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putative_RNA_dependent_RNA_polymerase

Euk-Vir

Gompholobium_virus_A

putative_RNA_dependent_RNA_polymerase__YP_009270620__Gompholobium_virus_A__1884832

Identity

Accession:: YP_009270620 ↗
Protein ID:: putative_RNA_dependent_RNA_polymerase
Kingdom:: euk

Quality

80.5 mean pLDDT

Cluster

View cluster (58 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 97-202

PDB

Domain cluster: rep: P1__YP_009552849__Apple_luteovirus_1__2170544__D293-391

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF08500.17 best	Tombus_P33	29.1	1.60e-06	88.7%	54.8%

D2 high residues 205-245

PDB

Domain cluster: representative

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1oywA03	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	0.61	53.0	3.45e-01	97.6%	27.3%

D3 high residues 629-776

PDB

Domain cluster: rep: P95_replicase__YP_009259667__Pelargonium_leaf_curl_virus__35280__D527-559_693-852

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00998.29 best	RdRP_3	115.0	5.50e-33	89.2%	28.0%

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3fyaB00	1.10.260.40	Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains	0.63	26.0	3.56e-01	87.2%	74.0%
2x48A00	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.59	24.0	3.70e-01	83.8%	100.0%
3o6xA02	1.20.120.1560	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) ›	0.58	28.0	2.81e-01	79.1%	43.2%
1aepA00	1.20.120.20	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein	0.57	34.0	3.40e-01	87.2%	55.6%
3n3dB00	1.10.600.10	Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase	0.50	35.0	2.81e-01	72.3%	96.8%

ECOD (3)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3010831	4967.1.1.14 ↗	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 › Flavi_NS5_thumb	0.66	56.0	4.94e-01	89.9%	78.6%
3185613	5001.1.1.120 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › TRP	0.52	46.0	3.50e-01	100.0%	78.7%
5000490	633.15.1.0 ↗	alpha bundles › Bromodomain-like › alpha-ketoacid dehydrogenase kinase-N › alpha-ketoacid dehydrogenase kinase-N	0.51	34.0	3.72e-01	93.9%	84.2%

D4 medium residues 259-390_410-426

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009337688__Beihai_tombus-like_virus_7__1922728__D528-588_642-697_774-796

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00998.29 best	RdRP_3	79.3	3.60e-22	73.8%	19.8%

D5 medium residues 391-409_427-454_497-553

PDB

Domain cluster: rep: hypothetical_protein_2__YP_009337432__Changjiang_tombus-like_virus_5__1922819__D23-82_137-181

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00998.29 best	RdRP_3	70.0	2.50e-19	58.7%	12.3%

CATH (3)

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 ›	0.72	62.0	5.21e-01	94.2%	71.6%
2qx2A00	3.10.570.10	Alpha Beta › Roll › sex pheromone staph- cam373 precursor fold › sex pheromone staph- cam373 precursor domain	0.59	42.0	3.06e-01	76.0%	74.8%
6fbtA01	1.10.1240.20	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Lytic transglycosylase, superhelical linker domain	0.52	29.0	3.31e-01	71.2%	73.7%

ECOD (12)

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	0.72	65.0	4.91e-01	100.0%	60.8%
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	0.71	65.0	4.38e-01	100.0%	46.7%
3241316	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	64.0	4.45e-01	100.0%	48.1%
5014895	2007.15.1.0 ↗	a/b three-layered sandwiches › Flavodoxin-like › N-deoxyribosyltransferase › N-deoxyribosyltransferase	0.55	36.0	3.33e-01	100.0%	51.1%
3584990	391.1.1.0 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module	0.54	22.0	3.30e-01	88.5%	88.6%
4977954	2004.1.1.791 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GvpD_bR2	0.54	44.0	3.39e-01	90.4%	85.5%
5069572	2004.1.1.146 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase	0.54	43.0	3.40e-01	86.5%	89.3%
4048642	101.1.1.304 ↗	alpha arrays › HTH › HTH › Three-helical HTH › GatB_Yqey	0.53	31.0	3.84e-01	92.3%	96.8%
4930745	2004.1.1.1219 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF7504	0.52	42.0	3.34e-01	90.4%	77.8%
5067460	2004.1.1.146 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase	0.52	43.0	3.31e-01	92.3%	72.2%
5081181	2004.1.1.0 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases	0.51	42.0	3.27e-01	91.3%	69.0%
3179675	3873.1.1.1 ↗	a+b two layers › Serine/threonine-protein kinase GCN2 C-terminal domain › Serine/threonine-protein kinase GCN2 C-terminal domain › Serine/threonine-protein kinase GCN2 C-terminal domain › HGTP_anticodon2	0.51	38.0	3.70e-01	85.6%	69.2%

D6 medium residues 455-496_554-628

PDB

Domain cluster: rep: hypothetical_protein_1__YP_009337274__Changjiang_tombus-like_virus_14__1922807__D158-196_253-344

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00998.29 best	RdRP_3	93.7	1.60e-26	64.1%	15.6%
PF00998.29	RdRP_3	58.6	6.80e-16	35.9%	8.6%