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putative_RNA-dependent_RNA_polymerase

Euk-Vir

Gentian_ovary_ringspot_virus

putative_RNA-dependent_RNA_polymerase__YP_009047252__Gentian_ovary_ringspot_virus__1920772

Identity

Accession:
YP_009047252 ↗
Protein ID:
putative_RNA-dependent_RNA_polymerase
Kingdom:
euk

Quality

90.7 mean pLDDT

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 20-74
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 36.2 4.60e-09 100.0% 12.3%
D2 high residues 366-459
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 68.5 7.70e-19 100.0% 20.7%
D3 medium residues 80-202_241-312
PDB
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 119.2 3.00e-34 64.1% 28.6%
PF00978.27 RdRP_2 60.2 2.50e-16 36.9% 15.9%
D4 medium residues 203-240_313-365
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00978.27 best RdRP_2 53.8 2.10e-14 59.3% 11.6%
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mukA02 3.90.1850.10 Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 0.76 70.0 4.29e-01 100.0% 45.1%
6qwtA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.75 69.0 5.89e-01 100.0% 86.5%
5wm1A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.72 53.0 5.03e-01 76.9% 87.2%
1khvA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.71 64.0 5.67e-01 98.9% 100.0%
1z1dB00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.71 50.0 4.41e-01 73.6% 65.6%
4pwuC00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.69 48.0 5.12e-01 71.4% 98.7%
1s7hA01 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 47.0 5.02e-01 71.4% 98.8%
4zmuA02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.69 61.0 5.12e-01 98.9% 87.7%
7e6gA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.69 58.0 4.93e-01 93.4% 89.3%
3mtkA00 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.69 60.0 4.98e-01 97.8% 82.2%
2rilA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 47.0 4.71e-01 71.4% 95.8%
2d9oA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.68 46.0 4.51e-01 70.3% 82.0%
1wf1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.66 46.0 4.70e-01 72.5% 84.4%
4ushA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 45.0 4.30e-01 70.3% 78.6%
2la4A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.65 46.0 4.51e-01 74.7% 75.2%
1kviA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 44.0 4.72e-01 71.4% 98.7%
5cqgA04 3.30.70.2630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 58.0 5.55e-01 100.0% 84.9%
6w72A01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 44.0 3.91e-01 72.5% 96.2%
1jwwA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 43.0 4.54e-01 72.5% 95.0%
2nyiA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 42.0 4.39e-01 71.4% 98.8%
1vi7A02 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 41.0 4.49e-01 70.3% 100.0%
2lg7A00 2.60.60.50 Mainly Beta › Sandwich › Lipoxygenase-1 › 0.59 40.0 3.60e-01 70.3% 73.6%
2v4jA02 3.30.70.2500 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 40.0 3.87e-01 70.3% 81.2%
3w6wB02 2.60.310.20 Mainly Beta › Sandwich › Hemocyanin; Chain: A, domain 2 › 0.57 43.0 3.84e-01 82.4% 85.3%
3tzyA02 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.57 39.0 4.37e-01 71.4% 97.1%
8owfA01 2.60.40.290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 39.0 3.68e-01 71.4% 64.9%
2jfdA03 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.57 39.0 4.41e-01 72.5% 98.5%
2cfxA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.56 44.0 4.49e-01 84.6% 95.6%
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 0.56 40.0 4.17e-01 75.8% 100.0%
3qc5X01 2.60.40.3260 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 40.0 3.43e-01 75.8% 51.4%
2rttA00 2.60.40.290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 38.0 3.66e-01 72.5% 65.7%
4nhxA02 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.53 42.0 3.26e-01 89.0% 87.7%
1o5wB02 3.90.660.10 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.53 43.0 3.59e-01 91.2% 82.8%
3bv8A00 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.53 38.0 3.90e-01 73.6% 80.0%
3i6dA02 3.90.660.20 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › Protoporphyrinogen oxidase, mitochondrial; domain 2 0.53 44.0 3.45e-01 90.1% 73.4%
3wdhA01 2.60.40.2320 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 35.0 3.45e-01 70.3% 84.4%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.80 74.0 5.04e-01 100.0% 55.1%
3483524 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 0.75 68.0 4.65e-01 100.0% 56.7%
4361688 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 0.72 64.0 4.25e-01 100.0% 53.3%
5036777 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.72 50.0 5.46e-01 72.5% 97.3%
4101334 304.28.1.3 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › SecD-TM1 0.70 49.0 4.92e-01 71.4% 85.6%
139439 304.48.1.14 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GGDEF 0.69 60.0 4.98e-01 97.8% 82.2%
