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NC_041929.1__YP_009601246.1__FDH46_gp357__00121

Bact-Vir

NC_041929.1__YP_009601246.1__FDH46_gp357__00121

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

79.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

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 7-56
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1df0A02 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.74 62.0 5.14e-01 100.0% 52.2%
1sf9A02 2.30.30.340 Mainly Beta › Roll › SH3 type barrels. › Hypothetical protein YfhH like domains 0.73 58.0 5.71e-01 100.0% 81.5%
6e55A01 2.30.30.90 Mainly Beta › Roll › SH3 type barrels. › Ferrous iron transport protein A (FeoA) 0.68 59.0 5.27e-01 100.0% 89.2%
4x9cD00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.68 56.0 5.33e-01 100.0% 76.7%
7cfdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.68 57.0 4.98e-01 100.0% 63.0%
3h8zA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.67 53.0 5.42e-01 90.0% 89.6%
2aj2A01 3.40.1740.10 Alpha Beta › 3-Layer(aba) Sandwich › VC0467-like › VC0467-like 0.67 60.0 4.78e-01 100.0% 55.7%
3lx7A01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.66 51.0 5.29e-01 100.0% 91.3%
4ytlA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.66 53.0 5.36e-01 100.0% 92.0%
3h8zA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.66 54.0 5.02e-01 100.0% 71.9%
3fb9B00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.65 57.0 4.86e-01 100.0% 67.9%
1b7tA02 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.65 54.0 5.36e-01 100.0% 88.5%
5i4eA01 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.64 49.0 5.09e-01 90.0% 91.3%
2e70A00 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.64 52.0 4.66e-01 100.0% 64.8%
6bogA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.64 52.0 5.18e-01 100.0% 90.4%
7afrX02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.62 55.0 5.19e-01 100.0% 83.3%
2cudA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.62 54.0 4.71e-01 100.0% 70.9%
1lckA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.62 54.0 5.17e-01 100.0% 94.9%
4b9dB01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.62 48.0 4.05e-01 90.0% 78.5%
4c5eC02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.61 53.0 4.33e-01 100.0% 79.2%
4m4zA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.60 50.0 5.18e-01 94.0% 100.0%
1hh2P02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 45.0 4.19e-01 86.0% 66.7%
2ej9A02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.57 44.0 4.43e-01 100.0% 91.8%
1sg5A01 2.30.30.400 Mainly Beta › Roll › SH3 type barrels. › Rof-like 0.56 45.0 4.12e-01 100.0% 67.5%
6qkgA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 47.0 3.70e-01 98.0% 58.6%
3mcaB01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.54 45.0 3.75e-01 100.0% 54.2%
1inlC02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.54 44.0 4.17e-01 96.0% 76.6%
3p54A02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.53 43.0 3.98e-01 100.0% 71.8%
1w0pA03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 45.0 3.11e-01 100.0% 46.5%
5bn3A03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.53 36.0 3.43e-01 74.0% 98.5%
6p2kB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 42.0 2.61e-01 100.0% 85.8%
2rprA00 2.20.25.240 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.52 43.0 3.71e-01 100.0% 75.9%
3zleA03 2.10.70.70 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.50 33.0 3.56e-01 72.0% 87.2%
1yg9A03 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.50 36.0 2.89e-01 80.0% 84.6%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4975150 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.77 63.0 6.01e-01 100.0% 76.7%
4995678 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.76 65.0 6.35e-01 100.0% 87.3%
5013892 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.76 62.0 6.09e-01 100.0% 83.6%
