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NC_041929.1__YP_009601225.1__FDH46_gp100__00100

Bact-Vir

NC_041929.1__YP_009601225.1__FDH46_gp100__00100

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

90.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

Cluster

View cluster (7 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 31-78_167-189
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF11246.15 best Phage_gp53 27.6 3.10e-06 90.1% 21.5%
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4b8vA03 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.75 50.0 5.91e-01 70.4% 100.0%
2djpA00 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.73 54.0 5.28e-01 78.9% 72.7%
2mtzA01 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.72 49.0 5.65e-01 74.6% 100.0%
2gu1A01 3.10.450.350 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.60 46.0 4.36e-01 84.5% 90.9%
7csxA02 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.60 42.0 4.27e-01 78.9% 73.6%
1whwA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 42.0 3.81e-01 78.9% 58.5%
7wezA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.56 39.0 3.82e-01 71.8% 68.0%
2pffB05 3.30.70.2430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 35.0 3.74e-01 76.1% 73.8%
2rt3A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 38.0 3.48e-01 80.3% 53.6%
2cphA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 37.0 3.65e-01 77.5% 64.6%
3g7qA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.54 40.0 2.91e-01 83.1% 82.1%
2v4jA02 3.30.70.2500 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 42.0 3.71e-01 84.5% 97.0%
3sluB01 3.10.450.350 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 43.0 4.04e-01 91.5% 93.4%
5i41B00 1.10.1660.10 Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › 0.52 36.0 3.69e-01 71.8% 92.5%
8gccA02 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.52 36.0 3.42e-01 76.1% 59.3%
1byrA00 3.30.870.10 Alpha Beta › 2-Layer Sandwich › Endonuclease; Chain A › Endonuclease Chain A 0.52 41.0 3.36e-01 93.0% 94.7%
3d68A01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.52 37.0 3.47e-01 84.5% 59.8%
2l9wA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.51 37.0 3.33e-01 80.3% 51.9%
2pg4A00 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 0.51 35.0 3.35e-01 74.6% 85.7%
2cpeA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.50 38.0 3.64e-01 81.7% 75.3%
1kkhA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.50 38.0 3.14e-01 81.7% 81.7%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5004560 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.82 61.0 6.87e-01 77.5% 100.0%
3250125 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.81 58.0 6.07e-01 74.6% 84.6%
3587382 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.80 59.0 6.64e-01 80.3% 100.0%
4177991 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.80 59.0 6.63e-01 77.5% 100.0%
3331840 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.79 58.0 6.46e-01 78.9% 98.2%
3230171 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.79 54.0 6.31e-01 77.5% 100.0%
4995817 101.15.1.4 ↗ alpha arrays › HTH › LysM domain › LysM domain › Phage_gp53 0.78 70.0 7.13e-01 100.0% 100.0%
3974521 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.77 58.0 6.28e-01 78.9% 93.3%
3633502 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.77 56.0 5.41e-01 81.7% 69.2%
3413357 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.76 57.0 5.82e-01 83.1% 80.0%
3925474 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.76 52.0 6.03e-01 78.9% 100.0%
3456918 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.76 58.0 5.12e-01 80.3% 61.0%
4468802 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.76 54.0 5.26e-01 80.3% 67.1%
3898121 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.76 54.0 6.08e-01 77.5% 96.4%
1758716 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.76 53.0 6.12e-01 73.2% 100.0%
3413453 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.76 51.0 5.97e-01 78.9% 100.0%
3337080 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.76 57.0 6.13e-01 78.9% 93.3%
3324708 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.76 58.0 6.24e-01 81.7% 95.0%
3232962 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.75 55.0 5.95e-01 83.1% 91.7%
3846469 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.75 55.0 5.07e-01 83.1% 61.1%
