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gag

Euk-Vir

White-tufted-ear_marmoset_simian_foamy_virus

gag__YP_009508576__White-tufted-ear_marmoset_simian_foamy_virus__2170205

Identity

Accession:
YP_009508576 ↗
Protein ID:
gag
Kingdom:
euk

Quality

59.3 mean pLDDT

Taxonomy

Pararnavirae› Artverviricota› Revtraviricetes› Ortervirales› Retroviridae› Simiispumavirus› White-tufted-ear_marmoset_simian_foamy_virus

TaxID: 2170205

Cluster

View cluster (13 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 10-97
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03276.20 best Gag_spuma_N 108.7 3.20e-31 96.6% 59.2%
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2b02A01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.60 44.0 4.22e-01 78.4% 97.1%
4hiaA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.58 45.0 3.63e-01 84.1% 86.9%
7a6pB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 42.0 3.67e-01 79.5% 76.8%
5iu1B00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 43.0 4.06e-01 84.1% 93.8%
5svgC00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 42.0 3.79e-01 79.5% 92.6%
7prrB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 41.0 3.41e-01 79.5% 68.6%
3cloC01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 44.0 3.47e-01 86.4% 73.1%
2z6cA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 42.0 3.86e-01 81.8% 87.6%
3mjqA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 41.0 3.92e-01 79.5% 90.7%
4d10F01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.56 42.0 3.33e-01 80.7% 90.5%
2kdkA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 42.0 3.96e-01 83.0% 97.2%
2v0uA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 42.0 3.65e-01 84.1% 76.0%
6kjuB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 40.0 3.70e-01 78.4% 87.2%
3nqhA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.55 41.0 2.91e-01 81.8% 92.4%
2y3vD00 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.54 38.0 3.26e-01 75.0% 89.0%
4hoiB00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 40.0 3.71e-01 78.4% 91.2%
4ywzB00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 40.0 3.41e-01 78.4% 62.3%
3q0xA01 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.54 39.0 3.25e-01 75.0% 86.5%
4m4xA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 38.0 3.46e-01 76.1% 88.1%
4ckmB00 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.53 38.0 3.26e-01 75.0% 94.4%
5zl6A01 2.40.37.10 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › Lyase, Ornithine Decarboxylase; Chain A, domain 1 0.53 38.0 3.19e-01 75.0% 99.3%
3mqqB00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 39.0 3.60e-01 79.5% 83.9%
3bwlB00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 39.0 3.53e-01 79.5% 78.0%
2gj3A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 38.0 3.55e-01 79.5% 82.4%
2ebkA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.52 45.0 3.95e-01 94.3% 81.2%
6pzjA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 38.0 3.26e-01 78.4% 73.6%
4xmqA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.51 36.0 3.26e-01 76.1% 69.9%
1na6A01 2.40.330.10 Mainly Beta › Beta Barrel › At1g16640 B3 domain › DNA-binding pseudobarrel domain 0.51 43.0 3.58e-01 98.9% 71.9%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1019414 6122.1.1.1 ↗ a+b two layers › N-terminal domain of spumavirus gag protein › N-terminal domain of spumavirus gag protein › N-terminal domain of spumavirus gag protein › Gag_spuma_N 0.90 85.0 6.61e-01 100.0% 50.9%
3588721 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.60 44.0 4.10e-01 78.4% 84.3%
5008201 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.59 44.0 4.34e-01 78.4% 89.5%
4986976 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.59 44.0 3.99e-01 79.5% 87.5%
3735309 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.58 43.0 4.35e-01 79.5% 95.6%
1840644 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.56 43.0 4.06e-01 84.1% 93.8%
4017509 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.56 42.0 3.63e-01 79.5% 73.6%
4551342 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.56 38.0 3.92e-01 70.5% 81.2%
