| 1CSH |
| ID: | 1411604667 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 435 (406) | ||
| Sequences: | 1756 (870.6) | ||
| Seq/Len: | 4.325 | ||
| Nf(neff/√len): | 43.2 |
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: 4.325).
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 |
| 249_V | 262_A | 6.815 | 1.00 |
| 246_S | 263_A | 3.862 | 1.00 |
| 68_S | 71_E | 3.343 | 1.00 |
| 98_Q | 104_Q | 3.307 | 1.00 |
| 102_P | 106_S | 3.090 | 1.00 |
| 306_T | 311_R | 2.910 | 1.00 |
| 249_V | 266_G | 2.846 | 1.00 |
| 284_S | 381_Q | 2.545 | 1.00 |
| 350_Q | 353_K | 2.467 | 1.00 |
| 209_H | 223_T | 2.454 | 1.00 |
| 245_T | 266_G | 2.395 | 1.00 |
| 210_N | 214_M | 2.345 | 1.00 |
| 298_K | 301_D | 2.308 | 1.00 |
| 241_V | 252_A | 2.307 | 1.00 |
| 206_D | 209_H | 2.269 | 1.00 |
| 252_A | 266_G | 2.253 | 1.00 |
| 248_L | 418_E | 2.237 | 1.00 |
| 101_T | 104_Q | 2.185 | 1.00 |
| 89_G | 105_V | 2.166 | 1.00 |
| 206_D | 223_T | 2.106 | 1.00 |
| 229_Y | 380_L | 2.020 | 1.00 |
| 205_L | 209_H | 2.015 | 1.00 |
| 143_I | 264_M | 1.993 | 1.00 |
| 336_L | 349_A | 1.985 | 1.00 |
| 86_L | 105_V | 1.977 | 1.00 |
| 140_S | 265_N | 1.955 | 1.00 |
| 95_V | 177_I | 1.945 | 1.00 |
| 222_F | 383_Y | 1.929 | 1.00 |
| 88_E | 112_W | 1.919 | 1.00 |
| 348_V | 378_V | 1.914 | 1.00 |
| 134_H | 277_Q | 1.902 | 1.00 |
| 300_R | 350_Q | 1.893 | 1.00 |
| 254_S | 268_A | 1.864 | 1.00 |
| 44_R | 416_P | 1.860 | 1.00 |
| 335_A | 378_V | 1.838 | 1.00 |
| 184_A | 397_V | 1.789 | 1.00 |
| 140_S | 144_T | 1.779 | 1.00 |
| 385_M | 394_L | 1.763 | 1.00 |
| 141_A | 144_T | 1.745 | 0.99 |
| 277_Q | 281_L | 1.737 | 0.99 |
| 189_R | 196_S | 1.721 | 0.99 |
| 208_S | 227_R | 1.706 | 0.99 |
| 124_T | 127_D | 1.685 | 0.99 |
| 241_V | 266_G | 1.679 | 0.99 |
| 67_F | 98_Q | 1.679 | 0.99 |
| 91_F | 401_L | 1.669 | 0.99 |
| 301_D | 305_N | 1.646 | 0.99 |
| 215_L | 385_M | 1.629 | 0.99 |
| 224_E | 227_R | 1.604 | 0.99 |
| 302_Y | 306_T | 1.579 | 0.99 |
| 173_A | 404_L | 1.577 | 0.99 |
| 262_A | 266_G | 1.576 | 0.99 |
| 350_Q | 354_I | 1.574 | 0.99 |
| 258_L | 268_A | 1.569 | 0.99 |
| 44_R | 319_A | 1.544 | 0.98 |
| 92_W | 98_Q | 1.536 | 0.98 |
| 184_A | 393_V | 1.520 | 0.98 |
| 245_T | 249_V | 1.514 | 0.98 |
| 303_I | 355_V | 1.511 | 0.98 |
| 234_S | 401_L | 1.508 | 0.98 |
| 229_Y | 331_Q | 1.490 | 0.98 |
