←Back to structures

NC_070869.1__YP_010659509.1__PP763_gp02__00002

Bact-Vir

NC_070869.1__YP_010659509.1__PP763_gp02__00002

Identity

Accession:
NC_070869 ↗
Kingdom:
phage

Quality

90.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Gamaleyavirus› Escherichia_phage_vB_EcoP_SP5M

TaxID: 2750853

Cluster

Singleton — not in a non-trivial cluster

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 1-112
PDB
Domain cluster: representative
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.81 41.0 5.74e-01 97.3% 95.0%
1s5jA04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.78 38.0 4.99e-01 98.2% 85.2%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.78 37.0 4.99e-01 95.5% 86.4%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 38.0 4.48e-01 100.0% 66.7%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.75 38.0 4.32e-01 100.0% 64.7%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 40.0 4.93e-01 79.5% 83.1%
1ykhA00 6.10.140.200 Special › Helix non-globular › Helix Hairpins › 0.73 36.0 3.95e-01 80.4% 55.8%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 40.0 5.39e-01 97.3% 96.9%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.73 37.0 4.75e-01 98.2% 85.9%
2gsqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.72 36.0 3.68e-01 93.8% 49.1%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 36.0 4.35e-01 100.0% 74.0%
2pusA04 6.10.140.300 Special › Helix non-globular › Helix Hairpins › 0.70 35.0 3.56e-01 95.5% 48.1%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.69 37.0 4.41e-01 75.0% 76.6%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 33.0 4.29e-01 97.3% 83.6%
3v5uA01 6.10.280.80 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › NCX, peripheral helical region 0.68 36.0 4.30e-01 80.4% 76.3%
4q20A01 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.68 37.0 4.30e-01 92.9% 73.2%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 36.0 4.33e-01 95.5% 78.1%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 33.0 4.24e-01 98.2% 86.0%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.67 35.0 4.21e-01 78.6% 76.7%
1vcsA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.65 39.0 4.10e-01 100.0% 64.7%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.65 36.0 4.65e-01 75.9% 96.9%
2c5iT00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 40.0 4.31e-01 100.0% 73.4%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 42.0 4.33e-01 100.0% 75.0%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.61 36.0 4.44e-01 91.1% 100.0%
1u5pA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 40.0 4.08e-01 100.0% 70.4%
3l1nA02 1.20.1280.140 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.60 35.0 3.90e-01 100.0% 73.6%
3fb2A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 39.0 4.06e-01 100.0% 72.4%
2mpnA00 6.10.140.1340 Special › Helix non-globular › Helix Hairpins › 0.57 31.0 3.78e-01 78.6% 83.8%
1s35A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 38.0 4.00e-01 100.0% 76.2%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 40.0 4.15e-01 100.0% 78.5%
6qumQ00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.56 31.0 3.66e-01 78.6% 81.1%
6p73A02 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.55 39.0 3.56e-01 77.7% 56.6%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.55 42.0 4.21e-01 96.4% 79.5%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.55 35.0 3.60e-01 92.9% 64.5%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.53 36.0 4.10e-01 75.9% 91.8%
3tulB00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.53 43.0 4.03e-01 94.6% 70.7%
4mt4A00 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.51 47.0 3.03e-01 98.2% 87.5%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4530714 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.80 36.0 5.36e-01 100.0% 98.0%
4248629 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.79 34.0 5.05e-01 97.3% 100.0%
3385950 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.79 42.0 5.38e-01 78.6% 85.7%
5030543 159.1.3.0 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › putative NTP pyrophosphohydrolase Exig_1061 0.76 40.0 4.28e-01 82.1% 58.0%
3644495 7022.1.1.0 ↗ alpha bundles › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein 0.76 38.0 3.63e-01 81.2% 42.4%
4973477 159.1.1.1 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › MazG 0.76 37.0 4.08e-01 100.0% 57.8%
3803573 7022.1.1.0 ↗ alpha bundles › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein 0.76 38.0 3.02e-01 100.0% 25.1%
4650330 603.5.1.0 ↗ alpha bundles › STAT-like › FlgN-like › FlgN-like 0.75 37.0 3.68e-01 75.9% 46.1%
3588068 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.73 40.0 4.45e-01 75.0% 66.7%
3932372 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.73 42.0 3.90e-01 100.0% 45.7%
4286197 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.71 39.0 4.55e-01 77.7% 75.0%
3712097 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.71 35.0 3.85e-01 98.2% 57.8%
5039854 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.70 39.0 4.67e-01 75.0% 81.3%
3631853 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.69 39.0 3.37e-01 89.3% 36.1%
4475138 606.1.1.16 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Transposase_20 0.69 37.0 3.07e-01 92.0% 29.0%
3387443 603.5.1.1 ↗ alpha bundles › STAT-like › FlgN-like › FlgN-like › FlgN 0.68 33.0 3.35e-01 74.1% 44.3%
3884123 601.4.1.75 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › PF27561 0.68 37.0 3.12e-01 76.8% 32.2%
3786136 603.1.1.3 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › V-SNARE 0.66 40.0 4.01e-01 100.0% 58.3%
3962634 150.5.1.11 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › T7SS_ESX_EspC 0.64 35.0 3.98e-01 97.3% 69.4%
3243586 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.63 35.0 4.10e-01 94.6% 76.2%
2035519 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.63 41.0 4.04e-01 100.0% 62.2%
3929776 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 44.0 2.79e-01 73.2% 18.9%
2035594 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.62 39.0 4.20e-01 100.0% 75.3%
3580368 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.62 41.0 3.81e-01 100.0% 52.4%
3392164 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.61 33.0 3.83e-01 100.0% 72.5%
4039014 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.59 45.0 4.56e-01 95.5% 79.1%
3497911 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.59 41.0 3.87e-01 100.0% 58.5%
2893266 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.59 36.0 3.92e-01 91.1% 72.8%
4266268 192.8.1.376 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › RRP36 0.59 37.0 3.40e-01 70.5% 46.7%
4024396 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.59 44.0 4.13e-01 100.0% 64.4%
4457403 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.58 43.0 3.12e-01 75.0% 79.3%
3930836 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.57 42.0 4.12e-01 100.0% 70.8%
3707409 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.56 44.0 4.38e-01 100.0% 80.0%
5027990 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.56 31.0 3.54e-01 78.6% 74.4%
3592036 3291.1.1.16 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Flagellar_rod 0.56 39.0 3.21e-01 100.0% 38.6%
3516129 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 40.0 4.18e-01 100.0% 81.0%
3741747 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.55 39.0 2.92e-01 73.2% 29.8%
3731974 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.55 38.0 3.91e-01 92.0% 72.7%
4337633 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.54 41.0 2.94e-01 78.6% 97.3%
3187479 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.54 35.0 3.90e-01 73.2% 83.3%
None — 0.54 39.0 2.46e-01 75.0% 23.9%
3949413 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.54 38.0 3.57e-01 73.2% 78.5%
4569106 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.52 37.0 2.43e-01 74.1% 60.8%
4675002 3755.1.1.0 ↗ alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.51 38.0 3.66e-01 78.6% 81.5%
3195070 109.4.1.128 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G_like_2 0.51 46.0 3.32e-01 100.0% 38.5%
3739245 4177.1.1.14 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_2 0.50 39.0 3.13e-01 82.1% 60.9%