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VP1

Euk-Vir

Rotavirus_F_chicken_03V0568_DEU_2003

VP1__YP_008145313__Rotavirus_F_chicken_03V0568_DEU_2003__994994

Identity

Accession:
YP_008145313 ↗
Protein ID:
VP1
Kingdom:
euk

Quality

85.8 mean pLDDT

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 medium residues 1-79
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1v9vA01 1.20.1480.20 Mainly Alpha › Up-down Bundle › hypothetical protein mp506/mpn330, domain 1 › MAST3 pre-PK domain-like 0.67 49.0 4.68e-01 78.5% 89.5%
1vjxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.65 47.0 3.83e-01 75.9% 92.6%
3t46A00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.61 44.0 4.50e-01 77.2% 92.0%
3rfyA02 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 0.59 50.0 4.63e-01 98.7% 99.1%
4c3eM00 1.20.120.1350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pneumovirus matrix protein 2 (M2), zinc-binding domain 0.54 43.0 3.54e-01 88.6% 77.4%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3461715 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.76 56.0 5.14e-01 77.2% 94.0%
4397450 632.22.1.163 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › Latarcin 0.74 56.0 4.91e-01 79.7% 86.1%
3731064 633.6.1.0 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like 0.74 55.0 4.89e-01 78.5% 94.5%
3686609 6026.1.1.0 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.68 50.0 4.80e-01 77.2% 84.4%
3612019 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 45.0 4.34e-01 79.7% 95.6%
5038046 3896.1.1.0 ↗ alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase 0.57 47.0 3.58e-01 91.1% 53.2%
3618557 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 0.57 50.0 4.82e-01 97.5% 90.0%
3286382 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.56 47.0 3.87e-01 94.9% 91.3%
D2 medium residues 80-96_700-773
PDB
Domain cluster: rep: VP1__YP_003896046__Rotavirus_D_chicken_05V0049_DEU_2005__884200__D70-83_693-762
D3 medium residues 248-336_670-699
PDB
Domain cluster: representative
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
223785 4963.1.1.1 ↗ alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › RdRP_4 0.98 71.0 4.91e-01 74.8% 26.6%
3387236 2004.1.1.220 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SWI2_SNF2 0.52 45.0 3.70e-01 95.8% 64.0%
D4 medium residues 337-388_443-465_490-599
PDB
Domain cluster: rep: VP1__YP_002302227__Rotavirus_A__28875__D336-386_450-491_506-597
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 64.0 1.90e-17 66.0% 20.2%
D5 medium residues 389-442_466-489
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mukA02 3.90.1850.10 Alpha Beta › Alpha-Beta Complex › RNA-directed RNA polymerase lambda-3 › RNA-directed RNA polymerase lambda-3 0.66 58.0 3.56e-01 100.0% 22.0%
3cl3A02 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.57 44.0 4.29e-01 84.6% 88.6%
2v7kA02 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 42.0 3.02e-01 83.3% 77.6%
1ce7A02 4.10.470.10 Few Secondary Structures › Irregular › Ricin (A Subunit), domain 2 › Ricin (A Subunit), domain 2 0.53 32.0 3.19e-01 88.5% 58.2%
1dkqA02 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.52 40.0 3.49e-01 84.6% 89.5%
3ga8A00 3.10.20.860 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.50 31.0 3.28e-01 88.5% 70.1%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
223786 304.48.1.16 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4 0.92 87.0 5.54e-01 100.0% 31.3%
5061207 102.1.2.10 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase › Q_salvage 0.59 49.0 3.40e-01 96.2% 38.7%
1247620 101.1.1.72 ↗ alpha arrays › HTH › HTH › Three-helical HTH › GP3_package 0.58 36.0 3.05e-01 88.5% 35.3%
4875850 4967.1.1.14 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › Flavi_NS5_thumb 0.54 28.0 2.89e-01 75.6% 48.7%
3622481 604.29.1.1 ↗ alpha bundles › Spectrin repeat-like › Trehalose-6-phosphate phosphatase N-terminal helical bundle › Trehalose-6-phosphate phosphatase N-terminal helical bundle › T6PP_N 0.53 33.0 2.96e-01 84.6% 41.7%
3690741 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 38.0 2.60e-01 79.5% 53.5%
3743600 109.4.1.1297 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TIMELESS, PF27570 0.52 38.0 2.26e-01 79.5% 53.2%
4934384 101.1.2.947 ↗ alpha arrays › HTH › HTH › winged helix domain › PF27234 0.51 30.0 2.99e-01 88.5% 54.1%
4392073 246.2.1.14 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › FBPase_2 0.50 38.0 2.38e-01 82.1% 59.7%
D6 medium residues 600-669
PDB
Domain cluster: representative
