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MN047793.1__QDJ96496.1__Xoosp13_310__00310

Bact-Vir

MN047793.1__QDJ96496.1__Xoosp13_310__00310

Identity

Accession:
MN047793 ↗
Kingdom:
phage

Quality

90.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Xanthomonas_phage_Xoo-sp13

TaxID: 2591401

Cluster

View cluster (2 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 131-187
PDB
Domain cluster: rep: OR142618.1__WMI31869.1__GBBBJNDB_00166__00166__D119-175
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fxdA05 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.66 44.0 3.47e-01 94.7% 33.3%
4pt4B00 4.10.520.10 Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins 0.66 38.0 3.18e-01 98.2% 34.0%
1egaA02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.58 48.0 4.04e-01 100.0% 52.8%
2v8qA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.57 40.0 3.56e-01 96.5% 49.4%
2q7aA00 2.60.40.1850 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 42.0 3.13e-01 98.2% 31.6%
3pp9B00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 44.0 3.16e-01 89.5% 59.2%
1bd3A00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 38.0 2.59e-01 73.7% 46.4%
4lq0A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.55 45.0 3.53e-01 100.0% 72.2%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.54 43.0 4.10e-01 91.2% 88.4%
4qqgG00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.54 36.0 3.33e-01 91.2% 54.2%
5inwA02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.54 38.0 3.16e-01 96.5% 40.7%
4wjmA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.53 40.0 2.58e-01 84.2% 95.2%
1se8A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 43.0 3.52e-01 91.2% 79.3%
1adoA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 38.0 2.40e-01 80.7% 91.2%
3vsjA00 3.40.830.10 Alpha Beta › 3-Layer(aba) Sandwich › Protocatechuate 4,5-dioxygenase; Chain B › LigB-like 0.52 39.0 2.61e-01 84.2% 69.6%
1azoA00 3.40.600.10 Alpha Beta › 3-Layer(aba) Sandwich › ECO RV Endonuclease; Chain A › DNA mismatch repair MutH/Restriction endonuclease, type II 0.52 42.0 3.02e-01 100.0% 69.2%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.52 38.0 3.23e-01 80.7% 63.1%
3aqoA02 3.30.1360.200 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.52 41.0 3.19e-01 91.2% 48.2%
1nqzA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.52 38.0 2.82e-01 82.5% 77.2%
3nlcA01 3.30.70.2700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.33e-01 77.2% 56.6%
4ofqA02 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 39.0 2.96e-01 89.5% 58.1%
5u3fB01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.50 41.0 3.23e-01 100.0% 40.7%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3942500 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.68 40.0 4.12e-01 93.0% 60.0%
3027359 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.65 39.0 4.44e-01 94.7% 86.5%
3349141 375.1.1.182 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF7086 0.65 50.0 3.76e-01 84.2% 70.0%
1238064 101.1.1.20 ↗ alpha arrays › HTH › HTH › Three-helical HTH › CPSF_A 0.63 52.0 4.63e-01 96.5% 90.7%
4426161 327.6.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like › NifU 0.63 50.0 4.26e-01 100.0% 53.7%
3313182 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.61 43.0 4.03e-01 86.0% 60.0%
3264034 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.60 40.0 3.87e-01 77.2% 60.0%
3251044 242.1.1.2 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2 0.60 41.0 3.13e-01 75.4% 28.6%
3459368 109.4.1.1668 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF27696 0.59 46.0 2.65e-01 86.0% 20.9%
3994311 389.1.3.0 ↗ few secondary structure elements › EGF-like › EGF-related › TNF receptor-like 0.58 34.0 3.85e-01 82.5% 80.0%
4165557 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 0.58 50.0 3.98e-01 100.0% 49.2%
2725646 4.8.1.29 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › SH3_AEBP2_C 0.58 40.0 3.13e-01 73.7% 52.4%
3288067 3326.1.1.1 ↗ alpha arrays › DNA-binding domain in UvrA › DNA-binding domain in UvrA › DNA-binding domain in UvrA › UvrA_DNA-bind 0.57 39.0 3.21e-01 70.2% 85.5%
4025837 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.57 50.0 4.28e-01 100.0% 62.1%
3656766 1.1.9.5 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.57 42.0 3.25e-01 84.2% 76.0%
4583759 3382.1.1.1 ↗ alpha arrays › Protein Wnt-8 › Protein Wnt-8 › Protein Wnt-8 › wnt 0.57 46.0 2.98e-01 96.5% 37.5%
4886572 3326.1.1.1 ↗ alpha arrays › DNA-binding domain in UvrA › DNA-binding domain in UvrA › DNA-binding domain in UvrA › UvrA_DNA-bind 0.56 38.0 3.12e-01 71.9% 85.0%
