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polymerase

Euk-Vir

Colombian_potato_soil-borne_virus

polymerase__YP_009220367__Colombian_potato_soil-borne_virus__1758139

Identity

Accession:
YP_009220367 ↗
Protein ID:
polymerase
Kingdom:
euk

Quality

66.4 mean pLDDT

Cluster

View cluster (6 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 1040-1181
PDB
Domain cluster: rep: KX578043.1__AOT27930.1__X__00015__D87-267
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF01443.25 best Viral_helicase1 90.5 2.00e-25 94.4% 53.5%
PF13245.13 AAA_19 27.0 6.30e-06 84.5% 90.3%
D2 high residues 1207-1333
PDB
Domain cluster: rep: TGB1_protein__NP_619560__Garlic_latent_virus__12458__D129-228
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01443.25 best Viral_helicase1 56.2 6.20e-15 80.3% 33.3%
D3 medium residues 91-138_200-355
PDB
Domain cluster: rep: uncovered_polypeptide_polyprotein__YP_001086452_0-758__Chrysanthemum_virus_B__12165__D72-292
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01660.23 best Vmethyltransf 110.1 1.60e-31 100.0% 66.9%
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3e8sA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.70 62.0 6.03e-01 91.7% 87.7%
3vc1J00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.68 60.0 5.36e-01 91.7% 88.0%
4krgA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.66 60.0 5.58e-01 96.1% 85.5%
5cm2Z00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.66 55.0 5.79e-01 91.2% 97.3%
2o57A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.64 50.0 5.56e-01 93.1% 99.4%
5gm2K01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.64 56.0 5.49e-01 92.6% 97.2%
2hx1A02 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.63 38.0 4.75e-01 85.3% 100.0%
3fzgA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.62 49.0 5.02e-01 92.2% 84.7%
4hg2B01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.62 49.0 5.36e-01 92.6% 98.8%
3tixB02 3.40.1010.30 Alpha Beta › 3-Layer(aba) Sandwich › Cobalt-precorrin-4 Transmethylase; domain 1 › 0.62 35.0 4.37e-01 89.2% 89.5%
3rghA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 21.0 3.05e-01 79.9% 62.5%
1zkdA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.61 49.0 5.34e-01 91.2% 99.4%
3rrkA03 3.30.70.2750 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 18.0 3.05e-01 84.8% 71.6%
7u7hA01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.61 44.0 4.30e-01 88.7% 67.3%
5rl9B01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.60 34.0 3.93e-01 91.7% 74.5%
1zjjA02 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.60 36.0 4.48e-01 87.7% 100.0%
1ovmA03 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.60 46.0 4.78e-01 90.7% 86.7%
1zq9A01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 50.0 5.31e-01 93.6% 98.9%
1qyrA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.59 50.0 5.28e-01 93.1% 98.4%
2vbiA03 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.59 47.0 4.89e-01 92.2% 90.5%
2dibA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 22.0 3.04e-01 79.9% 67.0%
3lidA03 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.58 25.0 3.45e-01 89.2% 80.2%
6denA03 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.57 47.0 4.59e-01 91.7% 78.1%
2bbeA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 21.0 2.84e-01 82.8% 61.2%
3ostA00 3.30.310.220 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Fungal kinase associated-1 domain 0.57 22.0 2.82e-01 94.1% 56.3%
3io5A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 42.0 3.80e-01 100.0% 56.8%
5ahkA03 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.56 46.0 4.78e-01 91.7% 93.1%
3ix9A00 3.40.430.10 Alpha Beta › 3-Layer(aba) Sandwich › Dihydrofolate Reductase, subunit A › Dihydrofolate Reductase, subunit A 0.55 39.0 4.23e-01 93.6% 87.3%
7pt4A01 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.55 45.0 4.65e-01 100.0% 91.2%
2w9hA00 3.40.430.10 Alpha Beta › 3-Layer(aba) Sandwich › Dihydrofolate Reductase, subunit A › Dihydrofolate Reductase, subunit A 0.54 38.0 4.18e-01 92.2% 90.4%
4ixoA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.54 44.0 4.17e-01 98.5% 73.5%
7dluA03 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 16.0 2.58e-01 94.6% 65.8%
3sl1A00 3.40.800.10 Alpha Beta › 3-Layer(aba) Sandwich › Arginase; Chain A › Ureohydrolase domain 0.52 39.0 3.47e-01 79.4% 95.5%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4988836 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.73 53.0 6.03e-01 91.2% 98.1%
4958614 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.68 55.0 5.73e-01 92.6% 89.5%
1179692 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.68 60.0 5.27e-01 91.7% 84.4%
