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gag_protein
Euk-VirReticuloendotheliosis_virus
gag_protein__YP_223870__Reticuloendotheliosis_virus__11636
Identity
- Accession:
- YP_223870 ↗
- Protein ID:
- gag_protein
- Kingdom:
- euk
Quality
70.8
mean pLDDT
Taxonomy
Pararnavirae›
Artverviricota›
Revtraviricetes›
Ortervirales›
Retroviridae›
Gammaretrovirus›
Reticuloendotheliosis_virus
TaxID: 11636
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 12-103
Domain cluster:
rep: truncated_gag-pro-pol__YP_004680223__PreXMRV-1__1038068__D8-91
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01140.25 best | Gag_MA | 67.9 | 9.50e-19 | 100.0% | 80.5% |
D2
medium
residues 342-424
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 |
|---|---|---|---|---|---|
| PF02093.21 best | Gag_p30 | 83.5 | 2.20e-23 | 100.0% | 40.8% |
CATH (11)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1bajA00 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.88 | 72.0 | 7.71e-01 | 92.8% | 100.0% |
| 5dckA00 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.82 | 67.0 | 7.19e-01 | 94.0% | 100.0% |
| 1qrjA02 | 1.10.1200.30 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Retrovirus capsid C-terminal domain | 0.79 | 70.0 | 6.94e-01 | 100.0% | 92.9% |
| 1vhnA02 | 1.10.1200.80 | Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Putative flavin oxidoreducatase; domain 2 | 0.62 | 48.0 | 5.07e-01 | 85.5% | 100.0% |
| 1mkiA02 | 1.10.1500.10 | Mainly Alpha › Orthogonal Bundle › Probable Glutaminase Ybgj; Chain: A, domain 2 › | 0.58 | 44.0 | 3.72e-01 | 80.7% | 97.1% |
| 4lvpA00 | 1.10.418.70 | Mainly Alpha › Orthogonal Bundle › Actin-binding Protein, T-fimbrin; domain 1 › Intraflagellar transport protein 81, N-terminal domain | 0.56 | 45.0 | 3.97e-01 | 86.7% | 73.4% |
| 1ls1A01 | 1.20.120.140 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain | 0.54 | 42.0 | 4.18e-01 | 86.7% | 97.8% |
| 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 | 0.53 | 43.0 | 3.77e-01 | 91.6% | 75.9% |
| 4xc7B01 | 3.40.50.280 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain | 0.52 | 40.0 | 3.39e-01 | 84.3% | 74.3% |
| 2qzcA00 | 1.20.910.10 | Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like | 0.51 | 38.0 | 2.98e-01 | 83.1% | 73.2% |
| 5gkxA00 | 3.90.1640.20 | Alpha Beta › Alpha-Beta Complex › inorganic pyrophosphatase (n-terminal core) › TON_0340 | 0.51 | 39.0 | 2.88e-01 | 86.7% | 76.8% |
ECOD (56)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2428300 | 170.1.1.2 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p30 | 0.98 | 94.0 | 9.28e-01 | 100.0% | 95.4% |
| 3519786 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.91 | 80.0 | 7.94e-01 | 100.0% | 90.6% |
| 3199067 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.88 | 76.0 | 7.46e-01 | 100.0% | 85.4% |
| 3501300 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.86 | 78.0 | 7.25e-01 | 100.0% | 80.0% |
| 3633075 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.85 | 75.0 | 7.32e-01 | 100.0% | 87.8% |
| 3431511 | 170.1.1.22 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PF30901 | 0.85 | 72.0 | 6.74e-01 | 100.0% | 75.0% |
| 3916896 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.84 | 78.0 | 6.91e-01 | 100.0% | 78.3% |
| 3746214 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.84 | 71.0 | 7.41e-01 | 94.0% | 98.7% |
| 3881657 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.84 | 72.0 | 7.38e-01 | 100.0% | 96.2% |
| 3519399 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.83 | 73.0 | 7.08e-01 | 100.0% | 86.7% |
| 3893949 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.82 | 75.0 | 7.31e-01 | 100.0% | 90.0% |
| 3817236 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.82 | 71.0 | 7.29e-01 | 98.8% | 97.5% |
| 3424718 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.81 | 71.0 | 6.76e-01 | 100.0% | 82.1% |
| 3787102 | 170.1.1.22 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PF30901 | 0.80 | 69.0 | 6.59e-01 | 100.0% | 81.1% |
| 2984623 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.80 | 74.0 | 7.08e-01 | 100.0% | 89.5% |
| 1175290 | 170.1.1.5 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Gag_p24_C | 0.80 | 69.0 | 6.96e-01 | 100.0% | 92.9% |
| 3762196 | 170.1.1.22 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PF30901 | 0.79 | 66.0 | 6.42e-01 | 100.0% | 83.3% |
| 3821057 | 170.1.1.22 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PF30901 | 0.79 | 65.0 | 6.81e-01 | 100.0% | 98.7% |
| 3573690 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.78 | 62.0 | 6.60e-01 | 96.4% | 100.0% |