3408597 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.68 50.0 5.17e-01 76.9% 92.9%
5012390 304.11.1.16 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 › DUF2110_C 0.67 46.0 5.13e-01 70.3% 100.0%
4950570 304.163.1.0 a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.66 46.0 5.27e-01 71.4% 100.0%
4931433 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.66 46.0 5.17e-01 71.4% 100.0%
4016694 304.9.1.31 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_9 0.66 47.0 4.63e-01 73.6% 93.7%
4032264 304.8.1.94 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DrrA1-3_C 0.66 45.0 5.21e-01 72.5% 100.0%
4957085 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.66 45.0 5.21e-01 71.4% 100.0%
3265364 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.65 45.0 4.32e-01 71.4% 99.0%
4025515 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.64 47.0 4.07e-01 75.8% 75.6%
4937175 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.64 43.0 4.99e-01 70.3% 100.0%
5040118 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.64 43.0 4.82e-01 70.3% 98.6%
3963438 304.15.1.0 a+b two layers › Alpha-beta plaits › Viral DNA-binding domain › Viral DNA-binding domain 0.63 43.0 4.91e-01 70.3% 100.0%
4461494 304.117.1.1 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in YebC › Ferredoxin-like domain in YebC › Transcrip_reg 0.63 42.0 4.85e-01 72.5% 96.9%
5009657 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.62 43.0 4.81e-01 72.5% 98.6%
4970578 304.11.1.16 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 › DUF2110_C 0.62 44.0 4.49e-01 74.7% 82.2%
3635926 304.7.1.0 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.62 42.0 4.85e-01 71.4% 98.5%
3333353 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.62 43.0 4.70e-01 73.6% 100.0%
3689276 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 0.61 42.0 4.60e-01 72.5% 90.7%
5010216 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.61 43.0 4.77e-01 73.6% 98.6%
3273461 304.46.1.1 a+b two layers › Alpha-beta plaits › eEF1-gamma domain › eEF1-gamma domain › EF1G 0.61 54.0 4.52e-01 100.0% 83.1%
3908315 898.1.1.1 a+b two layers › a+b domain in Ribosomal protein L1 › a+b domain in Ribosomal protein L1 › a+b domain in Ribosomal protein L1 › Ribosomal_L1 0.61 43.0 3.87e-01 74.7% 65.4%
4025551 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 0.60 41.0 4.09e-01 70.3% 80.0%
4995433 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.60 42.0 4.35e-01 72.5% 82.4%
4267491 304.147.1.1 a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.59 37.0 3.73e-01 70.3% 61.1%
5062189 304.24.1.5 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.59 41.0 4.48e-01 73.6% 93.3%
3974593 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.59 42.0 4.36e-01 75.8% 94.1%
1826980 10.32.1.52 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › GH115_C 0.58 40.0 3.21e-01 72.5% 50.8%
5005647 11.1.5.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.57 40.0 4.00e-01 72.5% 73.4%
3649851 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.57 37.0 4.29e-01 70.3% 93.8%
4455319 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 0.57 40.0 4.19e-01 72.5% 93.8%
4950919 11.1.1.257 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Top6b_C 0.56 38.0 3.62e-01 70.3% 59.0%
4321638 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.56 39.0 4.18e-01 71.4% 98.6%
3598569 10.15.1.1 beta sandwiches › jelly-roll › Smp-1-like › Smp-1-like › DUF1935 0.56 37.0 3.44e-01 70.3% 52.2%
3958482 11.1.5.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › CBM_2 0.56 39.0 3.74e-01 72.5% 68.6%
3279471 304.11.1.12 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 › WCX 0.56 37.0 3.94e-01 70.3% 77.5%
4657391 11.1.1.1264 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF27334 0.55 38.0 3.52e-01 72.5% 65.0%
3705936 10.15.1.1 beta sandwiches › jelly-roll › Smp-1-like › Smp-1-like › DUF1935 0.54 36.0 3.27e-01 70.3% 49.6%
4976636 304.24.1.5 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.53 38.0 4.20e-01 74.7% 98.6%
4626429 304.112.1.10 a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain › Med13_N 0.53 39.0 3.18e-01 79.1% 48.9%
4991904 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 37.0 3.09e-01 72.5% 49.1%
5007943 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.53 37.0 4.08e-01 75.8% 94.3%
4931128 11.1.1.257 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Top6b_C 0.53 36.0 3.41e-01 70.3% 81.7%
4102298 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.53 37.0 3.93e-01 73.6% 96.0%
5044202 304.164.1.0 a+b two layers › Alpha-beta plaits › Hypothetical protein NegoA.19184.a C-terminal domain › Hypothetical protein NegoA.19184.a C-terminal domain 0.51 35.0 3.83e-01 70.3% 91.4%
4073486 304.147.1.1 a+b two layers › Alpha-beta plaits › Tetrahydrodipicolinate acetyltransferase N-terminal domain › Tetrahydrodipicolinate acetyltransferase N-terminal domain › DapH_N 0.51 35.0 3.54e-01 71.4% 74.4%