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primase

Euk-Vir

Noumeavirus

primase__YP_009345453__Noumeavirus__1955558

Identity

Accession:
YP_009345453 ↗
Protein ID:
primase
Kingdom:
euk

Quality

78.8 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Marseilleviridae› Marseillevirus› Noumeavirus

TaxID: 1955558

Cluster

View cluster (27 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 12-194
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23162.2 best AEP_C962R 135.3 4.00e-39 82.5% 75.1%
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4evuB00 3.30.1660.10 Alpha Beta › 2-Layer Sandwich › Dodecin subunit-like › Flavin-binding protein dodecin 0.71 22.0 3.69e-01 83.6% 75.0%
5wpjA02 3.30.70.420 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain 0.68 41.0 5.10e-01 99.5% 100.0%
5is2A01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.66 34.0 4.59e-01 98.4% 96.7%
2fyxA00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.65 41.0 4.81e-01 74.9% 88.5%
1b64A00 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.64 32.0 4.39e-01 100.0% 94.5%
6h8oA00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.63 34.0 4.43e-01 89.6% 96.8%
4djbA00 3.30.70.2870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Mastadenovirus E4 ORF3 0.61 38.0 4.63e-01 99.5% 97.5%
1ivzA00 3.30.70.960 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › SEA domain 0.60 40.0 4.60e-01 72.1% 92.4%
4fprB00 3.30.70.2910 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 39.0 4.59e-01 92.3% 100.0%
3i4hX01 3.30.70.1890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 38.0 4.43e-01 99.5% 98.4%
4clfA02 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.56 38.0 3.87e-01 74.9% 68.5%
1m55A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.54 50.0 4.93e-01 99.5% 97.4%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5017694 304.55.2.1 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › Y1_Tnp 0.68 39.0 4.29e-01 91.3% 68.7%
4028741 304.20.1.1 ↗ a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP_RNA-bind 0.66 45.0 5.20e-01 77.6% 94.8%
3930380 304.166.1.0 ↗ a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain 0.65 38.0 4.82e-01 72.7% 100.0%
3525488 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.64 44.0 5.14e-01 98.4% 98.5%
3844655 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.64 41.0 4.91e-01 100.0% 96.7%
3922086 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.64 40.0 4.79e-01 98.9% 95.0%
3866917 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.63 44.0 5.04e-01 80.3% 98.5%
3543605 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.63 41.0 4.93e-01 100.0% 99.2%
4976988 304.8.1.9 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_6 0.63 32.0 4.37e-01 98.9% 96.7%
3753506 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.63 44.0 5.03e-01 79.2% 98.5%
3394262 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.62 41.0 4.82e-01 99.5% 97.6%
3753559 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.62 42.0 4.92e-01 80.3% 100.0%
4022825 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.62 34.0 4.26e-01 99.5% 90.5%
4994922 304.31.1.1 ↗ a+b two layers › Alpha-beta plaits › HMG-CoA reductase › NAD-binding domain of HMG-CoA reductase › HMG-CoA_red 0.62 38.0 4.64e-01 99.5% 100.0%
3559614 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.61 43.0 4.77e-01 72.1% 93.1%
4212379 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.61 48.0 4.28e-01 85.8% 58.8%
3724729 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.61 36.0 4.19e-01 100.0% 81.5%
1146572 304.152.1.1 ↗ a+b two layers › Alpha-beta plaits › E4-ORF3 › E4-ORF3 › Adeno_E4_ORF3 0.61 38.0 4.66e-01 99.5% 99.1%
3588046 304.55.1.14 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Y2_Tnp 0.61 53.0 4.67e-01 92.9% 88.8%
3791139 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 39.0 4.63e-01 71.6% 98.3%
3962778 304.31.1.1 ↗ a+b two layers › Alpha-beta plaits › HMG-CoA reductase › NAD-binding domain of HMG-CoA reductase › HMG-CoA_red 0.60 39.0 4.59e-01 94.0% 96.0%
3499543 304.47.1.0 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain 0.59 42.0 4.78e-01 100.0% 97.8%
4030594 304.46.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF1-gamma domain › eEF1-gamma domain › EF1G 0.58 37.0 3.93e-01 83.6% 71.9%
3932173 304.31.1.0 ↗ a+b two layers › Alpha-beta plaits › HMG-CoA reductase › NAD-binding domain of HMG-CoA reductase 0.58 44.0 4.84e-01 98.9% 98.0%
4098715 304.4.1.7 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Cyclase_polyket 0.57 35.0 4.28e-01 94.0% 99.1%
