←Back to structures

NC_042082.1__YP_009619897.1__FDJ07_gp002__00002

Bact-Vir

NC_042082.1__YP_009619897.1__FDJ07_gp002__00002

Identity

Accession:
NC_042082 ↗
Kingdom:
phage

Quality

80.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Delepquintavirus› Stenotrophomonas_phage_vB_SmaS_DLP_5

TaxID: 2044561

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 high residues 310-429
PDB
Domain cluster: rep: LacPavin_0818_WC40_scaffold_575784_prodigal-single.1__X__X__00015__D313-479
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vz0A01 3.90.1530.30 Alpha Beta › Alpha-Beta Complex › Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain › 0.69 36.0 4.91e-01 87.5% 98.4%
1wdcC01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.55 33.0 4.03e-01 93.3% 93.6%
3uo9C01 1.10.238.210 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › 0.54 31.0 3.76e-01 92.5% 88.3%
3c8zA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.50 44.0 3.28e-01 97.5% 55.4%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3283211 876.1.1.0 ↗ a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin 0.70 48.0 4.62e-01 71.7% 90.0%
1409395 876.1.1.3 ↗ a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin › PFIN 0.64 51.0 4.34e-01 83.3% 83.5%
4930273 876.1.1.0 ↗ a+b complex topology › ParB/Sulfiredoxin › ParB/Sulfiredoxin › ParB/Sulfiredoxin 0.62 47.0 4.22e-01 80.0% 96.4%
3573862 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 33.0 2.71e-01 90.8% 36.7%
D2 medium residues 1-186
PDB
Domain cluster: representative
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4f4cA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.69 62.0 4.10e-01 94.6% 91.1%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.64 27.0 3.32e-01 93.0% 59.3%
1jadA00 1.20.1230.10 Mainly Alpha › Up-down Bundle › Phospholipase C Beta; Chain: A › Phospholipase C beta, distal C-terminal domain 0.63 44.0 4.03e-01 71.0% 91.7%
3ljbA00 1.20.120.1240 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Dynamin, middle domain 0.63 58.0 5.50e-01 99.5% 85.8%
4bejB02 1.20.120.1240 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Dynamin, middle domain 0.61 56.0 5.30e-01 99.5% 84.8%
3q1xA01 1.10.3130.10 Mainly Alpha › Orthogonal Bundle › serine acetyltransferase, domain 1 › serine acetyltransferase, domain 1 0.60 37.0 4.27e-01 86.6% 83.5%
2qupA00 1.20.120.490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hypothetical protein TM1646-like domain 0.59 35.0 4.25e-01 93.5% 89.9%
7nmqA01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.59 44.0 3.52e-01 75.8% 95.7%
4ap2B01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.59 29.0 3.34e-01 84.4% 62.7%
5azpB01 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.58 44.0 3.53e-01 78.5% 58.8%
1wp1B01 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.58 43.0 3.40e-01 75.8% 67.3%
3s84A02 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.57 44.0 4.78e-01 80.6% 97.5%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.57 35.0 4.25e-01 78.0% 93.3%
2e87A01 1.20.120.1190 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.57 41.0 4.37e-01 86.6% 84.4%
5tgzA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.57 38.0 3.27e-01 87.6% 42.5%
3jz0A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.56 33.0 3.82e-01 94.1% 80.0%
1h6gA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.56 36.0 4.24e-01 78.0% 95.2%
7zd5C01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.55 44.0 3.71e-01 85.5% 99.7%
1y4cA03 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.54 32.0 3.95e-01 76.3% 94.7%
2d1lA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.54 45.0 4.07e-01 88.2% 82.7%
8h8jC01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.54 38.0 3.35e-01 88.7% 48.7%
4yvoA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 24.0 3.04e-01 98.4% 67.2%
5tj5E00 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.53 36.0 4.14e-01 83.9% 94.2%
3ihuA02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.53 38.0 4.33e-01 95.2% 99.3%
2v0oB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.53 41.0 3.65e-01 82.3% 82.3%
4iggB06 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.52 38.0 3.69e-01 83.3% 66.0%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.51 29.0 3.81e-01 93.0% 99.0%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4018386 601.19.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.69 64.0 4.19e-01 100.0% 33.2%
