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KU963248.1__AMS02668.1__SEA_YVONNETASTIC_124__00119

Bact-Vir

KU963248.1__AMS02668.1__SEA_YVONNETASTIC_124__00119

Identity

Accession:
KU963248 ↗
Kingdom:
phage

Quality

89.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Yvonnevirus› Gordonia_phage_Yvonnetastic

TaxID: 1821566

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 7-80
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 44.0 3.84e-01 77.0% 84.3%
1ye8A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 35.0 2.65e-01 73.0% 25.1%
2d9xA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 42.0 3.79e-01 81.1% 93.6%
7byjA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 41.0 3.84e-01 81.1% 77.9%
5ziyA01 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.55 49.0 3.62e-01 100.0% 89.7%
1rsgA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 41.0 2.91e-01 82.4% 84.9%
3uqcD02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.54 40.0 3.28e-01 81.1% 73.2%
1f44A01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.54 42.0 3.22e-01 87.8% 44.8%
2h3gX02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 40.0 3.16e-01 97.3% 37.1%
2rloA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 40.0 3.38e-01 83.8% 99.2%
2oap101 3.30.450.380 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 38.0 2.88e-01 82.4% 50.7%
1l3aA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.52 42.0 3.41e-01 97.3% 97.6%
1v57A03 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 36.0 2.99e-01 75.7% 68.1%
2pm6D01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 38.0 2.69e-01 85.1% 60.0%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3723770 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.77 34.0 3.28e-01 98.6% 37.6%
3652692 2485.1.1.86 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Alba 0.67 37.0 2.72e-01 81.1% 21.1%
3513128 220.1.1.50 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_17 0.65 44.0 3.54e-01 70.3% 69.3%
4023242 220.1.1.187 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › VPS13_C 0.64 48.0 4.09e-01 81.1% 93.6%
3190184 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.64 56.0 5.18e-01 100.0% 94.7%
4483586 2003.1.2.150 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3, GGR_cat 0.63 54.0 3.49e-01 100.0% 78.4%
3720028 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.62 48.0 4.23e-01 85.1% 99.1%
3595799 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 48.0 3.71e-01 86.5% 56.5%
3411789 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.61 44.0 3.68e-01 79.7% 97.9%
4280539 109.21.1.8 ↗ alpha superhelices › Repetitive alpha hairpins › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › WD40 0.60 50.0 2.89e-01 93.2% 37.0%
3525358 220.1.1.50 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_17 0.60 43.0 3.75e-01 77.0% 80.0%
4034336 4.8.1.13 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › ComK 0.60 48.0 3.98e-01 91.9% 64.1%
3513810 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 45.0 3.78e-01 82.4% 85.2%
4953970 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 43.0 3.71e-01 77.0% 91.7%
4874139 186.1.1.27 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › ResT-TelK_cat 0.58 45.0 4.22e-01 86.5% 73.2%
3417954 2.1.1.39 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RNA_pol_Rbc25 0.58 40.0 3.53e-01 74.3% 94.2%
5001380 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 38.0 3.76e-01 75.7% 62.5%
4085259 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.58 41.0 2.81e-01 74.3% 45.7%
4152161 206.1.1.70 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1 0.57 39.0 2.64e-01 71.6% 45.4%
3939128 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 43.0 3.87e-01 83.8% 80.9%
3219161 220.1.1.50 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_17 0.57 40.0 3.62e-01 75.7% 91.8%
3931963 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 42.0 3.61e-01 81.1% 67.2%
3493556 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 42.0 3.81e-01 85.1% 81.8%
4943984 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.55 43.0 3.27e-01 86.5% 83.2%
4313114 378.1.1.30 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › PF30178 0.55 40.0 3.56e-01 82.4% 69.2%
4533523 4263.2.1.1 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain › FtsH_ext 0.54 34.0 3.60e-01 71.6% 72.3%
3176064 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.54 34.0 2.69e-01 100.0% 31.0%
4987289 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 41.0 2.55e-01 85.1% 22.1%
4968259 3926.1.1.0 ↗ alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D 0.53 47.0 3.79e-01 100.0% 97.9%
3777040 220.1.1.120 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GARIL_Rab2_bd 0.52 38.0 3.20e-01 82.4% 56.0%
3952995 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.52 44.0 4.30e-01 97.3% 89.4%
4299488 2003.1.1.51 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › DFP 0.52 35.0 2.53e-01 70.3% 30.3%
3585813 220.1.1.50 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_17 0.52 36.0 3.81e-01 73.0% 96.9%
4979752 2003.2.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Formate dehydrogenase/DMSO reductase, domains 2 and 3 › Formate dehydrogenase/DMSO reductase, domains 2 and 3 0.52 41.0 2.81e-01 89.2% 65.4%
1833392 2003.1.2.16 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3,NAD_binding_8 0.51 36.0 2.86e-01 74.3% 54.4%
3742330 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.51 39.0 3.49e-01 86.5% 87.0%
3399725 220.1.1.50 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_17 0.51 38.0 3.35e-01 82.4% 93.0%
3712990 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 34.0 3.55e-01 71.6% 80.0%
4224102 874.1.1.1 ↗ a+b duplicates or obligate multimers › Smc hinge domain › Smc hinge domain › Smc hinge domain › SMC_hinge 0.51 46.0 2.87e-01 100.0% 82.1%
3697152 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 0.50 45.0 3.04e-01 100.0% 69.3%
3733618 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 44.0 3.25e-01 97.3% 51.8%
D2 high residues 91-139
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3au3A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.58 47.0 2.97e-01 100.0% 16.9%
1zp2A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.57 43.0 3.40e-01 85.7% 38.4%
7ojuA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 47.0 3.16e-01 95.9% 65.5%
5xfaA04 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.56 45.0 3.95e-01 100.0% 62.4%
3m8jA00 1.10.10.2690 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.52 38.0 3.15e-01 79.6% 43.3%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.51 36.0 3.55e-01 75.5% 71.7%
2i00C01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 41.0 3.07e-01 95.9% 47.2%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4018510 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.59 40.0 3.27e-01 75.5% 36.8%
4947697 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 38.0 3.65e-01 87.8% 55.0%
4522783 101.1.2.715 ↗ alpha arrays › HTH › HTH › winged helix domain › CheF-arch 0.58 48.0 3.11e-01 100.0% 78.2%
4587402 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.56 47.0 3.93e-01 98.0% 97.8%
3188707 132.1.1.6 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › DUF7080 0.54 43.0 3.52e-01 93.9% 86.0%
2528261 8002.1.1.1 ↗ alpha bundles › Zn-binding domain in glutaminyl-tRNA synthetase › Zn-binding domain in glutaminyl-tRNA synthetase › Zn-binding domain in glutaminyl-tRNA synthetase › tRNA-synt_1c 0.50 35.0 2.89e-01 75.5% 83.7%
3488091 109.24.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Helical domain in dedicator of cytokinesis protein 9 › Helical domain in dedicator of cytokinesis protein 9 › DHR-2_Lobe_A 0.50 40.0 3.09e-01 100.0% 37.1%