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NC_041929.1__YP_009601431.1__FDH46_gp172__00306

Bact-Vir

NC_041929.1__YP_009601431.1__FDH46_gp172__00306

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

94.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

Cluster

View cluster (3 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 3-76
PDB
Domain cluster: rep: OQ504961.1__WID42094.1__X__00032__D2-65
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3l50A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.60 38.0 3.14e-01 75.7% 34.6%
1vq8B03 3.30.1430.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L3; Chain: B; domain 2, › 0.58 45.0 4.00e-01 86.5% 96.4%
1z4vA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.58 50.0 3.15e-01 100.0% 38.7%
7qzqA01 2.120.10.80 Mainly Beta › 6 Propeller › Neuraminidase › Kelch-type beta propeller 0.57 52.0 3.34e-01 100.0% 34.2%
2yh6D00 3.30.530.50 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.57 44.0 3.92e-01 86.5% 58.2%
3g4eA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.56 49.0 3.26e-01 98.6% 50.2%
4hceA00 2.40.50.860 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.55 42.0 3.55e-01 82.4% 99.2%
2yfsA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.55 47.0 2.92e-01 98.6% 47.7%
4uf7B00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.54 45.0 2.93e-01 100.0% 32.8%
1eq6A00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.54 47.0 3.57e-01 100.0% 46.6%
2l9pA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 41.0 3.21e-01 82.4% 61.0%
2b3uB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 40.0 3.17e-01 83.8% 56.1%
2r76A00 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.53 41.0 3.52e-01 89.2% 76.5%
6a5gA01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 39.0 3.31e-01 82.4% 58.1%
1kiaA01 3.30.46.10 Alpha Beta › 2-Layer Sandwich › Glycine N-methyltransferase; chain A, domain 1 › Glycine N-methyltransferase, chain A, domain 1 0.53 38.0 3.69e-01 78.4% 71.1%
1d3bB00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.52 39.0 3.85e-01 97.3% 75.3%
1y7bA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.52 46.0 3.03e-01 100.0% 37.8%
1ekbB02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 39.0 3.52e-01 82.4% 78.9%
2hq9B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 39.0 3.31e-01 85.1% 86.1%
5fi9A01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.52 43.0 2.81e-01 100.0% 91.4%
1vl7A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 39.0 3.36e-01 87.8% 92.6%
5ek8A01 2.60.40.3330 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 42.0 3.69e-01 98.6% 86.5%
1dmzA00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.51 40.0 3.19e-01 87.8% 68.4%
2oggA01 3.40.1410.10 Alpha Beta › 3-Layer(aba) Sandwich › Chorismate lyase › Chorismate lyase-like 0.51 39.0 3.23e-01 83.8% 94.8%
2p13A00 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.50 29.0 2.82e-01 82.4% 48.2%
3n0aA02 2.60.40.1110 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 41.0 3.49e-01 95.9% 93.3%
4hiaA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.50 43.0 3.36e-01 100.0% 64.2%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3957641 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.76 46.0 5.27e-01 90.5% 81.8%
3803140 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.71 50.0 4.32e-01 87.8% 47.8%
3787221 3257.1.1.1 ↗ a+b complex topology › Phosphoinositide phosphatase SAC1 N-terminal domain › Phosphoinositide phosphatase SAC1 N-terminal domain › Phosphoinositide phosphatase SAC1 N-terminal domain › Syja_N 0.69 52.0 3.77e-01 100.0% 28.0%
4158830 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.68 47.0 3.91e-01 87.8% 40.8%
3881665 385.1.1.11 ↗ few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines › IL17 0.68 38.0 3.41e-01 85.1% 40.0%
3193241 223.2.1.22 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Folliculin 0.66 50.0 4.15e-01 100.0% 46.2%
3383629 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.65 52.0 4.26e-01 86.5% 55.6%
3427136 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 52.0 4.28e-01 87.8% 56.9%
3338824 5.1.3.144 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › b-prop_At3g26010-like 0.64 57.0 3.67e-01 100.0% 28.4%
4981234 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.63 46.0 4.81e-01 87.8% 87.7%
3945393 7089.1.1.2 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › DUF5405 0.63 55.0 5.34e-01 94.6% 91.3%
4407986 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.62 44.0 3.61e-01 87.8% 39.6%
3252114 223.2.1.56 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Afi1, DENND11 0.62 47.0 3.65e-01 98.6% 35.9%
