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gag_precursor
Euk-VirJembrana_disease_virus
gag_precursor__NP_042684__Jembrana_disease_virus__36370
Identity
- Accession:
- NP_042684 ↗
- Protein ID:
- gag_precursor
- Kingdom:
- euk
Quality
77.4
mean pLDDT
Taxonomy
Pararnavirae›
Artverviricota›
Revtraviricetes›
Ortervirales›
Retroviridae›
Lentivirus›
Jembrana_disease_virus
TaxID: 36370
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 3-124
Domain cluster:
rep: gag_protein__NP_054369__Simian_immunodeficiency_virus__11723__D11-108
CATH (21)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1ed1A00 | 1.10.150.90 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Immunodeficiency lentiviruses, gag gene matrix protein p17 | 0.89 | 73.0 | 7.59e-01 | 90.2% | 90.4% |
| 2n1rA00 | 1.10.150.90 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Immunodeficiency lentiviruses, gag gene matrix protein p17 | 0.80 | 68.0 | 6.60e-01 | 89.3% | 82.1% |
| 7odyC01 | 1.10.287.1080 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like | 0.68 | 40.0 | 4.58e-01 | 73.8% | 78.3% |
| 2a3vB01 | 1.10.150.130 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain | 0.65 | 45.0 | 4.94e-01 | 86.9% | 91.5% |
| 5jc3A02 | 1.20.1320.30 | Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › | 0.60 | 40.0 | 3.96e-01 | 76.2% | 65.1% |
| 2jqqA00 | 1.20.58.1240 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.60 | 41.0 | 3.81e-01 | 70.5% | 77.9% |
| 2n04A00 | 1.10.287.110 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain | 0.59 | 43.0 | 4.64e-01 | 78.7% | 89.5% |
| 3f7cA00 | 1.20.1590.10 | Mainly Alpha › Up-down Bundle › YP_001051499.1 fold like › YP_001051499.1 domain like | 0.58 | 43.0 | 3.68e-01 | 77.9% | 52.3% |
| 2kobA01 | 1.10.150.130 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain | 0.57 | 40.0 | 4.47e-01 | 86.1% | 94.6% |
| 2q9rA01 | 1.20.1590.10 | Mainly Alpha › Up-down Bundle › YP_001051499.1 fold like › YP_001051499.1 domain like | 0.56 | 41.0 | 3.56e-01 | 76.2% | 55.4% |
| 3i5xA02 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.56 | 39.0 | 3.03e-01 | 70.5% | 86.9% |
| 2wg7A00 | 1.20.90.10 | Mainly Alpha › Up-down Bundle › Phospholipase A2 › Phospholipase A2 domain | 0.56 | 39.0 | 4.01e-01 | 73.0% | 96.7% |
| 2raeA02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.54 | 38.0 | 3.65e-01 | 70.5% | 97.8% |
| 1cnt200 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.54 | 40.0 | 3.90e-01 | 87.7% | 70.8% |
| 1f7cA00 | 1.10.555.10 | Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein | 0.53 | 37.0 | 3.33e-01 | 72.1% | 84.1% |
| 6ks6Z01 | 1.10.560.10 | Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain | 0.53 | 46.0 | 3.59e-01 | 94.3% | 45.0% |
| 6ks6q01 | 1.10.560.10 | Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain | 0.53 | 45.0 | 3.46e-01 | 91.0% | 66.3% |
| 1q8cA00 | 1.10.940.10 | Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like | 0.52 | 31.0 | 3.10e-01 | 73.0% | 54.5% |
| 3d2yA02 | 1.10.101.10 | Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD | 0.51 | 29.0 | 3.38e-01 | 81.1% | 79.8% |
| 8b70A01 | 1.20.1740.10 | Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I | 0.51 | 44.0 | 3.08e-01 | 95.9% | 93.5% |
| 2fd5A02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.50 | 35.0 | 3.46e-01 | 72.1% | 87.9% |
ECOD (26)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2777770 | 612.1.1.1 ↗ | alpha arrays › Retroviral matrix proteins › Retroviral matrix proteins › Retroviral matrix proteins › Gag_p17 | 0.89 | 72.0 | 7.59e-01 | 86.9% | 91.8% |
| 199484 | 612.1.1.1 ↗ | alpha arrays › Retroviral matrix proteins › Retroviral matrix proteins › Retroviral matrix proteins › Gag_p17 | 0.85 | 75.0 | 7.23e-01 | 95.9% | 83.6% |
| 1556812 | 612.1.1.0 ↗ | alpha arrays › Retroviral matrix proteins › Retroviral matrix proteins › Retroviral matrix proteins | 0.80 | 68.0 | 6.60e-01 | 89.3% | 82.1% |
| 5081699 | 186.1.1.4 ↗ | alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_4 | 0.69 | 47.0 | 5.35e-01 | 86.9% | 94.4% |
| 5004033 | 6155.1.1.1 ↗ | alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › MtN3_slv | 0.64 | 34.0 | 3.88e-01 | 73.0% | 68.9% |
| 5019543 | 6155.1.1.2 ↗ | alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop | 0.64 | 34.0 | 3.70e-01 | 73.0% | 62.0% |
| 5079385 | 3930.1.1.3 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical | 0.61 | 46.0 | 4.51e-01 | 79.5% | 80.7% |
| 5066065 | 3930.1.1.3 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical | 0.59 | 45.0 | 4.51e-01 | 80.3% | 80.0% |
| 5067508 | 3930.1.1.3 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical | 0.59 | 45.0 | 4.38e-01 | 80.3% | 75.6% |
| 3236092 | 101.11.1.0 ↗ | alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 0.59 | 38.0 | 4.46e-01 | 73.0% | 98.8% |
