| GNRH_R_1_328 |
| ID: | 1483460719 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 328 (280) | ||
| Sequences: | 27176 (15705.7) | ||
| Seq/Len: | 97.057 | ||
| Nf(neff/√len): | 938.6 |
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: 97.057).
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 | 4.359 | 1.00 |
| 82_H | 164_W | 4.039 | 1.00 |
| 196_C | 200_C | 3.920 | 1.00 |
| 229_I | 233_K | 3.467 | 1.00 |
| 82_H | 131_M | 2.998 | 1.00 |
| 140_S | 233_K | 2.384 | 1.00 |
| 232_A | 236_F | 2.370 | 1.00 |
| 112_L | 116_V | 2.280 | 1.00 |
| 134_V | 163_A | 2.278 | 1.00 |
| 226_I | 230_C | 2.105 | 1.00 |
| 145_R | 148_A | 2.097 | 1.00 |
| 123_F | 168_S | 2.091 | 1.00 |
| 233_K | 236_F | 2.074 | 1.00 |
| 111_E | 115_K | 2.069 | 1.00 |
| 140_S | 145_R | 2.052 | 1.00 |
| 268_M | 326_F | 2.023 | 1.00 |
| 140_S | 230_C | 2.018 | 1.00 |
| 86_A | 127_A | 1.988 | 1.00 |
| 140_S | 144_T | 1.967 | 1.00 |
| 154_K | 158_S | 1.932 | 1.00 |
| 89_L | 124_S | 1.894 | 1.00 |
| 233_K | 237_T | 1.875 | 1.00 |
| 280_W | 312_A | 1.806 | 1.00 |
| 57_L | 81_K | 1.798 | 1.00 |
| 127_A | 167_S | 1.782 | 1.00 |
| 133_V | 230_C | 1.752 | 1.00 |
| 82_H | 160_V | 1.723 | 1.00 |
| 54_A | 58_L | 1.687 | 1.00 |
| 275_S | 322_I | 1.672 | 1.00 |
| 107_W | 110_G | 1.658 | 1.00 |
| 144_T | 237_T | 1.658 | 1.00 |
| 134_V | 159_M | 1.655 | 1.00 |
| 285_V | 289_W | 1.655 | 1.00 |
| 157_Q | 161_G | 1.640 | 1.00 |
| 119_Y | 123_F | 1.639 | 1.00 |
| 131_M | 160_V | 1.621 | 1.00 |
| 114_C | 196_C | 1.617 | 1.00 |
| 236_F | 240_R | 1.607 | 1.00 |
| 141_L | 145_R | 1.605 | 1.00 |
| 159_M | 163_A | 1.601 | 1.00 |
| 138_D | 142_A | 1.598 | 1.00 |
| 87_N | 319_D | 1.555 | 1.00 |
| 78_L | 160_V | 1.546 | 1.00 |
| 81_K | 85_L | 1.513 | 1.00 |
| 60_L | 81_K | 1.512 | 1.00 |
| 84_T | 87_N | 1.496 | 1.00 |
| 137_L | 230_C | 1.494 | 1.00 |
| 235_I | 239_T | 1.492 | 1.00 |
| 237_T | 240_R | 1.485 | 1.00 |
| 158_S | 162_L | 1.484 | 1.00 |
| 241_V | 245_D | 1.478 | 1.00 |
| 133_V | 226_I | 1.466 | 1.00 |
| 127_A | 131_M | 1.448 | 1.00 |
| 130_F | 223_P | 1.443 | 1.00 |
| 154_K | 157_Q | 1.409 | 1.00 |
| 319_D | 323_Y | 1.394 | 0.99 |
| 304_V | 308_F | 1.388 | 0.99 |
| 51_T | 54_A | 1.387 | 0.99 |
| 167_S | 171_A | 1.356 | 0.99 |
| 131_M | 164_W | 1.355 | 0.99 |
| 265_T | 268_M | 1.349 | 0.99 |
| 86_A | 128_P | 1.341 | 0.99 |
| 110_G | 113_L | 1.338 | 0.99 |
| 224_L | 277_T | 1.337 | 0.99 |
| 314_L | 318_F | 1.331 | 0.99 |
| 262_R | 266_L | 1.327 | 0.99 |
| 87_N | 128_P | 1.327 | 0.99 |
| 185_D | 188_G | 1.314 | 0.99 |
| 172_G | 176_Y | 1.305 | 0.99 |
| 136_S | 231_N | 1.301 | 0.99 |
| 137_L | 141_L | 1.289 | 0.99 |
| 281_T | 285_V | 1.271 | 0.99 |
