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NC_041911.1__YP_009598745.1__FDH28_gp052__00052

Bact-Vir

NC_041911.1__YP_009598745.1__FDH28_gp052__00052

Identity

Accession:
NC_041911 ↗
Kingdom:
phage

Quality

75.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Ripduovirus› Ralstonia_phage_RP12

TaxID: 1923889

Cluster

View cluster (6 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 medium residues 43-180
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ltyA02 3.30.160.720 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 33.0 4.56e-01 96.4% 98.4%
5ck3F00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.67 38.0 3.79e-01 100.0% 52.4%
3tnjA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.66 37.0 3.96e-01 100.0% 62.0%
2o3rA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.66 40.0 4.19e-01 100.0% 66.9%
5dn8A02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.65 36.0 3.40e-01 100.0% 44.2%
2ielA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.65 38.0 3.97e-01 100.0% 61.4%
1ao0A02 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.62 33.0 3.45e-01 100.0% 54.5%
1j24A00 3.40.50.10130 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 35.0 3.59e-01 100.0% 57.1%
3if5A02 3.30.750.24 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › STAS domain 0.61 32.0 3.91e-01 97.1% 78.7%
4rz2B00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 37.0 3.04e-01 100.0% 33.2%
2bgwB01 3.40.50.10130 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 35.0 3.62e-01 100.0% 58.8%
3t1iA02 3.30.110.110 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Mre11, capping domain 0.60 41.0 4.70e-01 97.8% 100.0%
7ch9L01 3.30.750.24 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › STAS domain 0.60 33.0 3.96e-01 96.4% 82.8%
1z85B02 3.40.1280.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha/beta knot › SPOUT methyltransferase, trefoil knot domain 0.58 33.0 3.29e-01 100.0% 51.0%
1f2dA02 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 32.0 3.69e-01 100.0% 72.5%
1jhdA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.58 35.0 3.11e-01 100.0% 41.4%
2ymbA00 3.30.870.30 Alpha Beta › 2-Layer Sandwich › Endonuclease; Chain A › MITD, C-terminal phospholipase D-like domain 0.57 33.0 3.26e-01 100.0% 49.7%
3a2kA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.57 36.0 3.66e-01 100.0% 63.7%
4da2A02 3.40.1350.60 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.57 38.0 3.75e-01 100.0% 61.8%
3lyhA00 3.40.50.1400 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 40.0 4.28e-01 100.0% 87.5%
1wy5A01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 33.0 2.87e-01 100.0% 39.6%
2c20A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 39.0 3.48e-01 100.0% 52.7%
1vkhA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 38.0 3.12e-01 100.0% 40.2%
2q0xA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 46.0 3.65e-01 100.0% 49.5%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4931052 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.76 42.0 4.34e-01 100.0% 56.3%
4021340 2007.9.1.9 ↗ a/b three-layered sandwiches › Flavodoxin-like › Toll/Interleukin receptor TIR domain › Toll/Interleukin receptor TIR domain › PF29907 0.73 45.0 4.05e-01 100.0% 46.7%
3388478 2007.9.1.9 ↗ a/b three-layered sandwiches › Flavodoxin-like › Toll/Interleukin receptor TIR domain › Toll/Interleukin receptor TIR domain › PF29907 0.72 45.0 3.99e-01 100.0% 44.7%
3216718 2007.9.1.9 ↗ a/b three-layered sandwiches › Flavodoxin-like › Toll/Interleukin receptor TIR domain › Toll/Interleukin receptor TIR domain › PF29907 0.70 44.0 3.99e-01 100.0% 47.8%
3838141 2004.1.1.67 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CbiA 0.69 40.0 3.45e-01 100.0% 36.7%
3511061 2005.1.1.36 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.67 40.0 3.80e-01 100.0% 50.6%
4927459 3979.1.1.0 ↗ a+b four layers › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain 0.67 35.0 4.59e-01 99.3% 97.1%
3964887 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.66 38.0 3.88e-01 97.1% 57.0%
5053786 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.64 38.0 3.49e-01 100.0% 44.6%
3389112 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.63 36.0 3.21e-01 100.0% 39.0%
4962915 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.62 35.0 3.71e-01 100.0% 61.7%
3245213 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 34.0 3.87e-01 100.0% 71.2%
3999486 2496.1.1.0 ↗ a/b three-layered sandwiches › SpoIIaa-like › SpoIIaa-like › SpoIIaa-like 0.60 35.0 3.97e-01 97.1% 77.0%
3670467 2002.1.1.115 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_79n 0.59 40.0 3.23e-01 97.8% 35.5%
3924732 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 33.0 3.05e-01 100.0% 40.0%