| 180_L | 400_A | 1.488 | 0.98 |
| 142_A | 183_V | 1.473 | 0.98 |
| 305_N | 309_S | 1.469 | 0.98 |
| 64_F | 234_S | 1.459 | 0.97 |
| 253_L | 271_L | 1.458 | 0.97 |
| 296_D | 353_K | 1.447 | 0.97 |
| 193_R | 389_N | 1.429 | 0.97 |
| 21_T | 25_Q | 1.429 | 0.97 |
| 103_E | 106_S | 1.428 | 0.97 |
| 139_L | 184_A | 1.422 | 0.97 |
| 276_N | 373_D | 1.420 | 0.97 |
| 185_A | 211_F | 1.413 | 0.97 |
| 233_H | 372_V | 1.403 | 0.97 |
| 410_S | 414_G | 1.391 | 0.96 |
| 106_S | 109_S | 1.389 | 0.96 |
| 333_E | 337_K | 1.386 | 0.96 |
| 119_P | 130_P | 1.375 | 0.96 |
| 182_C | 201_I | 1.367 | 0.96 |
| 90_L | 231_T | 1.361 | 0.96 |
| 205_L | 210_N | 1.360 | 0.96 |
| 67_F | 99_I | 1.357 | 0.96 |
| 250_G | 407_L | 1.354 | 0.96 |
| 304_W | 308_N | 1.349 | 0.95 |
| 140_S | 261_A | 1.337 | 0.95 |
| 58_P | 61_G | 1.333 | 0.95 |
| 300_R | 357_N | 1.328 | 0.95 |
| 136_M | 276_N | 1.327 | 0.95 |
| 118_L | 186_K | 1.325 | 0.95 |
| 106_S | 110_K | 1.320 | 0.95 |
| 342_D | 381_Q | 1.301 | 0.94 |
| 83_E | 333_E | 1.292 | 0.94 |
| 250_G | 259_S | 1.286 | 0.94 |
| 331_Q | 372_V | 1.271 | 0.93 |
| 245_T | 262_A | 1.267 | 0.93 |
| 313_V | 366_K | 1.267 | 0.93 |
| 303_I | 354_I | 1.266 | 0.93 |
| 291_G | 298_K | 1.266 | 0.93 |
| 224_E | 228_L | 1.264 | 0.93 |
| 286_L | 302_Y | 1.248 | 0.92 |
| 70_P | 329_T | 1.247 | 0.92 |
| 335_A | 348_V | 1.238 | 0.92 |
| 115_R | 175_D | 1.235 | 0.92 |
| 243_A | 247_H | 1.231 | 0.92 |
| 112_W | 174_M | 1.220 | 0.91 |
| 233_H | 276_N | 1.218 | 0.91 |
| 332_R | 336_L | 1.212 | 0.91 |
| 353_K | 361_E | 1.210 | 0.91 |
| 199_G | 213_N | 1.207 | 0.90 |
| 125_M | 145_A | 1.207 | 0.90 |
| 124_T | 128_N | 1.203 | 0.90 |
| 62_I | 409_W | 1.201 | 0.90 |
| 85_P | 89_G | 1.198 | 0.90 |
| 76_L | 231_T | 1.197 | 0.90 |
| 116_A | 207_W | 1.195 | 0.90 |
| 237_E | 421_K | 1.193 | 0.90 |
| 123_V | 186_K | 1.184 | 0.89 |
| 280_L | 391_Y | 1.183 | 0.89 |
| 120_S | 124_T | 1.181 | 0.89 |
| 208_S | 226_M | 1.181 | 0.89 |
| 126_L | 142_A | 1.179 | 0.89 |
| 304_W | 361_E | 1.176 | 0.89 |
| 286_L | 306_T | 1.175 | 0.89 |
| 65_R | 97_G | 1.171 | 0.89 |
| 201_I | 214_M | 1.170 | 0.89 |
| 249_V | 259_S | 1.167 | 0.88 |
| 64_F | 231_T | 1.166 | 0.88 |
| 304_W | 362_Q | 1.157 | 0.88 |
| 138_Q | 187_I | 1.154 | 0.88 |
| 125_M | 128_N | 1.153 | 0.88 |
| 205_L | 223_T | 1.149 | 0.87 |
| 237_E | 368_P | 1.149 | 0.87 |
