| SMARCE1 50-170 |
| ID: | 1513026259 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (104) | ||
| Sequences: | 198 (136.5) | ||
| Seq/Len: | 1.904 | ||
| Nf(neff/√len): | 13.4 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.904).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 25_M | 52_G | 1.847 | 0.98 |
| 17_P | 77_Y | 1.702 | 0.96 |
| 64_Q | 68_N | 1.607 | 0.94 |
| 18_D | 32_W | 1.553 | 0.92 |
| 53_G | 57_D | 1.538 | 0.92 |
| 30_K | 66_Y | 1.490 | 0.90 |
| 31_V | 54_M | 1.485 | 0.90 |
| 61_E | 99_R | 1.420 | 0.87 |
| 73_E | 76_E | 1.418 | 0.87 |
| 78_N | 101_E | 1.413 | 0.86 |
| 49_K | 74_K | 1.364 | 0.84 |
| 77_Y | 82_K | 1.354 | 0.83 |
| 46_E | 58_L | 1.343 | 0.82 |
| 49_K | 76_E | 1.308 | 0.80 |
| 104_L | 107_E | 1.290 | 0.79 |
| 106_E | 109_R | 1.290 | 0.79 |
| 104_L | 108_S | 1.288 | 0.79 |
| 84_Y | 88_P | 1.278 | 0.78 |
| 52_G | 56_R | 1.275 | 0.78 |
| 105_E | 108_S | 1.230 | 0.74 |
| 26_R | 74_K | 1.222 | 0.73 |
| 62_E | 83_A | 1.216 | 0.73 |
| 77_Y | 81_M | 1.191 | 0.71 |
| 28_S | 70_Y | 1.181 | 0.70 |
| 98_S | 102_A | 1.174 | 0.69 |
| 20_P | 74_K | 1.172 | 0.69 |
| 25_M | 44_L | 1.165 | 0.68 |
| 77_Y | 86_N | 1.163 | 0.68 |
| 103_A | 106_E | 1.158 | 0.67 |
| 102_A | 107_E | 1.155 | 0.67 |
| 76_E | 80_S | 1.154 | 0.67 |
| 47_I | 102_A | 1.152 | 0.67 |
| 19_K | 46_E | 1.152 | 0.67 |
| 103_A | 107_E | 1.142 | 0.66 |
| 101_E | 105_E | 1.140 | 0.66 |
| 93_Y | 98_S | 1.134 | 0.65 |
| 9_T | 68_N | 1.127 | 0.64 |
| 6_S | 9_T | 1.098 | 0.61 |
| 72_A | 95_N | 1.087 | 0.60 |
| 22_M | 69_E | 1.084 | 0.60 |
| 79_E | 101_E | 1.083 | 0.60 |
| 26_R | 69_E | 1.073 | 0.59 |
| 13_P | 18_D | 1.071 | 0.59 |
| 41_D | 64_Q | 1.063 | 0.58 |
| 7_G | 38_S | 1.055 | 0.57 |
| 17_P | 81_M | 1.051 | 0.56 |
| 28_S | 82_K | 1.049 | 0.56 |
| 19_K | 48_G | 1.046 | 0.56 |
| 25_M | 29_R | 1.041 | 0.55 |
| 48_G | 56_R | 1.036 | 0.55 |
| 23_P | 30_K | 1.029 | 0.54 |
| 28_S | 48_G | 1.026 | 0.54 |
| 46_E | 49_K | 1.024 | 0.53 |
| 81_M | 95_N | 1.022 | 0.53 |
| 46_E | 72_A | 1.011 | 0.52 |
| 11_P | 27_Y | 1.009 | 0.52 |
| 105_E | 109_R | 1.003 | 0.51 |
| 9_T | 81_M | 1.003 | 0.51 |
| 19_K | 43_K | 1.000 | 0.51 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 2co9A | 1 | 0.8347 | 99.9 | 0.379 | Contact Map |
| 2lhjA | 1 | 0.7355 | 99.9 | 0.393 | Contact Map |
| 2crjA | 1 | 0.7603 | 99.9 | 0.393 | Contact Map |
| 1cg7A | 1 | 0.7355 | 99.9 | 0.394 | Contact Map |
| 2e6oA | 1 | 0.7107 | 99.9 | 0.399 | Contact Map |
| 4euwA | 1 | 0.595 | 99.9 | 0.402 | Contact Map |
| 3tmmA | 1 | 0.9256 | 99.8 | 0.409 | Contact Map |
| 1hryA | 1 | 0.6033 | 99.8 | 0.409 | Contact Map |
| 2eqzA | 1 | 0.6942 | 99.8 | 0.41 | Contact Map |
| 1i11A | 1 | 0.5785 | 99.8 | 0.414 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)