RNA-dependent_RNA_polymerase_1b

Euk-Vir

Blackberry_vein_banding-associated_virus

RNA-dependent_RNA_polymerase_1b__YP_008411010__Blackberry_vein_banding-associated_virus__1381464

Identity

81.8 mean pLDDT

Orthornavirae› Kitrinoviricota› Alsuviricetes› Martellivirales› Closteroviridae› Ampelovirus› Blackberry_vein_banding-associated_virus

TaxID: 1381464

View cluster (450 members)

Download PDB Download Scores JSON

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

D1 medium residues 90-117_178-237_312-333

PDB

Domain cluster: rep: replicase_P2__YP_008519305__Blueberry_shock_virus__747056__D388-478

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00978.27 best	RdRP_2	67.3	1.70e-18	67.3%	14.1%

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2x9oA00	3.40.1500.20	Alpha Beta › 3-Layer(aba) Sandwich › oxygen-dependent coproporphyrinogen oxidase ›	0.53	37.0	2.92e-01	70.9%	100.0%
2zxkA00	3.40.1500.20	Alpha Beta › 3-Layer(aba) Sandwich › oxygen-dependent coproporphyrinogen oxidase ›	0.52	37.0	2.83e-01	72.7%	96.6%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3454701	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	47.0	3.47e-01	74.5%	55.4%

D2 medium residues 118-177_280-311

PDB

Domain cluster: rep: ORF_1b__YP_003289291__Strawberry_pallidosis-associated_virus__227507__D117-174_213-235_276-309

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3ciaA03	1.10.390.10	Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2	0.55	28.0	2.37e-01	98.9%	27.1%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3174650	138.1.1.31 ↗	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 › PF29703	0.53	29.0	3.06e-01	75.0%	57.6%
3681302	109.4.1.420 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR	0.53	31.0	2.93e-01	92.4%	49.1%

D3 medium residues 238-279_334-432

PDB

Domain cluster: rep: RdRp,_partial__YP_008858531__Carnation_yellow_fleck_virus__940280__D190-234_286-374

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00978.27 best	RdRP_2	125.1	5.10e-36	70.2%	21.8%