
3er6A00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.50 36.0 2.93e-01 73.0% 91.1%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5012980 2498.1.1.9 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M1 0.56 45.0 3.42e-01 88.0% 69.2%
166464 2007.1.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › DJ-1_PfpI 0.52 39.0 3.15e-01 81.0% 92.1%
3250254 2007.1.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › DJ-1_PfpI 0.52 36.0 2.96e-01 72.0% 90.4%
3281421 2007.1.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › DJ-1_PfpI 0.52 39.0 3.19e-01 81.0% 96.5%
3988445 2007.1.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › DJ-1_PfpI 0.51 36.0 2.99e-01 72.0% 91.1%
1498182 2007.1.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › DJ-1_PfpI 0.51 36.0 3.02e-01 72.0% 92.9%
3413735 3435.1.1.6 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC › DUF155 0.51 38.0 3.31e-01 79.0% 100.0%
3290169 2007.1.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › DJ-1_PfpI 0.51 36.0 2.76e-01 73.0% 68.6%
4087573 2004.1.1.73 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.51 35.0 3.03e-01 72.0% 90.6%
394933 2007.1.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › DJ-1_PfpI 0.51 35.0 2.77e-01 73.0% 71.0%
8997 2002.3.1.3 ↗ a/b barrels › TIM beta/alpha-barrel › Glycoside hydrolase/deacetylase › Glycoside hydrolase/deacetylase › Glyco_hydro_57 0.50 38.0 2.60e-01 81.0% 95.5%
3887886 604.3.1.11 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › DUF155 0.50 38.0 2.88e-01 80.0% 70.6%
3602410 604.1.1.235 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF27233 0.50 38.0 2.91e-01 83.0% 90.4%
D2 high residues 112-190
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.68 56.0 5.02e-01 89.9% 90.0%
3vw4A01 1.10.340.50 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › 0.65 55.0 5.25e-01 93.7% 80.4%
4a64A02 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.65 54.0 4.75e-01 91.1% 91.5%
2gbbB00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.63 54.0 4.35e-01 94.9% 52.3%
2icwG02 1.10.10.530 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › mam-mhc complex, Chain D, Domain 2 0.62 50.0 4.87e-01 92.4% 78.7%
2a0uB01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.61 52.0 4.19e-01 94.9% 55.0%
1u61A00 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.61 45.0 3.95e-01 81.0% 75.6%
1te2A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.61 41.0 4.29e-01 91.1% 76.4%
8sbeA01 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.61 50.0 3.82e-01 93.7% 75.5%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.59 47.0 4.59e-01 84.8% 83.5%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.59 45.0 4.61e-01 83.5% 85.7%
1yozA00 1.10.3200.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › AF0941-like 0.58 47.0 4.30e-01 94.9% 78.8%
1hciA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 44.0 3.79e-01 83.5% 72.2%
3bjdA01 1.10.1240.20 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Lytic transglycosylase, superhelical linker domain 0.57 48.0 4.66e-01 94.9% 83.0%
1zvuA03 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.57 44.0 3.64e-01 97.5% 47.1%
2xq9A02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.56 45.0 4.04e-01 93.7% 80.2%
1zx3A01 1.10.287.1020 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › NE0241-like 0.56 35.0 3.42e-01 98.7% 57.6%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.55 43.0 4.37e-01 88.6% 92.4%
1tvlA00 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.55 47.0 3.04e-01 97.5% 37.7%
7zxkC01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.54 42.0 3.39e-01 82.3% 90.0%
5nl6B01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 44.0 3.95e-01 94.9% 86.8%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.54 43.0 3.91e-01 87.3% 70.4%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.53 44.0 4.37e-01 96.2% 84.7%
2odvA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 42.0 3.87e-01 91.1% 89.3%
1cunA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 41.0 3.90e-01 89.9% 93.1%
3k2jA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.53 37.0 3.31e-01 75.9% 66.1%
3oxfA05 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 38.0 3.96e-01 86.1% 84.0%
3fm9A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 38.0 3.85e-01 93.7% 78.2%
4nqfA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.52 44.0 3.57e-01 91.1% 79.3%
2gfhA02 1.20.120.710 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain 0.52 40.0 3.94e-01 88.6% 75.6%
8h72B01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.51 44.0 3.04e-01 100.0% 36.3%
1zc6A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 38.0 3.13e-01 82.3% 76.3%
4ri6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 42.0 3.69e-01 91.1% 65.5%
