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MK016663.1__QBP05851.1__X__00001

Bact-Vir

MK016663.1__QBP05851.1__X__00001

Identity

Accession:
MK016663 ↗
Kingdom:
phage

Quality

81.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Synechococcus_phage_S-H68

TaxID: 2545436

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 3-61
PDB
Domain cluster: rep: NC_020859.1__YP_007675634.1__SWTG_00144__00168__D4-51
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ej9A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.65 47.0 3.34e-01 78.0% 32.4%
1q57G01 2.20.25.180 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.61 43.0 4.08e-01 74.6% 86.3%
3t4nA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.59 43.0 3.77e-01 79.7% 66.7%
5n70A02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.59 46.0 3.44e-01 86.4% 62.7%
1uh9A02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.57 45.0 3.38e-01 86.4% 66.4%
8ajqA01 3.90.1590.10 Alpha Beta › Alpha-Beta Complex › glutathione-dependent formaldehyde- activating enzyme (gfa) › glutathione-dependent formaldehyde- activating enzyme (gfa) 0.56 37.0 3.09e-01 78.0% 34.8%
1v8cA02 3.30.1370.80 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Molybdopterin cofactor biosynthesis MoaD-related, C-terminal domain 0.56 42.0 3.88e-01 83.1% 68.8%
2jmbA00 2.40.128.290 Mainly Beta › Beta Barrel › Lipocalin › Uncharacterised protein family Atu4866 0.55 40.0 3.71e-01 79.7% 83.5%
5bv3D01 3.30.200.40 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Scavenger mRNA decapping enzyme, N-terminal domain 0.53 36.0 3.05e-01 72.9% 91.1%
3sk2A00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 36.0 2.83e-01 72.9% 75.8%
4hr6C01 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.52 40.0 3.15e-01 86.4% 69.9%
3duzA03 6.10.250.3010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.51 38.0 3.57e-01 98.3% 64.9%
3s93A00 3.30.420.610 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › LOTUS domain-like 0.50 35.0 3.22e-01 74.6% 67.5%
6kguA01 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.50 32.0 2.90e-01 88.1% 44.2%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3490040 708.1.2.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like 0.69 47.0 3.92e-01 76.3% 39.4%
3891605 708.1.2.7 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like › RIG-I_C-RD 0.65 45.0 3.57e-01 74.6% 42.3%
4451003 387.1.1.13 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related › Toxin_12 0.64 33.0 3.96e-01 78.0% 76.3%
3271184 314.1.1.6 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › BPL_LplA_LipB 0.62 50.0 3.39e-01 91.5% 62.6%
3213512 387.1.3.21 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › Colipase-like › PF29459 0.61 31.0 3.94e-01 76.3% 93.3%
3254963 226.1.1.0 ↗ a+b two layers › POZ domain › POZ domain › POZ domain 0.59 45.0 3.26e-01 84.7% 34.9%
5010220 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 35.0 3.74e-01 78.0% 71.7%
4590318 11.1.1.335 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › GlgB_N 0.55 38.0 3.38e-01 76.3% 94.7%
3831261 844.1.1.5 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › DUF3527 0.50 40.0 2.84e-01 94.9% 74.2%
4943932 7538.1.1.0 ↗ a/b three-layered sandwiches › Hypothetical protein MT938 (MTH938) › Hypothetical protein MT938 (MTH938) › Hypothetical protein MT938 (MTH938) 0.50 31.0 2.45e-01 76.3% 30.1%
D2 medium residues 109-184_222-288
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5k3hB04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.54 34.0 3.56e-01 77.6% 68.4%
5azsC01 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.54 42.0 3.11e-01 81.1% 77.4%
D3 medium residues 289-328_459-491
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3sp1A02 1.20.120.1910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cysteine-tRNA ligase, C-terminal anti-codon recognition domain 0.54 43.0 3.49e-01 90.4% 69.5%
4ri6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 35.0 2.99e-01 79.5% 42.9%
4uz0A00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.51 36.0 3.45e-01 74.0% 72.4%
3cx5A02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.51 42.0 3.10e-01 98.6% 70.4%
2db0B00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.50 39.0 2.73e-01 84.9% 32.1%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4174435 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 0.59 41.0 3.81e-01 72.6% 80.0%
