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p88K_polymerase

Euk-Vir

Adonis_mosaic_virus

p88K_polymerase__YP_009553479__Adonis_mosaic_virus__1883104

Identity

Accession:: YP_009553479 ↗
Protein ID:: p88K_polymerase
Kingdom:: euk

Quality

79.2 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Tolucaviricetes› Tolivirales› Tombusviridae› Alphacarmovirus› Adonis_mosaic_virus

TaxID: 1883104

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 615-763

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	113.2	2.00e-32	89.9%	28.0%

D2 medium residues 90-179

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	32.4	1.50e-07	98.9%	52.6%

CATH (28)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3tl4X02	1.10.10.2420	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A ›	0.75	49.0	5.38e-01	98.9%	83.3%
2khmA01	1.10.10.1350	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain	0.73	51.0	4.79e-01	72.2%	66.7%
3vw4A01	1.10.340.50	Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 ›	0.73	50.0	5.00e-01	71.1%	71.7%
2klqA00	1.20.58.870	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.65	45.0	4.21e-01	72.2%	87.7%
3go9A02	3.30.830.10	Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like	0.64	45.0	3.40e-01	72.2%	68.2%
2dofA00	1.10.10.440	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain	0.63	41.0	4.18e-01	72.2%	68.2%
3fbzA01	1.20.58.800	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.63	44.0	4.30e-01	73.3%	64.7%
3h36A00	1.10.10.400	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain	0.61	43.0	4.58e-01	73.3%	96.2%
8jx6A02	2.30.30.780	Mainly Beta › Roll › SH3 type barrels. ›	0.60	43.0	4.12e-01	84.4%	65.0%
1bccA02	3.30.830.10	Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like	0.60	40.0	3.18e-01	70.0%	74.0%
1tt5B02	1.10.10.520	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Ubiquitin activating enzymes (Uba3). Chain: B, domain 2	0.57	40.0	4.30e-01	96.7%	87.0%
1ls1A01	1.20.120.140	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain	0.57	43.0	4.35e-01	100.0%	80.9%
7e5aB02	1.20.1000.10	Mainly Alpha › Up-down Bundle › Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 › Guanylate-binding protein, C-terminal domain	0.56	45.0	3.78e-01	97.8%	48.8%
3umgA02	1.10.150.240	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2	0.56	39.0	4.33e-01	72.2%	100.0%
1ldjA03	1.20.1310.10	Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats	0.55	49.0	4.55e-01	100.0%	88.7%
2nrlA00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.55	38.0	3.28e-01	71.1%	93.1%
7shlA02	1.20.1310.10	Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats	0.55	48.0	4.37e-01	100.0%	93.4%
1h97A00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.54	37.0	3.24e-01	71.1%	91.8%
3rmiA00	1.20.59.10	Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase	0.54	37.0	3.61e-01	72.2%	70.5%
1q6aA00	1.10.1240.30	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain	0.54	38.0	3.66e-01	74.4%	69.2%
6cnzF00	1.20.59.10	Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase	0.53	39.0	3.31e-01	100.0%	44.9%
1ldjA02	1.20.1310.10	Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats	0.53	46.0	4.24e-01	100.0%	96.7%
3shgA00	1.10.3290.10	Mainly Alpha › Orthogonal Bundle › Fic-like fold › Fido-like domain	0.53	45.0	3.53e-01	94.4%	75.3%
2wzkA03	1.20.1310.10	Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats	0.53	47.0	4.42e-01	100.0%	90.0%
6bmeA00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.52	42.0	3.79e-01	90.0%	85.0%
3ztaA00	1.10.490.130	Mainly Alpha › Orthogonal Bundle › Globin-like ›	0.51	42.0	3.70e-01	100.0%	59.7%
3kh1A00	1.10.3210.10	Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432	0.51	41.0	3.29e-01	91.1%	85.6%
3pmcA00	1.10.490.70	Mainly Alpha › Orthogonal Bundle › Globin-like › Histidine kinase N-terminal domain	0.50	42.0	3.77e-01	94.4%	100.0%

