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RNA-dependent_RNA_polymerase
Euk-VirHubei_narna-like_virus_24
RNA-dependent_RNA_polymerase__YP_009329842__Hubei_narna-like_virus_24__1922955
Identity
- Accession:
- YP_009329842 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
74.3
mean pLDDT
Cluster
View cluster (26 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
medium
residues 1-131
Domain cluster:
representative
CATH (14)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 7nmqA01 | 1.20.1170.10 | Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › | 0.63 | 46.0 | 3.40e-01 | 76.3% | 46.6% |
| 3ug9A02 | 1.20.1070.10 | Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins | 0.61 | 45.0 | 3.71e-01 | 74.8% | 80.0% |
| 6xkyA01 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.59 | 43.0 | 3.83e-01 | 75.6% | 79.1% |
| 1xmxA03 | 1.10.10.680 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Hypothetical protein VC1899 (Restriction endonuclease-like) | 0.58 | 39.0 | 4.56e-01 | 86.3% | 100.0% |
| 5ziyA01 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.58 | 42.0 | 3.75e-01 | 76.3% | 83.0% |
| 2nrjA01 | 1.20.1170.10 | Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › | 0.57 | 46.0 | 3.40e-01 | 85.5% | 94.8% |
| 1sqgA01 | 1.10.940.10 | Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like | 0.56 | 34.0 | 3.39e-01 | 85.5% | 55.3% |
| 3dyjA02 | 1.20.1420.10 | Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain | 0.55 | 44.0 | 4.17e-01 | 83.2% | 87.4% |
| 2jokA01 | 1.10.4120.10 | Mainly Alpha › Orthogonal Bundle › SopE-like GEF fold › SopE-like, GEF domain | 0.54 | 45.0 | 4.12e-01 | 89.3% | 75.4% |
| 1rp3A01 | 1.10.1740.10 | Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif | 0.54 | 25.0 | 3.01e-01 | 90.1% | 63.5% |
| 3pwxA01 | 1.20.1330.10 | Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain | 0.54 | 39.0 | 3.53e-01 | 75.6% | 70.1% |
| 1cnt200 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.53 | 34.0 | 3.46e-01 | 97.7% | 65.4% |
| 7c1iA01 | 1.20.120.160 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain | 0.52 | 38.0 | 4.31e-01 | 77.1% | 100.0% |
| 5azpB01 | 1.20.1600.10 | Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) | 0.51 | 46.0 | 3.31e-01 | 97.7% | 90.5% |
ECOD (19)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4124062 | 5050.1.1.9 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 | 0.67 | 38.0 | 3.18e-01 | 90.8% | 34.4% |
| 4008486 | 1075.5.1.0 ↗ | alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter | 0.61 | 43.0 | 3.63e-01 | 71.0% | 83.8% |
| 3781461 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.58 | 31.0 | 2.28e-01 | 87.8% | 18.3% |
| 3972015 | 5050.1.1.9 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 | 0.56 | 43.0 | 3.40e-01 | 80.2% | 77.8% |
| 3903240 | 5050.1.1.1 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr | 0.56 | 40.0 | 3.19e-01 | 73.3% | 75.1% |
| 5051518 | 1075.5.1.0 ↗ | alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter | 0.56 | 39.0 | 3.03e-01 | 71.0% | 66.0% |
| 3522682 | 601.19.1.17 ↗ | alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Niban2 | 0.56 | 41.0 | 3.33e-01 | 77.9% | 88.6% |
| 3978498 | 5050.1.1.9 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 | 0.55 | 43.0 | 3.71e-01 | 83.2% | 85.7% |
| 5004675 | 5050.1.1.53 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MarC | 0.54 | 45.0 | 3.95e-01 | 91.6% | 79.5% |
| 5018515 | 5050.1.1.53 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MarC | 0.54 | 45.0 | 3.95e-01 | 91.6% | 79.5% |
| 3567090 | 5079.1.1.1 ↗ | alpha duplicates or obligate multimers › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › MgtE | 0.53 | 43.0 | 3.65e-01 | 87.8% | 72.6% |
| 3604350 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.53 | 39.0 | 4.11e-01 | 75.6% | 95.8% |
| 3833548 | 5050.1.1.58 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › NFD4_C | 0.53 | 39.0 | 3.33e-01 | 76.3% | 90.5% |
| 3839175 | 601.51.1.1 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-helical domain in phase 1 flagellin › alpha-helical domain in phase 1 flagellin › Flagellin_N | 0.53 | 39.0 | 3.01e-01 | 76.3% | 63.7% |
