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XRN1_5-3_exonuclease
Euk-VirGolden_Marseillevirus
XRN1_5-3_exonuclease__YP_009310329__Golden_Marseillevirus__1720526
Identity
- Accession:
- YP_009310329 ↗
- Protein ID:
- XRN1_5-3_exonuclease
- Kingdom:
- euk
Quality
70.4
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Pimascovirales›
Marseilleviridae›
Marseillevirus›
Golden_Marseillevirus
TaxID: 1720526
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 29-188
Domain cluster:
representative
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF03159.25 best | XRN_N | 58.2 | 1.20e-15 | 56.9% | 32.4% |
| PF03159.25 | XRN_N | 26.3 | 6.70e-06 | 45.0% | 26.6% |
CATH (26)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1dnpA01 | 3.40.50.620 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs | 0.70 | 44.0 | 4.84e-01 | 100.0% | 76.9% |
| 3geeA03 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.67 | 38.0 | 4.15e-01 | 97.5% | 66.2% |
| 1j0aA02 | 3.40.50.1100 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.61 | 34.0 | 4.01e-01 | 100.0% | 80.8% |
| 7tjbA01 | 3.40.50.1110 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase | 0.58 | 48.0 | 4.38e-01 | 96.2% | 67.0% |
| 8gr2A01 | 3.40.50.1110 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase | 0.58 | 46.0 | 4.32e-01 | 93.8% | 69.2% |
| 3rotA02 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.57 | 39.0 | 4.18e-01 | 75.0% | 80.3% |
| 4o6vA00 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.57 | 46.0 | 4.06e-01 | 96.2% | 59.4% |
| 6feaB01 | 3.40.50.1980 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain | 0.56 | 44.0 | 4.57e-01 | 93.8% | 88.4% |
| 6feaA01 | 3.40.50.1980 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain | 0.55 | 42.0 | 3.93e-01 | 93.1% | 64.8% |
| 4h0oA02 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.54 | 46.0 | 4.20e-01 | 89.4% | 83.4% |
| 3ngxA02 | 3.40.50.10860 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 | 0.54 | 29.0 | 3.88e-01 | 100.0% | 100.0% |
| 6nplA01 | 1.20.1740.10 | Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I | 0.53 | 40.0 | 2.87e-01 | 76.9% | 95.9% |
| 3n4pC00 | 3.30.420.320 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › DNA-packaging terminase, C-terminal nuclease domain | 0.53 | 46.0 | 4.09e-01 | 91.9% | 87.2% |
| 3emzA00 | 3.20.20.80 | Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases | 0.52 | 48.0 | 3.77e-01 | 100.0% | 65.6% |
| 1ufoA00 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.52 | 47.0 | 4.06e-01 | 96.2% | 90.7% |
| 3ucxA00 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.52 | 47.0 | 3.95e-01 | 96.2% | 60.9% |
| 1auoA00 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.52 | 46.0 | 4.13e-01 | 95.6% | 94.0% |
| 1nmnA00 | 3.30.420.140 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain | 0.52 | 37.0 | 4.24e-01 | 93.8% | 100.0% |
| 2gm3A00 | 3.40.50.620 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs | 0.52 | 42.0 | 4.31e-01 | 100.0% | 89.5% |
| 2e9yB00 | 3.40.1160.10 | Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like | 0.51 | 47.0 | 3.76e-01 | 100.0% | 98.1% |
| 6yuqA01 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.51 | 42.0 | 3.65e-01 | 94.4% | 57.2% |
| 2dtxA00 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.51 | 45.0 | 3.84e-01 | 95.0% | 87.8% |
| 4da9B00 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.51 | 45.0 | 4.08e-01 | 96.2% | 90.3% |
| 1huxA02 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.50 | 39.0 | 4.14e-01 | 80.6% | 100.0% |
| 7w6bA01 | 3.40.50.410 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain | 0.50 | 42.0 | 3.56e-01 | 91.3% | 100.0% |
| 3r8eA01 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.50 | 41.0 | 4.41e-01 | 94.4% | 100.0% |
ECOD (45)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3294273 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.80 | 72.0 | 5.92e-01 | 100.0% | 56.3% |
| 3595159 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.79 | 74.0 | 6.36e-01 | 100.0% | 65.4% |
| 4443696 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.79 | 76.0 | 5.76e-01 | 100.0% | 54.6% |
| 4628515 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.79 | 75.0 | 6.12e-01 | 100.0% | 67.9% |
| 3612297 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.79 | 70.0 | 5.99e-01 | 100.0% | 62.1% |
| 3300817 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.79 | 75.0 | 5.71e-01 | 100.0% | 54.3% |
| 4027656 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.78 | 74.0 | 6.36e-01 | 100.0% | 67.1% |
