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NC_041911.1__YP_009598749.1__FDH28_gp056__00056

Bact-Vir

NC_041911.1__YP_009598749.1__FDH28_gp056__00056

Identity

Accession:
NC_041911 ↗
Kingdom:
phage

Quality

91.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Ripduovirus› Ralstonia_phage_RP12

TaxID: 1923889

Cluster

View cluster (2 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 1-94
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3imkA00 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.75 63.0 5.16e-01 88.3% 75.9%
2qbuA01 3.40.1010.10 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › Tetrapyrrole methylase, N-terminal domain 0.67 50.0 4.50e-01 79.8% 65.9%
3qyfA01 3.40.50.10770 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Hypothetical protein VC1899 like domain (Restriction endonuclease-like) 0.65 48.0 4.05e-01 79.8% 73.3%
4c0rA02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.64 37.0 3.61e-01 80.9% 51.0%
3n8hA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.63 49.0 4.03e-01 84.0% 85.8%
4h18A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.63 48.0 3.40e-01 81.9% 69.5%
3gybA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.63 47.0 4.21e-01 80.9% 67.4%
3qitB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.62 51.0 3.64e-01 89.4% 76.0%
5egnA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.61 49.0 3.66e-01 89.4% 75.4%
1pjrA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 50.0 4.00e-01 92.6% 57.4%
2y6uA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.60 48.0 3.35e-01 89.4% 65.4%
5b1yA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.60 51.0 3.84e-01 94.7% 60.7%
2xuaA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 47.0 3.53e-01 89.4% 70.0%
1kqpA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.59 45.0 3.27e-01 80.9% 87.8%
3a11B02 3.40.50.10470 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Translation initiation factor eif-2b; domain 2 0.59 54.0 4.21e-01 100.0% 52.3%
4n03A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.59 45.0 3.72e-01 81.9% 76.1%
2xvyA02 3.40.50.1400 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 43.0 3.97e-01 77.7% 95.2%
1fuyB01 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 45.0 3.78e-01 83.0% 72.6%
2wjwA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 44.0 3.75e-01 81.9% 63.2%
2wueA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.58 46.0 3.36e-01 88.3% 85.5%
1qydA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 45.0 3.65e-01 85.1% 63.9%
6twjA01 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.58 42.0 3.68e-01 77.7% 76.0%
4yo7A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 45.0 3.85e-01 85.1% 63.5%
1ufvA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.57 44.0 3.70e-01 84.0% 82.6%
2jfzA02 3.40.50.1860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 42.0 3.94e-01 77.7% 99.2%
3ke8A01 3.40.1010.20 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain 0.57 42.0 3.98e-01 77.7% 74.3%
4zeoH02 3.40.50.10470 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Translation initiation factor eif-2b; domain 2 0.56 47.0 4.00e-01 92.6% 69.4%
1m2vB04 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.56 41.0 3.11e-01 76.6% 85.6%
1hv8A02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 43.0 3.77e-01 85.1% 66.2%
3g5jA00 3.40.250.10 Alpha Beta › 3-Layer(aba) Sandwich › Oxidized Rhodanese; domain 1 › Rhodanese-like domain 0.56 42.0 3.81e-01 80.9% 76.2%
4c6rA00 3.40.50.10140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Toll/interleukin-1 receptor homology (TIR) domain 0.55 46.0 3.96e-01 95.7% 67.9%
3dnfB01 3.40.1010.20 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain 0.55 41.0 4.03e-01 78.7% 83.0%
4wesB04 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.55 41.0 4.10e-01 79.8% 84.7%
4q6bA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 40.0 3.61e-01 79.8% 54.5%
2y27B01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.55 47.0 3.29e-01 96.8% 64.0%
6gt9A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 46.0 3.83e-01 94.7% 77.6%
3rotA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 43.0 3.83e-01 86.2% 73.0%
1o4wA00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.54 41.0 3.68e-01 78.7% 86.4%
4c4aA03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 39.0 3.43e-01 77.7% 70.1%
4evwA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.53 43.0 3.33e-01 94.7% 82.7%
2kpoA00 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 37.0 3.60e-01 78.7% 64.5%
3iplB01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.52 42.0 2.88e-01 89.4% 48.6%
1nv8A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 37.0 2.96e-01 74.5% 54.8%
2f9fA00 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.52 38.0 3.27e-01 79.8% 56.6%
2yhaA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 38.0 3.44e-01 79.8% 69.1%
3gy1B02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.51 40.0 3.03e-01 85.1% 58.8%
2aznA00 3.40.430.10 Alpha Beta › 3-Layer(aba) Sandwich › Dihydrofolate Reductase, subunit A › Dihydrofolate Reductase, subunit A 0.51 41.0 3.24e-01 92.6% 62.1%
