| GNRH_R_1_328 |
| ID: | 1483583597 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 328 (291) | ||
| Sequences: | 13717 (7588.8) | ||
| Seq/Len: | 47.137 | ||
| Nf(neff/√len): | 444.9 |
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: 47.137).
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 |
| 49_S | 91_T | 5.777 | 1.00 |
| 82_H | 164_W | 3.981 | 1.00 |
| 229_I | 233_K | 3.843 | 1.00 |
| 82_H | 131_M | 3.012 | 1.00 |
| 196_C | 200_C | 2.874 | 1.00 |
| 134_V | 163_A | 2.778 | 1.00 |
| 112_L | 116_V | 2.656 | 1.00 |
| 140_S | 145_R | 2.560 | 1.00 |
| 111_E | 115_K | 2.533 | 1.00 |
| 154_K | 158_S | 2.514 | 1.00 |
| 119_Y | 123_F | 2.368 | 1.00 |
| 134_V | 159_M | 2.256 | 1.00 |
| 57_L | 81_K | 2.250 | 1.00 |
| 226_I | 230_C | 2.234 | 1.00 |
| 233_K | 236_F | 2.230 | 1.00 |
| 123_F | 168_S | 2.210 | 1.00 |
| 114_C | 196_C | 2.207 | 1.00 |
| 107_W | 110_G | 2.202 | 1.00 |
| 232_A | 236_F | 2.189 | 1.00 |
| 78_L | 160_V | 2.163 | 1.00 |
| 60_L | 81_K | 2.096 | 1.00 |
| 268_M | 326_F | 2.095 | 1.00 |
| 275_S | 322_I | 2.058 | 1.00 |
| 140_S | 233_K | 2.030 | 1.00 |
| 140_S | 144_T | 1.981 | 1.00 |
| 54_A | 58_L | 1.935 | 1.00 |
| 82_H | 160_V | 1.920 | 1.00 |
| 158_S | 162_L | 1.920 | 1.00 |
| 89_L | 124_S | 1.865 | 1.00 |
| 131_M | 160_V | 1.860 | 1.00 |
| 86_A | 127_A | 1.858 | 1.00 |
| 145_R | 148_A | 1.857 | 1.00 |
| 285_V | 289_W | 1.837 | 1.00 |
| 280_W | 312_A | 1.831 | 1.00 |
| 79_L | 156_G | 1.788 | 1.00 |
| 157_Q | 161_G | 1.763 | 1.00 |
| 87_N | 128_P | 1.741 | 1.00 |
| 228_L | 232_A | 1.643 | 1.00 |
| 172_G | 176_Y | 1.640 | 1.00 |
| 159_M | 163_A | 1.639 | 1.00 |
| 127_A | 167_S | 1.630 | 1.00 |
| 119_Y | 175_L | 1.622 | 1.00 |
| 144_T | 237_T | 1.608 | 1.00 |
| 224_L | 277_T | 1.604 | 1.00 |
| 49_S | 317_C | 1.600 | 1.00 |
| 214_F | 218_C | 1.592 | 1.00 |
| 236_F | 240_R | 1.590 | 1.00 |
| 87_N | 319_D | 1.575 | 1.00 |
| 281_T | 285_V | 1.574 | 1.00 |
| 78_L | 157_Q | 1.563 | 1.00 |
| 235_I | 239_T | 1.562 | 1.00 |
| 72_K | 77_K | 1.533 | 1.00 |
| 138_D | 142_A | 1.533 | 1.00 |
| 137_L | 230_C | 1.517 | 1.00 |
| 300_L | 304_V | 1.516 | 1.00 |
| 57_L | 88_L | 1.500 | 1.00 |
| 52_F | 317_C | 1.489 | 1.00 |
| 46_F | 99_G | 1.484 | 1.00 |
| 56_F | 60_L | 1.482 | 1.00 |
| 319_D | 323_Y | 1.460 | 1.00 |
| 233_K | 237_T | 1.455 | 1.00 |
| 86_A | 128_P | 1.451 | 1.00 |
| 142_A | 146_P | 1.448 | 1.00 |
| 154_K | 157_Q | 1.444 | 1.00 |
| 81_K | 85_L | 1.427 | 1.00 |
| 54_A | 88_L | 1.427 | 1.00 |
| 152_N | 155_V | 1.422 | 1.00 |
| 84_T | 87_N | 1.400 | 0.99 |
| 100_M | 109_A | 1.396 | 0.99 |
| 90_E | 316_P | 1.377 | 0.99 |
| 74_S | 77_K | 1.376 | 0.99 |
| 127_A | 131_M | 1.361 | 0.99 |
| 314_L | 318_F | 1.358 | 0.99 |
| 235_I | 266_L | 1.345 | 0.99 |
| 140_S | 230_C | 1.328 | 0.99 |