CATH (63)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r7rA04 3.30.70.2480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.97 93.0 6.83e-01 100.0% 44.6%
7nasX01 3.30.300.70 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › RimP-like superfamily, N-terminal 0.75 64.0 6.22e-01 95.7% 92.4%
1qf6A02 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.75 67.0 5.82e-01 100.0% 66.0%
2iruA02 3.30.70.3300 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.74 65.0 5.25e-01 100.0% 62.3%
4er8A00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.73 64.0 4.92e-01 100.0% 43.6%
2phcB01 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.73 60.0 5.71e-01 90.0% 75.9%
2a6mA00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.73 65.0 5.30e-01 100.0% 62.3%
2iusD01 3.30.980.40 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › 0.72 62.0 5.61e-01 100.0% 69.4%
1z1dB00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.72 57.0 4.70e-01 98.6% 47.3%
8a9xA01 3.30.1360.100 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › General secretion pathway protein M, EpsM 0.72 53.0 5.23e-01 92.9% 74.7%
1v4pC01 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.72 62.0 5.46e-01 100.0% 77.8%
1sc6A03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.71 59.0 5.65e-01 98.6% 78.0%
2faoA01 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.71 62.0 4.15e-01 100.0% 30.1%
3tviA02 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.71 58.0 4.44e-01 98.6% 39.6%
3kewB02 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.71 61.0 4.93e-01 100.0% 84.0%
2e7gA01 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.71 61.0 5.38e-01 100.0% 84.0%
5wm1A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.71 62.0 5.40e-01 100.0% 64.2%
4oi3A00 3.30.70.3090 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ORF SCO4226, nickel-binding ferredoxin-like monomer 0.70 55.0 5.33e-01 100.0% 75.3%
2khdA00 3.30.70.860 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 55.0 4.78e-01 85.7% 55.6%
3tf8B00 3.90.1520.10 Alpha Beta › Alpha-Beta Complex › H-NOX domain › H-NOX domain 0.70 60.0 4.40e-01 94.3% 40.2%
6lxgA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.70 58.0 5.77e-01 98.6% 90.4%
2e1bA02 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.70 60.0 5.00e-01 100.0% 82.2%
3n79A01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.70 55.0 5.37e-01 98.6% 79.5%
4clfA02 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.69 59.0 4.48e-01 100.0% 44.0%
2ewhA01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.69 57.0 5.41e-01 98.6% 77.6%
4mt1A07 3.30.70.1440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.69 60.0 5.35e-01 100.0% 71.6%
2wbmA03 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 51.0 5.18e-01 97.1% 81.4%
4gs5A02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.68 60.0 5.29e-01 100.0% 75.2%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.68 58.0 5.55e-01 98.6% 81.0%
2f5gA00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.68 58.0 4.82e-01 100.0% 60.8%
1nyrB02 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.68 58.0 4.62e-01 100.0% 80.7%
1uv7A00 3.30.1360.100 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › General secretion pathway protein M, EpsM 0.67 58.0 5.64e-01 100.0% 88.2%
2lqjA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.67 59.0 5.38e-01 100.0% 74.5%
4okoA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.67 54.0 3.62e-01 90.0% 29.0%
1vx4407 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 53.0 5.35e-01 98.6% 89.9%
1fjeB01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.67 54.0 5.18e-01 100.0% 79.0%
1js3A03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.67 53.0 4.81e-01 88.6% 63.9%
2v50D07 3.30.70.1440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.66 56.0 5.16e-01 100.0% 77.9%
1m0sA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.66 51.0 5.08e-01 95.7% 81.9%
1darA05 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 51.0 4.79e-01 98.6% 70.1%
2asyA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 56.0 5.01e-01 98.6% 69.3%
4e1oA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.64 51.0 4.60e-01 90.0% 63.3%
7qh2C03 3.30.70.2740 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 49.0 4.84e-01 90.0% 83.3%
2rk0A01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.62 44.0 3.68e-01 74.3% 87.6%
1vehA01 3.30.300.130 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › Fe-S cluster assembly (FSCA) 0.62 52.0 5.14e-01 100.0% 98.7%
3ewgA00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.61 47.0 4.55e-01 100.0% 76.2%
2cxiA01 3.30.56.10 Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › 0.61 44.0 4.29e-01 78.6% 72.2%
