| I_sub_Membound |
| ID: | 1428351372 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 330 (321) | ||
| Sequences: | 918 (625.7) | ||
| Seq/Len: | 2.860 | ||
| Nf(neff/√len): | 34.9 |
HHblits Results: (2013_03)
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: 2.860).
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 |
| 169_H | 172_H | 3.218 | 1.00 |
| 51_Y | 92_V | 2.593 | 1.00 |
| 44_I | 96_V | 2.591 | 1.00 |
| 13_S | 319_P | 2.538 | 1.00 |
| 152_M | 239_H | 2.532 | 1.00 |
| 22_T | 315_E | 2.432 | 1.00 |
| 97_V | 101_I | 2.397 | 1.00 |
| 44_I | 100_L | 2.284 | 1.00 |
| 156_G | 306_F | 2.269 | 1.00 |
| 235_H | 308_T | 2.122 | 1.00 |
| 36_W | 242_I | 2.100 | 1.00 |
| 54_G | 92_V | 2.066 | 1.00 |
| 2_P | 5_V | 2.061 | 1.00 |
| 249_G | 290_T | 2.059 | 1.00 |
| 49_L | 287_L | 2.041 | 1.00 |
| 290_T | 293_G | 2.011 | 1.00 |
| 48_L | 51_Y | 1.888 | 0.99 |
| 19_K | 316_N | 1.865 | 0.99 |
| 45_G | 106_F | 1.813 | 0.99 |
| 235_H | 298_P | 1.791 | 0.99 |
| 137_T | 140_L | 1.787 | 0.99 |
| 48_L | 96_V | 1.752 | 0.99 |
| 92_V | 96_V | 1.741 | 0.98 |
| 66_P | 70_D | 1.711 | 0.98 |
| 212_V | 215_L | 1.681 | 0.98 |
| 213_F | 217_V | 1.621 | 0.97 |
| 292_L | 295_M | 1.602 | 0.97 |
| 93_F | 97_V | 1.592 | 0.97 |
| 38_G | 98_W | 1.573 | 0.97 |
| 240_I | 246_G | 1.566 | 0.97 |
| 160_R | 176_G | 1.562 | 0.96 |
| 142_I | 240_I | 1.534 | 0.96 |
| 289_L | 293_G | 1.515 | 0.96 |
| 245_V | 294_H | 1.498 | 0.95 |
| 237_L | 255_L | 1.486 | 0.95 |
| 7_P | 10_L | 1.459 | 0.94 |
| 41_V | 290_T | 1.445 | 0.94 |
| 34_P | 94_W | 1.442 | 0.94 |
| 41_V | 249_G | 1.426 | 0.93 |
| 63_R | 67_L | 1.405 | 0.93 |
| 290_T | 294_H | 1.398 | 0.92 |
| 306_F | 312_F | 1.388 | 0.92 |
| 1_N | 9_E | 1.388 | 0.92 |
| 52_L | 56_W | 1.380 | 0.92 |
| 255_L | 289_L | 1.377 | 0.92 |
| 44_I | 105_F | 1.363 | 0.91 |
| 161_A | 165_L | 1.344 | 0.90 |
| 54_G | 85_V | 1.321 | 0.89 |
| 34_P | 104_E | 1.319 | 0.89 |
| 51_Y | 96_V | 1.308 | 0.89 |
| 46_Y | 286_I | 1.299 | 0.88 |
| 309_K | 312_F | 1.297 | 0.88 |
| 239_H | 304_V | 1.293 | 0.88 |
| 48_L | 105_F | 1.293 | 0.88 |
| 154_F | 184_L | 1.289 | 0.88 |
| 67_L | 70_D | 1.284 | 0.87 |
| 28_V | 159_L | 1.284 | 0.87 |
| 64_N | 67_L | 1.277 | 0.87 |
| 309_K | 317_G | 1.268 | 0.86 |
| 260_G | 279_A | 1.260 | 0.86 |
| 276_I | 280_G | 1.259 | 0.86 |
| 152_M | 156_G | 1.259 | 0.86 |
| 42_G | 98_W | 1.254 | 0.86 |
| 173_F | 185_G | 1.252 | 0.86 |
| 256_L | 285_L | 1.252 | 0.86 |
| 298_P | 308_T | 1.251 | 0.85 |
| 143_L | 276_I | 1.245 | 0.85 |
| 54_G | 89_N | 1.232 | 0.84 |
| 211_G | 214_L | 1.231 | 0.84 |
| 57_L | 67_L | 1.225 | 0.84 |
| 168_R | 324_K | 1.224 | 0.84 |
| 295_M | 302_I | 1.209 | 0.83 |
| 210_F | 217_V | 1.200 | 0.82 |
| 19_K | 314_E | 1.197 | 0.82 |
| 256_L | 282_L | 1.192 | 0.82 |
| 207_Y | 211_G | 1.192 | 0.82 |
| 46_Y | 283_H | 1.192 | 0.82 |