3cxbA03 1.10.1740.30 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Secreted effector protein SifA helical domain 0.50 46.0 4.55e-01 96.2% 93.8%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3626901 109.4.1.31 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MA3 0.68 47.0 3.35e-01 91.1% 25.3%
3216384 197.1.1.0 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like 0.67 61.0 5.20e-01 100.0% 65.6%
5001458 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.65 54.0 4.12e-01 92.4% 68.9%
5046564 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.65 56.0 4.28e-01 100.0% 86.2%
3936678 164.1.1.0 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II 0.61 50.0 5.01e-01 89.9% 92.5%
5026844 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.61 51.0 4.41e-01 94.9% 90.8%
5006033 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.61 53.0 3.98e-01 98.7% 83.0%
3192586 145.1.1.3 ↗ alpha arrays › F-box domain › F-box domain › F-box domain › F-box-like 0.60 42.0 3.59e-01 94.9% 43.6%
3990885 164.1.1.0 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II 0.60 48.0 4.65e-01 88.6% 84.4%
3954871 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.60 52.0 3.94e-01 100.0% 75.1%
3495156 109.58.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › DNA repair protein Rev1 C-terminal domain › DNA repair protein Rev1 C-terminal domain › REV1_C 0.60 47.0 4.66e-01 92.4% 82.4%
5017736 3625.1.1.0 ↗ alpha bundles › CRISPR RNA silencing complex Cmr2 subunit second helical domain › CRISPR RNA silencing complex Cmr2 subunit second helical domain › CRISPR RNA silencing complex Cmr2 subunit second helical domain 0.60 46.0 4.24e-01 83.5% 62.9%
5043597 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.60 49.0 3.70e-01 92.4% 61.5%
4047530 3754.1.1.1 ↗ alpha bundles › Bacterial cell wall synthesis membrane enzyme MraY-related › Bacterial cell wall synthesis membrane enzyme MraY-related › Bacterial cell wall synthesis membrane enzyme MraY-related › Glycos_transf_4 0.59 49.0 3.17e-01 89.9% 71.0%
4991909 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.59 51.0 4.00e-01 97.5% 82.9%
5035803 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.59 52.0 3.97e-01 98.7% 82.6%
1088836 101.38.1.0 ↗ alpha arrays › HTH › DNA-binding domain of the replication initiator protein ColE2-Rep › DNA-binding domain of the replication initiator protein ColE2-Rep 0.59 49.0 4.34e-01 94.9% 61.5%
4995712 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.58 43.0 4.03e-01 75.9% 75.8%
5039732 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.58 44.0 4.01e-01 83.5% 89.4%
3475109 140.1.1.5 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon_1 0.58 47.0 3.62e-01 91.1% 49.7%
5037709 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.58 47.0 4.21e-01 93.7% 92.5%
4396053 140.1.1.11 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DALR_1 0.58 44.0 3.57e-01 81.0% 47.1%
3253767 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.58 49.0 3.91e-01 92.4% 83.9%
5045083 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.58 48.0 3.69e-01 93.7% 67.4%
4108720 140.1.1.11 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DALR_1 0.57 45.0 3.40e-01 86.1% 38.0%
3984588 4044.1.1.1 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Prismane 0.56 41.0 3.36e-01 74.7% 45.2%
4155154 140.1.1.11 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DALR_1 0.56 43.0 3.61e-01 83.5% 52.9%
5077016 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.56 47.0 3.67e-01 100.0% 90.5%
4980491 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 44.0 3.12e-01 87.3% 52.7%
4286656 140.1.1.11 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DALR_1 0.56 42.0 3.83e-01 82.3% 67.3%
4093318 166.1.1.1 ↗ alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.55 46.0 4.31e-01 89.9% 73.7%
3403059 540.1.1.1 ↗ few secondary structure elements › Cytochrome c oxidase subunit h › Cytochrome c oxidase subunit h › Cytochrome c oxidase subunit h › COX6B 0.55 42.0 4.17e-01 91.1% 78.8%
3579534 192.29.1.144 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › SK_channel 0.55 45.0 3.48e-01 91.1% 67.6%
4927779 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.54 37.0 2.69e-01 70.9% 83.7%
3638435 1073.1.1.14 ↗ alpha arrays › Mitochondrial calcium uniporter (MCU) › Mitochondrial calcium uniporter (MCU) › Mitochondrial calcium uniporter (MCU) › LMBR1 0.53 40.0 3.56e-01 81.0% 99.1%
4042010 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.52 36.0 3.76e-01 73.4% 76.0%
4108657 140.1.1.11 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DALR_1 0.52 38.0 3.54e-01 82.3% 64.5%
4954909 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.52 37.0 3.67e-01 77.2% 70.6%
3799135 633.15.1.0 ↗ alpha bundles › Bromodomain-like › alpha-ketoacid dehydrogenase kinase-N › alpha-ketoacid dehydrogenase kinase-N 0.50 37.0 3.11e-01 81.0% 63.3%