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RNA-dependent_RNA_polymerase

Euk-Vir

Ageratum_latent_virus_1998

RNA-dependent_RNA_polymerase__YP_008470970__Ageratum_latent_virus_1998__2755028

Identity

Accession:
YP_008470970 ↗
Protein ID:
RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

68.6 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Martellivirales› Bromoviridae› Ilarvirus› Ageratum_latent_virus_1998

TaxID: 2755028

Cluster

View cluster (23 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 606-687
PDB
Domain cluster: rep: replication-associated_polyprotein_2a__YP_009165997__Privet_ringspot_virus__2169960__D620-694
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 50.7 1.90e-13 100.0% 17.3%
D2 medium residues 1-72
PDB
D3 medium residues 233-268_288-309
PDB
Domain cluster: rep: replication-associated_polyprotein_2a__YP_009165997__Privet_ringspot_virus__2169960__D236-291
D4 medium residues 310-407_419-429_474-488
PDB
Domain cluster: rep: ORF_1b__YP_003289291__Strawberry_pallidosis-associated_virus__227507__D117-174_213-235_276-309
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 69.1 5.10e-19 100.0% 24.3%
D5 medium residues 408-418_430-473_489-605
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009337040__Changjiang_tombus-like_virus_21__1922815__D1-47_99-181
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 184.9 3.70e-54 98.8% 40.0%
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h5xA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.72 48.0 5.82e-01 84.3% 100.0%
1gx5A03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.72 50.0 5.96e-01 86.6% 100.0%
1ra6A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.71 44.0 5.52e-01 79.7% 100.0%
5jxsA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.70 54.0 5.96e-01 91.9% 96.5%
1mwyA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 32.0 4.72e-01 70.9% 100.0%
6qwtA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.69 53.0 5.79e-01 93.6% 96.5%
3jcmH04 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.65 31.0 4.43e-01 75.6% 100.0%
2x3gA00 3.30.70.1910 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 41.0 4.85e-01 80.8% 92.2%
1mw7A03 3.30.70.980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › YebC, transcriptional regulation domain 0.64 30.0 4.33e-01 75.6% 100.0%
2r7rA04 3.30.70.2480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 44.0 4.60e-01 87.2% 77.7%
3to8A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.62 32.0 4.00e-01 72.1% 81.6%
1itpA00 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.61 28.0 3.98e-01 70.3% 93.5%
3rrkA03 3.30.70.2750 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 28.0 4.12e-01 72.1% 100.0%
3o1lB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.60 32.0 4.26e-01 72.1% 97.7%
2efpA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.60 34.0 4.29e-01 80.2% 93.9%
1scjB00 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.60 27.0 3.92e-01 74.4% 97.2%
1s7hA02 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 30.0 4.10e-01 75.6% 98.8%
3s8sA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 32.0 3.96e-01 73.3% 83.2%
7npaA02 3.30.70.3340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 28.0 3.74e-01 70.9% 85.9%
2dy1A03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.59 28.0 3.92e-01 73.3% 97.4%
2p5vA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.58 30.0 4.09e-01 74.4% 100.0%
2qz8A02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.57 29.0 3.98e-01 72.1% 100.0%
1x4hA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 31.0 3.87e-01 73.8% 82.9%
1s79A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 30.0 3.78e-01 72.7% 83.5%
1hi8A03 3.30.70.1600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 52.0 5.16e-01 96.5% 98.9%
2mzqA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 32.0 4.06e-01 88.4% 97.0%
6i0y501 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.53 36.0 4.04e-01 80.2% 90.8%
5huoE01 3.90.1170.20 Alpha Beta › Alpha-Beta Complex › Aldehyde Oxidoreductase; domain 3 › Quinolinate phosphoribosyl transferase, N-terminal domain 0.52 33.0 3.62e-01 76.2% 77.0%
3ct9A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 32.0 3.94e-01 70.3% 100.0%
2b7nA01 3.90.1170.20 Alpha Beta › Alpha-Beta Complex › Aldehyde Oxidoreductase; domain 3 › Quinolinate phosphoribosyl transferase, N-terminal domain 0.51 30.0 3.45e-01 70.3% 78.7%
