| 1ake |
| ID: | 1506711032 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 214 (208) | ||
| Sequences: | 5421 (3164.8) | ||
| Seq/Len: | 26.062 | ||
| Nf(neff/√len): | 219.4 |
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: 26.062).
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 |
| 113_D | 172_H | 4.211 | 1.00 |
| 23_K | 210_E | 3.049 | 1.00 |
| 52_I | 60_T | 2.700 | 1.00 |
| 35_L | 64_V | 2.638 | 1.00 |
| 118_D | 136_K | 2.568 | 1.00 |
| 19_F | 206_R | 2.539 | 1.00 |
| 169_V | 173_Q | 2.535 | 1.00 |
| 110_D | 195_K | 2.358 | 1.00 |
| 120_I | 164_V | 2.352 | 1.00 |
| 97_K | 185_E | 2.320 | 1.00 |
| 65_I | 86_F | 2.304 | 1.00 |
| 183_S | 195_K | 2.147 | 1.00 |
| 37_A | 41_S | 2.140 | 1.00 |
| 115_L | 118_D | 2.131 | 1.00 |
| 38_A | 70_E | 2.094 | 1.00 |
| 50_K | 54_D | 2.072 | 1.00 |
| 124_R | 135_V | 2.043 | 1.00 |
| 23_K | 206_R | 2.012 | 1.00 |
| 127_A | 154_T | 1.980 | 1.00 |
| 126_H | 129_S | 1.977 | 1.00 |
| 71_R | 76_D | 1.963 | 1.00 |
| 117_V | 165_R | 1.940 | 1.00 |
| 200_K | 208_D | 1.873 | 1.00 |
| 109_F | 198_G | 1.866 | 1.00 |
| 65_I | 95_A | 1.862 | 1.00 |
| 16_Q | 209_L | 1.861 | 1.00 |
| 51_D | 55_A | 1.857 | 1.00 |
| 52_I | 57_K | 1.826 | 1.00 |
| 127_A | 151_E | 1.823 | 1.00 |
| 122_G | 134_H | 1.797 | 1.00 |
| 176_A | 180_G | 1.782 | 1.00 |
| 48_Q | 51_D | 1.759 | 1.00 |
| 38_A | 43_S | 1.755 | 1.00 |
| 161_E | 165_R | 1.739 | 1.00 |
| 197_D | 200_K | 1.644 | 1.00 |
| 172_H | 176_A | 1.639 | 1.00 |
| 131_R | 148_V | 1.631 | 1.00 |
| 32_G | 36_R | 1.593 | 1.00 |
| 129_S | 149_T | 1.580 | 1.00 |
| 97_K | 182_Y | 1.577 | 1.00 |
| 142_V | 145_K | 1.567 | 1.00 |
| 61_D | 92_Q | 1.549 | 1.00 |
| 206_R | 210_E | 1.546 | 1.00 |
| 200_K | 204_E | 1.512 | 1.00 |
| 44_E | 48_Q | 1.496 | 1.00 |
| 113_D | 169_V | 1.492 | 1.00 |
| 18_Q | 22_E | 1.477 | 1.00 |
| 113_D | 165_R | 1.472 | 1.00 |
| 44_E | 47_K | 1.459 | 1.00 |
| 10_G | 120_I | 1.442 | 1.00 |
| 90_I | 94_D | 1.440 | 1.00 |
| 124_R | 155_T | 1.412 | 1.00 |
| 126_H | 146_D | 1.394 | 0.99 |
| 141_K | 147_D | 1.388 | 0.99 |
| 97_K | 181_Y | 1.387 | 0.99 |
| 146_D | 149_T | 1.381 | 0.99 |
| 166_K | 169_V | 1.373 | 0.99 |
| 171_Y | 175_T | 1.361 | 0.99 |
| 113_D | 168_L | 1.320 | 0.99 |
