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Ribonuclease_H
Euk-VirChrysochromulina_ericina_virus
Ribonuclease_H__YP_009173583__Chrysochromulina_ericina_virus__455364
Identity
- Accession:
- YP_009173583 ↗
- Protein ID:
- Ribonuclease_H
- Kingdom:
- euk
Quality
88.6
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Algavirales›
Phycodnaviridae›
Chrysochromulina_ericina_virus
TaxID: 455364
Cluster
View cluster (44 members)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 5-178_250-260
Domain cluster:
rep: Hypothetical_protein_SPPV_50__NP_659626__Sheeppox_virus__10266__D1-82_143-236
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02739.23 best | 5_3_exonuc_N | 65.6 | 6.30e-18 | 98.9% | 90.8% |
CATH (15)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3zdbA01 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.89 | 69.0 | 7.50e-01 | 94.1% | 93.6% |
| 1tfrA01 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.82 | 74.0 | 7.16e-01 | 100.0% | 84.5% |
| 1xo1A02 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.80 | 65.0 | 7.04e-01 | 100.0% | 98.1% |
| 1cmwA01 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.72 | 55.0 | 6.09e-01 | 88.1% | 96.0% |
| 1a76A01 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.68 | 61.0 | 5.87e-01 | 94.1% | 86.5% |
| 2bgwB01 | 3.40.50.10130 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.66 | 34.0 | 3.96e-01 | 75.7% | 68.7% |
| 2kpoA00 | 3.40.50.11230 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.65 | 33.0 | 4.20e-01 | 91.9% | 81.8% |
| 5ywwA01 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.60 | 38.0 | 4.56e-01 | 88.1% | 100.0% |
| 3o90B00 | 3.40.50.850 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Isochorismatase-like | 0.57 | 49.0 | 4.95e-01 | 94.1% | 91.5% |
| 3hu5A00 | 3.40.50.850 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Isochorismatase-like | 0.55 | 47.0 | 4.73e-01 | 94.1% | 89.5% |
| 3olqA00 | 3.40.50.12370 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.54 | 42.0 | 3.56e-01 | 90.8% | 48.7% |
| 3hcwA02 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.54 | 38.0 | 4.26e-01 | 70.8% | 97.2% |
| 3ksrA02 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.51 | 37.0 | 3.58e-01 | 75.1% | 66.7% |
| 4h08A00 | 3.40.50.1110 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase | 0.51 | 38.0 | 3.73e-01 | 76.8% | 90.0% |
| 2w02B01 | 1.10.150.640 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle | 0.51 | 22.0 | 3.37e-01 | 91.4% | 100.0% |
ECOD (35)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3387660 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.86 | 72.0 | 7.49e-01 | 94.1% | 93.5% |
| 3261281 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.86 | 73.0 | 7.67e-01 | 94.1% | 96.4% |
| 4125023 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.85 | 72.0 | 7.51e-01 | 94.1% | 94.7% |
| 3838776 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.85 | 70.0 | 7.43e-01 | 94.1% | 95.2% |
| 4355422 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.85 | 74.0 | 7.67e-01 | 100.0% | 95.4% |
| 4157264 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.85 | 75.0 | 7.64e-01 | 94.1% | 93.9% |
| 4995752 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.85 | 71.0 | 7.54e-01 | 94.1% | 97.0% |
| 3969358 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.85 | 71.0 | 7.66e-01 | 93.5% | 100.0% |
| 3964138 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.84 | 76.0 | 7.74e-01 | 100.0% | 96.1% |
| 4238071 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.84 | 74.0 | 7.61e-01 | 94.1% | 96.0% |
| 2074443 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.84 | 70.0 | 7.28e-01 | 93.5% | 92.5% |
| 4031817 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.83 | 72.0 | 7.50e-01 | 94.1% | 97.1% |
| 4165496 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.83 | 76.0 | 7.62e-01 | 100.0% | 95.1% |
| 3831671 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.83 | 75.0 | 7.36e-01 | 94.1% | 95.9% |
| 4324598 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.82 | 73.0 | 7.37e-01 | 100.0% | 91.9% |