| 4984025 | 5050.1.1.9 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 | 0.52 | 39.0 | 3.49e-01 | 77.1% | 66.9% |
| 4087220 | 613.1.1.1 ↗ | alpha complex topology › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › tRNA-synt_2c | 0.51 | 39.0 | 3.32e-01 | 83.2% | 57.0% |
| 3500773 | 3832.1.1.1 ↗ | alpha bundles › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › Tumor necrosis factor alpha-induced protein 8-like protein 2 › DUF758 | 0.51 | 44.0 | 4.04e-01 | 96.9% | 90.9% |
| 5008558 | 5050.1.1.9 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 | 0.50 | 38.0 | 3.31e-01 | 79.4% | 66.8% |
| 2642997 | 5050.1.1.9 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 | 0.50 | 38.0 | 3.37e-01 | 80.2% | 95.9% |
D2
medium
residues 132-152_173-301_342-389
Domain cluster:
representative
CATH (4)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1mukA02 | 3.90.1850.10 | Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 | 0.63 | 58.0 | 4.23e-01 | 98.5% | 59.8% |
| 2r7rA05 | 1.10.357.80 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › | 0.54 | 46.0 | 4.85e-01 | 98.5% | 99.4% |
| 4e1oA03 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.51 | 18.0 | 2.46e-01 | 93.9% | 57.1% |
| 2z2mD01 | 3.90.1310.10 | Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) | 0.51 | 19.0 | 3.04e-01 | 78.3% | 100.0% |
ECOD (19)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4019374 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.64 | 59.0 | 4.63e-01 | 100.0% | 75.8% |
| 3173834 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.62 | 53.0 | 4.11e-01 | 89.4% | 47.8% |
| 3589612 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.62 | 53.0 | 4.38e-01 | 89.4% | 62.1% |
| 4004424 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.62 | 53.0 | 4.20e-01 | 89.4% | 54.1% |
| 3097450 | 304.48.1.12 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Mononeg_RNA_pol | 0.62 | 54.0 | 4.26e-01 | 92.9% | 79.0% |
| 3945039 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.62 | 53.0 | 4.39e-01 | 89.4% | 59.4% |
| 4461237 | 4967.1.1.0 ↗ | alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases | 0.61 | 52.0 | 3.75e-01 | 89.4% | 37.7% |
| 4071235 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.61 | 52.0 | 3.77e-01 | 89.4% | 38.6% |
| 4516798 | 304.48.1.0 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like | 0.61 | 52.0 | 3.88e-01 | 89.4% | 42.9% |
| 3983816 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.60 | 42.0 | 3.88e-01 | 70.2% | 64.0% |
| 4497954 | 304.48.1.73 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1, RVT_N | 0.60 | 51.0 | 4.37e-01 | 89.4% | 64.8% |
| 5018583 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.60 | 51.0 | 4.29e-01 | 89.4% | 61.0% |
| 4152428 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.59 | 49.0 | 4.03e-01 | 87.9% | 57.7% |
| 223786 | 304.48.1.16 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4 | 0.58 | 53.0 | 4.50e-01 | 98.5% | 75.9% |
| 5002351 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.58 | 49.0 | 3.95e-01 | 89.4% | 53.6% |
| 5078830 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.55 | 44.0 | 4.00e-01 | 84.3% | 75.8% |
| 5029718 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.55 | 46.0 | 3.77e-01 | 87.9% | 58.5% |
| 4138932 | 304.48.1.72 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_N | 0.53 | 45.0 | 3.87e-01 | 89.4% | 66.3% |
| 4872037 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.52 | 44.0 | 4.00e-01 | 89.4% | 68.4% |
D3
medium
residues 153-172_390-470
Domain cluster:
representative
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3k49A00 | 1.25.10.10 | Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant | 0.52 | 37.0 | 2.56e-01 | 73.3% | 45.9% |
D4
medium
residues 302-341_471-551
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009272901__Fusarium_poae_mitovirus_4__1848153__D300-342_409-485
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF05919.17 best | Mitovir_RNA_pol | 35.6 | 8.20e-09 | 51.2% | 9.3% |
| PF05919.17 | Mitovir_RNA_pol | 25.2 | 1.10e-05 | 36.4% | 7.6% |