3641145 109.4.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Arm 0.58 37.0 2.88e-01 89.0% 27.9%
4554825 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 0.58 41.0 3.85e-01 75.3% 84.4%
4547664 109.4.1.337 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Ipi1_N 0.52 43.0 2.93e-01 93.2% 49.5%
3416007 109.4.1.947 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_DAAF5 0.51 37.0 2.59e-01 79.5% 34.0%
301487 109.4.1.33 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT 0.50 39.0 2.73e-01 84.9% 32.1%
D4 medium residues 329-458
PDB
Domain cluster: representative
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5070853 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.79 40.0 4.90e-01 72.3% 75.3%
1144783 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.73 43.0 3.99e-01 95.4% 46.9%
185780 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.73 39.0 4.50e-01 70.8% 70.1%
3587782 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.70 41.0 4.50e-01 96.9% 69.1%
D5 medium residues 492-666
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6xz3A01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.72 41.0 4.88e-01 72.6% 82.9%
4w8pA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.70 40.0 4.63e-01 72.6% 75.4%
3dyjA01 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.69 41.0 4.28e-01 74.9% 62.7%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.66 40.0 4.50e-01 74.9% 76.9%
5h5mA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.65 40.0 4.61e-01 73.1% 83.1%
2oerA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.64 38.0 3.86e-01 93.1% 57.5%
2b1eA04 1.20.1280.170 Mainly Alpha › Up-down Bundle › Monooxygenase › Exocyst complex component Exo70 0.63 37.0 4.25e-01 94.9% 78.7%
6k6iA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.62 40.0 3.73e-01 80.0% 51.1%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.62 22.0 3.92e-01 72.0% 98.3%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.62 23.0 3.97e-01 73.7% 100.0%
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.61 37.0 4.21e-01 89.1% 77.8%
7cj3A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.60 39.0 3.45e-01 80.0% 44.2%
2o36A01 1.20.1050.40 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › Endopeptidase. Chain P; domain 1 0.56 39.0 4.41e-01 97.1% 94.5%
3fhnA04 1.20.58.670 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain D 0.56 34.0 3.81e-01 93.1% 77.1%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.56 34.0 4.05e-01 86.9% 90.4%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.52 30.0 3.66e-01 77.7% 88.9%
5z7qA00 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.52 31.0 3.18e-01 78.9% 58.5%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3531143 109.4.1.375 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TRC8_N 0.62 40.0 3.76e-01 80.0% 52.1%
5051683 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.58 33.0 4.08e-01 94.3% 88.2%
4187493 603.1.1.103 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF29732 0.57 35.0 3.84e-01 94.3% 73.8%
3401837 3890.1.1.0 ↗ alpha bundles › Transmembrane Bax inhibitor motif (TMBIM) proteins › Transmembrane Bax inhibitor motif (TMBIM) proteins › Transmembrane Bax inhibitor motif (TMBIM) proteins 0.57 35.0 3.20e-01 76.6% 46.2%
3770412 109.4.1.465 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SPO22 0.55 42.0 3.75e-01 98.9% 55.9%
3410900 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.55 38.0 4.10e-01 73.1% 84.1%
3565766 603.1.1.103 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF29732 0.55 38.0 4.01e-01 94.9% 76.9%
3386988 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.54 47.0 4.34e-01 94.9% 92.9%
4028009 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.53 39.0 4.23e-01 94.3% 88.0%
3245047 603.1.1.213 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF29152 0.52 33.0 3.84e-01 94.9% 93.0%
4017914 601.55.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › anti-complement domain of BBK32 › anti-complement domain of BBK32 0.52 38.0 3.89e-01 75.4% 78.2%
4945172 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 43.0 4.07e-01 86.9% 75.9%
3810760 1075.1.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane 0.51 45.0 3.80e-01 96.0% 77.6%
4025954 3758.1.1.0 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins 0.51 37.0 3.33e-01 75.4% 81.2%
4175970 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 0.50 41.0 3.95e-01 89.1% 75.1%