| Cat_GnRH |
| ID: | 1495147569 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 327 (271) | ||
| Sequences: | 58506 (22730.5) | ||
| Seq/Len: | 215.889 | ||
| Nf(neff/√len): | 1380.8 |
Jackhmmer Results: (2016_04)
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: 215.889).
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 |
| 48_S | 90_T | 4.735 | 1.00 |
| 81_H | 163_W | 3.349 | 1.00 |
| 228_I | 232_K | 3.071 | 1.00 |
| 81_H | 130_M | 2.809 | 1.00 |
| 153_K | 157_S | 2.379 | 1.00 |
| 292_D | 295_M | 2.209 | 1.00 |
| 133_V | 162_A | 2.207 | 1.00 |
| 88_L | 123_S | 2.200 | 1.00 |
| 231_A | 235_F | 2.178 | 1.00 |
| 113_C | 195_C | 2.127 | 1.00 |
| 56_L | 80_K | 2.122 | 1.00 |
| 144_R | 147_A | 2.116 | 1.00 |
| 110_E | 114_K | 2.114 | 1.00 |
| 111_L | 115_V | 2.102 | 1.00 |
| 122_F | 167_S | 2.097 | 1.00 |
| 232_K | 235_F | 2.054 | 1.00 |
| 59_L | 80_K | 2.047 | 1.00 |
| 85_A | 126_A | 2.015 | 1.00 |
| 143_T | 236_T | 1.949 | 1.00 |
| 35_K | 39_T | 1.917 | 1.00 |
| 139_S | 232_K | 1.913 | 1.00 |
| 284_V | 288_W | 1.910 | 1.00 |
| 171_G | 175_Y | 1.874 | 1.00 |
| 139_S | 144_R | 1.873 | 1.00 |
| 151_N | 154_L | 1.867 | 1.00 |
| 225_I | 229_C | 1.864 | 1.00 |
| 53_A | 57_L | 1.844 | 1.00 |
| 133_V | 158_M | 1.838 | 1.00 |
| 96_L | 100_W | 1.750 | 1.00 |
| 235_F | 239_Q | 1.730 | 1.00 |
| 45_F | 91_L | 1.722 | 1.00 |
| 232_K | 236_T | 1.707 | 1.00 |
| 81_H | 159_I | 1.675 | 1.00 |
| 71_K | 76_K | 1.669 | 1.00 |
| 106_W | 109_G | 1.663 | 1.00 |
| 139_S | 143_T | 1.662 | 1.00 |
| 48_S | 316_C | 1.626 | 1.00 |
| 126_A | 166_S | 1.624 | 1.00 |
| 60_Q | 80_K | 1.618 | 1.00 |
| 77_M | 159_I | 1.591 | 1.00 |
| 279_W | 311_A | 1.552 | 1.00 |
| 303_V | 307_F | 1.538 | 1.00 |
| 157_S | 161_L | 1.536 | 1.00 |
| 156_Q | 160_G | 1.532 | 1.00 |
| 118_Y | 122_F | 1.527 | 1.00 |
| 152_G | 156_Q | 1.517 | 1.00 |
| 78_L | 155_G | 1.512 | 1.00 |
| 234_I | 238_T | 1.490 | 1.00 |
| 139_S | 229_C | 1.475 | 1.00 |
| 158_M | 162_A | 1.472 | 1.00 |
| 53_A | 87_L | 1.468 | 1.00 |
| 38_V | 98_G | 1.463 | 1.00 |
| 274_S | 321_I | 1.461 | 1.00 |
| 147_A | 150_S | 1.441 | 1.00 |
| 114_K | 178_R | 1.434 | 1.00 |
| 125_Y | 218_L | 1.426 | 1.00 |
| 62_W | 70_K | 1.411 | 1.00 |
| 130_M | 159_I | 1.410 | 1.00 |
| 57_L | 61_K | 1.395 | 0.99 |
| 38_V | 102_I | 1.393 | 0.99 |
| 205_W | 209_F | 1.382 | 0.99 |
| 49_T | 87_L | 1.373 | 0.99 |
| 299_V | 303_V | 1.371 | 0.99 |
| 136_L | 229_C | 1.369 | 0.99 |
| 209_F | 213_F | 1.368 | 0.99 |
| 166_S | 170_A | 1.364 | 0.99 |
| 110_E | 178_R | 1.349 | 0.99 |
| 86_N | 318_D | 1.346 | 0.99 |
| 132_V | 229_C | 1.338 | 0.99 |
| 51_F | 316_C | 1.331 | 0.99 |
| 118_Y | 174_L | 1.319 | 0.99 |
| 45_F | 98_G | 1.318 | 0.99 |
| 47_L | 316_C | 1.308 | 0.99 |
| 99_M | 103_T | 1.295 | 0.99 |
| 109_G | 112_L | 1.292 | 0.99 |
