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RNA-dependent_RNA_polymerase
Euk-VirHubei_narna-like_virus_23
RNA-dependent_RNA_polymerase__YP_009336767__Hubei_narna-like_virus_23__1922954
Identity
- Accession:
- YP_009336767 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
77.9
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
high
residues 534-593
D2
medium
residues 1-117
Domain cluster:
rep: RNA-dependent_RNA_polymerase__YP_009329842__Hubei_narna-like_virus_24__1922955__D1-131
CATH (10)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1t3qA02 | 1.10.150.120 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain | 0.62 | 39.0 | 4.58e-01 | 100.0% | 91.4% |
| 6ks6q01 | 1.10.560.10 | Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain | 0.60 | 53.0 | 4.10e-01 | 100.0% | 91.2% |
| 3sk9A00 | 1.10.3210.30 | Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › | 0.57 | 43.0 | 3.48e-01 | 79.5% | 76.1% |
| 7p2yd01 | 1.10.520.20 | Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase | 0.57 | 45.0 | 4.80e-01 | 88.0% | 100.0% |
| 4l7aA00 | 3.40.390.70 | Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › | 0.55 | 41.0 | 3.25e-01 | 80.3% | 88.1% |
| 3a06B03 | 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 | 27.0 | 3.14e-01 | 75.2% | 64.8% |
| 2d2sA01 | 1.20.58.1210 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, N-terminal helical domain | 0.53 | 33.0 | 3.35e-01 | 83.8% | 62.1% |
| 5g5gA02 | 1.10.150.120 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain | 0.53 | 38.0 | 4.23e-01 | 73.5% | 96.7% |
| 3k1hA00 | 3.30.1120.180 | Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Flagellar FLiS export co-chaperone, HP1076 | 0.53 | 40.0 | 4.05e-01 | 79.5% | 96.5% |
| 6a3kA00 | 1.20.120.10 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 | 0.50 | 35.0 | 3.40e-01 | 70.9% | 90.7% |
ECOD (16)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3249832 | 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 | 0.64 | 39.0 | 3.23e-01 | 86.3% | 36.0% |
| 3839239 | 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 | 0.63 | 38.0 | 3.20e-01 | 87.2% | 35.5% |
| 4032844 | 5051.1.1.10 ↗ | alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › AA_permease_2 | 0.62 | 45.0 | 3.01e-01 | 75.2% | 64.7% |
| 4943810 | 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 | 0.61 | 38.0 | 3.12e-01 | 87.2% | 35.1% |
| 4134989 | 138.1.1.6 ↗ | alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA_pol3_delt_C | 0.60 | 44.0 | 4.38e-01 | 88.0% | 72.8% |
| 3494376 | 109.46.1.1 ↗ | alpha superhelices › Repetitive alpha hairpins › Helical domain in TOPLESS related protein 2 (TPR2) › Helical domain in TOPLESS related protein 2 (TPR2) › CTLH | 0.59 | 41.0 | 4.08e-01 | 71.8% | 72.8% |
| 4196844 | 109.46.1.1 ↗ | alpha superhelices › Repetitive alpha hairpins › Helical domain in TOPLESS related protein 2 (TPR2) › Helical domain in TOPLESS related protein 2 (TPR2) › CTLH | 0.58 | 41.0 | 3.57e-01 | 71.8% | 49.1% |
| 146380 | 131.1.1.14 ↗ | alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › Cas3_HD | 0.57 | 43.0 | 3.48e-01 | 79.5% | 76.1% |
| 4942452 | 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 | 0.56 | 47.0 | 3.90e-01 | 89.7% | 77.6% |
| 4171218 | 109.46.1.1 ↗ | alpha superhelices › Repetitive alpha hairpins › Helical domain in TOPLESS related protein 2 (TPR2) › Helical domain in TOPLESS related protein 2 (TPR2) › CTLH | 0.56 | 48.0 | 3.70e-01 | 92.3% | 83.5% |
| 5017264 | 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 | 0.56 | 46.0 | 3.96e-01 | 89.7% | 77.3% |
| 5005973 | 3625.1.1.0 ↗ | alpha bundles › CRISPR RNA silencing complex Cmr2 subunit second helical domain › CRISPR RNA silencing complex Cmr2 subunit second helical domain › CRISPR RNA silencing complex Cmr2 subunit second helical domain | 0.55 | 40.0 | 4.43e-01 | 82.1% | 100.0% |