3lwsF02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.60 45.0 4.01e-01 82.9% 59.6%
2gffA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 49.0 4.49e-01 100.0% 79.2%
3bguA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 49.0 4.50e-01 100.0% 77.1%
4bkwA03 3.30.500.40 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.56 43.0 3.68e-01 94.3% 49.2%
4r80A00 3.10.450.630 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 48.0 4.74e-01 100.0% 90.8%
6ztgA01 3.30.70.1070 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sporulation related repeat 0.55 43.0 4.26e-01 100.0% 81.3%
3ulbA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 39.0 3.70e-01 75.7% 94.0%
3v8hC00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.54 47.0 3.19e-01 100.0% 28.1%
4g6xA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.53 39.0 3.25e-01 78.6% 84.5%
4p78C00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.52 37.0 3.77e-01 82.9% 78.8%
3zs6A03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.52 44.0 3.22e-01 100.0% 54.4%
2lfvA00 3.30.70.1070 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sporulation related repeat 0.52 39.0 3.56e-01 98.6% 57.5%
1cksB00 3.30.170.10 Alpha Beta › 2-Layer Sandwich › Cyclin-Dependent Kinase Subunit Type 2 › Cyclin-dependent kinase, regulatory subunit 0.52 36.0 3.55e-01 74.3% 70.5%
3ihlB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 43.0 3.12e-01 100.0% 76.9%
2zdiC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 38.0 2.94e-01 78.6% 98.0%
1bd3A00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 44.0 3.13e-01 100.0% 92.9%
ECOD (80)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
223786 304.48.1.16 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4 0.97 93.0 5.76e-01 100.0% 21.7%
4458453 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.77 69.0 6.63e-01 100.0% 92.5%
3357746 304.12.1.8 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › bHLH-TF_ACT-like_plant 0.77 59.0 5.94e-01 90.0% 82.9%
4229033 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.76 68.0 5.16e-01 100.0% 77.0%
4022864 309.1.2.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain 0.76 68.0 5.09e-01 100.0% 84.7%
3487113 309.1.2.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain 0.75 66.0 4.84e-01 100.0% 70.0%
3621728 304.18.1.0 ↗ a+b two layers › Alpha-beta plaits › Anticodon-binding domain of PheRS › Anticodon-binding domain of PheRS 0.75 66.0 6.34e-01 100.0% 91.3%
4103713 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.74 65.0 4.76e-01 100.0% 77.4%
5012054 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.74 60.0 6.08e-01 98.6% 90.0%
3963906 304.55.2.0 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like 0.73 59.0 5.39e-01 91.4% 65.3%
4526652 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.73 65.0 4.81e-01 100.0% 74.4%
5014815 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.73 64.0 4.94e-01 100.0% 77.5%
4432169 309.1.2.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain 0.73 64.0 4.91e-01 100.0% 78.8%
3986660 304.55.2.0 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like 0.73 64.0 5.72e-01 100.0% 72.0%
4371408 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.73 64.0 4.62e-01 100.0% 66.5%
5021890 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.72 63.0 5.00e-01 100.0% 84.7%
5047352 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.72 63.0 4.98e-01 100.0% 86.7%
4028003 327.6.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like › NifU 0.72 63.0 4.79e-01 100.0% 44.7%
4469636 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.72 63.0 5.95e-01 98.6% 83.5%
4968588 304.55.2.1 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › Y1_Tnp 0.72 59.0 5.18e-01 92.9% 70.0%
3515089 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.72 57.0 5.83e-01 100.0% 89.7%
3348724 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.72 62.0 5.51e-01 100.0% 69.5%
3707938 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.72 62.0 5.36e-01 100.0% 70.4%
3317095 304.9.1.122 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › bHLH-TF_ACT-like_plant 0.71 52.0 5.29e-01 78.6% 82.9%
3715301 304.55.2.0 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like 0.71 61.0 4.97e-01 100.0% 55.7%
4929473 304.39.1.0 ↗ a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.71 57.0 5.41e-01 90.0% 77.6%
4621829 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.71 61.0 4.46e-01 100.0% 61.5%
4107133 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.71 55.0 5.38e-01 98.6% 78.7%
