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MN234216.1__QFG13232.1__SEA_GILGAMESH_40__00040

Bact-Vir

MN234216.1__QFG13232.1__SEA_GILGAMESH_40__00040

Identity

Accession:
MN234216 ↗
Kingdom:
phage

Quality

89.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Gilgameshvirus› Streptomyces_phage_Gilgamesh

TaxID: 2599890

Cluster

View cluster (4 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 24-138
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4qclA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.76 70.0 5.24e-01 100.0% 89.7%
4fvmA03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.75 69.0 5.38e-01 99.1% 68.8%
2xriA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.65 59.0 4.86e-01 99.1% 93.7%
2py5A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 52.0 4.44e-01 100.0% 63.6%
1yvuA04 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 51.0 4.14e-01 99.1% 71.5%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.56 36.0 3.96e-01 89.6% 79.8%
4ep4A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 50.0 4.45e-01 98.3% 100.0%
4ibnA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 50.0 4.27e-01 100.0% 69.7%
4okeA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 49.0 4.40e-01 96.5% 73.8%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.56 36.0 4.00e-01 82.6% 82.6%
4c0hA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 48.0 3.81e-01 98.3% 64.3%
3qcpA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 37.0 3.30e-01 71.3% 77.2%
3p5jA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.52 46.0 3.96e-01 100.0% 72.6%
1c3kA00 2.100.10.30 Mainly Beta › Aligned Prism › Vitelline Membrane Outer Layer Protein I, subunit A › Jacalin-like lectin domain 0.52 32.0 3.04e-01 99.1% 49.7%
1uuzB00 3.40.1420.10 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › Inhibitor of vertebrate lysozyme 0.52 35.0 3.37e-01 93.9% 60.9%
4v0hD00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.51 45.0 3.68e-01 99.1% 92.8%
3ejvA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 34.0 3.08e-01 85.2% 49.1%
4ohxA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 45.0 3.64e-01 100.0% 72.8%
4c23B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.50 44.0 3.57e-01 100.0% 97.4%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3193111 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.77 71.0 4.85e-01 100.0% 83.9%
3492151 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.75 70.0 4.93e-01 100.0% 84.8%
4874454 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.75 69.0 5.19e-01 100.0% 90.6%
1790898 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.74 69.0 5.12e-01 100.0% 88.6%
3256261 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.74 67.0 5.12e-01 98.3% 91.0%
5035328 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.68 63.0 4.88e-01 99.1% 89.4%
3491266 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.67 60.0 4.87e-01 98.3% 97.7%
3497103 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.67 60.0 4.70e-01 98.3% 84.9%
3206356 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.67 61.0 4.18e-01 100.0% 41.0%
5062283 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.66 60.0 4.94e-01 99.1% 58.8%
3684974 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.66 60.0 3.71e-01 100.0% 23.5%
3988431 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.65 57.0 4.85e-01 98.3% 60.0%
2714249 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 57.0 4.73e-01 98.3% 91.4%
3936953 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.62 58.0 4.18e-01 100.0% 72.6%
4976732 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.60 53.0 3.84e-01 100.0% 73.9%
4028087 2484.1.1.20 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_A_exo1 0.58 53.0 4.26e-01 99.1% 86.5%
4243242 11.1.5.7 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › Adap_comp_sub 0.57 42.0 3.78e-01 76.5% 90.3%
3168063 11.1.5.7 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › Adap_comp_sub 0.56 41.0 3.64e-01 76.5% 83.5%
5083090 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 50.0 3.64e-01 99.1% 71.6%
4927205 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.55 50.0 3.72e-01 100.0% 66.9%
4985492 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.54 48.0 3.69e-01 99.1% 66.3%
3191460 11.1.5.37 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › muHD 0.54 38.0 3.68e-01 73.0% 95.4%
3651744 2484.1.1.15 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › GDA1_CD39 0.54 40.0 4.01e-01 76.5% 77.4%
2771373 2484.1.1.4 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.53 47.0 4.09e-01 98.3% 70.2%
5037955 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 46.0 3.39e-01 100.0% 66.2%
3219500 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.52 47.0 3.42e-01 100.0% 44.4%
3642967 246.3.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like 0.52 36.0 2.68e-01 100.0% 27.1%
3459933 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.52 45.0 4.07e-01 99.1% 68.5%
4014581 4081.1.1.0 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related 0.52 45.0 3.80e-01 98.3% 89.3%
4947601 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.52 45.0 3.41e-01 100.0% 67.5%
3930773 633.23.1.17 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › DuoxA 0.51 38.0 2.99e-01 79.1% 94.4%
4933484 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.51 45.0 3.47e-01 99.1% 72.0%
2792216 922.1.1.1 ↗ few secondary structure elements › TSP-1 type 1 repeat › TSP-1 type 1 repeat › TSP-1 type 1 repeat › TSP_1 0.51 25.0 3.36e-01 83.5% 93.1%
3928228 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.51 46.0 3.60e-01 99.1% 70.8%
4660860 2484.1.1.222 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UPF0236 0.51 45.0 3.45e-01 100.0% 61.8%
4052992 2484.1.1.222 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UPF0236 0.50 45.0 3.84e-01 100.0% 65.8%
3939873 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.50 45.0 3.39e-01 100.0% 51.0%
5001074 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.50 43.0 3.14e-01 99.1% 64.3%
5001466 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.50 43.0 3.19e-01 98.3% 59.1%
3962204 2003.4.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Tryptophan synthase beta subunit-like PLP-dependent enzymes › Tryptophan synthase beta subunit-like PLP-dependent enzymes 0.50 40.0 3.40e-01 86.1% 90.5%
D2 medium residues 139-249
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2wdqC00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.67 47.0 4.57e-01 72.1% 84.3%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.57 38.0 3.84e-01 89.2% 67.3%
2l7nA00 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.53 45.0 3.91e-01 91.9% 89.9%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4938272 601.7.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.59 44.0 4.29e-01 79.3% 100.0%
4012158 3543.1.1.0 ↗ alpha complex topology › Acid-activated urea channel › Acid-activated urea channel › Acid-activated urea channel 0.58 46.0 3.81e-01 85.6% 95.6%
3588587 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.54 41.0 4.06e-01 79.3% 89.6%