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RNA-dependent_RNA_polymerase
Euk-VirMacrophomina_phaseolina_chrysovirus_1
RNA-dependent_RNA_polymerase__YP_009667008__Macrophomina_phaseolina_chrysovirus_1__1708483
Identity
- Accession:
- YP_009667008 ↗
- Protein ID:
- RNA-dependent_RNA_polymerase
- Kingdom:
- euk
Quality
75.2
mean pLDDT
Taxonomy
Orthornavirae›
Duplornaviricota›
Chrymotiviricetes›
Ghabrivirales›
Chrysoviridae›
Alphachrysovirus›
Macrophomina_phaseolina_chrysovirus_1
TaxID: 1708483
Cluster
View cluster (8 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 42-228
Domain cluster:
rep: VP2__YP_009665170__Eriocheir_sinensis_reovirus__273810__D721-872
D2
medium
residues 229-310
D3
medium
residues 328-448
Domain cluster:
representative
CATH (5)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3hdeC00 | 1.10.530.40 | Mainly Alpha › Orthogonal Bundle › Lysozyme › | 0.58 | 48.0 | 4.34e-01 | 89.3% | 93.9% |
| 5xs2B02 | 1.10.472.10 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like | 0.55 | 40.0 | 3.87e-01 | 74.4% | 84.8% |
| 5gl7A01 | 1.10.730.10 | Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 | 0.53 | 39.0 | 3.53e-01 | 76.0% | 77.7% |
| 1y4cA03 | 1.20.120.660 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain | 0.51 | 33.0 | 3.43e-01 | 84.3% | 69.0% |
| 1u89A00 | 1.20.120.230 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like | 0.51 | 45.0 | 4.36e-01 | 99.2% | 93.5% |
ECOD (7)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5020092 | 5067.1.1.4 ↗ | alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › MMPL | 0.60 | 51.0 | 4.23e-01 | 95.0% | 75.9% |
| 3783029 | 633.31.1.0 ↗ | alpha bundles › Bromodomain-like › Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase › Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase | 0.53 | 35.0 | 4.10e-01 | 86.0% | 100.0% |
| 3724936 | 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 | 45.0 | 3.65e-01 | 97.5% | 78.3% |
| 5032558 | 604.5.1.1 ↗ | alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU_div | 0.52 | 45.0 | 3.77e-01 | 96.7% | 94.7% |
| 4955536 | 4121.1.1.1 ↗ | a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA | 0.51 | 37.0 | 3.06e-01 | 75.2% | 89.1% |
| 3247350 | 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 | 0.51 | 44.0 | 3.61e-01 | 96.7% | 85.7% |
| 3927248 | 5059.1.1.0 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter | 0.51 | 38.0 | 2.92e-01 | 80.2% | 44.0% |
D4
medium
residues 449-506_660-742
Domain cluster:
rep: hypothetical_protein_3__YP_009336917__Hubei_toti-like_virus_17__1923305__D93-140_272-388
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02123.22 best | RdRP_4 | 55.2 | 8.80e-15 | 79.4% | 17.0% |
CATH (13)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3cuqA02 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.68 | 24.0 | 3.11e-01 | 86.5% | 54.3% |
| 1u5pA01 | 1.20.58.60 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.64 | 27.0 | 3.10e-01 | 83.0% | 51.9% |
| 3cxbA03 | 1.10.1740.30 | Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Secreted effector protein SifA helical domain | 0.63 | 29.0 | 3.69e-01 | 88.7% | 72.8% |
| 2mabA00 | 1.10.10.1350 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain | 0.63 | 27.0 | 3.06e-01 | 85.1% | 49.5% |
| 2g3kA00 | 1.20.120.1130 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vps28 C-terminal domain | 0.60 | 30.0 | 3.65e-01 | 92.9% | 72.3% |
| 2j9wB00 | 1.20.120.1130 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vps28 C-terminal domain | 0.59 | 31.0 | 3.65e-01 | 93.6% | 71.7% |
| 1wn0A00 | 1.20.120.160 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain | 0.58 | 31.0 | 3.24e-01 | 99.3% | 54.2% |
| 2uubT00 | 1.20.58.110 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 | 0.58 | 26.0 | 3.05e-01 | 74.5% | 57.6% |
| 5u56A02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.52 | 27.0 | 2.96e-01 | 84.4% | 58.9% |
| 4ha8A01 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.52 | 20.0 | 2.88e-01 | 83.0% | 74.6% |
| 3nskB00 | 1.10.238.10 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand | 0.52 | 24.0 | 2.90e-01 | 80.1% | 63.0% |
