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NC_028829.1__YP_009201482.1__AVU32_gp379__00379

Bact-Vir

NC_028829.1__YP_009201482.1__AVU32_gp379__00379

Identity

Accession:
NC_028829 ↗
Kingdom:
phage

Quality

85.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Schizotequatrovirus› Vibrio_phage_ValKK3

TaxID: 1610855

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 5-161_262-296
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1k32A04 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.52 21.0 2.83e-01 72.9% 68.4%
2kx2A00 3.30.780.30 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › 0.51 23.0 3.15e-01 90.1% 82.3%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3185580 3613.1.1.0 ↗ beta barrels › Protein CLP1 C-terminal domain › Protein CLP1 C-terminal domain › Protein CLP1 C-terminal domain 0.56 33.0 3.86e-01 79.7% 80.7%
3249603 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.53 23.0 3.44e-01 80.7% 98.7%
D2 high residues 177-247
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2e62A01 6.10.140.420 Special › Helix non-globular › Helix Hairpins › 0.73 50.0 5.77e-01 84.5% 98.1%
2oerA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.72 52.0 3.86e-01 76.1% 63.7%
4m0mA04 1.20.1270.440 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.71 50.0 4.27e-01 74.6% 53.0%
4oe8C00 1.10.8.1170 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.67 48.0 4.48e-01 74.6% 86.2%
2k3oA00 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.66 43.0 3.60e-01 71.8% 37.2%
1c17M00 1.20.120.220 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ATP synthase, F0 complex, subunit A 0.66 57.0 4.61e-01 100.0% 95.8%
3buxB01 1.20.930.20 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Adaptor protein Cbl, N-terminal domain 0.65 47.0 3.89e-01 77.5% 65.9%
1jb0K00 1.20.860.20 Mainly Alpha › Up-down Bundle › Alpha-t-alpha › Photosystem I PsaK, reaction centre 0.64 41.0 4.80e-01 76.1% 100.0%
3w0lD02 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.64 51.0 3.35e-01 91.5% 91.5%
6mh4A03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.63 43.0 4.17e-01 71.8% 63.3%
3b8bA01 3.30.540.10 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › Fructose-1,6-Bisphosphatase, subunit A, domain 1 0.63 48.0 3.74e-01 88.7% 37.1%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.62 50.0 4.78e-01 95.8% 75.3%
2ewfA03 3.40.91.50 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › 0.62 47.0 3.37e-01 83.1% 99.6%
5svlA01 1.10.287.940 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › atp-gated p2x4 ion channel 0.62 49.0 5.04e-01 88.7% 97.1%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.61 48.0 4.13e-01 84.5% 100.0%
2bduA02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.61 42.0 4.24e-01 74.6% 82.4%
2rt6A00 1.20.1270.340 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.60 43.0 3.88e-01 76.1% 90.8%
3d85C00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.59 46.0 3.75e-01 83.1% 97.7%
1xjaB00 2.60.120.280 Mainly Beta › Sandwich › Jelly Rolls › Regulatory protein AraC 0.59 41.0 3.28e-01 73.2% 37.7%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.59 45.0 4.52e-01 83.1% 98.6%
1f7uA02 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.58 45.0 3.73e-01 84.5% 56.8%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.57 41.0 4.04e-01 76.1% 73.7%
4q20A01 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.54 48.0 4.60e-01 100.0% 85.4%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.50 42.0 4.15e-01 100.0% 89.6%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4011398 633.24.1.0 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain 0.87 60.0 5.64e-01 71.8% 60.0%
3956826 150.8.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PPE › PPE 0.80 58.0 4.33e-01 76.1% 85.9%
3245015 3831.1.1.0 ↗ alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 0.78 56.0 5.38e-01 76.1% 81.2%
4583055 316.1.1.11 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › GrpB 0.75 54.0 4.12e-01 76.1% 35.6%
4032308 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.74 63.0 4.58e-01 94.4% 37.1%
5040843 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.72 61.0 5.60e-01 100.0% 71.6%
4217669 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.72 62.0 4.28e-01 100.0% 28.4%
3716257 1189.1.1.0 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor 0.71 51.0 4.08e-01 74.6% 84.4%
3193842 145.1.1.0 ↗ alpha arrays › F-box domain › F-box domain › F-box domain 0.71 56.0 4.66e-01 85.9% 68.0%
2984622 3396.1.1.1 ↗ extended segments › HIG1 domain family member 1A › HIG1 domain family member 1A › HIG1 domain family member 1A › HIG_1_N 0.71 55.0 5.64e-01 90.1% 85.5%
3438464 5063.1.1.0 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK 0.71 47.0 5.44e-01 76.1% 98.0%
3970168 5045.1.1.0 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A 0.70 62.0 4.14e-01 100.0% 60.9%
4979934 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.69 53.0 4.28e-01 83.1% 44.6%
4663861 5069.1.3.78 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › MIS13 0.68 52.0 4.99e-01 85.9% 71.2%