| 4997392 | 3930.1.1.3 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical | 0.59 | 44.0 | 4.26e-01 | 79.5% | 77.9% |
| 352936 | 3813.1.1.1 ↗ | alpha bundles › DUF416 › DUF416 › DUF416 › DUF416 | 0.58 | 43.0 | 3.68e-01 | 77.9% | 52.3% |
| 4173849 | 186.1.1.1 ↗ | alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 | 0.58 | 43.0 | 4.54e-01 | 86.9% | 88.2% |
| 3583634 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.58 | 44.0 | 3.77e-01 | 81.1% | 65.4% |
| 3715346 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.57 | 44.0 | 3.61e-01 | 82.0% | 75.3% |
| 5040355 | 3930.1.1.3 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical | 0.57 | 43.0 | 4.27e-01 | 78.7% | 80.8% |
| 3829962 | 109.4.1.1497 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT, CLASP_N, XMAP215_CLASP_TOG | 0.57 | 43.0 | 2.42e-01 | 78.7% | 8.8% |
| 4385779 | 186.1.1.1 ↗ | alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 | 0.56 | 44.0 | 4.52e-01 | 86.1% | 85.8% |
| 4981587 | 3930.1.1.0 ↗ | alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase | 0.56 | 42.0 | 4.20e-01 | 80.3% | 76.2% |
| 3958903 | 186.1.1.0 ↗ | alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N | 0.55 | 43.0 | 4.54e-01 | 84.4% | 96.2% |
| 3400801 | 604.12.1.0 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain | 0.54 | 37.0 | 3.65e-01 | 70.5% | 71.1% |
| 3585882 | 633.1.1.1 ↗ | alpha bundles › Bromodomain-like › Bromodomain › Bromodomain › Bromodomain | 0.54 | 47.0 | 4.37e-01 | 98.4% | 86.3% |
| 3271602 | 109.4.1.1715 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ARM_TANGO6 | 0.51 | 37.0 | 2.77e-01 | 73.8% | 31.3% |
| 4025263 | 6055.1.1.35 ↗ | extended segments › Preprotein translocase subunit YajC › Preprotein translocase subunit YajC › Preprotein translocase subunit YajC › RIFIN | 0.51 | 37.0 | 3.09e-01 | 74.6% | 49.8% |
| 5054937 | 140.1.1.14 ↗ | alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › tRNA-synt_1e | 0.50 | 33.0 | 3.05e-01 | 79.5% | 52.3% |
| 3239720 | 2484.1.1.50 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Dimer_Tnp_hAT | 0.50 | 44.0 | 2.97e-01 | 100.0% | 69.2% |
D2
medium
residues 142-267
Domain cluster:
rep: gag_protein__YP_009305199__Simian_retrovirus_8__1904439__D302-440
D3
medium
residues 282-354
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF19317.5 best | Gag_p24_C | 33.8 | 3.00e-08 | 78.1% | 73.0% |
CATH (13)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5dckA00 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.96 | 75.0 | 7.67e-01 | 80.8% | 83.1% |
| 1d1dA02 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.70 | 57.0 | 5.59e-01 | 93.2% | 83.7% |
| 1j8yF01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.68 | 51.0 | 4.89e-01 | 82.2% | 96.5% |
| 5h5mA02 | 1.20.120.230 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like | 0.60 | 49.0 | 4.16e-01 | 93.2% | 96.2% |
| 1j1vA00 | 1.10.1750.10 | Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain | 0.60 | 42.0 | 3.88e-01 | 74.0% | 60.6% |
| 1u78A02 | 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 | 0.59 | 29.0 | 3.51e-01 | 71.2% | 71.1% |
| 7zmgL01 | 1.10.287.3510 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.55 | 37.0 | 3.62e-01 | 100.0% | 62.5% |
| 3h5qA01 | 1.20.970.10 | Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C | 0.55 | 29.0 | 2.96e-01 | 76.7% | 51.4% |
| 2gslF00 | 1.10.1520.10 | Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain | 0.55 | 44.0 | 3.63e-01 | 86.3% | 63.8% |
| 1y8aA02 | 1.10.3870.10 | Mainly Alpha › Orthogonal Bundle › AF1437-like domain fold › AF1437-like domain superfamily | 0.53 | 38.0 | 3.32e-01 | 76.7% | 48.3% |
| 3owaA01 | 1.10.540.10 | Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain | 0.52 | 37.0 | 3.01e-01 | 74.0% | 56.5% |
| 1b48A02 | 1.20.1050.10 | Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › | 0.52 | 40.0 | 3.54e-01 | 83.6% | 81.7% |
| 2ii2A04 | 1.10.220.10 | Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin | 0.52 | 37.0 | 3.66e-01 | 76.7% | 96.2% |
ECOD (7)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3746214 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.93 | 74.0 | 7.35e-01 | 82.2% | 81.3% |
| 2984623 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.93 | 88.0 | 7.94e-01 | 100.0% | 82.1% |
| 2568930 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.91 | 86.0 | 7.97e-01 | 100.0% | 83.0% |
| 3924866 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.76 | 62.0 | 5.70e-01 | 89.0% | 71.6% |
| 3930503 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.71 | 62.0 | 5.67e-01 | 97.3% | 75.8% |
| 5078781 | 148.1.3.0 ↗ | alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain | 0.61 | 41.0 | 3.86e-01 | 86.3% | 56.7% |
| 3798911 | 170.2.1.8 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › DUF1759 | 0.59 | 50.0 | 4.96e-01 | 98.6% | 92.5% |