4563029 327.6.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like › NifU 0.71 61.0 6.06e-01 100.0% 98.7%
4360595 304.156.1.1 ↗ a+b two layers › Alpha-beta plaits › DNA translocase FtsK N-terminal domain › DNA translocase FtsK N-terminal domain › FtsK_alpha 0.70 61.0 5.34e-01 100.0% 63.6%
5018524 304.55.2.1 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › Y1_Tnp 0.70 59.0 5.23e-01 98.6% 73.6%
4401174 327.6.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like › NifU 0.70 60.0 5.96e-01 98.6% 94.7%
4178103 309.1.2.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain 0.70 62.0 4.76e-01 100.0% 82.5%
5079181 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.70 61.0 4.73e-01 100.0% 75.0%
4478921 304.156.1.1 ↗ a+b two layers › Alpha-beta plaits › DNA translocase FtsK N-terminal domain › DNA translocase FtsK N-terminal domain › FtsK_alpha 0.70 60.0 5.71e-01 100.0% 84.7%
4945797 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.69 60.0 4.64e-01 100.0% 81.2%
4497845 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.69 59.0 4.55e-01 100.0% 76.0%
5017694 304.55.2.1 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › Y1_Tnp 0.69 59.0 4.74e-01 100.0% 56.0%
4416497 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.69 59.0 4.56e-01 100.0% 77.6%
5001172 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.69 53.0 4.68e-01 88.6% 56.2%
4975021 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.69 60.0 5.62e-01 100.0% 81.8%
4057632 3012.1.1.10 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › ISN1 0.69 61.0 5.73e-01 100.0% 91.8%
4032118 304.55.2.1 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › Y1_Tnp 0.69 59.0 4.80e-01 100.0% 57.9%
2698946 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.69 55.0 4.77e-01 98.6% 54.6%
5072410 306.6.1.6 ↗ a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like › GH3_C 0.69 57.0 5.25e-01 91.4% 74.4%
4342311 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.68 59.0 4.36e-01 100.0% 69.2%
4316388 309.1.2.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain 0.68 58.0 4.60e-01 97.1% 84.0%
3815383 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.67 54.0 5.09e-01 88.6% 76.5%
3961531 314.1.1.1 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2 0.67 55.0 4.11e-01 91.4% 68.9%
4052460 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.67 57.0 4.41e-01 100.0% 74.7%
4939665 304.120.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI 0.67 52.0 5.15e-01 100.0% 81.3%
5078562 304.55.2.1 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › Y1_Tnp 0.66 57.0 4.28e-01 100.0% 41.6%
4991070 304.8.1.43 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_5 0.66 53.0 5.33e-01 97.1% 91.4%
4304389 5086.1.1.119 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › RRG1_C 0.66 38.0 2.62e-01 75.7% 18.6%
3191211 304.8.1.21 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_9 0.66 55.0 5.23e-01 100.0% 77.6%
4995957 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.65 56.0 5.63e-01 98.6% 100.0%
5011351 327.18.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › 40S ribosomal protein S7-A › 40S ribosomal protein S7-A 0.65 52.0 5.39e-01 90.0% 96.9%
5898 327.6.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like › NifU 0.65 55.0 5.50e-01 100.0% 97.3%
4217144 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.64 55.0 5.34e-01 98.6% 85.0%
4411246 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.64 55.0 5.31e-01 98.6% 87.5%
4873911 4070.1.1.2 ↗ alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like › Peptidase_M50 0.61 52.0 3.81e-01 100.0% 78.6%
3419043 327.10.1.9 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N-like_STI 0.61 48.0 4.62e-01 90.0% 85.9%
4589697 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.61 48.0 4.68e-01 97.1% 81.2%
4182376 323.1.1.25 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › SIDD_N 0.60 47.0 3.70e-01 90.0% 89.4%
3348248 3012.1.1.14 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › KH_2 0.60 48.0 4.88e-01 90.0% 100.0%
3702916 5104.1.1.3 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA2 0.60 46.0 3.61e-01 82.9% 40.0%
3439658 327.10.1.9 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N-like_STI 0.59 48.0 4.73e-01 94.3% 97.3%
5037971 309.1.2.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain 0.59 47.0 3.95e-01 88.6% 49.6%
3260876 304.4.1.15 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › NIPSNAP 0.57 47.0 4.52e-01 100.0% 81.2%
3174687 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.57 43.0 4.28e-01 94.3% 78.7%
3942380 101.1.8.0 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.57 47.0 3.69e-01 97.1% 100.0%
