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RNA-dependent_RNA_polymerase

Euk-Vir

Blotched_snakehead_virus

RNA-dependent_RNA_polymerase__YP_052864__Blotched_snakehead_virus__311176

Identity

Accession:: YP_052864 ↗
Protein ID:: RNA-dependent_RNA_polymerase
Kingdom:: euk

Quality

73.0 mean pLDDT

Taxonomy

Orthornavirae› Birnaviridae› Blosnavirus› Blotched_snakehead_virus

TaxID: 311176

Cluster

View cluster (6 members)

3D Structure

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Domains

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

D1 high residues 712-752_766-791

PDB

D2 medium residues 222-242_258-286

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF04197.18 best	Birna_RdRp_palm	34.8	1.30e-08	100.0%	12.6%

CATH (10)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2ipcA04	1.10.3060.10	Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA	0.66	56.0	3.56e-01	96.0%	63.2%
3d5lB01	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	0.62	54.0	4.31e-01	100.0%	93.1%
1pu1A00	3.30.300.100	Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like	0.62	52.0	4.23e-01	92.0%	82.4%
6p3xB01	3.40.140.10	Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2	0.62	47.0	3.20e-01	82.0%	41.2%
2gtaA00	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.60	46.0	3.70e-01	82.0%	48.5%
8be0A01	3.40.91.90	Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain	0.59	51.0	3.43e-01	96.0%	33.0%
1e6cA00	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.59	49.0	3.41e-01	94.0%	80.0%
4onsB00	6.10.250.2780	Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces ›	0.57	44.0	4.29e-01	86.0%	75.0%
1jb7A01	2.40.50.140	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins	0.56	49.0	3.36e-01	100.0%	33.3%
2zc1A00	3.20.20.140	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases	0.54	46.0	2.78e-01	94.0%	82.0%

D3 medium residues 243-257_287-327_459-470

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF04197.18 best	Birna_RdRp_palm	75.0	8.70e-21	63.2%	7.7%

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2pggA01	3.90.1730.10	Alpha Beta › Alpha-Beta Complex › Infectious bursal virus vp1 polymerase fold › Infectious bursal virus vp1 polymerase domain	0.91	85.0	5.22e-01	100.0%	49.9%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3243038	3382.1.1.1 ↗	alpha arrays › Protein Wnt-8 › Protein Wnt-8 › Protein Wnt-8 › wnt	0.52	43.0	2.86e-01	100.0%	67.2%
3494371	386.1.1.0 ↗	few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers	0.52	39.0	3.04e-01	83.8%	69.7%

D4 medium residues 328-458_471-524

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF04197.18 best	Birna_RdRp_palm	363.1	4.20e-108	100.0%	37.1%

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3drwB01	3.40.1190.20	Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase	0.52	39.0	3.27e-01	78.4%	95.8%

ECOD (5)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
None	—		0.96	94.0	6.55e-01	100.0%	39.5%
1145898	304.48.2.1 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Birna_RdRp_palm	0.96	94.0	6.48e-01	100.0%	38.6%
4247937	295.1.1.0 ↗	a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain	0.68	24.0	3.11e-01	82.7%	52.7%
4171382	295.1.1.12 ↗	a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › UPF0231	0.58	26.0	3.18e-01	82.2%	61.7%
5005139	4337.1.1.1 ↗	a+b two layers › DNA mismatch repair protein MutL dimerization subdomain › DNA mismatch repair protein MutL dimerization subdomain › DNA mismatch repair protein MutL dimerization subdomain › MutL_C	0.53	33.0	3.97e-01	95.1%	92.8%

D5 medium residues 525-583

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF20488.4 best	Birna_VP1_thumb	101.3	7.20e-29	98.3%	34.1%

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
6p8uA01	3.30.460.10	Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2	0.58	50.0	3.81e-01	98.3%	59.7%
4kbmB01	2.40.10.170	Mainly Beta › Beta Barrel › Thrombin, subunit H ›	0.55	37.0	3.85e-01	91.5%	78.2%
1adjB02	3.40.50.800	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain	0.54	39.0	3.48e-01	100.0%	51.1%
1httA02	3.40.50.800	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain	0.53	38.0	3.35e-01	100.0%	49.0%
6bhdA03	2.30.30.140	Mainly Beta › Roll › SH3 type barrels. ›	0.53	36.0	3.57e-01	98.3%	68.3%
2do3A01	2.30.30.30	Mainly Beta › Roll › SH3 type barrels. ›	0.52	37.0	3.88e-01	96.6%	86.3%
2gumB03	2.30.29.100	Mainly Beta › Roll › PH-domain like ›	0.50	40.0	3.22e-01	96.6%	43.8%

ECOD (12)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1578946	4967.1.1.15 ↗	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 › Birna_VP1_thumb	0.95	88.0	6.05e-01	98.3%	33.5%
3398420	391.1.1.0 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module	0.59	34.0	3.82e-01	94.9%	80.0%
3482420	375.1.1.0 ↗	few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related	0.57	31.0	3.68e-01	83.1%	100.0%
3893040	391.1.1.0 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module	0.56	34.0	3.65e-01	98.3%	75.6%
4198047	391.1.1.5 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › TILa	0.53	32.0	3.57e-01	94.9%	82.5%
3623599	377.1.1.83 ↗	few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › PF26040	0.53	32.0	3.61e-01	72.9%	97.1%
3392762	377.1.1.83 ↗	few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › PF26040	0.52	32.0	3.53e-01	74.6%	100.0%
4025894	375.1.1.0 ↗	few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related	0.52	36.0	3.07e-01	74.6%	62.4%
5032137	375.1.1.31 ↗	few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Elf1	0.51	35.0	3.35e-01	84.7%	61.4%
4948153	375.1.1.0 ↗	few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related	0.51	35.0	3.34e-01	84.7%	61.4%
3247046	377.1.1.83 ↗	few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › PF26040	0.50	31.0	3.38e-01	71.2%	87.5%
4656512	809.1.1.0 ↗	a+b two layers › BLIP-like › beta-lactamase-inhibitor protein, BLIP › beta-lactamase-inhibitor protein, BLIP	0.50	31.0	3.14e-01	71.2%	60.0%

D6 medium residues 584-695

PDB

Domain cluster: rep: VP1_RNA-dependent_RNA_polymerase__NP_690839__Infectious_bursal_disease_virus__10995__D603-698

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF20488.4 best	Birna_VP1_thumb	192.8	5.60e-57	97.3%	64.7%