| QueE |
| ID: | 1495831938 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 223 (220) | ||
| Sequences: | 1977 (994.8) | ||
| Seq/Len: | 8.986 | ||
| Nf(neff/√len): | 67.1 |
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: 8.986).
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 |
| 32_P | 120_S | 3.600 | 1.00 |
| 119_T | 135_V | 2.369 | 1.00 |
| 28_L | 91_I | 2.174 | 1.00 |
| 89_V | 108_L | 2.167 | 1.00 |
| 188_L | 204_T | 2.125 | 1.00 |
| 91_I | 100_D | 2.077 | 1.00 |
| 4_P | 99_H | 2.041 | 1.00 |
| 187_A | 211_R | 2.032 | 1.00 |
| 214_M | 219_Y | 1.979 | 1.00 |
| 109_E | 131_T | 1.961 | 1.00 |
| 17_Y | 187_A | 1.908 | 1.00 |
| 21_V | 114_S | 1.874 | 1.00 |
| 23_A | 88_H | 1.860 | 1.00 |
| 97_C | 125_V | 1.842 | 1.00 |
| 10_Q | 22_P | 1.823 | 1.00 |
| 8_M | 26_I | 1.822 | 1.00 |
| 215_Q | 218_K | 1.778 | 1.00 |
| 73_E | 107_L | 1.694 | 1.00 |
| 19_T | 216_T | 1.688 | 1.00 |
| 87_R | 113_F | 1.688 | 1.00 |
| 33_V | 120_S | 1.678 | 1.00 |
| 23_A | 90_V | 1.675 | 1.00 |
| 33_V | 122_T | 1.671 | 1.00 |
| 32_P | 123_H | 1.669 | 1.00 |
| 32_P | 122_T | 1.651 | 1.00 |
| 117_I | 125_V | 1.633 | 1.00 |
| 41_K | 44_W | 1.627 | 1.00 |
| 91_I | 108_L | 1.624 | 1.00 |
| 74_D | 77_A | 1.619 | 1.00 |
| 71_S | 74_D | 1.581 | 1.00 |
| 88_H | 116_Q | 1.552 | 1.00 |
| 21_V | 211_R | 1.524 | 1.00 |
| 79_I | 91_I | 1.517 | 1.00 |
| 8_M | 78_V | 1.510 | 1.00 |
| 117_I | 130_N | 1.505 | 1.00 |
| 39_D | 118_E | 1.490 | 1.00 |
| 205_C | 212_L | 1.480 | 1.00 |
| 189_Q | 215_Q | 1.476 | 1.00 |
| 8_M | 24_I | 1.436 | 0.99 |
| 8_M | 75_L | 1.434 | 0.99 |
| 73_E | 77_A | 1.409 | 0.99 |
| 40_T | 43_T | 1.407 | 0.99 |
| 106_D | 109_E | 1.405 | 0.99 |
| 133_V | 156_N | 1.395 | 0.99 |
| 203_E | 206_I | 1.378 | 0.99 |
| 149_S | 177_T | 1.368 | 0.99 |
| 5_I | 28_L | 1.354 | 0.99 |
| 27_R | 39_D | 1.352 | 0.99 |
| 10_Q | 86_A | 1.348 | 0.99 |
| 39_D | 159_K | 1.347 | 0.99 |
| 95_E | 120_S | 1.344 | 0.99 |
| 118_E | 138_K | 1.340 | 0.99 |
| 199_R | 203_E | 1.327 | 0.99 |
| 116_Q | 134_T | 1.326 | 0.99 |
| 134_T | 157_E | 1.316 | 0.99 |
| 77_A | 110_K | 1.310 | 0.99 |
| 24_I | 79_I | 1.305 | 0.99 |
| 202_I | 206_I | 1.298 | 0.99 |
| 156_N | 184_R | 1.290 | 0.99 |
| 62_K | 65_D | 1.264 | 0.98 |
