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replicase

Euk-Vir

Porcine_feces-associated_gemycircularvirus

replicase__YP_009408609__Porcine_feces-associated_gemycircularvirus__2017712

Identity

Accession:
YP_009408609 ↗
Protein ID:
replicase
Kingdom:
euk

Quality

84.4 mean pLDDT

Taxonomy

Shotokuvirae› Cressdnaviricota› Repensiviricetes› Geplafuvirales› Genomoviridae› Gemykibivirus› Porcine_feces-associated_gemycircularvirus

TaxID: 2017712

Cluster

View cluster (491 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 23-118
PDB
Domain cluster: rep: replication-associated_protein__YP_009552054__Stipagrostis_associaed_virus_Viruses.__X__D4-105
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00799.27 best Gemini_AL1 37.6 2.70e-09 99.0% 84.1%
D2 high residues 126-177
PDB
Domain cluster: rep: replication_associated_protein__YP_009551401__Lepus_americanus_faeces_associated_genomovirus_SHP7__2219120__D110-157
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4iggB02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.73 66.0 4.98e-01 100.0% 66.9%
2l1lB00 1.20.1440.250 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.73 62.0 4.58e-01 92.3% 52.0%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.72 61.0 4.62e-01 100.0% 70.1%
1mhyG02 1.20.1280.30 Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 2 0.71 61.0 5.47e-01 96.2% 94.5%
2etdA00 1.20.1440.20 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › LemA-like domain 0.71 61.0 4.38e-01 94.2% 53.9%
3ci6B00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.70 61.0 4.30e-01 98.1% 97.6%
2q0oA01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.70 58.0 4.06e-01 94.2% 97.0%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.70 45.0 3.98e-01 71.2% 45.3%
5llyA02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.70 58.0 3.96e-01 94.2% 100.0%
4y2fA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.69 56.0 4.13e-01 92.3% 95.1%
3b34A05 1.25.50.10 Mainly Alpha › Alpha Horseshoe › Zincin-like fold › Peptidase M1, alanyl aminopeptidase, C-terminal domain 0.66 52.0 3.22e-01 88.5% 14.8%
3bvoA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.66 56.0 4.87e-01 100.0% 91.9%
1lm3B00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.66 56.0 4.54e-01 100.0% 80.2%
5l10B00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.65 55.0 3.93e-01 100.0% 100.0%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.65 49.0 4.26e-01 82.7% 70.4%
3dcfA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.64 52.0 3.92e-01 96.2% 55.6%
5cwhA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.64 53.0 3.83e-01 96.2% 39.7%
4g12A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.63 51.0 3.81e-01 96.2% 55.7%
6srbA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.63 53.0 4.16e-01 94.2% 69.7%
3p01A01 6.10.140.590 Special › Helix non-globular › Helix Hairpins › 0.62 51.0 4.57e-01 100.0% 78.3%
4he8D00 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.62 53.0 3.83e-01 100.0% 47.5%
8ek4A01 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.61 50.0 3.88e-01 100.0% 88.0%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.61 50.0 3.94e-01 100.0% 60.3%
7eu3E01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 51.0 4.32e-01 94.2% 88.5%
3rkoG00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 53.0 4.35e-01 100.0% 86.0%
2zj2A03 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 46.0 4.00e-01 84.6% 63.1%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 48.0 4.40e-01 98.1% 73.1%
8e9gK01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 50.0 4.27e-01 100.0% 96.7%
2jpnA00 1.20.1280.210 Mainly Alpha › Up-down Bundle › Monooxygenase › Uncharacterised protein UvsW.1 0.60 48.0 4.39e-01 100.0% 81.0%
1f5mA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.60 48.0 3.44e-01 96.2% 90.9%
3pasA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.59 50.0 3.46e-01 98.1% 86.8%
1hx8A02 1.20.58.150 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › ANTH domain 0.58 45.0 3.69e-01 96.2% 82.1%
3kd4A02 3.10.620.30 Alpha Beta › Roll › C8orf32 fold › 0.57 46.0 3.35e-01 94.2% 63.7%
2dg8D00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.56 42.0 3.02e-01 84.6% 48.6%
3vuqB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.55 44.0 3.23e-01 100.0% 54.5%
2rbdA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 45.0 3.28e-01 98.1% 44.7%
3h20A04 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.53 42.0 3.66e-01 94.2% 61.8%
2plrA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 40.0 2.68e-01 84.6% 31.1%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3851394 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.76 69.0 5.06e-01 100.0% 62.3%
4876583 109.4.1.1905 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_Syf1_M, HAT_Syf1_CNRKL1_C, HAT_PRP39_N 0.75 62.0 3.61e-01 96.2% 14.7%
