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NC_025470.1__YP_009104056.1__S140_55__00055

Bact-Vir

NC_025470.1__YP_009104056.1__S140_55__00055

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

92.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shewanella_sp._phage_1/40

TaxID: 1458860

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 high residues 3-71
PDB
Domain cluster: rep: AB366653.2__BAG41732.1__X__00285__D136-196
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3sjqC00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.85 50.0 4.77e-01 100.0% 51.2%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.80 52.0 5.08e-01 100.0% 61.3%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.77 50.0 4.16e-01 100.0% 39.0%
4rg8A04 1.10.287.1240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 50.0 5.22e-01 100.0% 80.6%
2kz5A00 1.10.880.10 Mainly Alpha › Orthogonal Bundle › Transcription Factor Skn-1; Chain P › Transcription factor, Skn-1-like, DNA-binding domain 0.60 36.0 3.34e-01 88.4% 46.2%
2f1kC02 1.10.3660.10 Mainly Alpha › Orthogonal Bundle › 6-phosphogluconate dehydrogenase C-terminal fold › 6-phosphogluconate dehydrogenase C-terminal like domain 0.59 46.0 3.96e-01 100.0% 53.1%
3wmeA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.58 41.0 2.66e-01 100.0% 16.3%
8ctsB01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 51.0 4.77e-01 100.0% 82.8%
2hmcA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.57 48.0 3.18e-01 100.0% 21.3%
2yksA02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.55 39.0 3.38e-01 100.0% 45.3%
1f46B00 3.30.1400.10 Alpha Beta › 2-Layer Sandwich › Cell Division Protein Zipa; Chain: A, › ZipA, C-terminal FtsZ-binding domain 0.55 48.0 3.81e-01 97.1% 99.3%
3he0B00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.55 41.0 3.05e-01 79.7% 56.2%
2qksA01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 44.0 3.99e-01 100.0% 81.1%
2ewtA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.53 36.0 3.60e-01 97.1% 67.6%
1jvmB00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 47.0 4.18e-01 100.0% 82.0%
3s6jE02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.53 44.0 4.44e-01 95.7% 94.2%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.53 47.0 4.50e-01 98.6% 87.7%
3a1sA02 1.10.287.1770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 45.0 4.17e-01 95.7% 85.2%
4h33A00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 47.0 4.29e-01 100.0% 75.8%
4modA00 1.20.5.300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.51 45.0 4.40e-01 100.0% 89.5%
3okqA00 1.20.58.1540 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain 0.51 46.0 3.78e-01 100.0% 55.2%
2oceA01 1.10.10.650 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › RuvA domain 2-like 0.51 42.0 3.58e-01 89.9% 62.8%
8bauA01 1.10.357.40 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › YbiA-like 0.51 42.0 3.23e-01 97.1% 41.4%
1bl0A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.51 32.0 3.47e-01 76.8% 78.6%
3ktdD02 1.10.3660.10 Mainly Alpha › Orthogonal Bundle › 6-phosphogluconate dehydrogenase C-terminal fold › 6-phosphogluconate dehydrogenase C-terminal like domain 0.51 42.0 3.70e-01 98.6% 60.6%
3spcA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 43.0 3.63e-01 100.0% 71.7%
4xr7E01 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.50 42.0 2.85e-01 98.6% 94.5%
3fi7A01 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.50 42.0 3.54e-01 98.6% 99.2%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5046515 5069.1.1.44 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › CopD 0.84 53.0 3.94e-01 100.0% 28.5%
3221760 604.1.1.140 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF27005 0.76 51.0 4.73e-01 100.0% 56.5%
4311347 604.24.1.0 ↗ alpha bundles › Spectrin repeat-like › Helical bundle domain in putative transcriptional regulator Jann_0659-related proteins › Helical bundle domain in putative transcriptional regulator Jann_0659-related proteins 0.70 49.0 4.64e-01 100.0% 62.5%
3278924 604.2.1.1 ↗ alpha bundles › Spectrin repeat-like › Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain › Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain › Succ_DH_flav_C 0.69 41.0 3.21e-01 100.0% 27.6%
3999994 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.69 42.0 4.08e-01 92.8% 56.0%
3592587 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.67 48.0 3.95e-01 100.0% 42.4%
4959289 606.1.1.0 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.64 59.0 5.25e-01 100.0% 75.8%
1765248 604.2.1.0 ↗ alpha bundles › Spectrin repeat-like › Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain › Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain 0.64 38.0 3.08e-01 100.0% 28.8%
3935680 101.1.17.0 ↗ alpha arrays › HTH › HTH › FF domain 0.61 40.0 4.19e-01 98.6% 72.3%
3412402 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 37.0 3.25e-01 98.6% 36.5%
4937851 1075.1.1.7 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane_6 0.61 42.0 2.80e-01 72.5% 40.0%
3850575 633.10.1.20 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like › Piezo_TM1-24 0.60 52.0 4.08e-01 100.0% 74.2%
3290432 5086.1.1.184 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › DUF4407 0.59 51.0 4.50e-01 100.0% 65.0%
3522 129.1.1.18 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › PDH_C 0.59 47.0 3.97e-01 100.0% 52.6%
53265 129.1.1.0 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like 0.59 46.0 3.97e-01 100.0% 52.6%
3396168 633.2.1.4 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein › Piezo_TM1-24 0.58 50.0 4.03e-01 100.0% 80.0%
2756561 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.57 39.0 3.26e-01 97.1% 41.0%
5053233 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.57 48.0 4.52e-01 95.7% 98.8%
1790171 1050.1.1.1 ↗ alpha arrays › BID domain of Bartonella effector protein (Bep) › BID domain of Bartonella effector protein (Bep) › BID domain of Bartonella effector protein (Bep) › Bep_C_terminal 0.57 50.0 4.34e-01 100.0% 82.2%
3994340 605.1.1.229 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Piezo_TM1-24 0.57 52.0 4.55e-01 100.0% 69.0%
3713201 4323.1.1.1 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.56 52.0 4.01e-01 100.0% 49.7%
4062549 3755.3.1.288 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › LMBR1 0.56 49.0 3.98e-01 100.0% 54.1%
3506336 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.55 43.0 3.64e-01 100.0% 50.4%
3283397 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.55 50.0 4.48e-01 100.0% 87.4%
3601995 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 35.0 3.16e-01 95.7% 48.4%
3266150 620.1.1.0 ↗ alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases 0.53 45.0 3.69e-01 100.0% 78.6%
3394746 210.1.2.4 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › AAT 0.52 43.0 2.78e-01 94.2% 84.8%
2774099 2006.1.1.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase 0.51 40.0 2.85e-01 89.9% 27.4%
3925702 102.1.2.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase 0.50 43.0 4.13e-01 100.0% 95.0%