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NC_021331.1__YP_008059755.1__pSf1_0033__00033

Bact-Vir

NC_021331.1__YP_008059755.1__pSf1_0033__00033

Identity

Accession:
NC_021331 ↗
Kingdom:
phage

Quality

86.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Drexlerviridae› Hanrivervirus› Shigella_phage_pSf-1

TaxID: 2496551

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 2-104
PDB
Domain cluster: rep: MK095606.1__AZS06374.1__AAS23_gp61__00061__D3-78
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23796.2 best DUF7174 40.3 3.60e-10 100.0% 65.2%
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6lbsB01 3.30.1370.230 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Stn1, C-terminal wHTH domain 0.69 50.0 5.58e-01 85.4% 98.7%
3c6kB03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.66 48.0 3.92e-01 87.4% 41.2%
3keyA02 3.30.1370.230 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Stn1, C-terminal wHTH domain 0.66 51.0 5.46e-01 88.3% 96.6%
2ek0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.65 48.0 5.11e-01 90.3% 91.1%
1bdfA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.64 40.0 4.04e-01 71.8% 61.3%
4ponA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.62 41.0 3.45e-01 88.3% 40.1%
6jp6D01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 41.0 3.19e-01 87.4% 31.7%
3ue2A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.60 36.0 3.82e-01 70.9% 68.2%
1vw4L01 3.90.1030.10 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › Ribosomal protein L17 0.59 47.0 4.35e-01 87.4% 87.4%
2nraC02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 46.0 4.71e-01 85.4% 96.1%
5yd0D01 3.30.950.30 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Schlafen, AAA domain 0.58 47.0 4.15e-01 88.3% 64.3%
4xrpC01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.57 42.0 3.58e-01 83.5% 46.3%
1xcjA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.57 45.0 3.55e-01 87.4% 98.3%
3jwhA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 43.0 3.58e-01 88.3% 45.0%
3pm9A03 3.30.70.2190 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 37.0 3.56e-01 70.9% 57.9%
3tebB00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.55 44.0 3.30e-01 86.4% 33.7%
2rilA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 33.0 3.46e-01 70.9% 64.2%
3cueB00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.54 44.0 3.81e-01 89.3% 93.4%
1qf6A02 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.54 42.0 4.22e-01 82.5% 85.8%
2xbtA00 2.60.40.710 Mainly Beta › Sandwich › Immunoglobulin-like › Endoglucanase-like 0.54 39.0 3.44e-01 86.4% 50.0%
1pwkA00 3.30.740.10 Alpha Beta › 2-Layer Sandwich › Protein Inhibitor Of Neuronal Nitric Oxide Synthase › Protein Inhibitor Of Neuronal Nitric Oxide Synthase; 0.53 37.0 3.95e-01 71.8% 87.9%
3mtiB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 40.0 3.34e-01 86.4% 45.6%
4z7eA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 39.0 3.34e-01 83.5% 48.2%
1emsA02 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.52 41.0 3.86e-01 87.4% 83.8%
5k9aA00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.51 42.0 3.41e-01 92.2% 64.7%
4bluB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 41.0 3.06e-01 88.3% 40.6%
3ce8A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 37.0 3.94e-01 75.7% 98.9%
3l7xA00 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.51 40.0 3.53e-01 85.4% 56.7%
6blkC00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.51 39.0 3.36e-01 79.6% 91.8%
3cloC01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.50 35.0 2.91e-01 73.8% 68.4%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3188973 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.70 52.0 3.93e-01 98.1% 34.0%
5047334 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.63 33.0 3.42e-01 70.9% 53.7%
5082316 101.1.2.187 ↗ alpha arrays › HTH › HTH › winged helix domain › Rep3_C 0.61 47.0 4.84e-01 84.5% 88.4%
3472642 3937.1.1.2 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.61 45.0 3.01e-01 77.7% 67.2%
3385833 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.60 43.0 2.95e-01 73.8% 35.9%