4000045 7512.1.1.3 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 0.55 32.0 2.94e-01 100.0% 40.5%
5000410 7522.1.1.4 ↗ a/b three-layered sandwiches › TK C-terminal domain-like › TK C-terminal domain-like › TK C-terminal domain-like › PFOR_II 0.52 37.0 3.71e-01 100.0% 70.6%
4038287 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.51 35.0 3.55e-01 100.0% 69.6%
4117581 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.51 37.0 3.71e-01 100.0% 72.9%
4278305 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.51 36.0 3.65e-01 100.0% 72.5%
3489889 2005.1.1.11 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.50 35.0 3.38e-01 100.0% 61.9%
D2 medium residues 181-268
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4kqcA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 45.0 3.73e-01 96.6% 46.9%
3n75A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 42.0 3.72e-01 98.9% 53.5%
3lcmB00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.57 49.0 3.90e-01 98.9% 62.2%
3n8hA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.56 40.0 3.29e-01 76.1% 99.4%
1t3gB00 3.40.50.10140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Toll/interleukin-1 receptor homology (TIR) domain 0.56 47.0 4.01e-01 100.0% 55.6%
1h2bA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 40.0 3.56e-01 100.0% 49.3%
4q37A00 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.56 41.0 3.78e-01 100.0% 58.3%
3guwA00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.55 45.0 3.30e-01 88.6% 54.5%
3gffA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 46.0 3.20e-01 100.0% 30.7%
1krhA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.53 46.0 4.07e-01 100.0% 80.6%
3qvsA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 41.0 2.98e-01 89.8% 91.4%
5vegB00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.52 44.0 3.83e-01 100.0% 59.7%
2w42B02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 41.0 3.15e-01 90.9% 67.1%
3ctlA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.51 45.0 3.42e-01 100.0% 47.9%
4ol9A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 42.0 3.45e-01 100.0% 48.2%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5010972 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.60 45.0 3.36e-01 100.0% 28.6%
4013544 2007.2.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Flavoproteins 0.59 51.0 4.28e-01 98.9% 71.0%
4147569 2007.1.3.16 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › KaiA_N 0.58 42.0 3.69e-01 100.0% 49.3%
3631246 2007.2.1.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Flavoproteins › Flavodoxin_1 0.57 49.0 4.02e-01 100.0% 62.3%
3457387 2005.1.1.41 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.55 44.0 3.62e-01 89.8% 85.7%
3919325 2005.1.1.36 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.54 37.0 2.97e-01 71.6% 98.0%
3330674 2005.1.1.41 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.54 43.0 3.67e-01 89.8% 90.6%
3676583 2005.1.1.41 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.54 43.0 3.47e-01 89.8% 82.6%
4983514 2002.1.1.44 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase 0.54 44.0 3.24e-01 92.0% 63.2%
4883864 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.53 43.0 4.21e-01 100.0% 80.0%
3837596 2005.1.1.41 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.53 42.0 3.47e-01 88.6% 84.6%
5050025 7567.1.1.1 ↗ a/b three-layered sandwiches › LmbE-like › LmbE-like › LmbE-like › PIG-L 0.53 44.0 3.32e-01 95.5% 35.3%
5046104 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.52 41.0 3.37e-01 100.0% 44.7%
3471158 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.52 43.0 3.68e-01 90.9% 93.8%
3360085 2005.1.1.41 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.52 40.0 3.42e-01 87.5% 90.6%
3336896 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.52 44.0 3.45e-01 100.0% 68.6%
3604260 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.52 45.0 3.26e-01 100.0% 74.4%
5051563 7512.1.1.0 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.52 45.0 3.61e-01 100.0% 82.7%
5029063 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.52 35.0 2.58e-01 93.2% 22.5%
3484286 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.51 43.0 3.69e-01 92.0% 97.9%
5037656 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.51 43.0 3.05e-01 100.0% 43.7%
4468768 7514.1.1.1 ↗ a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › NAD_binding_1 0.51 44.0 3.72e-01 100.0% 72.3%
3270650 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.50 44.0 4.00e-01 100.0% 76.7%
3314969 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 39.0 3.37e-01 85.2% 73.8%
5048607 2007.3.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Succinyl-CoA synthetase domains › Succinyl-CoA synthetase domains › Succ_CoA_lig 0.50 42.0 3.51e-01 98.9% 52.0%