| M2TMe |
| ID: | 1482332575 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 350 (350) | ||
| Sequences: | 733 (482.3) | ||
| Seq/Len: | 2.094 | ||
| Nf(neff/√len): | 25.8 |
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: 2.094).
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 |
| 308_N | 311_I | 2.987 | 1.00 |
| 326_D | 330_K | 2.948 | 1.00 |
| 241_Y | 245_F | 2.799 | 1.00 |
| 109_E | 112_Q | 2.755 | 1.00 |
| 199_D | 317_T | 2.622 | 1.00 |
| 109_E | 129_Y | 2.555 | 1.00 |
| 199_D | 203_F | 2.531 | 1.00 |
| 242_L | 246_G | 2.157 | 1.00 |
| 330_K | 336_L | 2.061 | 0.99 |
| 330_K | 333_R | 2.027 | 0.99 |
| 112_Q | 135_N | 2.013 | 0.99 |
| 134_W | 138_D | 1.885 | 0.98 |
| 191_I | 194_K | 1.838 | 0.98 |
| 246_G | 249_P | 1.831 | 0.98 |
| 135_N | 138_D | 1.822 | 0.98 |
| 180_F | 205_F | 1.803 | 0.98 |
| 72_Y | 76_L | 1.800 | 0.98 |
| 97_A | 101_W | 1.704 | 0.97 |
| 61_P | 64_V | 1.687 | 0.96 |
| 215_G | 219_Q | 1.666 | 0.96 |
| 186_L | 196_M | 1.652 | 0.96 |
| 246_G | 251_Y | 1.639 | 0.95 |
| 129_Y | 135_N | 1.628 | 0.95 |
| 61_P | 65_F | 1.611 | 0.95 |
| 240_S | 246_G | 1.604 | 0.95 |
| 112_Q | 138_D | 1.598 | 0.95 |
| 108_E | 111_R | 1.569 | 0.94 |
| 306_L | 310_L | 1.555 | 0.93 |
| 333_R | 337_I | 1.521 | 0.92 |
| 308_N | 312_A | 1.514 | 0.92 |
| 313_M | 317_T | 1.502 | 0.92 |
| 190_I | 193_V | 1.483 | 0.91 |
| 295_L | 302_T | 1.471 | 0.91 |
| 109_E | 135_N | 1.465 | 0.90 |
| 112_Q | 129_Y | 1.455 | 0.90 |
| 11_G | 14_S | 1.443 | 0.90 |
| 61_P | 76_L | 1.425 | 0.89 |
| 311_I | 314_F | 1.417 | 0.88 |
| 138_D | 175_R | 1.412 | 0.88 |
| 326_D | 336_L | 1.405 | 0.88 |
| 305_L | 312_A | 1.401 | 0.88 |
| 317_T | 321_V | 1.401 | 0.88 |
| 247_Q | 250_G | 1.394 | 0.87 |
| 57_F | 63_V | 1.388 | 0.87 |
| 240_S | 249_P | 1.370 | 0.86 |
| 146_V | 150_T | 1.354 | 0.85 |
| 199_D | 313_M | 1.341 | 0.84 |
| 317_T | 343_R | 1.339 | 0.84 |
| 80_A | 169_F | 1.335 | 0.84 |
| 132_D | 138_D | 1.335 | 0.84 |
| 65_F | 75_F | 1.326 | 0.84 |
| 317_T | 337_I | 1.309 | 0.82 |
| 236_A | 241_Y | 1.307 | 0.82 |
| 329_W | 347_P | 1.305 | 0.82 |
| 331_F | 349_P | 1.301 | 0.82 |
| 132_D | 135_N | 1.295 | 0.81 |
| 215_G | 240_S | 1.290 | 0.81 |
| 333_R | 349_P | 1.286 | 0.81 |
| 306_L | 312_A | 1.281 | 0.81 |
| 186_L | 189_K | 1.258 | 0.79 |