4237660 1008.1.1.0 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain 0.68 54.0 4.51e-01 85.9% 50.8%
4623986 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.67 57.0 3.93e-01 100.0% 27.2%
3442159 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.66 56.0 5.21e-01 100.0% 97.9%
4499545 604.9.1.20 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › TMD_POM152 0.66 47.0 4.16e-01 77.5% 53.0%
3782757 304.102.1.4 ↗ a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › TruB_N 0.65 46.0 2.95e-01 74.6% 81.5%
3224304 4120.1.1.30 ↗ few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP › DUF842 0.64 46.0 4.36e-01 76.1% 94.1%
4139865 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.64 57.0 3.89e-01 100.0% 28.1%
4029754 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 0.63 55.0 5.25e-01 100.0% 87.1%
4959036 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.63 56.0 4.92e-01 98.6% 67.6%
4964984 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.63 54.0 4.90e-01 100.0% 70.0%
4964387 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.63 55.0 4.98e-01 100.0% 71.0%
4026047 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.61 51.0 4.82e-01 93.0% 77.6%
5041920 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.59 42.0 3.98e-01 76.1% 78.9%
5020110 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 53.0 4.70e-01 98.6% 72.0%
5063791 1075.3.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC importer transmembrane domain fold › Type I ABC importer transmembrane domain fold › BPD_transp_1 0.58 46.0 2.98e-01 88.7% 97.6%
3855461 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 0.53 38.0 3.70e-01 85.9% 67.1%
3556027 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 0.53 38.0 3.70e-01 85.9% 67.1%
D3 high residues 340-408
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2k19A00 1.20.1440.140 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.60 49.0 4.45e-01 94.2% 85.7%
2etdA00 1.20.1440.20 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › LemA-like domain 0.59 48.0 3.94e-01 95.7% 63.8%
1e6vB02 1.20.840.10 Mainly Alpha › Up-down Bundle › Methyl-coenzyme M Reductase; Chain B, domain 2 › Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal 0.58 49.0 3.33e-01 100.0% 69.2%
4ne4A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.57 42.0 3.19e-01 78.3% 94.0%
6a7hA01 1.20.140.180 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.57 38.0 3.16e-01 81.2% 36.4%
7e4mA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.52 40.0 2.80e-01 88.4% 34.6%
1jvaB02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.52 40.0 3.55e-01 88.4% 73.6%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5074606 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.64 48.0 4.31e-01 82.6% 69.0%
3597161 633.2.1.0 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.63 53.0 5.02e-01 94.2% 87.1%
3171529 5025.1.1.7 ↗ extended segments › PetL subunit of the cytochrome b6f complex › PetL subunit of the cytochrome b6f complex › PetL subunit of the cytochrome b6f complex › Erv26 0.60 52.0 4.29e-01 97.1% 90.4%
4030933 225.1.1.17 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c+His_kinase 0.60 51.0 3.72e-01 95.7% 49.2%
4094763 304.60.1.8 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10, PF27436 0.59 42.0 3.28e-01 76.8% 68.8%
3400507 109.27.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › BACK domain › BACK domain 0.56 37.0 3.20e-01 72.5% 42.7%
3598367 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 41.0 3.74e-01 78.3% 79.6%
3550061 101.1.2.127 ↗ alpha arrays › HTH › HTH › winged helix domain › Cullin_Nedd8 0.56 40.0 3.52e-01 76.8% 69.5%
3602284 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 38.0 3.57e-01 71.0% 65.9%
3408885 101.1.2.499 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_MCM7 0.56 40.0 3.90e-01 76.8% 89.3%
3490496 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.55 44.0 3.69e-01 92.8% 83.8%
3856178 101.1.2.304 ↗ alpha arrays › HTH › HTH › winged helix domain › E3_UFM1_ligase 0.55 38.0 4.04e-01 73.9% 95.0%
5000261 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 40.0 4.25e-01 87.0% 93.3%
3304822 7018.1.1.2 ↗ few secondary structure elements › gp76 helical domain › gp76 helical domain › gp76 helical domain › SAM_AAE17_18 0.54 44.0 4.20e-01 94.2% 96.5%
3204194 101.1.2.86 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_Nse1 0.54 39.0 3.56e-01 78.3% 87.4%
3958400 2005.1.1.5 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1c 0.53 42.0 3.25e-01 92.8% 88.1%
3250325 108.1.1.34 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_12 0.52 37.0 3.42e-01 76.8% 74.7%
4213802 3304.1.1.2 ↗ a+b two layers › Cellular targeting domain in sucrose synthase-1 › Cellular targeting domain in sucrose synthase-1 › Cellular targeting domain in sucrose synthase-1 › SUS_N 0.52 40.0 3.28e-01 87.0% 50.0%
5011622 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 40.0 3.72e-01 92.8% 91.4%
5002469 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.51 37.0 3.47e-01 82.6% 67.4%
3621166 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 41.0 3.77e-01 95.7% 94.7%