| NanR 25-255 |
| ID: | 1517460237 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 231 (227) | ||
| Sequences: | 18336 (12293.2) | ||
| Seq/Len: | 80.775 | ||
| Nf(neff/√len): | 815.9 |
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: 80.775).
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 |
| 128_A | 206_R | 4.010 | 1.00 |
| 113_R | 214_D | 3.546 | 1.00 |
| 209_D | 212_E | 3.278 | 1.00 |
| 26_G | 29_E | 3.229 | 1.00 |
| 19_M | 24_E | 2.918 | 1.00 |
| 135_S | 199_I | 2.628 | 1.00 |
| 99_H | 162_P | 2.582 | 1.00 |
| 106_F | 110_S | 2.563 | 1.00 |
| 19_M | 40_F | 2.540 | 1.00 |
| 34_E | 45_R | 2.401 | 1.00 |
| 17_E | 58_K | 2.264 | 1.00 |
| 126_L | 154_V | 2.262 | 1.00 |
| 13_E | 54_A | 2.234 | 1.00 |
| 105_L | 222_N | 2.172 | 1.00 |
| 62_Q | 72_S | 2.169 | 1.00 |
| 12_V | 43_V | 2.083 | 1.00 |
| 204_A | 212_E | 2.069 | 1.00 |
| 123_Q | 160_G | 2.067 | 1.00 |
| 102_Q | 114_Y | 2.060 | 1.00 |
| 12_V | 41_F | 2.047 | 1.00 |
| 120_T | 123_Q | 1.971 | 1.00 |
| 157_E | 165_M | 1.936 | 1.00 |
| 117_E | 210_P | 1.927 | 1.00 |
| 131_L | 202_V | 1.869 | 1.00 |
| 124_I | 206_R | 1.829 | 1.00 |
| 63_I | 69_A | 1.807 | 1.00 |
| 15_E | 19_M | 1.801 | 1.00 |
| 212_E | 216_A | 1.798 | 1.00 |
| 152_H | 198_H | 1.791 | 1.00 |
| 109_S | 218_Q | 1.781 | 1.00 |
| 197_Q | 223_S | 1.737 | 1.00 |
| 6_K | 14_E | 1.705 | 1.00 |
| 154_V | 157_E | 1.701 | 1.00 |
| 203_D | 207_R | 1.698 | 1.00 |
| 109_S | 214_D | 1.686 | 1.00 |
| 214_D | 218_Q | 1.685 | 1.00 |
| 103_L | 167_I | 1.674 | 1.00 |
| 200_A | 216_A | 1.611 | 1.00 |
| 37_L | 48_V | 1.585 | 1.00 |
| 113_R | 210_P | 1.577 | 1.00 |
| 110_S | 113_R | 1.572 | 1.00 |
| 207_R | 212_E | 1.545 | 1.00 |
| 18_Q | 22_R | 1.540 | 1.00 |
| 199_I | 203_D | 1.530 | 1.00 |
| 153_R | 169_V | 1.529 | 1.00 |
| 130_A | 147_S | 1.522 | 1.00 |
| 112_V | 213_A | 1.479 | 1.00 |
| 119_A | 124_I | 1.477 | 1.00 |
| 105_L | 218_Q | 1.463 | 1.00 |
| 105_L | 225_S | 1.452 | 1.00 |
| 156_A | 168_H | 1.447 | 1.00 |
| 64_N | 67_E | 1.441 | 1.00 |
| 128_A | 132_E | 1.436 | 1.00 |
| 128_A | 202_V | 1.429 | 1.00 |
| 113_R | 211_D | 1.426 | 1.00 |
| 140_N | 143_A | 1.411 | 1.00 |
| 166_A | 170_A | 1.409 | 1.00 |
| 215_R | 219_S | 1.398 | 0.99 |
| 131_L | 199_I | 1.397 | 0.99 |
| 11_M | 15_E | 1.393 | 0.99 |
| 35_R | 39_A | 1.382 | 0.99 |
| 133_I | 150_D | 1.374 | 0.99 |
| 123_Q | 158_I | 1.373 | 0.99 |
| 13_E | 58_K | 1.372 | 0.99 |
| 36_E | 40_F | 1.367 | 0.99 |
| 119_A | 208_H | 1.333 | 0.99 |
| 64_N | 70_R | 1.328 | 0.99 |