| 306_L | 336_L | 1.253 | 0.78 |
| 169_F | 200_V | 1.253 | 0.78 |
| 330_K | 337_I | 1.251 | 0.78 |
| 298_Y | 312_A | 1.249 | 0.78 |
| 306_L | 313_M | 1.244 | 0.78 |
| 246_G | 250_G | 1.243 | 0.78 |
| 45_Q | 48_G | 1.222 | 0.76 |
| 42_K | 45_Q | 1.221 | 0.76 |
| 120_C | 123_M | 1.217 | 0.76 |
| 247_Q | 252_I | 1.213 | 0.75 |
| 142_I | 294_L | 1.196 | 0.74 |
| 329_W | 349_P | 1.195 | 0.74 |
| 262_C | 274_C | 1.195 | 0.74 |
| 43_R | 47_V | 1.194 | 0.74 |
| 3_A | 7_K | 1.190 | 0.73 |
| 109_E | 132_D | 1.189 | 0.73 |
| 41_E | 47_V | 1.187 | 0.73 |
| 295_L | 300_L | 1.182 | 0.73 |
| 118_D | 121_G | 1.178 | 0.72 |
| 72_Y | 75_F | 1.177 | 0.72 |
| 129_Y | 138_D | 1.176 | 0.72 |
| 304_I | 308_N | 1.175 | 0.72 |
| 193_V | 206_L | 1.174 | 0.72 |
| 302_T | 305_L | 1.173 | 0.72 |
| 298_Y | 330_K | 1.159 | 0.70 |
| 65_F | 76_L | 1.157 | 0.70 |
| 326_D | 329_W | 1.154 | 0.70 |
| 1_I | 32_L | 1.153 | 0.70 |
| 244_I | 302_T | 1.153 | 0.70 |
| 71_S | 101_W | 1.140 | 0.69 |
| 205_F | 214_F | 1.137 | 0.68 |
| 329_W | 333_R | 1.137 | 0.68 |
| 192_I | 305_L | 1.134 | 0.68 |
| 43_R | 46_D | 1.129 | 0.67 |
| 18_G | 21_R | 1.128 | 0.67 |
| 62_V | 66_H | 1.127 | 0.67 |
| 146_V | 342_G | 1.121 | 0.67 |
| 314_F | 334_H | 1.120 | 0.67 |
| 41_E | 45_Q | 1.120 | 0.67 |
| 316_Y | 322_Q | 1.118 | 0.66 |
| 163_V | 221_I | 1.114 | 0.66 |
| 27_L | 30_P | 1.110 | 0.66 |
| 303_N | 314_F | 1.108 | 0.65 |
| 333_R | 348_P | 1.105 | 0.65 |
| 24_L | 27_L | 1.105 | 0.65 |
| 236_A | 240_S | 1.103 | 0.65 |
| 321_V | 345_A | 1.103 | 0.65 |
| 309_L | 317_T | 1.101 | 0.65 |
| 247_Q | 254_G | 1.101 | 0.65 |
| 42_K | 47_V | 1.099 | 0.64 |
| 5_L | 13_L | 1.096 | 0.64 |
| 339_E | 344_P | 1.095 | 0.64 |
| 64_V | 165_L | 1.092 | 0.64 |
| 77_C | 293_L | 1.091 | 0.64 |
| 346_A | 349_P | 1.090 | 0.64 |
| 92_S | 99_Y | 1.088 | 0.63 |
| 32_L | 38_S | 1.088 | 0.63 |
| 177_M | 191_I | 1.087 | 0.63 |
| 251_Y | 254_G | 1.087 | 0.63 |
| 298_Y | 307_L | 1.087 | 0.63 |
| 307_L | 328_I | 1.087 | 0.63 |
| 318_F | 331_F | 1.085 | 0.63 |
| 31_L | 34_T | 1.085 | 0.63 |
| 162_R | 188_P | 1.082 | 0.63 |
| 65_F | 188_P | 1.079 | 0.62 |
| 4_F | 8_V | 1.076 | 0.62 |
| 295_L | 303_N | 1.075 | 0.62 |
| 249_P | 252_I | 1.075 | 0.62 |
| 22_V | 33_L | 1.072 | 0.62 |
| 240_S | 247_Q | 1.072 | 0.62 |