| 3516986 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.78 | 71.0 | 6.93e-01 | 97.6% | 93.3% |
| 3931877 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.78 | 72.0 | 6.49e-01 | 100.0% | 93.6% |
| 3936705 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.76 | 65.0 | 6.06e-01 | 100.0% | 74.3% |
| 3375800 | 170.1.1.15 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › Retrotran_gag_2 | 0.76 | 66.0 | 6.39e-01 | 100.0% | 85.3% |
| 3173429 | 101.1.2.463 ↗ | alpha arrays › HTH › HTH › winged helix domain › TYA | 0.75 | 65.0 | 6.40e-01 | 100.0% | 90.0% |
| 3170562 | 2484.5.1.5 ↗ | mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › TYA | 0.74 | 65.0 | 6.41e-01 | 100.0% | 90.0% |
| 3927258 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.73 | 64.0 | 6.55e-01 | 97.6% | 100.0% |
| 3175328 | 601.30.1.3 ↗ | alpha bundles › Four-helical up-and-down bundle › Helical bundle domain in hypothetical protein PH1320 › Helical bundle domain in hypothetical protein PH1320 › TYA | 0.73 | 64.0 | 6.29e-01 | 100.0% | 90.0% |
| 3178411 | 101.1.1.311 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › TYA | 0.72 | 63.0 | 6.10e-01 | 100.0% | 85.3% |
| 3171256 | 304.48.1.58 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › TYA | 0.72 | 62.0 | 6.02e-01 | 100.0% | 85.3% |
| 3935441 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.72 | 59.0 | 6.04e-01 | 97.6% | 93.8% |
| 3763289 | 304.24.1.29 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › PNMA | 0.72 | 65.0 | 5.91e-01 | 100.0% | 84.5% |
| 3569143 | 170.2.1.28 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › PNMA | 0.72 | 65.0 | 5.89e-01 | 100.0% | 84.5% |
| 4634618 | 170.1.1.25 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PNMA | 0.71 | 64.0 | 5.86e-01 | 100.0% | 84.5% |
| 4247468 | 170.1.1.25 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PNMA | 0.71 | 63.0 | 5.66e-01 | 100.0% | 80.9% |
| 3563179 | 304.9.1.37 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › PNMA | 0.70 | 63.0 | 5.96e-01 | 100.0% | 86.0% |
| 3486419 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.70 | 54.0 | 5.84e-01 | 92.8% | 98.6% |
| 3633877 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.70 | 63.0 | 6.15e-01 | 100.0% | 100.0% |
| 3856673 | 396.1.1.8 ↗ | few secondary structure elements › CCHC-type 1 zinc finger › Retrovirus zinc finger-related domains › Retrovirus zinc finger-related domains › PNMA | 0.70 | 61.0 | 5.83e-01 | 100.0% | 88.0% |
| 3845048 | 170.1.1.25 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PNMA | 0.70 | 61.0 | 5.72e-01 | 100.0% | 84.8% |
| 4015330 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.70 | 62.0 | 5.80e-01 | 100.0% | 81.9% |
| 3573730 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.69 | 60.0 | 6.08e-01 | 100.0% | 100.0% |
| 4112344 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.68 | 59.0 | 6.05e-01 | 100.0% | 100.0% |
| 3868867 | 170.1.1.25 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C › PNMA | 0.68 | 59.0 | 5.63e-01 | 100.0% | 88.0% |
| 3523523 | 304.9.1.37 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › PNMA | 0.68 | 59.0 | 5.28e-01 | 100.0% | 73.3% |
| 3931493 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.67 | 59.0 | 5.61e-01 | 100.0% | 85.0% |
| 3579762 | 170.2.1.8 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › DUF1759 | 0.67 | 55.0 | 5.62e-01 | 98.8% | 93.8% |
| 4237957 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.67 | 58.0 | 5.89e-01 | 97.6% | 100.0% |
| 3941254 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.67 | 59.0 | 5.67e-01 | 100.0% | 87.4% |
| 3216085 | 170.2.1.29 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › DUF7083 | 0.67 | 60.0 | 5.84e-01 | 100.0% | 100.0% |
| 3631497 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.66 | 59.0 | 5.90e-01 | 100.0% | 98.8% |
| 3389120 | 170.1.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C | 0.65 | 59.0 | 5.62e-01 | 100.0% | 89.5% |
| 3300490 | 170.2.1.32 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › PF28884 | 0.65 | 54.0 | 5.41e-01 | 92.8% | 98.8% |
| 3437527 | 170.2.1.30 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › DUF4219 | 0.64 | 55.0 | 5.65e-01 | 97.6% | 100.0% |
| 3921524 | 601.7.1.36 ↗ | alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › UFL1 | 0.61 | 50.0 | 4.45e-01 | 89.2% | 90.8% |
| 3696944 | 2007.1.19.2 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › FabD/lysophospholipase-like › Patatin | 0.59 | 46.0 | 3.26e-01 | 84.3% | 32.2% |
| 3507982 | 632.2.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains | 0.56 | 47.0 | 4.35e-01 | 92.8% | 80.0% |