1491756 304.55.1.9 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › PV_NSP1 0.57 53.0 4.76e-01 99.5% 92.3%
3910541 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.56 39.0 4.50e-01 99.5% 100.0%
4007464 304.55.1.19 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Inovirus_Gp2 0.56 46.0 4.58e-01 87.4% 91.1%
4315665 304.8.1.91 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DUF1424 0.55 49.0 4.73e-01 95.6% 83.3%
4173640 304.55.1.27 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Phage_GPA 0.55 48.0 4.22e-01 95.6% 80.7%
3242509 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.55 37.0 4.15e-01 73.8% 91.1%
4319983 304.55.1.25 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Rep_1 0.54 49.0 4.51e-01 97.3% 76.2%
7321 886.1.1.2 ↗ a+b duplicates or obligate multimers › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › GyrI-like 0.52 40.0 4.23e-01 96.7% 87.0%
4939286 304.35.1.3 ↗ a+b two layers › Alpha-beta plaits › Methyl-coenzyme M reductase subunits › Methyl-coenzyme M reductase subunits › MCR_beta_N 0.50 35.0 3.59e-01 70.5% 77.2%
D2 high residues 748-828
PDB
Domain cluster: rep: D5_family_NTPase_ATPase__YP_010084866__Shrimp_hemocyte_iridescent_virus__2039780__D809-878
D3 medium residues 225-319
PDB
Domain cluster: rep: putative_primase__YP_009506829__Tunisvirus_fontaine2__1421067__D281-379
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08707.17 best PriCT_2 64.8 1.10e-17 79.0% 96.1%
D4 medium residues 320-503
PDB
Domain cluster: rep: VV_D5-like_helicase__YP_009000916__Pithovirus_sibericum__1450746__D372-558
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08706.17 best D5_N 61.4 1.70e-16 82.6% 89.1%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2khmA01 1.10.10.1350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain 0.60 33.0 4.13e-01 72.3% 88.0%
2lseA00 1.20.120.1360 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.54 26.0 3.26e-01 91.8% 76.2%
3tdoA00 1.20.1080.10 Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. 0.52 39.0 3.53e-01 78.3% 89.9%
D5 medium residues 504-538_689-747
PDB
Domain cluster: rep: putative_D5-ATPase-helicase__YP_009052397__Aureococcus_anophagefferens_virus__1474867__D587-621_752-814
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.63 31.0 3.00e-01 72.3% 39.1%
1z21A00 1.10.10.1000 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Type III secretion system virulence factor YopR, core domain 0.61 32.0 3.27e-01 74.5% 47.9%
1ma1A01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.60 30.0 3.55e-01 75.5% 68.8%
2hsbA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.59 33.0 3.01e-01 78.7% 40.5%
1bccH00 1.10.287.20 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain 0.56 29.0 3.47e-01 81.9% 72.7%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.55 29.0 3.26e-01 79.8% 64.0%
1w36C06 1.10.10.990 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.54 36.0 4.02e-01 78.7% 88.9%
1bgfA00 1.10.532.10 Mainly Alpha › Orthogonal Bundle › Transcription Factor, Stat-4 › STAT transcription factor, N-terminal domain 0.52 39.0 3.58e-01 79.8% 81.5%
1gcvB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 37.0 3.33e-01 77.7% 94.9%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4343661 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.59 39.0 3.65e-01 94.7% 55.3%
4066056 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.55 36.0 3.41e-01 93.6% 54.8%
4605138 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.53 38.0 3.60e-01 100.0% 61.7%
5028356 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.53 31.0 2.88e-01 79.8% 43.2%
4453306 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.53 37.0 3.57e-01 100.0% 61.4%
4270265 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.53 36.0 3.57e-01 98.9% 66.0%
3233589 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.52 29.0 3.21e-01 80.9% 66.7%
4209288 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.52 36.0 3.43e-01 100.0% 59.1%
4124492 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.52 38.0 3.58e-01 100.0% 63.5%
4634964 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.52 38.0 3.66e-01 100.0% 67.3%
4066542 150.3.1.7 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › IL4 0.51 41.0 3.59e-01 88.3% 65.7%
3652007 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.51 37.0 2.90e-01 77.7% 85.1%
3461004 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.51 29.0 3.15e-01 75.5% 68.0%
D6 medium residues 539-688
PDB
Domain cluster: rep: MN062720.1__QDP45567.1__SEA_FUZZBUSTER_83__00083__D568-722_747-764
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19263.6 best DUF5906 31.8 2.80e-07 79.3% 95.6%