| 129_Y | 134_W | 1.067 | 0.61 |
| 78_L | 94_C | 1.065 | 0.61 |
| 109_E | 138_D | 1.064 | 0.61 |
| 40_R | 46_D | 1.063 | 0.61 |
| 304_I | 307_L | 1.063 | 0.61 |
| 40_R | 44_L | 1.059 | 0.60 |
| 242_L | 247_Q | 1.059 | 0.60 |
| 290_L | 302_T | 1.057 | 0.60 |
| 328_I | 334_H | 1.057 | 0.60 |
| 150_T | 154_I | 1.056 | 0.60 |
| 129_Y | 132_D | 1.056 | 0.60 |
| 68_N | 340_Y | 1.056 | 0.60 |
| 330_K | 349_P | 1.055 | 0.60 |
| 306_L | 309_L | 1.055 | 0.60 |
| 188_P | 196_M | 1.055 | 0.60 |
| 144_L | 168_D | 1.054 | 0.60 |
| 46_D | 49_T | 1.052 | 0.59 |
| 334_H | 337_I | 1.051 | 0.59 |
| 42_K | 46_D | 1.050 | 0.59 |
| 203_F | 210_W | 1.048 | 0.59 |
| 193_V | 207_L | 1.046 | 0.59 |
| 195_R | 213_S | 1.033 | 0.57 |
| 60_A | 63_V | 1.031 | 0.57 |
| 319_Q | 323_E | 1.031 | 0.57 |
| 238_Y | 241_Y | 1.030 | 0.57 |
| 91_P | 96_C | 1.028 | 0.57 |
| 3_A | 8_V | 1.028 | 0.57 |
| 162_R | 172_F | 1.028 | 0.57 |
| 328_I | 332_Q | 1.027 | 0.57 |
| 174_L | 193_V | 1.027 | 0.57 |
| 340_Y | 349_P | 1.025 | 0.56 |
| 61_P | 75_F | 1.025 | 0.56 |
| 175_R | 187_G | 1.023 | 0.56 |
| 60_A | 84_M | 1.021 | 0.56 |
| 333_R | 350_F | 1.021 | 0.56 |
| 240_S | 243_T | 1.020 | 0.56 |
| 315_N | 318_F | 1.020 | 0.56 |
| 214_F | 218_K | 1.018 | 0.56 |
| 126_A | 146_V | 1.017 | 0.56 |
| 4_F | 7_K | 1.017 | 0.56 |
| 322_Q | 326_D | 1.014 | 0.55 |
| 241_Y | 300_L | 1.014 | 0.55 |
| 119_E | 123_M | 1.011 | 0.55 |
| 29_F | 33_L | 1.010 | 0.55 |
| 5_L | 11_G | 1.009 | 0.55 |
| 194_K | 200_V | 1.009 | 0.55 |
| 177_M | 180_F | 1.006 | 0.54 |
| 42_K | 48_G | 1.005 | 0.54 |
| 181_T | 184_K | 1.004 | 0.54 |
| 316_Y | 325_T | 1.003 | 0.54 |
| 169_F | 193_V | 1.002 | 0.54 |
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 | |
| 3j9pD | 4 | 0.7143 | 100 | 0.535 | Contact Map |
| 3j5pB | 4 | 0.84 | 100 | 0.567 | Contact Map |
| 4dxwA | 4 | 0.6371 | 99.7 | 0.781 | Contact Map |
| 3rvyA | 2 | 0.6114 | 99.6 | 0.805 | Contact Map |
| 4bgnA | 2 | 0.6029 | 99.6 | 0.813 | Contact Map |
| 3behA | 4 | 0.6343 | 98.7 | 0.872 | Contact Map |
| 2r9rB | 2 | 0.7743 | 98.4 | 0.884 | Contact Map |
| 4ltoA | 4 | 0.3457 | 97.2 | 0.911 | Contact Map |
| 1orqC | 1 | 0.6143 | 96.7 | 0.918 | Contact Map |
| 4cbcA | 4 | 0.2629 | 96.1 | 0.922 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)