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YP_010772789.1

Arc-Vir

NC_074655__YP_010772789.1__QIT52-gp32__00032

Identity

Accession:
NC_074655 ↗
Protein ID:
YP_010772789.1 ↗
Kingdom:
archaea

Quality

78.6 mean pLDDT

Taxonomy

Itzamnaviridae› Pletoitzamnavirus› Methanophagales_virus_PBV082

TaxID: 3071307

Cluster

View cluster (18 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 398-461
PDB
D2 medium residues 1-135
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4akgA06 1.10.8.710 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Dynein motor, AAA1 domain, small subdomain 0.60 33.0 3.68e-01 97.0% 65.4%
1op1A00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.60 33.0 4.00e-01 94.1% 85.4%
1qgtB00 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.56 33.0 3.29e-01 88.1% 53.8%
4nftC00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.56 49.0 4.43e-01 94.1% 86.5%
1e7pC00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.55 42.0 3.38e-01 79.3% 70.9%
3ls1A00 1.20.120.290 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle 0.54 31.0 3.17e-01 97.0% 55.6%
6lumG01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.53 39.0 4.29e-01 98.5% 93.8%
2wcjA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.53 38.0 3.82e-01 86.7% 72.3%
1mhyB00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.52 36.0 2.66e-01 70.4% 75.2%
4o6yB00 1.20.120.1770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 39.0 3.42e-01 80.0% 71.6%
2jx0A00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.52 32.0 3.28e-01 97.0% 61.8%
5h5mA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.52 36.0 3.71e-01 97.0% 74.6%
8ex5A01 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.51 36.0 3.24e-01 100.0% 50.8%
4hkrA00 1.20.140.140 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Calcium release-activated calcium channel protein Orai 0.51 37.0 3.53e-01 76.3% 76.4%
4ecgA00 1.20.1420.20 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › M75 peptidase, HXXE motif 0.51 37.0 2.77e-01 77.0% 96.7%
3kavA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.50 28.0 3.17e-01 94.8% 70.6%
1sziA02 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.50 32.0 3.18e-01 78.5% 61.3%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5027768 3352.1.1.2 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PMT_2 0.94 88.0 5.75e-01 98.5% 27.4%
4959788 3352.1.1.2 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PMT_2 0.93 87.0 5.85e-01 100.0% 31.0%
5055716 3352.1.1.2 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PMT_2 0.86 82.0 5.75e-01 100.0% 37.3%
5030341 3352.1.1.2 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PMT_2 0.85 78.0 5.39e-01 100.0% 32.3%
4998378 3352.1.1.2 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PMT_2 0.84 78.0 5.51e-01 100.0% 35.7%
4998643 3352.1.1.2 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PMT_2 0.83 79.0 5.45e-01 100.0% 34.4%
4941316 3352.1.1.1 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3 0.82 77.0 5.11e-01 100.0% 30.4%
3494243 3352.1.1.31 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › Mannosyl_trans, PIG-U 0.80 75.0 5.61e-01 100.0% 46.1%
4033051 632.19.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542 0.80 42.0 5.76e-01 95.6% 100.0%
5056667 3352.1.1.2 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PMT_2 0.80 75.0 5.12e-01 100.0% 36.8%
4941642 3352.1.1.0 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.80 72.0 5.01e-01 100.0% 33.0%
3184452 3352.1.1.9 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › Mannosyl_trans 0.79 72.0 5.29e-01 98.5% 42.9%
4997932 3352.1.1.9 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › Mannosyl_trans 0.79 73.0 5.39e-01 100.0% 41.2%
4967543 3352.1.1.2 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › PMT_2 0.77 70.0 5.11e-01 100.0% 38.3%
5003405 3352.1.1.0 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.74 69.0 4.79e-01 100.0% 36.8%
3970681 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.61 55.0 4.62e-01 97.8% 94.2%
3576591 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.53 34.0 3.41e-01 97.8% 62.2%
5030728 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.53 33.0 3.35e-01 97.0% 60.0%
3883101 5067.1.1.3 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Patched 0.53 43.0 3.53e-01 85.9% 93.3%