| 1p8dB00 | 1.10.565.10 | Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor | 0.51 | 38.0 | 3.15e-01 | 75.9% | 74.9% |
| 2ynqB00 | 1.25.40.680 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type VII secretion system EssB, C-terminal-like domain | 0.50 | 31.0 | 3.09e-01 | 71.6% | 57.0% |
ECOD (6)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1789314 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.68 | 63.0 | 4.53e-01 | 100.0% | 72.6% |
| 4946174 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.60 | 28.0 | 3.48e-01 | 81.6% | 68.9% |
| 3704187 | 601.28.1.1 ↗ | alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like › VPS28 | 0.58 | 33.0 | 3.74e-01 | 99.3% | 71.8% |
| 3587011 | 604.39.1.23 ↗ | alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters › Hpre_diP_synt_I | 0.53 | 40.0 | 3.76e-01 | 80.1% | 96.6% |
| 3608662 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.52 | 27.0 | 3.37e-01 | 79.4% | 80.0% |
| 3423387 | 611.9.1.0 ↗ | alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain | 0.51 | 33.0 | 3.64e-01 | 92.2% | 82.7% |
D5
medium
residues 507-518_567-625
Domain cluster:
representative
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2r7rA05 | 1.10.357.80 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › | 0.61 | 49.0 | 3.76e-01 | 100.0% | 36.9% |
| 2r1fA03 | 3.30.160.60 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger | 0.58 | 27.0 | 3.48e-01 | 87.3% | 79.5% |
| 2bf1A00 | 2.170.40.20 | Mainly Beta › Beta Complex › HIV Envelope Protein Gp120; Chain G › Human immunodeficiency virus 1, Gp160, envelope glycoprotein | 0.54 | 37.0 | 2.51e-01 | 73.2% | 87.8% |
| 1unnC00 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.54 | 27.0 | 2.33e-01 | 73.2% | 26.1% |
| 1bm9A00 | 1.10.10.10 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain | 0.52 | 36.0 | 3.03e-01 | 73.2% | 100.0% |
| 3bzvB00 | 3.40.1690.10 | Alpha Beta › 3-Layer(aba) Sandwich › name from scop › secretion proteins EscU | 0.51 | 29.0 | 2.86e-01 | 83.1% | 48.8% |
ECOD (18)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 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 | 0.71 | 55.0 | 3.73e-01 | 83.1% | 66.8% |
| 3954143 | 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 | 0.66 | 50.0 | 3.80e-01 | 83.1% | 40.0% |
| 4250601 | 186.1.1.0 ↗ | alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N | 0.63 | 53.0 | 4.05e-01 | 94.4% | 95.3% |
| 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 | 0.62 | 54.0 | 3.41e-01 | 100.0% | 64.0% |
| 4441043 | 101.1.10.0 ↗ | alpha arrays › HTH › HTH › Cyclin-like | 0.62 | 50.0 | 3.94e-01 | 91.5% | 98.8% |
| 4434853 | 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 | 49.0 | 3.48e-01 | 98.6% | 27.5% |
| 3275438 | 109.4.1.1945 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_Maestro, HEAT_Maestro_2, HEAT_MROH2B_1st, HEAT_MROH2B_C | 0.58 | 41.0 | 2.23e-01 | 76.1% | 4.6% |
| 2006900 | 302.4.1.0 ↗ | a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit | 0.58 | 34.0 | 3.00e-01 | 95.8% | 38.5% |
| 3271607 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.58 | 41.0 | 2.91e-01 | 76.1% | 50.6% |
| 3194847 | 3343.1.1.2 ↗ | alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal,GCP_N_terminal | 0.57 | 38.0 | 2.27e-01 | 70.4% | 14.4% |
| 3734132 | 3542.1.1.3 ↗ | alpha arrays › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Peptidase_A22B | 0.56 | 38.0 | 2.56e-01 | 71.8% | 35.6% |
| 4954187 | 221.10.1.1 ↗ | a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ | 0.55 | 24.0 | 2.69e-01 | 78.9% | 50.0% |
| 3682186 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.52 | 35.0 | 2.86e-01 | 74.6% | 34.0% |
| 4999286 | 101.1.2.48 ↗ | alpha arrays › HTH › HTH › winged helix domain › PadR | 0.51 | 34.0 | 2.58e-01 | 93.0% | 26.7% |
| 3198300 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.51 | 35.0 | 2.57e-01 | 71.8% | 82.4% |
| 3908365 | 109.4.1.363 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Tcf25 | 0.51 | 34.0 | 2.19e-01 | 70.4% | 90.8% |
| 3480552 | 323.1.1.0 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases | 0.51 | 35.0 | 2.65e-01 | 73.2% | 96.4% |
| 3280466 | 101.1.2.48 ↗ | alpha arrays › HTH › HTH › winged helix domain › PadR | 0.50 | 33.0 | 2.47e-01 | 93.0% | 25.3% |