5033075 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 58.0 5.69e-01 100.0% 78.2%
4947995 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.72 56.0 5.52e-01 100.0% 80.0%
4348606 4.1.1.440 ↗ beta barrels › SH3 › SH3 › SH3 › PF27165 0.72 64.0 5.85e-01 100.0% 78.5%
4963446 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 62.0 5.69e-01 100.0% 75.4%
5041872 4.1.1.40 ↗ beta barrels › SH3 › SH3 › SH3 › FeoA 0.70 62.0 5.42e-01 100.0% 82.7%
4429179 4.1.1.175 ↗ beta barrels › SH3 › SH3 › SH3 › MSSS 0.70 52.0 5.44e-01 100.0% 91.1%
5044373 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 57.0 5.42e-01 100.0% 76.7%
5017214 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.69 56.0 5.46e-01 100.0% 81.8%
4024914 4.1.1.249 ↗ beta barrels › SH3 › SH3 › SH3 › KOW2_Spt5 0.69 55.0 5.23e-01 96.0% 73.3%
3604264 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 54.0 4.48e-01 94.0% 70.0%
4962256 101.1.2.937 ↗ alpha arrays › HTH › HTH › winged helix domain › PF25943 0.68 58.0 4.57e-01 100.0% 65.5%
4550511 4.1.1.175 ↗ beta barrels › SH3 › SH3 › SH3 › MSSS 0.67 48.0 4.96e-01 96.0% 84.4%
None — 0.67 56.0 3.04e-01 100.0% 5.3%
3711384 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 58.0 4.92e-01 100.0% 63.5%
3684908 4.1.1.238 ↗ beta barrels › SH3 › SH3 › SH3 › KOW5_SPT5 0.67 55.0 4.81e-01 100.0% 61.3%
3586487 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 55.0 4.60e-01 100.0% 54.1%
None — 0.66 54.0 2.98e-01 100.0% 5.8%
3671986 4.1.1.238 ↗ beta barrels › SH3 › SH3 › SH3 › KOW5_SPT5 0.66 54.0 4.85e-01 100.0% 65.7%
3943751 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.65 54.0 4.99e-01 94.0% 81.5%
4890270 4.1.1.33 ↗ beta barrels › SH3 › SH3 › SH3 › Myosin_N 0.65 52.0 5.14e-01 100.0% 85.2%
3294392 4.1.1.43 ↗ beta barrels › SH3 › SH3 › SH3 › SMN_Tudor 0.64 54.0 4.54e-01 100.0% 55.3%
3330943 4.1.1.43 ↗ beta barrels › SH3 › SH3 › SH3 › SMN_Tudor 0.64 54.0 5.24e-01 100.0% 85.5%
4978946 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.64 49.0 4.64e-01 84.0% 96.7%
3721794 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 53.0 5.01e-01 100.0% 78.3%
5077969 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 54.0 4.71e-01 100.0% 70.0%
3466771 375.3.1.2 ↗ few secondary structure elements › Rubredoxin-like › CSL zinc finger › CSL zinc finger › zf-CSL 0.63 42.0 4.15e-01 76.0% 63.6%
3217770 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 54.0 4.37e-01 100.0% 53.0%
3323530 4.1.1.118 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_15 0.62 53.0 4.92e-01 100.0% 86.2%
3929881 220.1.1.61 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C_FAK1 0.62 53.0 4.12e-01 100.0% 64.3%
3479395 64.1.1.0 ↗ beta meanders › WW domain-like › WW domain › WW domain 0.62 40.0 4.51e-01 72.0% 100.0%
3616382 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.61 49.0 4.64e-01 90.0% 88.3%
4025781 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.59 44.0 4.22e-01 82.0% 80.0%
3765126 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.58 50.0 4.92e-01 100.0% 100.0%
3196012 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 49.0 4.24e-01 100.0% 77.1%
167340 4.1.1.28 ↗ beta barrels › SH3 › SH3 › SH3 › BPL_C 0.57 44.0 4.43e-01 100.0% 91.8%
3218417 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.57 43.0 3.69e-01 88.0% 50.6%
3266702 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 44.0 3.78e-01 100.0% 75.3%
3504860 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.52 45.0 4.06e-01 100.0% 91.4%
3593349 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.52 44.0 2.80e-01 100.0% 35.4%
3632665 325.1.7.1 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › Biotin_lipoyl 0.51 34.0 3.02e-01 72.0% 70.6%
3401149 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 41.0 2.85e-01 100.0% 41.0%
3396002 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 39.0 2.79e-01 98.0% 62.0%
3893039 6129.1.1.1 ↗ beta barrels › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › VWD 0.50 41.0 3.03e-01 100.0% 53.1%