| 111_E | 174_M | 1.146 | 0.87 |
| 116_A | 203_S | 1.144 | 0.87 |
| 398_S | 401_L | 1.140 | 0.87 |
| 95_V | 404_L | 1.136 | 0.87 |
| 111_E | 171_E | 1.136 | 0.87 |
| 270_P | 351_L | 1.130 | 0.86 |
| 54_S | 235_D | 1.124 | 0.86 |
| 96_T | 170_Y | 1.117 | 0.85 |
| 233_H | 376_S | 1.114 | 0.85 |
| 230_L | 397_V | 1.114 | 0.85 |
| 264_M | 396_G | 1.114 | 0.85 |
| 17_A | 21_T | 1.109 | 0.85 |
| 180_L | 183_V | 1.106 | 0.85 |
| 168_F | 172_D | 1.105 | 0.84 |
| 255_D | 268_A | 1.103 | 0.84 |
| 332_R | 352_Y | 1.101 | 0.84 |
| 111_E | 115_R | 1.096 | 0.84 |
| 267_L | 276_N | 1.093 | 0.84 |
| 296_D | 350_Q | 1.093 | 0.84 |
| 324_T | 329_T | 1.089 | 0.83 |
| 372_V | 376_S | 1.075 | 0.82 |
| 297_E | 301_D | 1.074 | 0.82 |
| 115_R | 174_M | 1.072 | 0.82 |
| 85_P | 227_R | 1.069 | 0.82 |
| 126_L | 187_I | 1.067 | 0.81 |
| 224_E | 337_K | 1.059 | 0.81 |
| 17_A | 26_H | 1.058 | 0.81 |
| 172_D | 256_P | 1.056 | 0.81 |
| 143_I | 180_L | 1.055 | 0.80 |
| 93_L | 99_I | 1.054 | 0.80 |
| 229_Y | 233_H | 1.048 | 0.80 |
| 285_Q | 311_R | 1.047 | 0.80 |
| 94_L | 401_L | 1.047 | 0.80 |
| 92_W | 104_Q | 1.035 | 0.79 |
| 239_G | 421_K | 1.034 | 0.79 |
| 143_I | 176_L | 1.034 | 0.79 |
| 256_P | 404_L | 1.032 | 0.78 |
| 280_L | 291_G | 1.031 | 0.78 |
| 64_F | 97_G | 1.031 | 0.78 |
| 202_D | 205_L | 1.030 | 0.78 |
| 282_W | 306_T | 1.028 | 0.78 |
| 122_V | 125_M | 1.028 | 0.78 |
| 92_W | 108_V | 1.024 | 0.78 |
| 226_M | 394_L | 1.014 | 0.77 |
| 296_D | 347_L | 1.010 | 0.76 |
| 20_K | 25_Q | 1.007 | 0.76 |
| 300_R | 361_E | 1.004 | 0.76 |
| 43_M | 46_M | 1.003 | 0.76 |
| 136_M | 267_L | 1.003 | 0.76 |
| 260_F | 400_A | 1.002 | 0.75 |
| 20_K | 24_Q | 1.001 | 0.75 |
| 295_S | 343_P | 1.000 | 0.75 |
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 | |
| 1cshA | 1 | 1 | 100 | 0.099 | Contact Map |
| 2ibpA | 2 | 0.9011 | 100 | 0.225 | Contact Map |
| 2h12A | 6 | 0.9218 | 100 | 0.226 | Contact Map |
| 3l96A | 2 | 0.9195 | 100 | 0.242 | Contact Map |
| 3msuA | 2 | 0.9057 | 100 | 0.242 | Contact Map |
| 1iomA | 1 | 0.8391 | 100 | 0.245 | Contact Map |
| 2c6xA | 4 | 0.8276 | 100 | 0.246 | Contact Map |
| 1vgmA | 2 | 0.8368 | 100 | 0.246 | Contact Map |
| 1o7xA | 4 | 0.8322 | 100 | 0.251 | Contact Map |
| 1aj8A | 2 | 0.8345 | 100 | 0.252 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)