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NC_006820.1__YP_195175.1__S-PM2p143__00146

Bact-Vir

NC_006820.1__YP_195175.1__S-PM2p143__00146

Identity

Accession:
NC_006820 ↗
Kingdom:
phage

Quality

76.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Nodensvirus› Synechococcus_phage_S-PM2

TaxID: 238854

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 5-172
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4xq7A01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.76 53.0 5.54e-01 91.1% 76.9%
4s3nA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.73 51.0 5.46e-01 91.7% 81.0%
1lqlA02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.67 40.0 5.00e-01 92.3% 97.1%
3oguA03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.66 43.0 4.85e-01 91.1% 87.8%
2ihmB03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.63 41.0 4.85e-01 90.5% 95.6%
2rjbA00 3.10.180.80 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › Uncharacterised protein PF07063, DUF1338 0.58 50.0 3.70e-01 91.1% 65.6%
3q2wA04 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.57 32.0 3.93e-01 79.8% 87.6%
5tfmA02 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.55 30.0 3.80e-01 76.8% 88.1%
5w4tB03 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.53 31.0 3.73e-01 78.0% 88.0%
1yliB00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.53 32.0 3.43e-01 95.2% 66.9%
5cyxA03 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.52 31.0 3.69e-01 79.2% 89.0%
5t4mB01 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.51 29.0 3.43e-01 78.0% 79.6%
1ywmA01 2.60.500.10 Mainly Beta › Sandwich › Surface Active Protein fold › Surface Active Protein domain 0.51 29.0 3.70e-01 88.7% 96.9%
3f65G01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 30.0 3.59e-01 78.6% 89.0%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3443030 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.65 25.0 3.53e-01 97.6% 72.5%
3608162 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.64 29.0 2.97e-01 72.0% 41.8%
3610425 316.1.1.23 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DNA_pol_B_thumb 0.63 45.0 4.12e-01 91.1% 54.4%
3703231 216.1.1.2 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › Autophagy_act_C 0.62 29.0 3.01e-01 73.8% 43.6%
4969719 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.61 35.0 3.74e-01 88.7% 62.0%
3264178 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.59 28.0 3.08e-01 91.1% 51.4%
4947993 283.2.1.19 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › NMD3 0.59 32.0 3.87e-01 82.7% 78.2%
3640795 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.56 38.0 3.57e-01 93.5% 53.0%
3411221 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.56 32.0 4.02e-01 92.3% 94.0%
4071803 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.54 37.0 3.62e-01 70.2% 77.9%
3616323 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.54 38.0 3.64e-01 71.4% 82.6%
3183677 523.1.1.3 ↗ a+b two layers › Ribosomal protein L9 C-domain › Ribosomal protein L9 C-domain › Ribosomal protein L9 C-domain › PF29994 0.53 30.0 3.66e-01 90.5% 84.5%
3768529 11.1.1.15 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PKD 0.53 33.0 3.88e-01 82.1% 90.4%
3587268 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 29.0 3.37e-01 87.5% 75.0%
3873771 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.52 25.0 2.96e-01 97.0% 64.5%
3543052 11.1.1.284 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PKD_4 0.52 33.0 3.93e-01 90.5% 95.5%
3700950 2004.1.1.26 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin 0.52 39.0 2.65e-01 78.0% 30.4%
3240574 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.51 36.0 3.57e-01 70.2% 80.0%
3705675 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 30.0 3.30e-01 90.5% 70.0%
3926817 219.1.1.25 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › LRAT 0.51 26.0 2.64e-01 82.7% 45.0%
3366570 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 30.0 3.56e-01 87.5% 87.3%
3450141 283.2.1.8 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › PF29994 0.51 28.0 3.56e-01 86.3% 91.0%
3808345 221.7.1.1 ↗ a+b two layers › beta-Grasp › E2-binding domain of E1 › E2-binding domain of E1 › E2_bind 0.50 30.0 3.57e-01 85.1% 90.5%
D2 high residues 177-322
PDB
Domain cluster: rep: IMGVR_UViG_3300000172_000086-3300000172-SI34jun09_200mDRAFT_100220910__D4-124
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ls1A01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.61 32.0 3.91e-01 85.6% 80.9%
6c6sD02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.57 24.0 3.48e-01 96.6% 90.0%
2ve3B00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.52 44.0 3.20e-01 91.8% 77.8%
5ycqA00 2.30.30.390 Mainly Beta › Roll › SH3 type barrels. › Hemimethylated DNA-binding domain 0.52 21.0 2.74e-01 93.8% 63.6%
3l9rA01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.50 40.0 3.75e-01 91.8% 69.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3828018 149.1.1.1 ↗ alpha arrays › Cytochrome P450 › Cytochrome P450 › Cytochrome P450 › p450 0.52 45.0 3.11e-01 94.5% 72.2%
3983938 608.1.1.0 ↗ alpha arrays › AhpD-like › AhpD-like › AhpD-like 0.51 37.0 3.54e-01 93.2% 64.7%
4464657 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.50 27.0 3.42e-01 78.1% 92.5%
D3 high residues 336-518
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6z74C02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.52 31.0 3.36e-01 88.0% 66.0%
6elqA01 1.20.1270.30 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.51 37.0 3.79e-01 74.9% 84.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3602675 1075.5.1.27 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE, Polysacc_synt 0.54 39.0 3.38e-01 90.2% 48.9%
3233647 5001.1.1.60 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srx 0.54 41.0 3.49e-01 78.1% 92.6%
4987543 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 36.0 3.63e-01 90.2% 65.8%
D4 medium residues 519-586
PDB