| 49_L | 284_L | 1.191 | 0.81 |
| 228_E | 235_H | 1.186 | 0.81 |
| 46_Y | 249_G | 1.183 | 0.81 |
| 210_F | 213_F | 1.179 | 0.81 |
| 245_V | 297_Q | 1.168 | 0.80 |
| 16_N | 303_W | 1.166 | 0.80 |
| 42_G | 102_Y | 1.164 | 0.79 |
| 58_S | 89_N | 1.164 | 0.79 |
| 249_G | 291_T | 1.163 | 0.79 |
| 48_L | 52_L | 1.154 | 0.79 |
| 55_R | 89_N | 1.148 | 0.78 |
| 13_S | 17_T | 1.144 | 0.78 |
| 2_P | 27_P | 1.141 | 0.77 |
| 188_A | 284_L | 1.138 | 0.77 |
| 51_Y | 89_N | 1.137 | 0.77 |
| 293_G | 297_Q | 1.133 | 0.77 |
| 243_Y | 249_G | 1.130 | 0.76 |
| 306_F | 323_F | 1.127 | 0.76 |
| 47_A | 96_V | 1.124 | 0.76 |
| 304_V | 309_K | 1.121 | 0.76 |
| 156_G | 312_F | 1.110 | 0.75 |
| 51_Y | 93_F | 1.104 | 0.74 |
| 48_L | 194_L | 1.102 | 0.74 |
| 209_G | 213_F | 1.100 | 0.74 |
| 206_M | 210_F | 1.097 | 0.73 |
| 1_N | 24_D | 1.093 | 0.73 |
| 198_Q | 201_W | 1.090 | 0.73 |
| 209_G | 212_V | 1.089 | 0.73 |
| 100_L | 105_F | 1.083 | 0.72 |
| 51_Y | 55_R | 1.082 | 0.72 |
| 286_I | 297_Q | 1.080 | 0.72 |
| 39_M | 102_Y | 1.075 | 0.71 |
| 138_A | 142_I | 1.074 | 0.71 |
| 93_F | 266_R | 1.073 | 0.71 |
| 206_M | 214_L | 1.073 | 0.71 |
| 285_L | 289_L | 1.071 | 0.71 |
| 269_L | 308_T | 1.069 | 0.71 |
| 63_R | 68_V | 1.067 | 0.70 |
| 101_I | 162_Y | 1.066 | 0.70 |
| 9_E | 13_S | 1.066 | 0.70 |
| 116_F | 119_P | 1.066 | 0.70 |
| 273_L | 280_G | 1.064 | 0.70 |
| 44_I | 110_L | 1.063 | 0.70 |
| 34_P | 228_E | 1.058 | 0.70 |
| 190_A | 194_L | 1.057 | 0.69 |
| 8_F | 11_L | 1.057 | 0.69 |
| 152_M | 297_Q | 1.056 | 0.69 |
| 293_G | 304_V | 1.054 | 0.69 |
| 295_M | 313_Y | 1.053 | 0.69 |
| 28_V | 38_G | 1.050 | 0.69 |
| 287_L | 308_T | 1.044 | 0.68 |
| 46_Y | 290_T | 1.044 | 0.68 |
| 8_F | 40_I | 1.042 | 0.68 |
| 68_V | 72_F | 1.040 | 0.68 |
| 12_V | 15_L | 1.027 | 0.66 |
| 40_I | 309_K | 1.026 | 0.66 |
| 307_F | 313_Y | 1.021 | 0.66 |
| 270_I | 277_V | 1.021 | 0.66 |
| 64_N | 68_V | 1.020 | 0.65 |
| 28_V | 152_M | 1.020 | 0.65 |
| 231_T | 292_L | 1.017 | 0.65 |
| 3_P | 6_K | 1.016 | 0.65 |
| 236_I | 249_G | 1.015 | 0.65 |
| 58_S | 86_Y | 1.009 | 0.64 |
| 172_H | 175_E | 1.009 | 0.64 |
| 249_G | 283_H | 1.007 | 0.64 |
| 156_G | 160_R | 1.006 | 0.64 |
| 303_W | 307_F | 1.006 | 0.64 |
| 229_I | 232_Q | 1.000 | 0.63 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2nvjA | 1 | 0.0758 | 96.8 | 0.927 | Contact Map |
| 2jtwA | 1 | 0.0758 | 96.4 | 0.929 | Contact Map |
| 1q90G | 1 | 0.0879 | 9.8 | 0.973 | Contact Map |
| 4ogqG | 1 | 0.1091 | 5.9 | 0.976 | Contact Map |
| 4wfeA | 2 | 0.4606 | 5.2 | 0.976 | Contact Map |
| 2cs7A | 3 | 0.0667 | 3.5 | 0.978 | Contact Map |
| 2kv5A | 1 | 0.1 | 2.5 | 0.98 | Contact Map |
| 4crwA | 1 | 0.1848 | 2.4 | 0.98 | Contact Map |
| 4fioA | 3 | 0.1818 | 2.3 | 0.98 | Contact Map |
| 2ih3C | 1 | 0.1879 | 2.3 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)