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replicase

Euk-Vir

Sweet_potato_collusive_virus

replicase__YP_004347415__Sweet_potato_collusive_virus__930168

Identity

Accession:
YP_004347415 ↗
Protein ID:
replicase
Kingdom:
euk

Quality

79.5 mean pLDDT

Taxonomy

Pararnavirae› Artverviricota› Revtraviricetes› Ortervirales› Caulimoviridae› Cavemovirus› Sweet_potato_collusive_virus

TaxID: 930168

Cluster

Singleton — not in a non-trivial cluster

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 5-117
PDB
Domain cluster: rep: NC_029048.2__YP_009221738.1__PHICD211_20135__00153__D2-127
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02160.20 best Peptidase_A3 52.1 8.70e-14 100.0% 51.4%
PF00077.26 RVP 27.4 4.70e-06 88.5% 83.2%
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3s8iA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.84 74.0 7.21e-01 100.0% 84.7%
3slzA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.81 69.0 6.88e-01 100.0% 89.5%
1fmbA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.80 65.0 6.76e-01 93.8% 92.3%
3sqfA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.78 62.0 6.70e-01 91.2% 98.9%
4ehcA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.77 72.0 5.26e-01 100.0% 48.2%
2fivA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.77 66.0 6.63e-01 92.9% 90.3%
3liyA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.77 67.0 6.67e-01 93.8% 90.5%
5c9dB00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.77 67.0 6.61e-01 99.1% 89.2%
2jysA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.76 59.0 6.47e-01 100.0% 100.0%
1mppA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.75 69.0 5.83e-01 100.0% 91.2%
1bxoA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.75 69.0 6.03e-01 100.0% 91.5%
1wkrA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.75 69.0 5.95e-01 100.0% 87.6%
1yg9A02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.74 62.0 5.93e-01 89.4% 98.5%
1mvpA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.74 62.0 6.28e-01 93.8% 90.2%
1uh9A02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.72 66.0 6.00e-01 100.0% 84.6%
4pphA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.69 63.0 5.23e-01 100.0% 73.3%
1miqA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.68 62.0 5.63e-01 100.0% 85.5%
2vijA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.67 62.0 5.84e-01 100.0% 100.0%
7tbdB02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.63 57.0 5.07e-01 100.0% 82.8%
1nvpD02 2.30.18.10 Mainly Beta › Roll › TATA box binding Protein, subunit D; domain 2 › Transcription factor IIA (TFIIA), beta-barrel domain 0.58 26.0 3.69e-01 74.3% 100.0%
1nh2C00 2.30.18.10 Mainly Beta › Roll › TATA box binding Protein, subunit D; domain 2 › Transcription factor IIA (TFIIA), beta-barrel domain 0.54 25.0 3.39e-01 72.6% 92.0%
ECOD (95)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3370298 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.89 80.0 8.16e-01 100.0% 98.2%
3735567 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.87 80.0 6.14e-01 100.0% 48.0%
3225435 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.87 72.0 7.23e-01 90.3% 85.8%
3334785 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.87 78.0 7.45e-01 100.0% 83.1%
3421072 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.87 79.0 7.89e-01 100.0% 94.8%
5032562 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.86 81.0 7.96e-01 100.0% 93.3%
3902845 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.86 81.0 7.71e-01 100.0% 90.0%
3868675 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.86 78.0 6.67e-01 100.0% 63.5%
4934668 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.86 81.0 7.69e-01 100.0% 96.9%
5031162 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.86 80.0 7.96e-01 100.0% 96.5%
3504655 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.86 74.0 7.44e-01 95.6% 89.6%
3511017 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.85 79.0 7.86e-01 100.0% 95.7%
3934130 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.85 81.0 7.67e-01 100.0% 88.5%
3878578 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.85 81.0 7.76e-01 100.0% 92.0%
3737912 1.1.1.13 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Peptidase_A2_2 0.85 71.0 7.55e-01 90.3% 98.0%
3724372 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.85 74.0 6.55e-01 91.2% 69.0%
3883471 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.85 80.0 7.62e-01 100.0% 90.0%
3274948 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.85 74.0 6.52e-01 100.0% 66.5%
3559341 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.85 80.0 7.36e-01 100.0% 83.6%
4933012 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.85 80.0 7.89e-01 100.0% 95.0%
3337491 1.1.2.29 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RVP 0.85 73.0 7.57e-01 100.0% 97.1%
4984762 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.85 78.0 7.68e-01 100.0% 92.5%
3518811 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.85 77.0 7.86e-01 99.1% 99.1%
3732052 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.85 73.0 7.44e-01 91.2% 99.1%
3923745 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.84 80.0 7.66e-01 100.0% 89.6%
3684739 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.84 79.0 7.76e-01 100.0% 95.8%
3923810 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.84 76.0 7.60e-01 95.6% 94.8%
3631178 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.84 79.0 7.27e-01 100.0% 85.0%
3436417 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.84 79.0 7.52e-01 100.0% 89.2%
3927612 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.84 77.0 7.67e-01 100.0% 95.7%
3927455 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.84 77.0 7.28e-01 97.3% 89.2%
3366156 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.84 78.0 7.69e-01 100.0% 93.3%
3933534 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.84 67.0 7.32e-01 88.5% 100.0%
3925981 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.84 71.0 7.22e-01 100.0% 91.8%
3529283 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.83 77.0 7.41e-01 98.2% 92.0%
3724349 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.83 76.0 7.00e-01 97.3% 96.4%
3922986 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.83 69.0 7.32e-01 87.6% 100.0%