3ik4A02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.50 40.0 3.07e-01 89.4% 58.9%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5004763 7563.1.1.4 ↗ a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related › YpsA 0.88 65.0 5.35e-01 76.6% 64.5%
4277518 7563.1.1.4 ↗ a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related › YpsA 0.79 61.0 4.79e-01 80.9% 61.7%
119404 7563.1.1.5 ↗ a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related › cpYpsA 0.75 63.0 5.16e-01 88.3% 75.9%
5080508 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.71 54.0 4.73e-01 79.8% 63.0%
3602124 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.69 52.0 4.63e-01 79.8% 63.0%
5009930 7592.1.1.6 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › Csa3_N 0.67 50.0 4.49e-01 80.9% 84.4%
5045614 7512.1.1.0 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.65 57.0 4.35e-01 96.8% 61.8%
3458229 2005.1.1.21 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Pantoate_ligase 0.65 50.0 3.92e-01 83.0% 86.3%
3966875 7577.1.1.3 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Aminotran_5 0.65 47.0 3.22e-01 76.6% 75.2%
4449595 2004.1.1.455 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD-helicase, UvrD_C, UvrD_C_2 0.63 54.0 3.27e-01 96.8% 78.5%
4412868 2005.1.1.21 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Pantoate_ligase 0.63 48.0 3.91e-01 84.0% 83.2%
4486112 7592.1.1.3 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › DUF6293_N 0.61 46.0 4.20e-01 79.8% 88.0%
4259515 2005.1.1.21 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Pantoate_ligase 0.61 46.0 3.70e-01 80.9% 80.5%
4615208 2007.2.2.7 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Phosphotyrosine protein phosphatases I-like › DUF2325 0.61 45.0 4.49e-01 78.7% 77.0%
3301514 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.61 46.0 3.39e-01 81.9% 57.8%
None — 0.60 52.0 3.57e-01 98.9% 37.2%
1565415 7579.1.1.44 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_6 0.59 48.0 3.23e-01 89.4% 59.7%
3959397 2004.1.1.49 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD-helicase 0.59 41.0 2.97e-01 72.3% 26.8%
4861321 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.59 40.0 3.47e-01 79.8% 43.8%
3673088 2004.1.1.186 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_12 0.58 41.0 3.48e-01 76.6% 61.8%
3934219 323.1.1.20 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding,ACAS_N 0.57 47.0 3.51e-01 93.6% 34.3%
3239102 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.57 41.0 3.43e-01 75.5% 53.9%
4439294 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.56 42.0 3.86e-01 80.9% 79.2%
3829758 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.56 43.0 3.51e-01 85.1% 42.7%
5010054 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.56 36.0 3.19e-01 78.7% 41.3%
3272687 2003.1.5.79 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_23 0.56 46.0 3.56e-01 94.7% 57.1%
4502261 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.55 41.0 3.77e-01 78.7% 74.4%
4956540 7597.1.1.0 ↗ a/b three-layered sandwiches › Endolysin C-terminal domain › Endolysin C-terminal domain › Endolysin C-terminal domain 0.55 39.0 4.08e-01 81.9% 83.5%
4103800 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.55 41.0 3.83e-01 79.8% 79.2%
4992778 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.55 46.0 3.63e-01 96.8% 87.7%
3729634 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.55 43.0 3.17e-01 85.1% 34.6%
5037855 7539.1.1.1 ↗ a/b three-layered sandwiches › Creatininase › Creatininase › Creatininase › Creatininase 0.55 45.0 3.60e-01 95.7% 84.7%
3735434 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.55 39.0 3.24e-01 79.8% 40.0%
3731438 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.54 43.0 3.14e-01 85.1% 33.2%
4218926 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.54 40.0 3.81e-01 80.9% 77.5%
5003854 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.54 40.0 3.83e-01 80.9% 79.1%
4979896 7584.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins 0.54 40.0 3.01e-01 79.8% 36.4%
4564292 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.54 40.0 3.85e-01 80.9% 80.0%
3727807 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.54 39.0 2.96e-01 78.7% 35.2%
5005881 7584.1.1.1 ↗ a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › AMP-binding 0.54 39.0 3.39e-01 79.8% 48.0%
3985686 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.53 38.0 3.38e-01 78.7% 50.7%
2393002 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.52 40.0 3.14e-01 83.0% 51.6%
3280738 2007.1.4.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Phosphofructokinase N-terminal domain 0.52 39.0 3.94e-01 80.9% 86.3%
3576390 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.52 35.0 2.95e-01 80.9% 38.2%
3935782 2007.2.5.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase › Rhodanese 0.52 40.0 3.74e-01 80.9% 66.1%
3597211 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.51 38.0 3.13e-01 79.8% 42.7%
4965060 7584.1.1.1 ↗ a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › AMP-binding 0.51 37.0 3.19e-01 79.8% 44.8%
4946985 2004.1.1.43 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SRP54 0.51 41.0 3.16e-01 89.4% 64.0%
3441883 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.50 37.0 3.34e-01 78.7% 63.7%