5076059 5073.1.2.23 ↗ alpha bundles › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain-related › Copper efflux ATPase transmembrane domain › Hydrolase 0.52 40.0 3.00e-01 80.7% 55.4%
4333625 5049.1.1.1 ↗ alpha complex topology › Ammonium transporter-related › Ammonium transporter-related › Ammonium transporter › Ammonium_transp 0.52 39.0 2.74e-01 77.8% 63.3%
3848829 5067.1.1.5 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Sterol-sensing 0.52 42.0 3.52e-01 86.7% 89.6%
3277874 5067.1.1.4 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › MMPL 0.50 42.0 3.52e-01 90.4% 89.1%
D3 medium residues 136-217
PDB
Domain cluster: rep: IMGVR_UViG_3300025163_000063-3300025163-Ga0209410_100050829__D138-212
D4 medium residues 218-391
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6gyhA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.60 42.0 3.88e-01 94.8% 55.1%
3ajmB02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.58 38.0 4.26e-01 94.3% 85.0%
2hujA00 1.20.120.440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YppE-like 0.58 38.0 4.35e-01 93.1% 92.0%
6k6iA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.57 41.0 3.84e-01 97.1% 58.4%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.57 30.0 4.02e-01 77.6% 100.0%
2pfdA03 1.20.120.680 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle 0.57 43.0 4.15e-01 79.3% 93.1%
1o5hA00 1.20.120.680 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle 0.56 42.0 4.07e-01 78.7% 89.5%
8gi9A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.56 40.0 3.64e-01 96.6% 55.0%
1st6A03 1.20.120.810 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vinculin, Vh2 four-helix bundle 0.55 40.0 3.69e-01 96.0% 57.2%
5d0yA00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.55 36.0 3.80e-01 91.4% 73.5%
4huqS00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.54 35.0 3.66e-01 92.5% 67.7%
4o6yB00 1.20.120.1770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.54 41.0 3.89e-01 78.7% 81.5%
1e2aA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.53 29.0 3.68e-01 75.9% 89.2%
4aifA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 32.0 3.46e-01 75.9% 70.1%
3solA00 1.20.58.1630 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Chaperone lipoprotein PulS/OutS 0.52 26.0 3.45e-01 83.9% 87.9%
4hzuS00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.52 35.0 3.64e-01 92.5% 71.3%
3er9B01 1.20.1270.320 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Poxvirus poly(A) polymerase, N domain 0.51 30.0 3.71e-01 83.3% 94.3%
4yvoA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.51 30.0 3.53e-01 76.4% 83.2%
2m6bA00 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.51 38.0 4.10e-01 92.0% 91.3%
3rkvA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.50 30.0 3.27e-01 75.3% 68.7%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3339293 3922.1.1.189 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › DUF630 0.59 52.0 4.59e-01 96.6% 92.7%
3247271 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.56 44.0 3.72e-01 81.0% 61.1%
4859202 1076.1.1.2 ↗ alpha bundles › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Aph-1 0.55 42.0 3.85e-01 79.9% 70.1%
5053783 5082.1.1.0 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like 0.55 40.0 4.32e-01 87.9% 88.0%
3470477 1076.1.1.2 ↗ alpha bundles › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Aph-1 0.54 42.0 3.82e-01 82.2% 97.0%
3563979 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.53 30.0 3.33e-01 79.3% 66.2%
3168689 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 37.0 3.50e-01 70.7% 59.5%
3217267 5001.1.1.27 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Sre 0.52 42.0 3.59e-01 83.9% 68.7%
3184336 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.52 33.0 3.44e-01 81.6% 69.7%
3623581 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.52 46.0 4.29e-01 98.9% 90.5%
3931007 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.51 40.0 3.39e-01 82.2% 63.0%
3977977 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 42.0 4.00e-01 87.4% 86.3%
4019589 5050.1.1.8 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › FPN1 0.51 42.0 3.77e-01 89.7% 72.8%
3181551 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 0.50 42.0 3.93e-01 89.1% 88.8%