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NC_041908.1__YP_009598447.1__FDH25_gp05__00005

Bact-Vir

NC_041908.1__YP_009598447.1__FDH25_gp05__00005

Identity

Accession:
NC_041908 ↗
Kingdom:
phage

Quality

91.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Kleczkowskavirus› Rhizobium_phage_RHEph04

TaxID: 1220604

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 6-92
PDB
Domain cluster: rep: OP009285.1__UUV44842.1__RCRUDOLPH_75__00075__D3-77
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3e19B01 2.30.30.90 Mainly Beta › Roll › SH3 type barrels. › Ferrous iron transport protein A (FeoA) 0.67 41.0 4.58e-01 75.9% 82.8%
6e55A01 2.30.30.90 Mainly Beta › Roll › SH3 type barrels. › Ferrous iron transport protein A (FeoA) 0.66 42.0 4.55e-01 77.0% 77.0%
1yt3A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.64 49.0 3.76e-01 81.6% 46.4%
2rdpA00 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 0.64 50.0 4.25e-01 100.0% 52.1%
4gyiA01 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 0.63 53.0 5.20e-01 100.0% 83.9%
1bdp001 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.63 47.0 3.65e-01 80.5% 43.8%
3p54A02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.59 36.0 3.92e-01 78.2% 74.6%
4g54A01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.56 41.0 3.64e-01 77.0% 89.6%
1okeB02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.56 38.0 4.02e-01 90.8% 80.5%
2fhdA02 2.30.30.810 Mainly Beta › Roll › SH3 type barrels. › 0.56 38.0 4.13e-01 73.6% 86.1%
1faoA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 41.0 3.95e-01 78.2% 92.0%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.55 45.0 4.04e-01 88.5% 95.0%
3d6wB01 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.55 40.0 4.35e-01 77.0% 100.0%
3h8zA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.55 31.0 3.48e-01 88.5% 73.4%
2cs7A00 3.10.50.90 Alpha Beta › Roll › Chitinase A; domain 3 › 0.54 34.0 4.05e-01 75.9% 100.0%
3orjA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 36.0 3.41e-01 71.3% 88.8%
4d8mA03 2.100.10.40 Mainly Beta › Aligned Prism › Vitelline Membrane Outer Layer Protein I, subunit A › 0.52 38.0 2.96e-01 77.0% 85.9%
5cdvA01 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.52 35.0 3.15e-01 70.1% 75.8%
1vmoA00 2.100.10.20 Mainly Beta › Aligned Prism › Vitelline Membrane Outer Layer Protein I, subunit A › Vitelline membrane outer layer protein I (VOMI) 0.51 38.0 3.09e-01 78.2% 55.2%
8siuA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 44.0 2.98e-01 98.9% 90.4%
3rbtD01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 35.0 3.12e-01 71.3% 65.6%
2krsA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.51 31.0 3.67e-01 71.3% 90.0%
6i7eA01 1.20.58.530 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 41.0 3.30e-01 88.5% 96.6%
1x43A01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.51 31.0 3.53e-01 73.6% 85.5%
2hgaA01 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.50 37.0 3.76e-01 78.2% 87.1%
2b9wA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.50 43.0 3.21e-01 93.1% 84.3%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3694123 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.67 38.0 2.42e-01 89.7% 11.7%
3664145 2484.1.1.20 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_A_exo1 0.63 48.0 3.67e-01 81.6% 52.7%
5013516 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 51.0 4.99e-01 100.0% 80.0%
4015761 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 52.0 5.12e-01 100.0% 82.1%
3212254 2484.1.1.20 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_A_exo1 0.62 48.0 3.45e-01 81.6% 35.1%
3923385 2003.1.2.18 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.62 51.0 3.33e-01 89.7% 87.4%
3927943 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 47.0 3.37e-01 81.6% 31.6%
3357118 2484.1.1.20 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_A_exo1 0.60 46.0 3.53e-01 81.6% 49.5%
1856688 101.1.2.35 ↗ alpha arrays › HTH › HTH › winged helix domain › TFIIF_beta 0.59 41.0 4.43e-01 100.0% 88.7%
3517415 4.1.1.287 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5641 0.59 37.0 4.12e-01 74.7% 83.1%
3604523 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.58 46.0 4.14e-01 100.0% 61.7%
5027238 2.1.1.25 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_pol_B_exo1 0.58 36.0 3.03e-01 70.1% 36.0%
3989307 220.1.1.88 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF956 0.58 44.0 4.11e-01 82.8% 82.7%
3750304 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.57 43.0 3.90e-01 81.6% 73.3%
3743553 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.56 40.0 2.86e-01 74.7% 61.2%
1175057 4.1.1.145 ↗ beta barrels › SH3 › SH3 › SH3 › Crb2_Tudor 0.55 38.0 3.83e-01 73.6% 70.5%
4023885 2004.1.1.17 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Myosin_head 0.54 46.0 2.68e-01 95.4% 51.3%
3666622 1.1.1.9 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › TAXi_C 0.52 43.0 3.15e-01 89.7% 72.8%
3931203 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.52 41.0 3.62e-01 87.4% 85.2%
3267367 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.52 43.0 2.79e-01 93.1% 75.6%
3512448 220.1.1.37 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_13 0.52 40.0 3.36e-01 86.2% 68.1%
3720521 318.1.1.1 ↗ a+b two layers › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal_L6 0.52 37.0 3.60e-01 93.1% 68.4%
3449498 4286.1.1.1 ↗ beta complex topology › At5g01610-like › At5g01610-like › At5g01610-like › DUF538 0.51 40.0 3.68e-01 86.2% 63.5%
4160400 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.51 36.0 2.54e-01 74.7% 57.1%
5052405 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.51 35.0 3.48e-01 70.1% 75.3%
3505711 4.1.1.287 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5641 0.51 35.0 3.60e-01 72.4% 92.9%
3900920 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.50 41.0 3.68e-01 89.7% 90.4%