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gag_protein
Euk-VirSimian_immunodeficiency_virus
gag_protein__NP_054369__Simian_immunodeficiency_virus__11723
Identity
- Accession:
- NP_054369 ↗
- Protein ID:
- gag_protein
- Kingdom:
- euk
Quality
70.7
mean pLDDT
Taxonomy
Pararnavirae›
Artverviricota›
Revtraviricetes›
Ortervirales›
Retroviridae›
Lentivirus›
Simian_immunodeficiency_virus
TaxID: 11723
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 11-108
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00540.24 best | Gag_p17 | 170.8 | 2.40e-50 | 100.0% | 69.3% |
CATH (13)
| 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 | 0.90 | 86.0 | 8.09e-01 | 100.0% | 90.4% |
| 3f2bA08 | 1.10.150.870 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › | 0.75 | 47.0 | 4.15e-01 | 80.6% | 45.3% |
| 4od8D00 | 6.10.140.1880 | Special › Helix non-globular › Helix Hairpins › | 0.70 | 36.0 | 4.80e-01 | 96.9% | 96.1% |
| 5figA00 | 1.20.1270.360 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.58 | 45.0 | 4.56e-01 | 83.7% | 98.0% |
| 2a3vB01 | 1.10.150.130 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain | 0.58 | 47.0 | 4.80e-01 | 98.0% | 91.5% |
| 4akgA04 | 1.20.58.1120 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dynein motor heavy chain, linker domain, subdomain 4 | 0.58 | 40.0 | 3.45e-01 | 70.4% | 96.2% |
| 3bt5A00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.57 | 45.0 | 3.91e-01 | 83.7% | 79.5% |
| 4jgwA01 | 1.20.870.10 | Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 | 0.55 | 39.0 | 3.42e-01 | 75.5% | 75.0% |
| 3a11B01 | 1.20.120.420 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 | 0.54 | 39.0 | 3.61e-01 | 74.5% | 76.0% |
| 2n04A00 | 1.10.287.110 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain | 0.53 | 43.0 | 4.24e-01 | 87.8% | 87.6% |
| 1rq5A02 | 1.50.10.10 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.53 | 38.0 | 2.44e-01 | 76.5% | 30.6% |
| 3onkA00 | 1.25.40.90 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.52 | 36.0 | 3.31e-01 | 72.4% | 83.2% |
| 2a2fX02 | 1.20.58.670 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain D | 0.51 | 37.0 | 3.48e-01 | 77.6% | 68.2% |
ECOD (8)
| 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 | 0.90 | 85.0 | 8.18e-01 | 100.0% | 94.5% |
| 199484 | 612.1.1.1 ↗ | alpha arrays › Retroviral matrix proteins › Retroviral matrix proteins › Retroviral matrix proteins › Gag_p17 | 0.89 | 85.0 | 7.48e-01 | 100.0% | 77.6% |
| 3185802 | 7015.1.1.0 ↗ | alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain | 0.66 | 50.0 | 4.50e-01 | 80.6% | 89.6% |
| 3896394 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.63 | 46.0 | 3.68e-01 | 75.5% | 84.3% |
| 3466334 | 174.1.1.0 ↗ | few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain | 0.62 | 47.0 | 4.33e-01 | 81.6% | 93.8% |
| 3279916 | 633.21.1.34 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › DUF7144 | 0.60 | 47.0 | 4.49e-01 | 83.7% | 98.3% |
| 3733554 | 4967.1.1.0 ↗ | 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 | 0.56 | 40.0 | 3.49e-01 | 74.5% | 80.7% |
| 3243563 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.50 | 42.0 | 3.53e-01 | 93.9% | 96.6% |
D2
high
residues 143-218_232-280
Domain cluster:
rep: gag_protein__YP_009305199__Simian_retrovirus_8__1904439__D302-440
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00607.26 best | Gag_p24 | 39.5 | 7.20e-10 | 94.4% | 96.9% |
D3
medium
residues 282-361
Domain cluster:
rep: p24_CA__NP_955618__Human_T-cell_leukemia_virus_type_I__11908__D133-202
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF19317.5 best | Gag_p24_C | 106.6 | 5.80e-31 | 88.8% | 93.2% |