4222853 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.54 42.0 3.62e-01 85.7% 77.4%
3196982 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.54 43.0 2.87e-01 91.4% 45.2%
5011183 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.54 43.0 3.78e-01 91.4% 77.3%
3981752 829.1.1.1 ↗ a+b duplicates or obligate multimers › NinB › NinB › NinB › NinB 0.53 43.0 3.56e-01 91.4% 57.7%
3595668 2003.1.2.7 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_2 0.53 41.0 2.97e-01 88.6% 96.4%
4173782 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.52 40.0 3.50e-01 85.7% 73.0%
4944403 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.52 39.0 3.31e-01 87.1% 96.3%
3989509 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.51 41.0 3.60e-01 91.4% 68.2%
3872228 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 44.0 2.83e-01 100.0% 24.1%
D7 medium residues 774-864
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12289.14 best Rotavirus_VP1 78.7 6.10e-22 98.9% 27.3%
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1b3qA01 1.10.287.560 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Histidine kinase CheA-like, homodimeric domain 0.61 31.0 3.67e-01 87.9% 71.0%
3g80A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.61 32.0 3.51e-01 91.2% 63.0%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.58 32.0 3.60e-01 94.5% 71.2%
1b06A01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.56 31.0 3.53e-01 82.4% 73.1%
4hehA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.53 30.0 3.13e-01 90.1% 57.8%
1wpaA01 6.10.140.340 Special › Helix non-globular › Helix Hairpins › 0.53 40.0 3.95e-01 80.2% 83.8%
4ywoA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 39.0 3.06e-01 80.2% 42.5%
2xheA03 3.90.830.10 Alpha Beta › Alpha-Beta Complex › Syntaxin Binding Protein 1; Chain A, domain 2 › Sec1/Munc18 (SM) protein, domain 3a 0.53 35.0 3.23e-01 76.9% 51.2%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.53 34.0 3.53e-01 70.3% 72.0%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.52 34.0 3.61e-01 74.7% 79.7%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.51 38.0 3.70e-01 79.1% 77.5%
3udcA01 1.10.287.1260 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.50 37.0 3.44e-01 96.7% 61.7%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1173790 4962.1.1.3 ↗ alpha complex topology › C-terminal additional helical subdomain in reovirus polymerase lambda3 › C-terminal additional helical subdomain in reovirus polymerase lambda3 › C-terminal additional helical subdomain in reovirus polymerase lambda3 › Rotavirus_VP1 0.89 83.0 5.46e-01 100.0% 27.4%
5074223 622.5.1.0 ↗ alpha bundles › YvfG-like › Probable 26S proteasome regulatory subunit p27 › Probable 26S proteasome regulatory subunit p27 0.60 45.0 4.56e-01 80.2% 82.2%
3467691 150.5.1.76 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › DUF1110 0.59 42.0 4.36e-01 79.1% 80.0%
4211999 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.58 42.0 3.75e-01 75.8% 76.9%
4140367 5045.1.1.1 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.58 49.0 4.29e-01 96.7% 81.1%
3586824 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.57 42.0 2.77e-01 78.0% 71.9%
4526829 6130.1.1.1 ↗ alpha complex topology › Selenocysteine synthase N-terminal domain › Selenocysteine synthase N-terminal domain › Selenocysteine synthase N-terminal domain › Se-cys_synth_N 0.57 32.0 3.53e-01 87.9% 68.0%
3304703 4957.1.1.0 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit 0.56 37.0 3.69e-01 95.6% 63.0%
3408266 3615.1.1.0 ↗ alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain 0.55 40.0 3.47e-01 76.9% 89.3%
4110261 3748.1.1.2 ↗ extended segments › 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain › 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain › 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain › CSN5_C 0.53 36.0 3.74e-01 75.8% 75.3%
3627459 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.52 36.0 3.09e-01 72.5% 94.2%
3964771 327.11.2.48 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › DUF7168 0.51 42.0 3.86e-01 90.1% 100.0%
3965811 3711.1.1.0 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.51 40.0 3.84e-01 85.7% 96.3%
4324117 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.51 38.0 2.57e-01 79.1% 90.6%
4482084 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.51 30.0 3.11e-01 79.1% 61.1%
D8 medium residues 865-921_988-1086
PDB
Domain cluster: rep: polymerase__YP_009163940__Fengkai_orbivirus__1692107__D1078-1116_1190-1260
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12289.14 best Rotavirus_VP1 97.3 1.30e-27 64.1% 31.8%