| 3250971 | 616.1.1.0 ↗ | alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain | 0.54 | 42.0 | 4.45e-01 | 88.0% | 98.0% |
| 5014890 | 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 | 38.0 | 3.33e-01 | 76.1% | 70.3% |
| 4029995 | 174.1.1.0 ↗ | few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain | 0.51 | 46.0 | 3.98e-01 | 100.0% | 80.6% |
| 3414852 | 3567.1.1.0 ↗ | a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer | 0.50 | 35.0 | 3.41e-01 | 71.8% | 65.4% |
D3
medium
residues 118-168
Domain cluster:
representative
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5ekaA00 | 4.10.520.10 | Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins | 0.55 | 37.0 | 3.24e-01 | 72.5% | 83.5% |
ECOD (3)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4337374 | 2005.1.1.11 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 | 0.56 | 38.0 | 2.44e-01 | 72.5% | 15.3% |
| 3597958 | 221.1.1.0 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like | 0.56 | 38.0 | 2.57e-01 | 72.5% | 20.5% |
| 4469854 | 109.4.1.3270 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT, TPR_8, HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N, HAT_PRP39_C | 0.51 | 38.0 | 2.23e-01 | 94.1% | 22.9% |
D4
medium
residues 169-268_356-374
Domain cluster:
representative
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2vhjA02 | 2.30.270.20 | Mainly Beta › Roll › duf1285 protein fold › | 0.51 | 21.0 | 2.75e-01 | 78.2% | 66.1% |
ECOD (10)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 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 | 0.54 | 50.0 | 3.37e-01 | 100.0% | 44.6% |
| 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 | 0.53 | 49.0 | 3.53e-01 | 100.0% | 58.2% |
| 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 | 0.53 | 49.0 | 3.16e-01 | 100.0% | 34.4% |
| 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 | 0.52 | 49.0 | 3.48e-01 | 100.0% | 55.5% |
| 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 | 0.52 | 48.0 | 3.33e-01 | 100.0% | 50.4% |
| 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 | 0.52 | 48.0 | 3.50e-01 | 100.0% | 60.0% |
| 3197950 | 256.1.1.0 ↗ | a+b two layers › MTH1598-like › MTH1598-like › MTH1598-like | 0.52 | 22.0 | 3.19e-01 | 82.4% | 97.8% |
| 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 | 0.51 | 47.0 | 3.40e-01 | 100.0% | 55.9% |
| 5041736 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.50 | 28.0 | 3.25e-01 | 75.6% | 81.3% |
| 3339169 | 4.1.1.415 ↗ | beta barrels › SH3 › SH3 › SH3 › PNPOx_N | 0.50 | 30.0 | 3.37e-01 | 84.0% | 80.0% |
D5
medium
residues 269-291_327-355_375-404
Domain cluster:
representative
CATH (5)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3c18A02 | 1.20.120.330 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 | 0.56 | 38.0 | 3.44e-01 | 70.7% | 80.5% |
| 3tp3A02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.55 | 48.0 | 4.00e-01 | 98.8% | 58.8% |
| 4etrB00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.53 | 46.0 | 4.10e-01 | 98.8% | 93.4% |
| 1blwC00 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.52 | 42.0 | 3.54e-01 | 89.0% | 77.3% |
| 2o36A01 | 1.20.1050.40 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › Endopeptidase. Chain P; domain 1 | 0.51 | 43.0 | 3.75e-01 | 95.1% | 86.7% |
ECOD (4)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3593236 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.56 | 48.0 | 4.45e-01 | 98.8% | 77.3% |
| 1680584 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.55 | 48.0 | 3.84e-01 | 97.6% | 95.8% |
| 4999123 | 604.12.1.135 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Oxidored_q2 | 0.52 | 46.0 | 4.25e-01 | 100.0% | 84.8% |
| 3581266 | 604.6.1.0 ↗ | alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain | 0.51 | 44.0 | 4.03e-01 | 98.8% | 87.3% |