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NC_025470.1__YP_009104169.1__S140_171__00168

Bact-Vir

NC_025470.1__YP_009104169.1__S140_171__00168

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

66.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shewanella_sp._phage_1/40

TaxID: 1458860

Cluster

View cluster (3 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 high residues 8-50
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 63.0 4.35e-01 100.0% 67.8%
7qovB01 1.10.472.20 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Nitrile hydratase, beta subunit 0.64 45.0 3.38e-01 76.7% 29.6%
3tw8A03 6.10.140.1000 Special › Helix non-globular › Helix Hairpins › 0.59 43.0 4.38e-01 81.4% 100.0%
2l09A01 1.10.8.550 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Proto-chlorophyllide reductase 57 kD subunit B 0.59 43.0 4.14e-01 83.7% 67.3%
2wm3A02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.55 37.0 2.85e-01 72.1% 91.2%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3684484 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.80 70.0 4.55e-01 100.0% 32.8%
3927560 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.75 61.0 5.43e-01 100.0% 65.0%
4172979 101.11.1.1 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.73 61.0 4.79e-01 100.0% 64.0%
3577476 109.4.1.514 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Vps54 0.72 64.0 4.29e-01 100.0% 39.4%
3503307 1203.1.2.1 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › ASD2 0.72 62.0 4.17e-01 100.0% 26.2%
3451236 397.4.1.3 ↗ few secondary structure elements › Toxic hairpin › VhTI-like › VhTI-like › PF31266 0.71 54.0 5.37e-01 86.0% 82.2%
4977442 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.70 61.0 4.00e-01 100.0% 55.1%
4337212 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.70 61.0 3.93e-01 100.0% 49.3%
3704161 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.69 53.0 3.37e-01 90.7% 16.9%
4853145 1042.1.1.1 ↗ a+b complex topology › S2 subunit of coronavirus spike glycoprotein › S2 subunit of coronavirus spike glycoprotein › S2 subunit of coronavirus spike glycoprotein › CoV_S2 0.66 55.0 3.66e-01 100.0% 25.0%
4585912 101.1.2.603 ↗ alpha arrays › HTH › HTH › winged helix domain › RNA_pol_Rpc82, HTH_9 0.62 49.0 2.98e-01 100.0% 12.0%
D2 medium residues 58-155
PDB
Domain cluster: rep: NC_004827.1__NP_852777.1__Aaphi23p49__00063__D109-193
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ibjA02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.62 45.0 3.77e-01 76.5% 88.6%
3mogA03 3.30.750.190 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.55 38.0 3.86e-01 70.4% 85.1%
1yqgA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 36.0 3.17e-01 71.4% 64.4%
3ws7A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 45.0 3.75e-01 98.0% 98.3%
5bseA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 38.0 3.20e-01 78.6% 96.0%
3tt2A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 41.0 2.90e-01 87.8% 37.1%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5003241 102.7.1.1 ↗ alpha arrays › HhH/H2TH › Baseplate wedge protein gp7 domain IV › Baseplate wedge protein gp7 domain IV › Tail_P2_I 0.75 70.0 6.59e-01 100.0% 98.3%
3942252 3261.1.1.8 ↗ a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › DUF2612 0.72 64.0 6.17e-01 98.0% 96.4%
3500879 327.11.1.9 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › Phage_Wedge1 0.69 49.0 5.20e-01 74.5% 92.9%
4979404 327.11.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › KH_2 0.60 54.0 4.77e-01 98.0% 90.0%
3691474 327.5.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins 0.60 46.0 3.11e-01 80.6% 61.7%
1718744 219.1.1.62 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › SidE_DUB 0.60 43.0 3.46e-01 75.5% 40.6%
3620592 6155.1.1.15 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › DUF846 0.52 36.0 3.27e-01 72.4% 97.9%
3295277 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.52 46.0 2.97e-01 100.0% 64.2%
D3 medium residues 159-239
PDB