| 303_P | 307_F | 1.303 | 0.99 |
| 129_A | 133_V | 1.288 | 0.99 |
| 132_M | 227_M | 1.286 | 0.99 |
| 50_A | 91_T | 1.285 | 0.99 |
| 237_T | 240_R | 1.280 | 0.99 |
| 142_A | 147_L | 1.260 | 0.99 |
| 275_S | 318_F | 1.251 | 0.99 |
| 110_G | 113_L | 1.238 | 0.98 |
| 36_K | 40_T | 1.235 | 0.98 |
| 304_V | 308_F | 1.230 | 0.98 |
| 83_L | 87_N | 1.227 | 0.98 |
| 286_L | 308_F | 1.227 | 0.98 |
| 57_L | 85_L | 1.227 | 0.98 |
| 83_L | 131_M | 1.219 | 0.98 |
| 79_L | 135_I | 1.205 | 0.98 |
| 75_R | 156_G | 1.198 | 0.98 |
| 270_V | 274_T | 1.198 | 0.98 |
| 43_F | 99_G | 1.195 | 0.98 |
| 167_S | 171_A | 1.191 | 0.98 |
| 140_S | 229_I | 1.189 | 0.98 |
| 142_A | 149_L | 1.189 | 0.98 |
| 130_F | 166_L | 1.185 | 0.98 |
| 279_C | 315_N | 1.184 | 0.98 |
| 50_A | 88_L | 1.177 | 0.98 |
| 130_F | 163_A | 1.176 | 0.98 |
| 238_L | 263_L | 1.167 | 0.97 |
| 46_F | 91_T | 1.163 | 0.97 |
| 133_V | 226_I | 1.150 | 0.97 |
| 48_L | 51_T | 1.147 | 0.97 |
| 133_V | 230_C | 1.134 | 0.97 |
| 129_A | 276_F | 1.134 | 0.97 |
| 137_L | 141_L | 1.132 | 0.97 |
| 271_A | 326_F | 1.128 | 0.97 |
| 127_A | 164_W | 1.122 | 0.97 |
| 174_Q | 177_I | 1.118 | 0.96 |
| 148_A | 151_S | 1.109 | 0.96 |
| 141_L | 145_R | 1.107 | 0.96 |
| 220_F | 276_F | 1.103 | 0.96 |
| 51_T | 54_A | 1.101 | 0.96 |
| 136_S | 230_C | 1.101 | 0.96 |
| 58_L | 62_K | 1.097 | 0.96 |
| 39_V | 99_G | 1.094 | 0.96 |
| 94_V | 313_F | 1.089 | 0.96 |
| 161_G | 165_I | 1.088 | 0.96 |
| 43_F | 103_I | 1.081 | 0.95 |
| 86_A | 124_S | 1.067 | 0.95 |
| 123_F | 171_A | 1.059 | 0.95 |
| 131_M | 164_W | 1.056 | 0.95 |
| 55_S | 59_K | 1.056 | 0.95 |
| 173_P | 211_Y | 1.053 | 0.95 |
| 86_A | 164_W | 1.053 | 0.95 |
| 57_L | 84_T | 1.045 | 0.94 |
| 126_Y | 167_S | 1.044 | 0.94 |
| 158_S | 161_G | 1.044 | 0.94 |
| 126_Y | 219_L | 1.037 | 0.94 |
| 259_P | 263_L | 1.030 | 0.94 |
| 136_S | 231_N | 1.029 | 0.94 |
| 271_A | 322_I | 1.024 | 0.93 |
| 56_F | 320_P | 1.021 | 0.93 |
| 61_Q | 81_K | 1.020 | 0.93 |
| 164_W | 320_P | 1.017 | 0.93 |
| 130_F | 133_V | 1.015 | 0.93 |
| 130_F | 219_L | 1.014 | 0.93 |
| 220_F | 224_L | 1.014 | 0.93 |
| 216_F | 221_I | 1.005 | 0.93 |
| 263_L | 267_K | 1.005 | 0.93 |
| 52_F | 321_L | 1.005 | 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 | |
| 4pxzA | 1 | 0.8659 | 100 | 0.31 | Contact Map |
| 4iarA | 1 | 0.8354 | 100 | 0.315 | Contact Map |
| 3uonA | 1 | 0.8506 | 100 | 0.316 | Contact Map |
| 2rh1A | 1 | 0.8567 | 100 | 0.317 | Contact Map |
| 3pblA | 2 | 0.811 | 100 | 0.325 | Contact Map |
| 3oduA | 2 | 0.878 | 100 | 0.327 | Contact Map |
| 3vw7A | 1 | 0.8811 | 100 | 0.329 | Contact Map |
| 4s0vA | 1 | 0.8598 | 100 | 0.33 | Contact Map |
| 4grvA | 1 | 0.8994 | 100 | 0.331 | Contact Map |
| 4dklA | 1 | 0.8628 | 100 | 0.332 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)