3560747 3382.1.1.1 ↗ alpha arrays › Protein Wnt-8 › Protein Wnt-8 › Protein Wnt-8 › wnt 0.56 47.0 2.98e-01 98.2% 34.0%
5004912 3326.1.1.1 ↗ alpha arrays › DNA-binding domain in UvrA › DNA-binding domain in UvrA › DNA-binding domain in UvrA › UvrA_DNA-bind 0.56 35.0 2.86e-01 91.2% 31.8%
4423403 330.1.1.14 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › RecT 0.56 43.0 3.33e-01 87.7% 62.1%
3838355 2006.1.4.3 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › NYN 0.55 38.0 2.97e-01 71.9% 42.2%
3486585 304.47.1.0 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain 0.55 44.0 3.57e-01 100.0% 43.3%
3923193 3382.1.1.1 ↗ alpha arrays › Protein Wnt-8 › Protein Wnt-8 › Protein Wnt-8 › wnt 0.55 46.0 2.90e-01 98.2% 33.3%
4020093 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 37.0 2.77e-01 70.2% 55.6%
4488006 2003.1.5.13 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Spermine_synth 0.55 38.0 2.40e-01 89.5% 14.2%
3267201 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.54 35.0 3.18e-01 96.5% 44.7%
3867644 3382.1.1.1 ↗ alpha arrays › Protein Wnt-8 › Protein Wnt-8 › Protein Wnt-8 › wnt 0.54 44.0 2.86e-01 96.5% 30.5%
3240679 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.54 47.0 3.41e-01 98.2% 63.1%
5053243 67.1.1.1 ↗ beta sandwiches › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › DnaJ_C 0.53 39.0 3.58e-01 82.5% 72.5%
3470394 3382.1.1.1 ↗ alpha arrays › Protein Wnt-8 › Protein Wnt-8 › Protein Wnt-8 › wnt 0.52 46.0 2.85e-01 100.0% 68.3%
4618123 286.1.1.4 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Pro_racemase 0.52 45.0 3.24e-01 100.0% 41.2%
3907851 3382.1.1.1 ↗ alpha arrays › Protein Wnt-8 › Protein Wnt-8 › Protein Wnt-8 › wnt 0.51 45.0 2.87e-01 100.0% 57.6%
3507097 304.20.1.3 ↗ a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › Nrap_D6 0.51 38.0 3.21e-01 93.0% 43.5%
3495008 3382.1.1.1 ↗ alpha arrays › Protein Wnt-8 › Protein Wnt-8 › Protein Wnt-8 › wnt 0.51 45.0 2.75e-01 100.0% 60.3%
4950538 3326.1.1.1 ↗ alpha arrays › DNA-binding domain in UvrA › DNA-binding domain in UvrA › DNA-binding domain in UvrA › UvrA_DNA-bind 0.51 34.0 2.74e-01 93.0% 33.9%
5051150 2003.1.2.12 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › DAO 0.51 40.0 2.49e-01 87.7% 30.7%
4023956 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.50 35.0 2.74e-01 75.4% 38.5%
D2 medium residues 12-63
PDB
Domain cluster: representative
D3 medium residues 64-130
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a7wA00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.65 47.0 4.77e-01 98.5% 75.0%
2yviA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.57 41.0 3.71e-01 74.6% 64.0%
2f9wA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 47.0 3.86e-01 89.6% 56.8%
3di2A00 1.20.1250.50 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.54 43.0 3.60e-01 98.5% 50.4%
7cyuA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.54 38.0 4.14e-01 85.1% 87.7%
3thxB02 3.30.420.110 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › MutS, connector domain 0.51 38.0 3.00e-01 80.6% 48.0%
4fd4A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 39.0 2.69e-01 79.1% 42.5%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3194715 2004.1.1.154 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_2,AAA_5 0.76 47.0 3.01e-01 85.1% 14.7%
3897619 3684.1.1.40 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PF28484 0.65 49.0 4.00e-01 100.0% 45.0%
1413973 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.65 45.0 3.55e-01 73.1% 90.8%
3449314 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.62 51.0 4.72e-01 88.1% 82.4%
4017838 2484.1.1.57 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ydc2-catalyt 0.57 48.0 3.26e-01 94.0% 40.4%
5001627 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 0.57 53.0 3.47e-01 100.0% 94.9%
3183304 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.55 42.0 3.28e-01 82.1% 91.7%
3648783 604.17.1.0 ↗ alpha bundles › Spectrin repeat-like › MTH_863 C-terminal domain-like › MTH_863 C-terminal domain-like 0.55 29.0 3.17e-01 70.1% 61.8%
3470874 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.55 51.0 4.80e-01 100.0% 85.0%
4962111 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 0.54 48.0 3.18e-01 98.5% 90.1%
3806359 148.1.3.205 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_At3g28540 0.54 46.0 4.65e-01 94.0% 95.4%
2163596 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.51 39.0 2.69e-01 80.6% 41.5%