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NIb
Euk-VirRose_yellow_mosaic_virus
NIb__YP_006908987__Rose_yellow_mosaic_virus__1048434
Identity
- Accession:
- YP_006908987 ↗
- Protein ID:
- NIb
- Kingdom:
- euk
Quality
90.2
mean pLDDT
Taxonomy
Orthornavirae›
Pisuviricota›
Stelpaviricetes›
Patatavirales›
Potyviridae›
Roymovirus›
Rose_yellow_mosaic_virus
TaxID: 1048434
Cluster
View cluster (450 members)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 392-489
Domain cluster:
rep: NIb__YP_007032445__Cassava_brown_streak_virus__137758__D405-481
D2
medium
residues 1-17_73-106_202-219_246-320
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00680.26 best | RdRP_1 | 52.6 | 4.60e-14 | 52.8% | 15.8% |
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1t02A02 | 3.90.770.10 | Alpha Beta › Alpha-Beta Complex › 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 › 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 | 0.57 | 41.0 | 3.35e-01 | 73.6% | 74.5% |
| 3zieD00 | 3.30.110.150 | Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › SepF-like protein | 0.50 | 24.0 | 2.97e-01 | 81.9% | 72.0% |
ECOD (2)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1789314 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.80 | 71.0 | 5.00e-01 | 93.1% | 85.5% |
| 217141 | 304.48.1.15 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_3 | 0.75 | 68.0 | 4.98e-01 | 96.5% | 79.0% |
D3
medium
residues 56-72_158-201
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00680.26 best | RdRP_1 | 35.7 | 5.90e-09 | 96.7% | 10.7% |
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4r80A00 | 3.10.450.630 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › | 0.53 | 39.0 | 3.71e-01 | 82.0% | 93.4% |
| 2cz4A00 | 3.30.70.120 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.52 | 38.0 | 3.37e-01 | 83.6% | 57.6% |
| 4zajA01 | 3.30.1360.70 | Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Arginyl tRNA synthetase N-terminal domain | 0.51 | 34.0 | 3.01e-01 | 90.2% | 44.2% |
| 2bjoA02 | 3.30.300.20 | Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain | 0.51 | 40.0 | 3.61e-01 | 91.8% | 72.3% |
| 2nrqA00 | 3.30.1440.10 | Alpha Beta › 2-Layer Sandwich › 50s Ribosomal Protein L5; Chain: A, › Ribosomal protein L5 | 0.51 | 38.0 | 3.08e-01 | 86.9% | 81.8% |
| 1vwxB03 | 3.30.1430.10 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L3; Chain: B; domain 2, › | 0.50 | 38.0 | 3.05e-01 | 82.0% | 63.4% |
ECOD (16)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5367 | 304.48.1.8 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 | 0.83 | 75.0 | 4.52e-01 | 100.0% | 42.6% |
| 3636696 | 3745.1.1.1 ↗ | alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex | 0.60 | 41.0 | 2.52e-01 | 72.1% | 59.0% |
| 3829789 | 101.1.2.245 ↗ | alpha arrays › HTH › HTH › winged helix domain › PORR | 0.60 | 45.0 | 3.68e-01 | 85.2% | 57.6% |
| 4943012 | 810.1.1.0 ↗ | a+b two layers › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) | 0.56 | 45.0 | 3.64e-01 | 93.4% | 99.2% |
| 4929586 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.55 | 40.0 | 3.70e-01 | 80.3% | 67.1% |
| 4984746 | 7592.1.1.0 ↗ | a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains | 0.54 | 38.0 | 2.65e-01 | 75.4% | 62.8% |
| 4996686 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.53 | 37.0 | 3.26e-01 | 75.4% | 53.0% |
| 3233196 | 304.51.1.0 ↗ | a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related | 0.53 | 38.0 | 3.25e-01 | 78.7% | 49.1% |
| 3934203 | 5001.1.1.5 ↗ | alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_3 | 0.53 | 44.0 | 2.90e-01 | 100.0% | 80.3% |
| 3856781 | 109.4.1.906 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › N-HEAT_ATR | 0.53 | 43.0 | 2.49e-01 | 100.0% | 39.7% |
| 3411543 | 2003.1.2.2 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GMC_oxred_N | 0.53 | 36.0 | 2.26e-01 | 72.1% | 76.3% |
| 3741555 | 4969.1.1.0 ↗ | alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I | 0.52 | 38.0 | 2.69e-01 | 80.3% | 26.1% |
| 4554366 | 304.114.1.0 ↗ | a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain | 0.52 | 39.0 | 3.27e-01 | 83.6% | 53.9% |
| 3508551 | 304.114.1.0 ↗ | a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain | 0.52 | 38.0 | 3.20e-01 | 83.6% | 51.7% |
| 3759055 | 304.114.1.0 ↗ | a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain | 0.51 | 38.0 | 3.16e-01 | 83.6% | 49.6% |
| 3550113 | 4969.1.1.0 ↗ | alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I | 0.51 | 38.0 | 3.15e-01 | 83.6% | 49.6% |
D4
medium
residues 107-157
Domain cluster:
rep: NIb__YP_004564597__Hardenbergia_mosaic_virus__409486__D110-163
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2dk8A01 | 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 | 0.66 | 40.0 | 3.67e-01 | 86.3% | 46.2% |
| 1huxA02 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.54 | 47.0 | 3.46e-01 | 100.0% | 72.9% |
ECOD (1)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4341780 | 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 | 0.53 | 46.0 | 4.22e-01 | 94.1% | 76.9% |
D5
medium
residues 220-245_321-391
Domain cluster:
rep: KR816341.1__AKQ06880.1__X__00021__D162-195_238-325