1zavA01 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.51 35.0 3.91e-01 79.7% 89.6%
1xjhA00 3.90.1280.10 Alpha Beta › Alpha-Beta Complex › CBS domain Like › HSP33 redox switch-like 0.50 16.0 2.60e-01 87.2% 74.2%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
217141 304.48.1.15 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 0.83 77.0 5.90e-01 97.1% 58.8%
4014158 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 0.79 74.0 6.05e-01 98.8% 84.4%
3479114 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 0.78 72.0 4.80e-01 98.8% 75.2%
3495499 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 0.77 72.0 5.84e-01 98.8% 68.2%
None — 0.76 67.0 5.14e-01 92.4% 51.9%
3737536 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 0.76 71.0 5.86e-01 98.8% 86.6%
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 0.76 70.0 5.48e-01 99.4% 60.6%
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 0.74 68.0 5.22e-01 99.4% 68.3%
3931851 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 62.0 5.35e-01 98.8% 60.8%
3934202 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 0.70 56.0 6.04e-01 87.2% 99.3%
3674421 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.68 30.0 4.51e-01 73.3% 100.0%
3946828 304.11.1.0 ↗ a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase 0.68 28.0 4.40e-01 70.9% 100.0%
5022444 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.66 29.0 4.11e-01 70.3% 87.5%
3457319 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.65 29.0 4.13e-01 71.5% 92.0%
4931433 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.65 29.0 4.25e-01 76.2% 100.0%
4586345 304.28.1.2 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Sec_GG 0.65 33.0 4.49e-01 74.4% 97.6%
4012791 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.64 31.0 4.41e-01 73.3% 98.8%
4676848 304.24.1.3 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.64 30.0 4.30e-01 70.3% 100.0%
3678489 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 0.63 54.0 5.16e-01 92.4% 78.0%
4380765 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.63 29.0 4.15e-01 70.3% 96.0%
5000640 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.63 27.0 4.09e-01 73.8% 100.0%
3373939 304.11.1.11 ↗ a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase › SBDS_C 0.63 30.0 4.18e-01 75.6% 93.8%
4939299 304.24.1.3 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.63 32.0 4.20e-01 77.3% 91.1%
3505715 304.24.1.3 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.63 30.0 4.25e-01 75.6% 97.5%
2776431 304.24.1.3 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.62 30.0 4.22e-01 78.5% 97.5%
4136209 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.61 31.0 4.28e-01 71.5% 98.8%
5020057 325.1.4.1 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Nicotinate/Quinolinate PRTase N-terminal domain-like › QRPTase_N 0.60 30.0 3.51e-01 70.3% 65.6%
3671314 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.60 36.0 3.12e-01 80.8% 39.0%
3743450 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.59 31.0 4.22e-01 77.9% 97.8%
3164817 304.28.1.2 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Sec_GG 0.59 31.0 4.16e-01 77.3% 100.0%
4938054 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.59 29.0 4.00e-01 72.7% 98.8%
5046295 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.58 31.0 4.00e-01 78.5% 89.0%
3396694 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.58 30.0 3.97e-01 70.9% 93.3%
4985748 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.58 31.0 4.05e-01 78.5% 95.7%
5013209 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.56 33.0 4.21e-01 82.0% 100.0%
3613380 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.56 30.0 3.94e-01 80.8% 100.0%
4979746 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.55 31.0 3.86e-01 79.7% 93.0%
3416938 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.53 31.0 3.69e-01 77.9% 85.2%
4948157 304.56.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like 0.53 31.0 3.90e-01 77.3% 99.0%
4396118 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.52 34.0 3.59e-01 80.2% 71.2%
4402752 309.1.2.2 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_bind_4 0.52 32.0 3.33e-01 70.3% 65.0%
4639557 304.60.1.2 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.51 36.0 3.63e-01 80.8% 70.3%
3602749 205.1.1.35 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4+Fer4_7 0.51 25.0 3.39e-01 70.9% 98.7%