| SMARCE1_50-150 |
| ID: | 1486753413 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (85) | ||
| Sequences: | 2856 (1826.5) | ||
| Seq/Len: | 33.600 | ||
| Nf(neff/√len): | 198.1 |
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: 33.600).
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 |
| 75_E | 79_S | 3.718 | 1.00 |
| 63_Q | 67_N | 3.068 | 1.00 |
| 72_E | 75_E | 2.931 | 1.00 |
| 30_V | 53_M | 2.577 | 1.00 |
| 30_V | 33_Q | 2.359 | 1.00 |
| 27_S | 50_I | 2.159 | 1.00 |
| 64_E | 68_E | 1.786 | 1.00 |
| 29_K | 65_Y | 1.751 | 1.00 |
| 25_R | 72_E | 1.747 | 1.00 |
| 59_D | 66_L | 1.740 | 1.00 |
| 58_T | 61_E | 1.731 | 1.00 |
| 57_L | 61_E | 1.646 | 1.00 |
| 49_I | 53_M | 1.627 | 1.00 |
| 52_G | 56_D | 1.595 | 1.00 |
| 74_I | 78_E | 1.536 | 1.00 |
| 20_L | 24_M | 1.520 | 1.00 |
| 67_N | 70_E | 1.506 | 1.00 |
| 49_I | 52_G | 1.487 | 1.00 |
| 71_A | 74_I | 1.478 | 1.00 |
| 30_V | 50_I | 1.472 | 1.00 |
| 70_E | 74_I | 1.444 | 1.00 |
| 80_M | 84_H | 1.423 | 1.00 |
| 25_R | 68_E | 1.389 | 0.99 |
| 68_E | 71_A | 1.356 | 0.99 |
| 68_E | 72_E | 1.348 | 0.99 |
| 47_G | 51_G | 1.336 | 0.99 |
| 74_I | 77_N | 1.328 | 0.99 |
| 20_L | 72_E | 1.283 | 0.99 |
| 32_D | 35_K | 1.283 | 0.99 |
| 75_E | 78_E | 1.248 | 0.99 |
| 73_K | 77_N | 1.220 | 0.98 |
| 24_M | 27_S | 1.216 | 0.98 |
| 12_P | 83_Y | 1.209 | 0.98 |
| 58_T | 64_E | 1.205 | 0.98 |
| 43_L | 47_G | 1.178 | 0.98 |
| 29_K | 68_E | 1.148 | 0.97 |
| 67_N | 71_A | 1.140 | 0.97 |
| 33_Q | 37_S | 1.132 | 0.97 |
| 45_E | 48_K | 1.125 | 0.97 |
| 32_D | 36_A | 1.125 | 0.97 |
| 20_L | 28_R | 1.119 | 0.96 |
| 26_Y | 57_L | 1.098 | 0.96 |
| 81_K | 85_N | 1.093 | 0.96 |
| 42_K | 45_E | 1.088 | 0.96 |
| 59_D | 63_Q | 1.080 | 0.95 |
| 27_S | 31_W | 1.051 | 0.94 |
| 61_E | 64_E | 1.043 | 0.94 |
| 57_L | 64_E | 1.024 | 0.93 |
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 | 0.99 | 99.8 | 0.2 | Contact Map |
| 1cg7A | 1 | 0.87 | 99.8 | 0.202 | Contact Map |
| 3tmmA | 1 | 0.92 | 99.8 | 0.205 | Contact Map |
| 2lhjA | 1 | 0.88 | 99.8 | 0.208 | Contact Map |
| 2crjA | 1 | 0.9 | 99.8 | 0.214 | Contact Map |
| 1hmeA | 1 | 0.77 | 99.8 | 0.215 | Contact Map |
| 2gzkA | 1 | 0.86 | 99.8 | 0.217 | Contact Map |
| 2yrqA | 1 | 0.87 | 99.7 | 0.219 | Contact Map |
| 1k99A | 1 | 0.91 | 99.7 | 0.22 | Contact Map |
| 4euwA | 1 | 0.72 | 99.7 | 0.223 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)