4591683 305.1.1.0 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase 0.60 38.0 3.99e-01 72.8% 69.5%
3697211 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.59 46.0 3.50e-01 89.3% 35.7%
4022825 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.59 36.0 3.64e-01 70.9% 58.1%
4969811 2003.1.5.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.59 40.0 2.94e-01 82.5% 25.6%
3262891 101.1.2.79 ↗ alpha arrays › HTH › HTH › winged helix domain › RNA_pol_I_A49 0.58 36.0 4.22e-01 86.4% 96.9%
4033445 7523.1.1.17 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › OpuAC 0.58 41.0 3.36e-01 81.6% 39.2%
3699934 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 47.0 4.76e-01 88.3% 93.3%
5000641 2003.1.5.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.57 40.0 2.96e-01 82.5% 27.9%
3725393 304.4.1.49 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AtuA 0.57 35.0 3.68e-01 70.9% 67.4%
3950775 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.56 41.0 3.49e-01 77.7% 47.0%
5082698 101.1.2.914 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF6015 0.56 35.0 3.73e-01 81.6% 71.1%
3588338 101.1.2.187 ↗ alpha arrays › HTH › HTH › winged helix domain › Rep3_C 0.56 47.0 4.03e-01 94.2% 83.5%
5044376 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.55 38.0 2.69e-01 70.9% 24.0%
3690383 304.4.1.58 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Dehydratase_hem 0.55 33.0 3.37e-01 71.8% 57.1%
4954449 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.55 41.0 4.20e-01 83.5% 80.8%
3811740 2003.1.5.14 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_3 0.55 45.0 3.46e-01 93.2% 37.6%
3515401 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 41.0 3.95e-01 82.5% 68.3%
4403450 305.1.1.1 ↗ a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.55 37.0 3.56e-01 76.7% 59.2%
3805545 101.1.2.24 ↗ alpha arrays › HTH › HTH › winged helix domain › MAGE 0.54 43.0 4.07e-01 89.3% 75.4%
3990818 312.1.1.2 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › HIT 0.53 43.0 3.71e-01 87.4% 70.9%
4629783 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.53 45.0 4.27e-01 92.2% 96.7%
3988477 848.1.1.1 ↗ a+b complex topology › Hsp33 domain › Hsp33 domain › Hsp33 domain › HSP33 0.53 38.0 2.97e-01 75.7% 77.0%
4971745 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.53 42.0 3.95e-01 87.4% 91.4%
2329747 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.52 30.0 3.19e-01 80.6% 63.0%
4937399 312.1.1.2 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › HIT 0.52 40.0 3.67e-01 85.4% 61.4%
3347816 101.1.2.394 ↗ alpha arrays › HTH › HTH › winged helix domain › eWH_GTF3C1 0.52 40.0 3.93e-01 87.4% 75.7%
5058218 312.1.1.2 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › HIT 0.51 40.0 3.64e-01 85.4% 62.2%
4464568 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.51 38.0 3.87e-01 86.4% 81.0%
4932382 312.1.1.2 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › HIT 0.51 40.0 3.57e-01 85.4% 60.0%
4602428 304.4.1.9 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Chlor_dismutase 0.51 35.0 3.11e-01 70.9% 86.7%
5024594 312.1.1.2 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › HIT 0.51 40.0 3.69e-01 86.4% 65.2%
4929188 312.1.1.2 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › HIT 0.51 39.0 3.78e-01 84.5% 75.0%
4284678 225.1.1.3 ↗ 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 0.51 38.0 3.25e-01 79.6% 85.3%
5074091 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.50 41.0 3.55e-01 89.3% 94.5%
3611256 101.1.2.236 ↗ alpha arrays › HTH › HTH › winged helix domain › POLR3C_WHD 0.50 44.0 2.81e-01 99.0% 27.2%
2850632 312.1.1.2 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › HIT 0.50 39.0 3.96e-01 85.4% 85.8%
5083964 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 39.0 3.96e-01 86.4% 86.0%
3788427 101.1.2.207 ↗ alpha arrays › HTH › HTH › winged helix domain › TFC3_eWH 0.50 38.0 3.94e-01 87.4% 85.0%
3827266 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 36.0 3.21e-01 84.5% 53.1%
4025884 312.1.1.8 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › DcpS_C 0.50 39.0 3.27e-01 84.5% 48.1%