| 4136793 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.81 | 78.0 | 7.41e-01 | 100.0% | 88.1% |
| 4040391 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.81 | 73.0 | 7.47e-01 | 94.1% | 97.8% |
| 3293941 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.81 | 77.0 | 7.36e-01 | 100.0% | 95.2% |
| 4322588 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.80 | 75.0 | 7.60e-01 | 99.5% | 98.9% |
| 3942445 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.80 | 73.0 | 7.32e-01 | 100.0% | 94.1% |
| 4029535 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.80 | 71.0 | 7.27e-01 | 94.1% | 95.6% |
| 3942272 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.80 | 70.0 | 7.34e-01 | 94.1% | 99.4% |
| 3838580 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.76 | 68.0 | 6.89e-01 | 97.3% | 95.6% |
| 3329169 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.75 | 63.0 | 6.51e-01 | 94.1% | 92.6% |
| 4028492 | 2006.1.4.25 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_I | 0.74 | 66.0 | 6.08e-01 | 93.5% | 83.0% |
| 3913336 | 2006.1.4.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I | 0.72 | 57.0 | 5.71e-01 | 93.5% | 81.1% |
| 3216159 | 2007.5.1.0 ↗ | a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase | 0.59 | 44.0 | 3.84e-01 | 76.8% | 56.1% |
| 5060902 | 2006.1.4.2 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN | 0.56 | 39.0 | 4.55e-01 | 89.2% | 99.2% |
| 4988572 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.55 | 43.0 | 4.68e-01 | 90.8% | 99.3% |
| 3682488 | 2007.5.1.8 ↗ | a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 | 0.54 | 39.0 | 4.16e-01 | 75.7% | 92.7% |
| 3776724 | 2007.5.1.0 ↗ | a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase | 0.53 | 41.0 | 3.61e-01 | 100.0% | 54.5% |
| 3950703 | 2004.1.1.60 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SKI | 0.51 | 39.0 | 3.94e-01 | 76.8% | 94.4% |
| 5077286 | 2004.1.1.79 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Thymidylate_kin | 0.51 | 42.0 | 3.98e-01 | 86.5% | 97.7% |
| 4183580 | 2004.1.1.79 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Thymidylate_kin | 0.51 | 38.0 | 3.82e-01 | 77.8% | 96.4% |
| 3273735 | 2008.1.1.7 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › ERCC4 | 0.50 | 39.0 | 3.73e-01 | 91.4% | 70.5% |
D2
high
residues 185-244
Domain cluster:
representative
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5hmlA02 | 1.10.150.20 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain | 0.85 | 80.0 | 7.14e-01 | 100.0% | 90.0% |
| 3zdbA02 | 1.10.150.20 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain | 0.77 | 68.0 | 6.00e-01 | 100.0% | 79.8% |
| 3h7iA02 | 1.10.150.20 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain | 0.74 | 65.0 | 6.03e-01 | 100.0% | 96.1% |
| 1yvjA02 | 1.10.510.10 | Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 | 0.58 | 43.0 | 3.09e-01 | 81.7% | 54.6% |
| 4ri1C00 | 3.40.630.30 | Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) | 0.54 | 45.0 | 3.34e-01 | 100.0% | 44.0% |
| 2qm0A01 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.51 | 37.0 | 2.54e-01 | 81.7% | 19.6% |
ECOD (9)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2074406 | 102.1.1.4 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc | 0.84 | 78.0 | 6.33e-01 | 100.0% | 67.9% |
| 3942250 | 102.1.1.4 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc | 0.83 | 77.0 | 5.77e-01 | 100.0% | 65.9% |
| 4995753 | 102.1.1.4 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc | 0.82 | 75.0 | 5.90e-01 | 100.0% | 59.7% |
| 3964109 | 102.1.1.4 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc | 0.81 | 74.0 | 6.85e-01 | 100.0% | 94.7% |
| 3283743 | 102.1.1.0 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like | 0.81 | 73.0 | 4.45e-01 | 98.3% | 20.9% |
| 4440292 | 102.1.1.4 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc | 0.81 | 73.0 | 5.82e-01 | 100.0% | 59.1% |
| None | — | 0.80 | 73.0 | 6.31e-01 | 100.0% | 80.0% | |
| 4319500 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.80 | 72.0 | 4.19e-01 | 100.0% | 15.4% |
| 4237116 | 102.1.1.4 ↗ | alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc | 0.79 | 72.0 | 6.49e-01 | 100.0% | 88.7% |