3969916 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.74 62.0 6.26e-01 91.5% 91.4%
3691772 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.74 54.0 6.01e-01 84.5% 98.2%
2809236 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.74 56.0 5.93e-01 80.3% 98.4%
3517460 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.74 53.0 5.93e-01 81.7% 98.2%
2124917 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.74 57.0 4.28e-01 81.7% 36.6%
3452845 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.74 54.0 6.13e-01 80.3% 100.0%
3457416 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.73 56.0 6.08e-01 80.3% 98.3%
3819870 101.15.1.6 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM2_CERK1_LYK3_4_5 0.73 56.0 4.47e-01 81.7% 95.6%
162111 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.73 54.0 5.28e-01 78.9% 72.7%
3365578 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.73 56.0 5.37e-01 81.7% 86.3%
3611431 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.72 50.0 5.37e-01 71.8% 95.0%
2895417 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.72 52.0 5.11e-01 77.5% 75.3%
3641672 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.71 55.0 5.42e-01 81.7% 84.0%
3353525 101.15.1.6 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM2_CERK1_LYK3_4_5 0.71 55.0 4.47e-01 81.7% 48.8%
4069716 101.15.1.14 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM, LysM2_CERK1_LYK3_4_5 0.71 57.0 4.71e-01 85.9% 51.7%
3666767 101.15.1.10 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM2_NFP 0.70 53.0 4.60e-01 80.3% 61.0%
3381619 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.69 58.0 3.80e-01 90.1% 62.5%
3604763 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.69 50.0 4.72e-01 76.1% 74.1%
3337328 101.15.1.14 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM, LysM2_CERK1_LYK3_4_5 0.69 58.0 3.79e-01 90.1% 64.8%
3166029 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.68 49.0 5.38e-01 78.9% 98.2%
4491522 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.68 50.0 5.35e-01 78.9% 91.7%
3698672 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.68 50.0 4.37e-01 77.5% 81.0%
3920054 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 0.58 36.0 3.62e-01 100.0% 62.9%
4215184 304.117.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.56 36.0 3.69e-01 78.9% 65.7%
4022794 2003.1.2.25 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.55 41.0 2.87e-01 85.9% 80.9%
3164516 101.15.1.2 ↗ alpha arrays › HTH › LysM domain › LysM domain › OapA 0.54 43.0 4.16e-01 91.5% 91.8%
3658706 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.54 38.0 3.79e-01 83.1% 70.7%
3286660 304.169.1.3 ↗ a+b two layers › Alpha-beta plaits › RspWYL1 C-terminal domain › RspWYL1 C-terminal domain › WCX 0.54 37.0 3.49e-01 81.7% 57.8%
4959005 300.1.1.0 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease 0.53 43.0 3.52e-01 94.4% 96.6%
3735227 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.53 39.0 2.68e-01 81.7% 81.0%
3342808 108.1.1.30 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_8 0.53 43.0 3.41e-01 100.0% 56.7%
3420784 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.52 40.0 3.52e-01 81.7% 57.1%
3706605 101.1.2.119 ↗ alpha arrays › HTH › HTH › winged helix domain › Tau95 0.52 35.0 2.48e-01 71.8% 27.1%
3783637 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 39.0 3.30e-01 80.3% 52.2%
143702 304.9.1.26 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_occluded 0.51 37.0 3.33e-01 80.3% 51.9%
3437099 304.7.1.2 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Inhibitor_I9 0.51 37.0 3.48e-01 80.3% 62.8%
3617015 304.120.1.12 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › PF26955 0.50 36.0 3.43e-01 80.3% 63.5%
D2 high residues 83-164
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2mh2A00 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 0.60 31.0 3.48e-01 92.7% 62.5%
3b0bC02 6.10.130.30 Special › Helix non-globular › GTP Cyclohydrolase I; Chain A, domain 1 › 0.60 32.0 3.94e-01 93.9% 95.3%
2l76A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.56 32.0 3.09e-01 72.0% 48.4%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2774435 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.55 31.0 2.92e-01 96.3% 41.0%
3704056 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.53 46.0 2.89e-01 100.0% 34.0%