| 129_K | 133_I | 1.323 | 0.99 |
| 210_P | 214_D | 1.314 | 0.99 |
| 148_D | 152_H | 1.311 | 0.99 |
| 15_E | 18_Q | 1.311 | 0.99 |
| 126_L | 157_E | 1.303 | 0.99 |
| 105_L | 109_S | 1.302 | 0.99 |
| 99_H | 163_I | 1.297 | 0.99 |
| 163_I | 174_W | 1.294 | 0.99 |
| 155_L | 205_I | 1.288 | 0.99 |
| 109_S | 113_R | 1.285 | 0.99 |
| 159_P | 165_M | 1.268 | 0.99 |
| 104_R | 108_E | 1.265 | 0.99 |
| 15_E | 41_F | 1.259 | 0.99 |
| 19_M | 41_F | 1.246 | 0.98 |
| 197_Q | 220_H | 1.245 | 0.98 |
| 102_Q | 161_N | 1.242 | 0.98 |
| 124_I | 208_H | 1.233 | 0.98 |
| 30_Q | 70_R | 1.226 | 0.98 |
| 130_A | 154_V | 1.209 | 0.98 |
| 202_V | 206_R | 1.208 | 0.98 |
| 133_I | 147_S | 1.201 | 0.98 |
| 124_I | 202_V | 1.200 | 0.98 |
| 153_R | 157_E | 1.200 | 0.98 |
| 150_D | 154_V | 1.176 | 0.98 |
| 146_R | 150_D | 1.170 | 0.97 |
| 111_L | 156_A | 1.155 | 0.97 |
| 212_E | 215_R | 1.146 | 0.97 |
| 148_D | 198_H | 1.142 | 0.97 |
| 112_V | 116_A | 1.141 | 0.97 |
| 218_Q | 222_N | 1.139 | 0.97 |
| 98_A | 225_S | 1.128 | 0.97 |
| 25_F | 71_V | 1.128 | 0.97 |
| 99_H | 161_N | 1.124 | 0.97 |
| 211_D | 215_R | 1.120 | 0.96 |
| 119_A | 158_I | 1.120 | 0.96 |
| 64_N | 68_R | 1.113 | 0.96 |
| 154_V | 158_I | 1.111 | 0.96 |
| 7_K | 10_E | 1.109 | 0.96 |
| 112_V | 217_L | 1.097 | 0.96 |
| 62_Q | 70_R | 1.096 | 0.96 |
| 143_A | 146_R | 1.096 | 0.96 |
| 110_S | 214_D | 1.089 | 0.96 |
| 200_A | 212_E | 1.080 | 0.95 |
| 119_A | 205_I | 1.078 | 0.95 |
| 6_K | 11_M | 1.077 | 0.95 |
| 200_A | 219_S | 1.069 | 0.95 |
| 196_Q | 200_A | 1.068 | 0.95 |
| 135_S | 195_Y | 1.068 | 0.95 |
| 56_K | 63_I | 1.061 | 0.95 |
| 151_F | 202_V | 1.058 | 0.95 |
| 56_K | 61_V | 1.058 | 0.95 |
| 33_S | 36_E | 1.055 | 0.95 |
| 108_E | 152_H | 1.036 | 0.94 |
| 114_Y | 118_H | 1.030 | 0.94 |
| 119_A | 123_Q | 1.028 | 0.94 |
| 198_H | 220_H | 1.016 | 0.93 |
| 126_L | 129_K | 1.012 | 0.93 |
| 102_Q | 118_H | 1.006 | 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 | |
| 3c7jA | 2 | 0.9048 | 100 | 0.103 | Contact Map |
| 4p96A | 2 | 0.974 | 100 | 0.109 | Contact Map |
| 3sxyA | 2 | 0.8528 | 100 | 0.113 | Contact Map |
| 2di3A | 2 | 0.961 | 100 | 0.115 | Contact Map |
| 2hs5A | 1 | 0.8788 | 100 | 0.126 | Contact Map |
| 3ihuA | 2 | 0.8701 | 100 | 0.128 | Contact Map |
| 4p9fA | 2 | 0.9004 | 100 | 0.14 | Contact Map |
| 1hw1A | 2 | 0.9567 | 100 | 0.152 | Contact Map |
| 3ic7A | 2 | 0.4805 | 99.8 | 0.496 | Contact Map |
| 3by6A | 5 | 0.5238 | 99.8 | 0.497 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)