| 3718959 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.78 | 74.0 | 6.42e-01 | 100.0% | 69.4% |
| 3596632 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.77 | 73.0 | 6.13e-01 | 100.0% | 73.6% |
| 4026642 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.77 | 72.0 | 6.22e-01 | 100.0% | 68.3% |
| 3251911 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.76 | 70.0 | 6.23e-01 | 100.0% | 71.4% |
| 3713303 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.75 | 71.0 | 6.03e-01 | 100.0% | 74.7% |
| 3293941 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.64 | 60.0 | 5.45e-01 | 100.0% | 81.0% |
| 3831671 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.64 | 59.0 | 5.54e-01 | 100.0% | 87.2% |
| 4136793 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.62 | 57.0 | 5.16e-01 | 100.0% | 75.7% |
| 5039733 | 7592.1.1.0 ↗ | a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains | 0.61 | 41.0 | 4.57e-01 | 100.0% | 84.6% |
| 4243731 | 2007.5.1.8 ↗ | a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 | 0.60 | 53.0 | 4.32e-01 | 96.2% | 66.6% |
| 3452345 | 2007.5.1.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL | 0.60 | 54.0 | 4.19e-01 | 97.5% | 62.4% |
| 3674675 | 2007.5.1.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL | 0.59 | 53.0 | 4.08e-01 | 96.2% | 60.0% |
| 4264908 | 2006.1.4.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I | 0.59 | 52.0 | 4.68e-01 | 100.0% | 70.2% |
| 3929291 | 1076.1.1.2 ↗ | alpha bundles › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Aph-1 | 0.57 | 41.0 | 3.85e-01 | 73.1% | 87.7% |
| 5079107 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.57 | 45.0 | 4.88e-01 | 86.9% | 100.0% |
| 2664650 | 2007.1.14.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like › Oxidored_nitro | 0.56 | 43.0 | 4.33e-01 | 93.1% | 77.8% |
| 4946373 | 1075.1.2.0 ↗ | alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain | 0.56 | 42.0 | 4.13e-01 | 78.1% | 93.1% |
| 3925925 | 300.1.1.9 ↗ | a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › MIT_C | 0.55 | 40.0 | 3.86e-01 | 100.0% | 66.7% |
| 4971822 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.55 | 48.0 | 4.73e-01 | 95.6% | 95.4% |
| 4030032 | 7579.1.1.0 ↗ | a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases | 0.53 | 44.0 | 3.44e-01 | 95.0% | 40.6% |
| 3581603 | 7579.1.1.18 ↗ | a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_2 | 0.53 | 47.0 | 4.09e-01 | 96.9% | 92.2% |
| 3968275 | 1075.1.1.1 ↗ | alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane | 0.52 | 38.0 | 3.40e-01 | 74.4% | 71.1% |
| 3466452 | 2484.1.1.10 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD | 0.52 | 48.0 | 4.08e-01 | 100.0% | 90.4% |
| 3465680 | 2004.1.1.56 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NB-ARC | 0.52 | 39.0 | 3.77e-01 | 78.1% | 90.8% |
| 3188177 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.52 | 38.0 | 3.43e-01 | 75.0% | 68.0% |
| 3689247 | 2484.1.1.10 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD | 0.52 | 48.0 | 4.05e-01 | 100.0% | 93.5% |
| 5062242 | 2484.1.1.21 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › BcrAD_BadFG | 0.52 | 45.0 | 4.40e-01 | 93.1% | 89.7% |
| 3252761 | 2007.1.19.1 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › FabD/lysophospholipase-like › Acyl_transf_1 | 0.51 | 47.0 | 3.78e-01 | 99.4% | 89.8% |
| 5064976 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.51 | 45.0 | 4.54e-01 | 96.9% | 94.4% |
| 4250774 | 7512.1.1.30 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_4 | 0.51 | 46.0 | 3.99e-01 | 96.2% | 85.8% |
| None | — | 0.51 | 46.0 | 3.89e-01 | 95.6% | 88.5% | |
| 5056072 | 7512.1.1.30 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_4 | 0.50 | 44.0 | 4.08e-01 | 93.8% | 99.5% |
| 3246007 | 7579.1.1.28 ↗ | a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S28 | 0.50 | 46.0 | 3.41e-01 | 98.1% | 70.9% |
| 5082709 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.50 | 41.0 | 4.34e-01 | 100.0% | 98.6% |
| 4932574 | 7512.1.1.8 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Epimerase_2 | 0.50 | 44.0 | 4.02e-01 | 95.0% | 100.0% |
| 4975222 | 2004.1.1.191 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_17 | 0.50 | 45.0 | 4.19e-01 | 96.9% | 98.5% |
| 4598609 | 2003.1.1.84 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › PRISE | 0.50 | 45.0 | 3.34e-01 | 96.9% | 45.2% |
| 5079477 | 1075.1.2.1 ↗ | alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX | 0.50 | 37.0 | 3.65e-01 | 76.9% | 98.9% |