4351646 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.61 44.0 3.42e-01 87.8% 31.9%
3993127 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.61 51.0 3.13e-01 93.2% 37.4%
3830573 331.4.1.1 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › KA1 0.60 45.0 3.91e-01 79.7% 60.5%
3607858 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 51.0 4.58e-01 95.9% 70.5%
3630686 206.1.3.12 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL 0.59 45.0 2.89e-01 82.4% 40.3%
3254845 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 47.0 3.89e-01 86.5% 56.2%
4028630 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.58 34.0 3.65e-01 73.0% 66.2%
3431863 5.1.5.37 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › DUF295 0.58 45.0 3.12e-01 87.8% 39.7%
3824503 5.1.4.550 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_FKB95 0.58 51.0 3.48e-01 100.0% 30.4%
4030216 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.58 50.0 3.33e-01 100.0% 29.3%
3465186 5.1.8.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › putative conserved lipoprotein NT01CX_1156 0.58 50.0 4.18e-01 97.3% 75.4%
3474038 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.58 46.0 3.81e-01 89.2% 66.4%
3704579 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.57 46.0 3.56e-01 98.6% 39.4%
4248616 5.1.5.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.57 50.0 3.09e-01 98.6% 32.4%
4501100 7504.1.1.3 ↗ a/b three-layered sandwiches › ITPase-like › ITPase-like › ITPase-like › Maf 0.57 49.0 3.54e-01 100.0% 98.7%
3265386 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.56 42.0 3.33e-01 79.7% 51.6%
3398140 4.1.1.326 ↗ beta barrels › SH3 › SH3 › SH3 › Chitin_bind_4 0.56 36.0 3.66e-01 77.0% 64.0%
3581093 4292.2.1.0 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.56 48.0 4.70e-01 98.6% 92.5%
3877211 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.56 47.0 2.96e-01 95.9% 35.7%
3240522 2492.1.1.2 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB 0.55 44.0 3.28e-01 89.2% 70.0%
5079898 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.55 44.0 3.74e-01 90.5% 93.1%
3531180 223.2.1.25 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Avl9 0.55 47.0 3.58e-01 98.6% 49.7%
4452393 304.112.1.10 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain › Med13_N 0.54 40.0 3.58e-01 79.7% 55.2%
3934645 2492.1.1.2 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB 0.54 45.0 3.35e-01 90.5% 75.3%
3995113 331.4.1.1 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › KA1 0.54 40.0 3.73e-01 82.4% 62.1%
3173167 223.2.1.28 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Afi1 0.54 46.0 3.46e-01 98.6% 36.9%
3270697 223.2.1.25 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Avl9 0.54 48.0 3.71e-01 100.0% 45.5%
3207857 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 45.0 2.97e-01 100.0% 30.4%
3531113 223.2.1.25 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Avl9 0.54 46.0 3.42e-01 98.6% 43.8%
4020386 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.54 46.0 3.51e-01 100.0% 57.4%
3737184 7502.1.1.2 ↗ 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 › Brix 0.53 44.0 3.07e-01 91.9% 76.8%
3593432 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 46.0 3.44e-01 100.0% 58.0%
4414940 5.1.2.5 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › Glyco_hydro_68 0.53 46.0 2.79e-01 98.6% 43.5%
4994978 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 42.0 2.74e-01 95.9% 19.7%
3635685 9.3.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Quinohemoprotein amine dehydrogenase A chain, domain 3-like › Quinohemoprotein amine dehydrogenase A chain, domain 3-like 0.53 46.0 3.58e-01 100.0% 81.2%
3927132 221.13.1.0 ↗ a+b two layers › beta-Grasp › Mitochondrial calcium uniporter N-terminal domain › Mitochondrial calcium uniporter N-terminal domain 0.52 40.0 3.54e-01 86.5% 96.5%
3927095 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.51 40.0 3.65e-01 87.8% 73.3%
3525336 5.1.3.130 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › HPS3_N 0.51 42.0 3.15e-01 97.3% 69.0%
3171377 7026.1.1.5 ↗ beta meanders › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 › ATG2_CAD 0.51 40.0 2.97e-01 89.2% 50.0%
3243301 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.51 42.0 2.84e-01 100.0% 22.1%
4943678 4178.1.1.0 ↗ beta sandwiches › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain › Putative glucosidase YicI, C-terminal domain 0.51 39.0 3.75e-01 83.8% 84.7%
5005288 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 41.0 3.31e-01 93.2% 87.1%