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NC_028850.1__YP_009203163.1__AVU16_gp07__00007

Bact-Vir

NC_028850.1__YP_009203163.1__AVU16_gp07__00007

Identity

Accession:
NC_028850 ↗
Kingdom:
phage

Quality

94.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Autographivirales› Autonotataviridae› Aghbyvirus› Yersinia_phage_vB_YenP_ISAO8

TaxID: 1675027

Cluster

Singleton — not in a non-trivial cluster

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 5-127
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23780.2 best S-AdoMet_lyase 77.9 1.00e-21 98.4% 99.2%
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6u26A01 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.69 42.0 4.83e-01 100.0% 84.1%
2r6fA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.69 32.0 4.08e-01 74.0% 75.0%
3go9A02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.66 48.0 3.97e-01 75.6% 91.2%
4mt1A07 3.30.70.1440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.63 47.0 5.11e-01 78.0% 94.1%
2cg8B02 3.30.70.560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK 0.60 54.0 5.29e-01 100.0% 98.5%
3kkfA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 42.0 4.51e-01 82.1% 88.6%
3f44A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 50.0 4.19e-01 95.1% 92.4%
1m55A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.56 48.0 4.20e-01 96.7% 94.8%
5t0oA02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.55 42.0 4.51e-01 95.1% 94.2%
3duwA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 46.0 3.80e-01 89.4% 92.2%
5mmiU01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 31.0 3.57e-01 76.4% 78.0%
3hx9B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 40.0 4.42e-01 95.1% 99.0%
5o6uB00 3.30.70.2540 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › CRISPR-associated endoribonuclease Cas6/Csy4 0.54 48.0 4.23e-01 99.2% 100.0%
6bhdA03 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.53 25.0 3.38e-01 72.4% 85.7%
3ow8C00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 46.0 3.47e-01 95.1% 73.0%
5l6gA02 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.53 45.0 3.76e-01 95.9% 78.6%
2fyxA00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.53 44.0 4.40e-01 92.7% 86.9%
2ovrB02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 42.0 3.07e-01 84.6% 59.9%
4j0wA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 45.0 3.34e-01 94.3% 69.4%
2ipiA02 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.52 45.0 3.67e-01 97.6% 72.6%
6hhnA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 36.0 4.09e-01 98.4% 96.7%
4xmqA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 43.0 4.18e-01 89.4% 96.2%
2cnxA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 43.0 3.27e-01 93.5% 83.7%
7t8tA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.50 35.0 3.49e-01 72.4% 80.2%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3477897 304.44.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 0.74 50.0 5.82e-01 97.6% 95.6%
5043596 304.15.1.0 ↗ a+b two layers › Alpha-beta plaits › Viral DNA-binding domain › Viral DNA-binding domain 0.72 50.0 5.15e-01 70.7% 91.3%
4044908 304.8.1.62 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › CitX 0.68 50.0 4.45e-01 75.6% 68.2%
3215882 304.8.1.72 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › SCVP 0.68 47.0 5.32e-01 70.7% 97.8%
5034097 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.68 46.0 5.34e-01 82.1% 100.0%
5005033 304.39.1.0 ↗ a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.67 42.0 5.03e-01 73.2% 95.0%
2533026 304.159.1.1 ↗ a+b two layers › Alpha-beta plaits › Alpha-beta plait domain in NisB › Alpha-beta plait domain in NisB › Lant_dehydr_C 0.66 47.0 4.94e-01 96.7% 81.7%
4477176 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 0.65 41.0 4.84e-01 89.4% 90.6%
3209679 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.65 45.0 4.97e-01 79.7% 91.6%
3211626 304.162.1.2 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › FLAD1_M 0.64 41.0 4.80e-01 100.0% 92.9%
3286580 304.159.1.1 ↗ a+b two layers › Alpha-beta plaits › Alpha-beta plait domain in NisB › Alpha-beta plait domain in NisB › Lant_dehydr_C 0.64 46.0 5.02e-01 98.4% 92.0%
4886650 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 0.62 39.0 4.60e-01 89.4% 90.6%
3963926 304.14.1.1 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) › SPOR 0.62 38.0 4.52e-01 82.1% 94.9%
3789491 304.162.1.0 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain 0.61 41.0 4.83e-01 91.1% 100.0%
5044376 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.60 51.0 3.76e-01 91.9% 89.2%
3990697 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.58 42.0 4.63e-01 81.3% 96.8%
3443914 7502.1.1.1 ↗ 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 › HGTP_anticodon 0.58 41.0 3.83e-01 86.2% 60.0%
3994783 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.56 39.0 3.87e-01 100.0% 66.9%
3505467 327.11.2.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.56 38.0 3.89e-01 91.9% 73.0%
3672118 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.56 43.0 4.46e-01 82.1% 95.7%
3279792 2003.1.5.14 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_3 0.55 46.0 3.84e-01 89.4% 94.0%
3368430 312.1.1.6 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › CwfJ_C_2,CwfJ_C_1 0.54 41.0 3.49e-01 80.5% 81.9%
4312788 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.54 47.0 3.68e-01 95.9% 65.8%
4587782 304.41.1.1 ↗ a+b two layers › Alpha-beta plaits › Glutamyl tRNA-reductase catalytic, N-terminal domain › Glutamyl tRNA-reductase catalytic, N-terminal domain › GlutR_N 0.54 48.0 4.60e-01 99.2% 95.2%
4358407 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.54 41.0 4.31e-01 81.3% 99.1%
4275104 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 0.53 40.0 4.11e-01 85.4% 82.6%
5078315 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.53 41.0 2.65e-01 80.5% 35.4%
3025907 2003.1.5.14 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_3 0.53 44.0 3.64e-01 90.2% 89.0%
3461988 5.1.3.54 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › DUF1668 0.53 44.0 3.26e-01 93.5% 60.0%
3996305 5.1.4.102 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40_3 0.52 45.0 3.24e-01 93.5% 80.8%
3692025 5.1.4.311 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, Beta-prop_NUP159_NUP214 0.52 44.0 3.27e-01 93.5% 68.6%
3924096 5.1.4.102 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40_3 0.52 44.0 3.33e-01 91.9% 89.7%
3616177 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.52 38.0 3.86e-01 80.5% 79.2%
3938865 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.51 44.0 3.19e-01 94.3% 63.3%
3708814 5.1.4.102 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40_3 0.51 43.0 3.35e-01 91.9% 90.4%
3180082 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.51 43.0 3.17e-01 94.3% 64.9%
3767991 5.1.4.254 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, Beta-prop_NOL10_N 0.51 43.0 3.24e-01 93.5% 67.3%
3518935 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.50 43.0 3.14e-01 93.5% 56.5%
3793409 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.50 41.0 3.38e-01 89.4% 48.0%
3912315 5.1.4.371 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Frtz 0.50 41.0 2.91e-01 93.5% 63.7%