| 27_R | 118_E | 1.261 | 0.98 |
| 6_N | 29_Q | 1.256 | 0.98 |
| 159_K | 189_Q | 1.255 | 0.98 |
| 18_F | 21_V | 1.228 | 0.98 |
| 163_G | 191_I | 1.225 | 0.98 |
| 2_Q | 58_L | 1.225 | 0.98 |
| 19_T | 213_S | 1.219 | 0.98 |
| 140_N | 170_A | 1.199 | 0.97 |
| 168_I | 204_T | 1.198 | 0.97 |
| 26_I | 89_V | 1.198 | 0.97 |
| 39_D | 138_K | 1.196 | 0.97 |
| 70_A | 75_L | 1.187 | 0.97 |
| 55_F | 59_A | 1.187 | 0.97 |
| 18_F | 88_H | 1.186 | 0.97 |
| 118_E | 159_K | 1.184 | 0.97 |
| 56_S | 59_A | 1.180 | 0.97 |
| 89_V | 113_F | 1.179 | 0.97 |
| 26_I | 79_I | 1.177 | 0.97 |
| 76_L | 107_L | 1.176 | 0.97 |
| 15_E | 27_R | 1.133 | 0.96 |
| 89_V | 107_L | 1.128 | 0.96 |
| 50_R | 65_D | 1.120 | 0.96 |
| 4_P | 58_L | 1.115 | 0.96 |
| 131_T | 186_I | 1.109 | 0.95 |
| 27_R | 159_K | 1.108 | 0.95 |
| 39_D | 92_T | 1.104 | 0.95 |
| 176_A | 207_A | 1.097 | 0.95 |
| 119_T | 133_V | 1.090 | 0.95 |
| 25_F | 39_D | 1.085 | 0.95 |
| 198_T | 212_L | 1.071 | 0.94 |
| 194_K | 197_A | 1.062 | 0.94 |
| 15_E | 20_G | 1.061 | 0.94 |
| 216_T | 219_Y | 1.059 | 0.94 |
| 79_I | 108_L | 1.058 | 0.94 |
| 116_Q | 157_E | 1.044 | 0.93 |
| 90_V | 136_S | 1.038 | 0.93 |
| 25_F | 118_E | 1.035 | 0.93 |
| 55_F | 58_L | 1.035 | 0.93 |
| 212_L | 216_T | 1.034 | 0.93 |
| 160_H | 186_I | 1.033 | 0.93 |
| 3_Y | 103_P | 1.030 | 0.92 |
| 62_K | 66_K | 1.030 | 0.92 |
| 22_P | 205_C | 1.026 | 0.92 |
| 18_F | 116_Q | 1.021 | 0.92 |
| 75_L | 104_L | 1.016 | 0.92 |
| 125_V | 133_V | 1.008 | 0.91 |
| 27_R | 92_T | 1.002 | 0.91 |
| 32_P | 95_E | 1.001 | 0.91 |
| 168_I | 172_D | 1.001 | 0.91 |
| 21_V | 88_H | 1.001 | 0.91 |
| 28_L | 101_L | 1.000 | 0.91 |
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 | |
| 4njhA | 2 | 0.8565 | 100 | 0.31 | Contact Map |
| 3c8fA | 1 | 0.843 | 99.9 | 0.611 | Contact Map |
| 1tv8A | 2 | 0.8924 | 99.6 | 0.704 | Contact Map |
| 3rfaA | 2 | 0.8879 | 99.6 | 0.706 | Contact Map |
| 2z2uA | 1 | 0.8251 | 99.5 | 0.729 | Contact Map |
| 2yx0A | 1 | 0.8744 | 99.5 | 0.73 | Contact Map |
| 2a5hA | 4 | 0.8969 | 99.5 | 0.733 | Contact Map |
| 4k36A | 2 | 0.8027 | 99.5 | 0.735 | Contact Map |
| 2qgqA | 8 | 0.7309 | 99.4 | 0.755 | Contact Map |
| 3canA | 1 | 0.5695 | 99.3 | 0.759 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)