| 108_E | 179_I | 1.311 | 0.99 |
| 38_A | 67_L | 1.302 | 0.99 |
| 14_G | 84_D | 1.299 | 0.99 |
| 91_P | 94_D | 1.294 | 0.99 |
| 134_H | 137_F | 1.289 | 0.99 |
| 168_L | 172_H | 1.285 | 0.99 |
| 112_P | 199_T | 1.269 | 0.99 |
| 129_S | 146_D | 1.265 | 0.99 |
| 208_D | 211_K | 1.263 | 0.99 |
| 2_R | 81_F | 1.262 | 0.99 |
| 180_G | 183_S | 1.262 | 0.99 |
| 180_G | 184_K | 1.257 | 0.99 |
| 48_Q | 66_A | 1.253 | 0.99 |
| 60_T | 63_L | 1.240 | 0.98 |
| 27_P | 71_R | 1.230 | 0.98 |
| 19_F | 203_A | 1.214 | 0.98 |
| 126_H | 149_T | 1.208 | 0.98 |
| 12_G | 15_T | 1.200 | 0.98 |
| 16_Q | 206_R | 1.200 | 0.98 |
| 109_F | 209_L | 1.195 | 0.98 |
| 201_P | 204_E | 1.194 | 0.98 |
| 43_S | 46_G | 1.193 | 0.98 |
| 11_A | 111_V | 1.191 | 0.98 |
| 71_R | 74_Q | 1.190 | 0.98 |
| 125_V | 132_V | 1.187 | 0.98 |
| 38_A | 41_S | 1.181 | 0.98 |
| 156_R | 159_D | 1.164 | 0.97 |
| 95_A | 98_E | 1.160 | 0.97 |
| 19_F | 22_E | 1.156 | 0.97 |
| 108_E | 195_K | 1.155 | 0.97 |
| 8_A | 171_Y | 1.147 | 0.97 |
| 5_L | 17_A | 1.143 | 0.97 |
| 115_L | 199_T | 1.137 | 0.97 |
| 37_A | 71_R | 1.101 | 0.96 |
| 35_L | 39_V | 1.096 | 0.96 |
| 94_D | 97_K | 1.096 | 0.96 |
| 122_G | 135_V | 1.088 | 0.96 |
| 196_V | 205_V | 1.082 | 0.96 |
| 6_L | 179_I | 1.079 | 0.95 |
| 39_V | 53_M | 1.073 | 0.95 |
| 200_K | 205_V | 1.049 | 0.94 |
| 24_Y | 210_E | 1.034 | 0.94 |
| 87_P | 92_Q | 1.032 | 0.94 |
| 8_A | 116_I | 1.031 | 0.94 |
| 106_V | 193_Y | 1.025 | 0.93 |
| 144_G | 147_D | 1.021 | 0.93 |
| 105_Y | 194_A | 1.018 | 0.93 |
| 111_V | 198_G | 1.013 | 0.93 |
| 160_Q | 163_T | 1.008 | 0.93 |
| 34_M | 38_A | 1.004 | 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 | |
| 4qbgB | 1 | 0.9766 | 100 | 0.274 | Contact Map |
| 4jzkA | 2 | 1 | 100 | 0.28 | Contact Map |
| 3gmtA | 2 | 0.9252 | 100 | 0.28 | Contact Map |
| 3be4A | 1 | 0.9626 | 100 | 0.282 | Contact Map |
| 4pzlA | 4 | 1 | 100 | 0.288 | Contact Map |
| 3tlxA | 4 | 0.9766 | 100 | 0.3 | Contact Map |
| 2xb4A | 1 | 0.972 | 100 | 0.302 | Contact Map |
| 1ak2A | 1 | 0.9766 | 100 | 0.316 | Contact Map |
| 1zd8A | 1 | 0.9626 | 100 | 0.319 | Contact Map |
| 1akyA | 1 | 0.9766 | 100 | 0.321 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)