| 140_L | 144_R | 1.291 | 0.99 |
| 80_K | 84_L | 1.289 | 0.99 |
| 56_L | 87_L | 1.279 | 0.99 |
| 77_M | 156_Q | 1.278 | 0.99 |
| 153_K | 156_Q | 1.266 | 0.99 |
| 132_V | 226_M | 1.264 | 0.99 |
| 132_V | 225_I | 1.262 | 0.99 |
| 154_L | 157_S | 1.260 | 0.99 |
| 32_L | 36_I | 1.255 | 0.99 |
| 85_A | 127_P | 1.251 | 0.99 |
| 125_Y | 166_S | 1.247 | 0.99 |
| 204_W | 208_A | 1.245 | 0.98 |
| 111_L | 114_K | 1.233 | 0.98 |
| 55_F | 323_G | 1.232 | 0.98 |
| 227_L | 231_A | 1.215 | 0.98 |
| 84_L | 88_L | 1.213 | 0.98 |
| 223_L | 276_T | 1.211 | 0.98 |
| 126_A | 163_W | 1.207 | 0.98 |
| 313_L | 317_F | 1.198 | 0.98 |
| 49_T | 90_T | 1.197 | 0.98 |
| 262_L | 266_K | 1.195 | 0.98 |
| 285_L | 307_F | 1.194 | 0.98 |
| 162_A | 166_S | 1.191 | 0.98 |
| 126_A | 130_M | 1.191 | 0.98 |
| 54_S | 58_K | 1.187 | 0.98 |
| 302_P | 306_F | 1.184 | 0.98 |
| 129_F | 165_L | 1.182 | 0.98 |
| 181_H | 202_P | 1.181 | 0.98 |
| 50_T | 53_A | 1.175 | 0.98 |
| 96_L | 112_L | 1.174 | 0.98 |
| 122_F | 170_A | 1.169 | 0.97 |
| 280_T | 284_V | 1.164 | 0.97 |
| 121_L | 170_A | 1.159 | 0.97 |
| 135_S | 229_C | 1.156 | 0.97 |
| 234_I | 265_L | 1.149 | 0.97 |
| 38_V | 42_F | 1.149 | 0.97 |
| 129_F | 218_L | 1.129 | 0.97 |
| 143_T | 232_K | 1.125 | 0.97 |
| 151_N | 155_G | 1.125 | 0.97 |
| 42_F | 98_G | 1.124 | 0.97 |
| 74_R | 155_G | 1.123 | 0.97 |
| 157_S | 160_G | 1.118 | 0.96 |
| 73_S | 76_K | 1.115 | 0.96 |
| 137_D | 141_A | 1.110 | 0.96 |
| 135_S | 230_N | 1.109 | 0.96 |
| 85_A | 123_S | 1.107 | 0.96 |
| 128_A | 222_P | 1.104 | 0.96 |
| 213_F | 217_C | 1.102 | 0.96 |
| 132_V | 222_P | 1.100 | 0.96 |
| 236_T | 239_Q | 1.097 | 0.96 |
| 99_M | 108_A | 1.097 | 0.96 |
| 216_S | 222_P | 1.076 | 0.95 |
| 139_S | 228_I | 1.075 | 0.95 |
| 56_L | 84_L | 1.072 | 0.95 |
| 219_F | 280_T | 1.061 | 0.95 |
| 288_W | 293_P | 1.058 | 0.95 |
| 286_G | 289_Y | 1.058 | 0.95 |
| 282_Y | 286_G | 1.048 | 0.94 |
| 103_T | 107_Y | 1.047 | 0.94 |
| 269_V | 273_T | 1.039 | 0.94 |
| 217_C | 222_P | 1.031 | 0.94 |
| 285_L | 303_V | 1.025 | 0.93 |
| 56_L | 83_T | 1.020 | 0.93 |
| 215_F | 220_I | 1.018 | 0.93 |
| 55_F | 59_L | 1.015 | 0.93 |
| 160_G | 164_L | 1.009 | 0.93 |
| 89_E | 315_P | 1.007 | 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 | 0.8685 | 100 | 0.243 | Contact Map |
| 4iarA | 1 | 0.8379 | 100 | 0.245 | Contact Map |
| 2rh1A | 1 | 0.8593 | 100 | 0.247 | Contact Map |
| 3uonA | 1 | 0.8532 | 100 | 0.25 | Contact Map |
| 4grvA | 1 | 0.8991 | 100 | 0.259 | Contact Map |
| 3pblA | 2 | 0.8135 | 100 | 0.259 | Contact Map |
| 3oduA | 2 | 0.8807 | 100 | 0.26 | Contact Map |
| 3vw7A | 1 | 0.8838 | 100 | 0.264 | Contact Map |
| 4s0vA | 1 | 0.8593 | 100 | 0.269 | Contact Map |
| 4dklA | 1 | 0.8654 | 100 | 0.27 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)