3773238 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.82 78.0 7.43e-01 100.0% 88.5%
3730035 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.82 68.0 7.26e-01 87.6% 100.0%
3937611 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.82 73.0 7.40e-01 96.5% 96.4%
3447999 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.82 77.0 7.57e-01 100.0% 96.7%
5031732 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.82 73.0 7.29e-01 100.0% 93.9%
3935726 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.82 74.0 7.41e-01 100.0% 95.6%
3510736 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.82 74.0 7.38e-01 100.0% 94.8%
3934416 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.82 71.0 7.01e-01 96.5% 87.5%
3926561 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.81 73.0 7.21e-01 100.0% 90.0%
5031038 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.81 76.0 7.32e-01 100.0% 96.8%
4969904 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.81 76.0 7.09e-01 100.0% 83.0%
3924493 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.81 65.0 7.02e-01 100.0% 98.9%
3933744 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.81 70.0 7.12e-01 92.0% 92.7%
5032263 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.81 75.0 7.16e-01 100.0% 94.6%
3502540 1.1.1.14 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › DUF1758 0.81 59.0 6.60e-01 76.1% 100.0%
3507687 1.1.1.14 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › DUF1758 0.81 76.0 7.19e-01 100.0% 95.4%
3912599 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.80 72.0 7.10e-01 100.0% 89.2%
5028105 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.80 74.0 6.97e-01 100.0% 88.1%
3691719 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.80 69.0 7.16e-01 91.2% 100.0%
5030771 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.80 71.0 7.10e-01 100.0% 93.9%
3579423 1.1.1.14 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › DUF1758 0.80 74.0 6.69e-01 100.0% 94.7%
4993154 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.80 74.0 7.07e-01 100.0% 87.5%
3833862 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.80 72.0 7.20e-01 100.0% 94.8%
3821648 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.80 75.0 7.24e-01 100.0% 94.4%
3731145 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.80 70.0 6.78e-01 93.8% 86.4%
3797424 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.79 74.0 6.45e-01 100.0% 88.5%
4992554 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.79 74.0 6.70e-01 100.0% 80.5%
3931384 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.79 71.0 7.28e-01 97.3% 98.2%
3793978 1.1.1.14 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › DUF1758 0.79 74.0 6.44e-01 100.0% 92.7%
4993656 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.79 74.0 7.24e-01 100.0% 95.8%
1697187 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.79 66.0 6.49e-01 100.0% 82.6%
3931849 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.79 73.0 7.10e-01 100.0% 89.6%
3506070 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.79 74.0 6.48e-01 100.0% 94.4%
3933581 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.79 71.0 7.27e-01 100.0% 100.0%
3514088 1.1.1.14 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › DUF1758 0.79 73.0 6.89e-01 100.0% 90.3%
3668951 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.79 60.0 6.69e-01 84.1% 100.0%
3509026 1.1.1.14 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › DUF1758 0.79 73.0 6.29e-01 100.0% 92.9%
4001904 1.1.1.14 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › DUF1758 0.79 58.0 6.32e-01 77.0% 95.8%
4964766 1.1.1.5 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Zn_protease 0.78 69.0 7.00e-01 97.3% 96.4%
5023444 1.1.1.5 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Zn_protease 0.78 71.0 7.24e-01 97.3% 100.0%
3506977 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.78 73.0 6.66e-01 100.0% 91.6%
5073196 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.78 72.0 6.98e-01 100.0% 90.2%
3516105 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.78 73.0 6.87e-01 100.0% 93.3%
4928555 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.78 72.0 6.99e-01 100.0% 92.7%
5032212 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.78 71.0 6.74e-01 100.0% 92.5%
5034399 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.78 72.0 6.82e-01 100.0% 87.2%
5032277 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.78 72.0 6.98e-01 100.0% 90.4%
139793 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.77 67.0 6.68e-01 93.8% 90.5%
3782336 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.77 71.0 6.80e-01 100.0% 90.0%
3184963 1.1.1.27 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_N 0.76 71.0 4.73e-01 100.0% 39.5%
3175153 1.1.1.19 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Pol_BBD 0.75 62.0 5.97e-01 86.7% 79.2%
4993389 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.75 69.0 6.75e-01 100.0% 93.3%
3517572 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.75 67.0 6.73e-01 100.0% 94.8%
3582847 1.1.2.30 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › DUF1758 0.74 70.0 6.74e-01 100.0% 96.0%
3437522 1.1.1.19 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Pol_BBD 0.70 60.0 5.82e-01 97.3% 83.2%
5064814 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.68 60.0 5.04e-01 100.0% 57.7%
3723709 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.62 47.0 5.16e-01 78.8% 98.9%
4932541 4.1.1.19 ↗ beta barrels › SH3 › SH3 › SH3 › LSM 0.58 27.0 3.21e-01 77.9% 63.0%
D2 high residues 413-493
PDB
Domain cluster: rep: polyprotein,_partial__YP_010085997__Schefflera_ringspot_virus__2169729__D61-133
D3 high residues 501-631
PDB
Domain cluster: rep: polyprotein__YP_002916057__Sweet_potato_badnavirus_B__647294__D493-623
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF17917.8 best RT_RNaseH 53.2 4.00e-14 80.2% 81.9%
PF17919.8 RT_RNaseH_2 46.3 5.30e-12 61.8% 66.0%
D4 medium residues 168-188_278-305_332-410
PDB
Domain cluster: rep: IMGVR_UViG_3300021288_000040-3300021288-Ga0214511_10009611__D472-499_578-609_637-721
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00078.33 best RVT_1 71.9 9.50e-20 62.5% 42.0%
D5 medium residues 189-277_306-331
PDB
Domain cluster: rep: pol_protein,_partial__YP_002308474__Simian_T-cell_lymphotropic_virus_6__481147__D16-81_108-143