3506163 223.1.1.29 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_11 0.56 43.0 3.89e-01 83.0% 85.5%
4102446 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 0.56 41.0 3.22e-01 79.5% 50.2%
4959121 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.55 42.0 3.87e-01 81.8% 87.8%
3511551 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 33.0 3.81e-01 85.2% 88.3%
4952200 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.54 39.0 2.92e-01 76.1% 42.5%
5069528 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.54 40.0 3.80e-01 80.7% 90.0%
5047587 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.54 40.0 3.62e-01 79.5% 80.0%
3821773 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.54 39.0 3.35e-01 78.4% 72.9%
3640509 304.9.1.21 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRP7,RRM_Rrp7 0.54 37.0 2.79e-01 71.6% 60.9%
3401903 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.54 39.0 3.70e-01 78.4% 86.4%
4949125 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.54 39.0 3.40e-01 79.5% 68.0%
3744425 5.1.4.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CNH 0.53 37.0 2.44e-01 73.9% 24.3%
3734529 304.9.1.21 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRP7,RRM_Rrp7 0.53 37.0 2.61e-01 72.7% 56.9%
5019134 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.53 38.0 3.30e-01 78.4% 66.0%
4962395 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.53 39.0 3.53e-01 79.5% 82.4%
3674460 2484.1.1.157 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4371 0.53 37.0 2.80e-01 73.9% 37.8%
3659671 4.25.1.0 ↗ beta barrels › SH3 › Auxin response factor dimerization domain and ancillary domain › Auxin response factor dimerization domain and ancillary domain 0.53 35.0 3.86e-01 89.8% 85.7%
5068526 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.53 38.0 3.73e-01 78.4% 96.0%
None — 0.51 35.0 3.02e-01 70.5% 77.2%
5008203 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.51 37.0 3.51e-01 79.5% 83.5%
4864011 1.1.7.41 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › UPF1_1B_dom 0.51 41.0 3.87e-01 96.6% 72.4%
207 1.1.11.2 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain › EcoRII-N 0.51 43.0 3.58e-01 98.9% 71.5%
3720530 223.1.1.85 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3+PAS_9 0.51 40.0 2.58e-01 89.8% 80.0%
4023469 216.1.1.0 ↗ a+b two layers › UBC-like › UBC-like › UBC-like 0.50 42.0 3.67e-01 94.3% 73.6%
4629016 60.1.2.1 ↗ beta barrels › SPOC domain-like › SPOC domain-related › Ku70/80 subunit middle domain › Ku 0.50 37.0 2.51e-01 78.4% 21.3%
3587863 3158.1.1.1 ↗ beta barrels › uncharacterized protein RUMGNA_01417 › uncharacterized protein RUMGNA_01417 › uncharacterized protein RUMGNA_01417 › DUF5348 0.50 38.0 3.85e-01 95.5% 83.5%
3959244 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.50 36.0 3.67e-01 78.4% 94.4%
D2 medium residues 129-180
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3uumA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.88 81.0 6.00e-01 100.0% 45.1%
2r9iA00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.79 71.0 6.35e-01 100.0% 77.5%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 69.0 6.13e-01 98.1% 72.6%
4i43B02 3.30.43.40 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain 0.74 50.0 3.85e-01 71.2% 32.5%
1vkeB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.67 49.0 3.93e-01 76.9% 51.5%
1v9mA03 1.20.1690.10 Mainly Alpha › Up-down Bundle › V-type ATP synthase subunit C fold › V-type ATP synthase subunit C domain 0.65 42.0 3.53e-01 75.0% 36.5%
2zyhA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.63 49.0 3.28e-01 86.5% 30.7%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3555578 633.22.1.15 ↗ alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) › OST3_OST6 0.84 65.0 5.06e-01 84.6% 41.8%
3607691 109.4.1.1554 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TARBP1 0.79 62.0 3.68e-01 86.5% 13.0%
D3 medium residues 280-447
PDB
Domain cluster: rep: gag__YP_009513241__Rhesus_macaque_simian_foamy_virus__2170199__D297-457
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF20672.4 best Gag_FV_central 249.5 2.00e-74 100.0% 97.1%