5073391 604.39.1.6 ↗ alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters › QueT 0.66 39.0 4.08e-01 91.9% 62.3%
4519670 5045.1.1.3 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › V_ATPase_I 0.61 54.0 4.77e-01 95.2% 94.3%
4537363 1075.4.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › ABC_membrane 0.61 56.0 3.81e-01 100.0% 86.2%
3193408 1075.4.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › ABC_membrane 0.60 55.0 3.72e-01 100.0% 89.2%
4002962 1075.4.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › ABC_membrane 0.59 55.0 3.53e-01 100.0% 77.6%
4632513 5045.1.1.1 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.59 50.0 4.58e-01 93.0% 68.6%
4581508 601.19.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Apolipoprotein 0.59 52.0 5.00e-01 98.9% 82.9%
4656035 5001.1.1.9 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › TAS2R 0.59 45.0 3.83e-01 87.1% 48.7%
4561197 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.56 44.0 4.25e-01 80.6% 76.6%
5065166 1075.5.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter 0.56 41.0 3.94e-01 90.9% 65.7%
4141759 5045.1.1.1 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.56 49.0 4.61e-01 95.7% 77.0%
3459613 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.56 39.0 4.15e-01 77.4% 80.0%
4112439 5045.1.1.1 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.55 47.0 4.39e-01 90.9% 74.2%
3239412 109.4.1.285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PSMD12-CSN4_N 0.55 26.0 3.00e-01 77.4% 60.0%
4077080 5045.1.1.1 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.54 48.0 4.36e-01 96.8% 71.0%
5020679 1075.5.1.8 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Polysacc_synt_3 0.54 39.0 3.82e-01 94.6% 67.5%
3258598 1075.4.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › ABC_membrane 0.54 46.0 3.79e-01 90.3% 95.2%
3609119 5050.1.1.15 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Nodulin-like 0.54 45.0 3.26e-01 90.3% 72.7%
3259226 3758.1.1.0 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins 0.54 43.0 4.19e-01 81.7% 98.0%
3700752 1075.5.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE 0.54 41.0 3.87e-01 93.5% 63.9%
3735343 1075.5.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE 0.54 42.0 3.92e-01 94.1% 65.1%
3742987 5045.1.1.1 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.53 44.0 4.00e-01 88.2% 69.6%
5065783 1075.5.1.4 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Polysacc_synt 0.53 40.0 3.54e-01 91.4% 54.1%
3589119 1075.5.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter 0.53 39.0 3.61e-01 91.9% 58.4%
4974383 1075.5.1.4 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Polysacc_synt 0.53 39.0 3.80e-01 94.1% 68.3%
3600161 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 0.53 45.0 3.30e-01 94.1% 95.0%
4297941 1075.5.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE 0.53 42.0 3.83e-01 93.5% 63.7%
3786208 1075.5.1.5 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Rft-1 0.53 40.0 3.78e-01 100.0% 64.3%
4978924 1075.5.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter 0.52 41.0 3.54e-01 91.4% 53.6%
5039268 1075.5.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter 0.52 40.0 3.58e-01 94.1% 56.5%
5028176 1075.5.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE 0.52 39.0 3.46e-01 93.5% 53.5%
3800161 4177.1.1.10 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › GMIP-like_FCH 0.52 40.0 3.68e-01 81.7% 80.8%
5028169 1075.5.1.2 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MurJ 0.52 39.0 3.57e-01 94.1% 58.8%
4990027 1075.5.1.8 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Polysacc_synt_3 0.51 39.0 3.52e-01 91.4% 57.6%
3691337 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.51 38.0 3.64e-01 76.3% 85.6%
3239812 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.51 39.0 3.65e-01 79.0% 92.9%
4996790 1075.5.1.8 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Polysacc_synt_3 0.51 38.0 3.38e-01 94.1% 54.3%
4950955 1075.5.1.2 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MurJ 0.50 38.0 3.45e-01 93.5% 56.2%
5048320 1075.5.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE 0.50 39.0 3.66e-01 93.5% 64.8%
3958112 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.50 38.0 3.49e-01 87.1% 58.8%
3971653 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 0.50 32.0 3.22e-01 93.5% 60.5%
D3 medium residues 187-298
PDB
Domain cluster: rep: OK381870.1__UHD87241.1__X__00034__D191-280