3994877 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.75 51.0 3.85e-01 75.0% 30.8%
4980717 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.74 65.0 4.69e-01 100.0% 100.0%
3959683 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.74 65.0 4.01e-01 100.0% 19.7%
3961415 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.74 64.0 3.96e-01 100.0% 19.0%
5002258 109.7.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Cytochrome c oxidase subunit E › Cytochrome c oxidase subunit E 0.74 61.0 5.29e-01 92.3% 70.0%
3719434 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.73 62.0 4.68e-01 96.2% 84.0%
4156528 261.1.1.1 ↗ a+b complex topology › Hect, E3 ligase catalytic domain › Hect, E3 ligase catalytic domain › Hect, E3 ligase catalytic domain › HECT 0.72 57.0 3.42e-01 90.4% 12.5%
4143568 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.71 63.0 5.26e-01 100.0% 92.2%
3370882 109.4.1.1683 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, PF30484 0.71 55.0 3.23e-01 82.7% 13.9%
5038239 3843.1.1.31 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › Oxidored_q3 0.71 62.0 5.52e-01 100.0% 94.7%
2323994 604.37.1.0 ↗ alpha bundles › Spectrin repeat-like › Legionella effector Lem22 › Legionella effector Lem22 0.70 58.0 4.88e-01 94.2% 87.8%
4162034 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.70 59.0 5.05e-01 100.0% 92.2%
3669330 604.1.1.148 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › TBCC_N 0.70 61.0 5.22e-01 100.0% 97.6%
3572303 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.69 55.0 4.21e-01 92.3% 69.2%
2485663 7021.1.1.1 ↗ alpha bundles › viral membrane assembly protein A6 homolog › viral membrane assembly protein A6 homolog › viral membrane assembly protein A6 homolog › Pox_A6 0.68 57.0 3.60e-01 90.4% 55.0%
4475943 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.68 59.0 5.05e-01 100.0% 97.6%
4429835 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.68 46.0 3.70e-01 71.2% 37.0%
3958773 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.67 58.0 3.99e-01 100.0% 88.9%
3776957 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.67 56.0 4.24e-01 98.1% 64.4%
3719708 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.66 54.0 4.28e-01 94.2% 45.2%
3421143 603.1.1.147 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF26753 0.66 55.0 3.84e-01 96.2% 78.3%
1907312 223.1.1.7 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › Autoind_bind 0.66 56.0 3.98e-01 100.0% 99.4%
3743127 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.65 54.0 4.83e-01 98.1% 66.3%
3290011 3843.1.1.4 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › PhaG_MnhG_YufB 0.65 54.0 4.46e-01 94.2% 83.2%
3828897 7516.1.1.7 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › UDPGP 0.65 52.0 2.96e-01 88.5% 16.4%
3358694 192.29.1.101 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › Rx_N 0.65 54.0 4.18e-01 96.2% 88.3%
3929241 627.1.1.1 ↗ alpha complex topology › VPS9 domain › VPS9 domain › VPS9 domain › VPS9 0.64 55.0 3.92e-01 100.0% 57.6%
2396196 601.1.2.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Vinculin 0.63 51.0 4.01e-01 100.0% 75.8%
5067760 283.1.1.0 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › Creatinase/aminopeptidase › Creatinase/aminopeptidase 0.62 54.0 4.56e-01 100.0% 95.6%
4960265 191.1.1.63 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_N 0.62 53.0 3.62e-01 100.0% 43.9%
4499656 3843.1.1.4 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › PhaG_MnhG_YufB 0.62 54.0 4.00e-01 100.0% 77.9%
4957898 191.1.1.63 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_N 0.62 51.0 3.49e-01 96.2% 42.0%
4324922 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.62 52.0 4.54e-01 100.0% 90.6%
4932209 3843.1.1.6 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › MrpF_PhaF 0.61 47.0 4.15e-01 86.5% 90.0%
5023802 3843.1.1.2 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › DUF2108 0.61 49.0 4.48e-01 90.4% 92.9%
4099504 604.17.1.0 ↗ alpha bundles › Spectrin repeat-like › MTH_863 C-terminal domain-like › MTH_863 C-terminal domain-like 0.60 51.0 4.95e-01 98.1% 98.3%
1503553 3796.1.1.1 ↗ alpha arrays › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain › Isd_H_B_linker 0.60 48.0 4.40e-01 98.1% 73.1%
3685099 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.59 41.0 3.86e-01 75.0% 63.1%
3958163 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.58 50.0 4.12e-01 100.0% 87.9%
4954727 3843.1.1.1 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › Oxidored_q2 0.56 48.0 3.91e-01 100.0% 91.0%
5009338 3843.1.1.1 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › Oxidored_q2 0.55 47.0 3.99e-01 100.0% 100.0%
D3 high residues 190-352
PDB
Domain cluster: rep: Rep_78_protein__YP_680423__adeno-associated_virus_2__10804__D308-421_457-489