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NC_041929.1__YP_009601486.1__FDH46_gp117__00361

Bact-Vir

NC_041929.1__YP_009601486.1__FDH46_gp117__00361

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

90.0 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 1-61
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.54 33.0 3.38e-01 85.2% 63.2%
1vyiA00 1.20.120.820 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Phosphoprotein, C-terminal domain 0.52 43.0 3.65e-01 98.4% 82.0%
4ec7A00 2.10.90.10 Mainly Beta › Ribbon › Cystine Knot Cytokines, subunit B › Cystine-knot cytokines 0.52 45.0 3.76e-01 100.0% 79.6%
4x0qA04 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.52 39.0 3.03e-01 91.8% 35.4%
3py8A04 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.51 38.0 2.97e-01 93.4% 35.4%
7txnA01 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 3.16e-01 73.8% 93.3%
4dsfA04 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.50 36.0 3.09e-01 95.1% 43.6%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.50 40.0 3.74e-01 88.5% 73.7%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4338978 314.1.1.2 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.64 54.0 3.46e-01 98.4% 21.2%
4970833 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.53 40.0 3.89e-01 100.0% 75.7%
3640563 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 37.0 3.57e-01 100.0% 66.7%
D2 medium residues 65-138_192-233
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1m5q101 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.56 32.0 3.99e-01 80.2% 95.6%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 33.0 3.65e-01 89.7% 74.7%
2lt1A00 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.56 32.0 3.80e-01 78.4% 85.3%
1zq1A01 2.30.30.520 Mainly Beta › Roll › SH3 type barrels. › 0.55 33.0 3.88e-01 89.7% 87.0%
2digA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.55 30.0 3.71e-01 86.2% 88.2%
2oviA00 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.55 40.0 3.65e-01 94.0% 56.3%
2fhdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.54 29.0 3.66e-01 72.4% 93.5%
7a0hA01 3.30.1140.60 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit 0.54 31.0 3.30e-01 96.6% 62.4%
6s8zA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.54 30.0 3.72e-01 81.0% 96.8%
2x5cA01 3.30.70.3590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 33.0 3.63e-01 85.3% 75.8%
3cpfA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.54 28.0 3.56e-01 82.8% 87.7%
1v4aA02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.53 38.0 3.46e-01 75.9% 65.7%
2f4qA01 3.30.66.10 Alpha Beta › 2-Layer Sandwich › Viral Topoisomerase I › DNA topoisomerase I domain 0.53 26.0 3.09e-01 91.4% 68.1%
4tyzA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 33.0 3.44e-01 91.4% 66.1%
1uebA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.53 29.0 3.64e-01 81.0% 95.2%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 29.0 3.58e-01 87.9% 100.0%
3oyyA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.52 28.0 3.51e-01 80.2% 89.4%
2f5kA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 25.0 3.29e-01 79.3% 100.0%
3oymA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.50 27.0 3.26e-01 80.2% 82.9%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4352326 2008.1.1.81 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF2726 0.63 52.0 5.19e-01 88.8% 96.7%
5056826 4.17.1.1 ↗ beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like › GatD_N 0.63 31.0 3.97e-01 83.6% 83.1%
5053906 4.17.1.1 ↗ beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like › GatD_N 0.62 31.0 4.10e-01 86.2% 91.7%
4932253 2008.1.1.100 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N_2 0.60 54.0 4.97e-01 96.6% 77.9%
5016968 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 50.0 4.77e-01 99.1% 80.7%
5004397 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 53.0 4.75e-01 100.0% 77.5%
4939428 56.2.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › CO dehydrogenase accessory protein CooT › CO dehydrogenase accessory protein CooT › CooT 0.57 31.0 4.04e-01 77.6% 100.0%
2413544 56.2.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › CO dehydrogenase accessory protein CooT › CO dehydrogenase accessory protein CooT › CooT 0.57 32.0 4.06e-01 80.2% 100.0%
4970510 56.2.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › CO dehydrogenase accessory protein CooT › CO dehydrogenase accessory protein CooT › CooT 0.57 33.0 4.06e-01 81.0% 98.5%
5050320 4.17.1.1 ↗ beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like › GatD_N 0.57 33.0 3.96e-01 89.7% 88.0%
4948433 4.17.1.1 ↗ beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like › GatD_N 0.57 31.0 3.86e-01 86.2% 89.7%
5081442 4.17.1.1 ↗ beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like › GatD_N 0.56 31.0 3.78e-01 86.2% 87.1%
5027289 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.56 49.0 4.22e-01 99.1% 71.4%
4971470 4.17.1.1 ↗ beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like › GatD_N 0.55 33.0 3.99e-01 86.2% 92.0%
4171461 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.55 48.0 4.16e-01 98.3% 95.1%
3936885 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 30.0 3.65e-01 82.8% 90.8%
4120629 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.54 32.0 3.72e-01 83.6% 86.7%
4944045 4.17.1.2 ↗ beta barrels › SH3 › GatD N-terminal domain-like › GatD N-terminal domain-like › Asparaginase 0.54 32.0 3.86e-01 87.1% 94.3%
4964370 2008.1.1.230 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF7527 0.54 47.0 3.81e-01 98.3% 99.6%
4238582 3174.2.1.1 ↗ beta barrels › Ribosomal protein L14-like › Barrel domain in flagellar protein FlgA › Barrel domain in flagellar protein FlgA › ChapFlgA 0.53 29.0 3.68e-01 93.1% 100.0%
4161673 4.1.1.105 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5604 0.52 29.0 3.30e-01 82.8% 70.6%
4646632 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.52 29.0 3.57e-01 81.9% 93.8%
3199204 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.51 40.0 4.24e-01 94.0% 93.3%
5075469 4.1.1.3 ↗ beta barrels › SH3 › SH3 › SH3 › KOW 0.51 29.0 3.52e-01 78.4% 95.4%
4010715 243.3.1.17 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › Imm-NTF2-2 0.50 30.0 3.66e-01 94.8% 95.7%
D3 medium residues 139-191_234-274
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4brcA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.57 46.0 3.51e-01 88.3% 61.8%
3lidA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 43.0 3.90e-01 92.6% 73.9%
1k4nA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 44.0 3.61e-01 96.8% 88.5%
1p49A01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.51 43.0 2.94e-01 95.7% 81.2%
1fsuA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.50 42.0 2.92e-01 95.7% 81.1%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5046708 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 46.0 4.11e-01 95.7% 88.9%
3447487 304.6.1.2 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › ALO 0.53 36.0 2.81e-01 71.3% 58.7%
3811165 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.53 45.0 3.48e-01 94.7% 50.2%
4265963 223.1.1.23 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_2 0.51 43.0 3.57e-01 96.8% 62.7%
4096733 3008.1.1.0 ↗ a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.51 36.0 3.85e-01 90.4% 87.5%