3640712 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.68 42.0 4.97e-01 100.0% 89.3%
3290424 2003.1.5.35 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › LCM 0.66 57.0 5.22e-01 90.7% 80.4%
3805802 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.66 51.0 5.13e-01 96.1% 79.0%
4961790 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.66 57.0 5.49e-01 91.7% 88.0%
3802438 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.66 49.0 4.70e-01 92.6% 66.8%
3407989 2007.1.2.30 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › IR75A_N 0.64 47.0 4.96e-01 99.0% 85.6%
3241239 2003.1.5.213 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › MTS, tRNA_U5-meth_tr 0.63 55.0 4.26e-01 91.2% 45.0%
3757398 2003.1.5.97 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_32 0.63 55.0 4.44e-01 92.6% 74.7%
4236550 2003.1.5.82 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_31 0.63 53.0 4.06e-01 90.7% 41.1%
3899941 2003.1.5.156 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr, Methyltransf_31 0.63 53.0 4.09e-01 91.2% 42.4%
4957465 2003.1.5.79 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_23 0.62 52.0 5.16e-01 88.7% 100.0%
4226862 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.62 49.0 3.97e-01 91.2% 46.1%
4151376 2003.1.5.182 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD, Methyltransf_11 0.61 52.0 5.27e-01 94.6% 91.0%
4029370 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.61 51.0 3.94e-01 91.2% 41.6%
3332978 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.61 50.0 4.63e-01 98.0% 68.6%
4179980 2003.1.5.182 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD, Methyltransf_11 0.61 53.0 5.44e-01 95.1% 96.4%
4499454 2003.1.5.155 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD, Methyltransf_25 0.61 52.0 5.43e-01 95.1% 97.4%
3371640 2003.1.5.156 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr, Methyltransf_31 0.60 52.0 3.90e-01 91.2% 42.6%
4677963 2003.1.5.2 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD 0.60 54.0 5.29e-01 94.1% 90.2%
4333133 2003.1.5.2 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD 0.59 52.0 5.24e-01 94.1% 91.7%
4176694 2003.1.5.2 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD 0.59 53.0 5.16e-01 96.1% 86.2%
4197001 2003.1.5.182 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › RrnaAD, Methyltransf_11 0.59 51.0 5.15e-01 96.1% 92.5%
5049929 2003.1.5.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.59 51.0 5.02e-01 91.7% 86.4%
3739670 2007.2.5.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase 0.58 32.0 4.08e-01 82.8% 92.2%
3298801 2006.1.1.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.58 39.0 4.59e-01 86.3% 100.0%
None — 0.58 48.0 5.02e-01 91.7% 94.6%
4967075 7574.1.1.5 ↗ a/b three-layered sandwiches › Thiamin diphosphate-binding fold (THDP-binding) › Thiamin diphosphate-binding fold (THDP-binding) › Thiamin diphosphate-binding fold (THDP-binding) › TPP_enzyme_C 0.57 50.0 4.72e-01 94.6% 91.0%
3967997 223.1.1.76 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_7 0.56 27.0 3.53e-01 94.6% 80.0%
3248873 7577.1.1.7 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Cys_Met_Meta_PP 0.56 40.0 3.81e-01 89.7% 60.8%
5019613 2007.2.5.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase › Rhodanese 0.55 29.0 3.71e-01 83.3% 87.8%
3389509 2007.2.5.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase › Rhodanese 0.55 29.0 3.49e-01 82.4% 74.8%
4055211 2007.2.5.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase › Rhodanese 0.53 29.0 3.62e-01 82.8% 86.2%
4064316 2007.2.5.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase › Rhodanese 0.52 29.0 3.54e-01 81.9% 84.8%
3984636 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.51 43.0 4.52e-01 94.6% 97.3%
4937627 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 23.0 3.26e-01 91.2% 93.3%
D4 medium residues 139-199
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7fciA01 1.20.1530.20 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › 0.68 59.0 3.85e-01 100.0% 93.4%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.68 53.0 4.19e-01 83.6% 43.8%
4p5aC00 3.30.1360.170 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.60 53.0 3.52e-01 95.1% 32.7%
6lpfA01 1.10.730.20 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › 0.55 49.0 3.60e-01 100.0% 46.0%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3185588 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.73 50.0 3.27e-01 72.1% 60.4%
3841428 6155.1.1.0 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.63 51.0 4.44e-01 86.9% 60.0%
D5 medium residues 356-467_491-520
PDB
D6 medium residues 862-986_1003-1039
PDB
Domain cluster: rep: replicase__NP_059451__Soil-borne_cereal_mosaic_virus__100887__D845-991