ECOD (32)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3952621	101.35.1.0 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX	0.77	54.0	6.03e-01	97.8%	94.2%
4124450	101.35.1.4 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3	0.75	52.0	5.87e-01	97.8%	95.6%
5044192	2004.1.1.42 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE	0.70	49.0	3.07e-01	72.2%	15.1%
3170802	101.1.1.133 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Vhr1	0.68	48.0	4.78e-01	74.4%	71.6%
3171699	101.1.1.133 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Vhr1	0.68	48.0	4.70e-01	74.4%	68.0%
4928310	4953.1.1.0 ↗	beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like	0.67	51.0	5.11e-01	100.0%	77.4%
5029167	206.1.1.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase	0.66	50.0	3.56e-01	97.8%	27.3%
4931674	4953.1.1.40 ↗	beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › T1RH-like_C	0.65	53.0	5.31e-01	100.0%	85.6%
3530124	386.1.1.0 ↗	few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers	0.63	41.0	4.38e-01	100.0%	75.0%
3261803	633.24.1.0 ↗	alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain	0.62	43.0	4.41e-01	71.1%	95.3%
4014527	532.2.1.0 ↗	alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains	0.60	49.0	4.88e-01	100.0%	85.3%
4930514	610.3.1.1 ↗	alpha arrays › ERP29 C domain-like › GatB/GatE C-terminal domain › GatB/GatE C-terminal domain › GatB_Yqey	0.59	51.0	4.13e-01	95.6%	53.1%
5074758	164.1.1.0 ↗	alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II	0.58	40.0	4.21e-01	72.2%	91.3%
4948274	164.1.1.1 ↗	alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2	0.56	39.0	4.15e-01	71.1%	98.7%
3789554	604.12.1.0 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain	0.56	42.0	4.26e-01	100.0%	80.0%
3776754	5055.1.1.0 ↗	extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel	0.56	35.0	3.96e-01	96.7%	86.2%
5030164	101.11.1.0 ↗	alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	0.56	41.0	4.53e-01	98.9%	100.0%
4943201	181.1.1.32 ↗	alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54	0.56	42.0	4.31e-01	100.0%	83.5%
4934951	164.1.1.1 ↗	alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2	0.56	39.0	3.90e-01	72.2%	81.1%
3504161	109.4.1.17 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cullin	0.55	48.0	3.61e-01	100.0%	47.9%
3708255	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.55	38.0	4.10e-01	71.1%	85.3%
4927512	164.1.1.1 ↗	alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2	0.55	38.0	3.86e-01	72.2%	82.2%
1063099	4040.1.1.1 ↗	alpha bundles › Fic-like › Fic-like › Fic-like › Fic	0.53	45.0	3.54e-01	94.4%	96.5%
3702110	593.1.1.0 ↗	alpha bundles › GroEL equatorial domain-like › GroEL equatorial domain-like › GroEL equatorial domain-like	0.53	47.0	3.41e-01	100.0%	95.0%
4277373	4994.1.1.1 ↗	alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507	0.52	41.0	4.07e-01	100.0%	82.8%
4464677	4198.1.1.0 ↗	alpha arrays › TerB-like › TerB-like › TerB-like	0.51	40.0	3.51e-01	94.4%	55.7%
4646569	4994.1.1.1 ↗	alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507	0.51	40.0	3.96e-01	100.0%	82.1%
3587219	2006.1.1.18 ↗	a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_2	0.51	34.0	2.67e-01	70.0%	79.5%
5077106	3861.1.1.0 ↗	alpha bundles › Mitochondrial translocator protein (TSPO) › Mitochondrial translocator protein (TSPO) › Mitochondrial translocator protein (TSPO)	0.51	41.0	3.81e-01	100.0%	70.2%
3364093	148.1.3.0 ↗	alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain	0.50	34.0	3.89e-01	94.4%	98.5%
3728950	650.1.1.0 ↗	alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain	0.50	34.0	3.68e-01	76.7%	85.3%
5005237	4967.1.1.11 ↗	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 › GIIM	0.50	40.0	3.41e-01	100.0%	51.2%

D3 medium residues 251-350_393-414

PDB

Domain cluster: rep: hypothetical_protein_1__YP_009337417__Changjiang_tombus-like_virus_9__1922823__D348-350_352-432_502-513

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00998.29 best	RdRP_3	61.7	8.30e-17	69.7%	16.5%

D4 medium residues 351-392_415-432_502-539

PDB

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

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00998.29 best	RdRP_3	30.5	2.40e-07	43.9%	8.6%
PF00998.29	RdRP_3	43.0	3.70e-11	40.8%	8.0%

D5 medium residues 433-501_540-614

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	90.7	1.30e-25	53.5%	15.8%
PF00998.29	RdRP_3	103.3	1.90e-29	48.6%	14.2%