| 127_A | 164_W | 1.263 | 0.99 |
| 228_L | 232_A | 1.258 | 0.99 |
| 152_N | 155_V | 1.251 | 0.99 |
| 83_L | 131_M | 1.248 | 0.99 |
| 303_P | 307_F | 1.246 | 0.98 |
| 82_H | 86_A | 1.244 | 0.98 |
| 174_Q | 177_I | 1.240 | 0.98 |
| 231_N | 234_I | 1.235 | 0.98 |
| 214_F | 218_C | 1.231 | 0.98 |
| 142_A | 147_L | 1.226 | 0.98 |
| 96_P | 99_G | 1.225 | 0.98 |
| 90_E | 316_P | 1.224 | 0.98 |
| 142_A | 146_P | 1.217 | 0.98 |
| 263_L | 267_K | 1.214 | 0.98 |
| 265_T | 269_T | 1.209 | 0.98 |
| 79_L | 156_G | 1.206 | 0.98 |
| 235_I | 266_L | 1.182 | 0.98 |
| 130_F | 166_L | 1.182 | 0.98 |
| 49_S | 53_N | 1.175 | 0.98 |
| 112_L | 115_K | 1.173 | 0.98 |
| 79_L | 135_I | 1.166 | 0.97 |
| 55_S | 59_K | 1.165 | 0.97 |
| 57_L | 84_T | 1.162 | 0.97 |
| 53_N | 56_F | 1.155 | 0.97 |
| 86_A | 124_S | 1.152 | 0.97 |
| 309_F | 313_F | 1.152 | 0.97 |
| 262_R | 265_T | 1.142 | 0.97 |
| 86_A | 164_W | 1.139 | 0.97 |
| 126_Y | 219_L | 1.139 | 0.97 |
| 72_K | 77_K | 1.133 | 0.97 |
| 123_F | 171_A | 1.129 | 0.97 |
| 78_L | 157_Q | 1.121 | 0.97 |
| 293_D | 296_M | 1.113 | 0.96 |
| 305_N | 309_F | 1.106 | 0.96 |
| 132_M | 227_M | 1.094 | 0.96 |
| 177_I | 180_M | 1.083 | 0.96 |
| 56_F | 60_L | 1.082 | 0.96 |
| 133_V | 223_P | 1.078 | 0.95 |
| 74_S | 77_K | 1.074 | 0.95 |
| 126_Y | 167_S | 1.069 | 0.95 |
| 119_Y | 175_L | 1.068 | 0.95 |
| 267_K | 271_A | 1.061 | 0.95 |
| 119_Y | 171_A | 1.056 | 0.95 |
| 57_L | 60_L | 1.054 | 0.95 |
| 317_C | 320_P | 1.050 | 0.94 |
| 220_F | 224_L | 1.048 | 0.94 |
| 129_A | 223_P | 1.046 | 0.94 |
| 50_A | 88_L | 1.040 | 0.94 |
| 155_V | 158_S | 1.038 | 0.94 |
| 54_A | 88_L | 1.038 | 0.94 |
| 122_L | 171_A | 1.030 | 0.94 |
| 300_L | 304_V | 1.029 | 0.94 |
| 136_S | 230_C | 1.028 | 0.94 |
| 130_F | 163_A | 1.027 | 0.94 |
| 141_L | 149_L | 1.024 | 0.93 |
| 275_S | 318_F | 1.024 | 0.93 |
| 148_A | 151_S | 1.023 | 0.93 |
| 277_T | 281_T | 1.021 | 0.93 |
| 140_S | 229_I | 1.019 | 0.93 |
| 144_T | 233_K | 1.018 | 0.93 |
| 79_L | 138_D | 1.018 | 0.93 |
| 49_S | 52_F | 1.017 | 0.93 |
| 235_I | 238_L | 1.012 | 0.93 |
| 50_A | 91_T | 1.008 | 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 | 0.28 | Contact Map |
| 4iarA | 1 | 0.8354 | 100 | 0.288 | Contact Map |
| 3uonA | 1 | 0.8506 | 100 | 0.289 | Contact Map |
| 2rh1A | 1 | 0.8598 | 100 | 0.291 | Contact Map |
| 3oduA | 2 | 0.875 | 100 | 0.294 | Contact Map |
| 4grvA | 1 | 0.8994 | 100 | 0.295 | Contact Map |
| 4s0vA | 1 | 0.8567 | 100 | 0.295 | Contact Map |
| 3vw7A | 1 | 0.8811 | 100 | 0.3 | Contact Map |
| 3pblA | 2 | 0.811 | 100 | 0.3 | Contact Map |
| 3emlA | 1 | 0.8506 | 100 | 0.307 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)