| iqgap1 962-1345 |
| ID: | 1492718019 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 384 (376) | ||
| Sequences: | 867 (559.1) | ||
| Seq/Len: | 2.306 | ||
| Nf(neff/√len): | 28.8 |
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: 2.306).
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 |
| 280_F | 291_N | 3.212 | 1.00 |
| 103_G | 234_Y | 2.872 | 1.00 |
| 87_N | 92_K | 2.275 | 1.00 |
| 117_E | 183_K | 2.243 | 1.00 |
| 243_D | 261_R | 2.189 | 1.00 |
| 267_I | 271_L | 1.906 | 0.99 |
| 364_H | 367_L | 1.897 | 0.99 |
| 293_Y | 297_S | 1.847 | 0.99 |
| 281_L | 286_H | 1.706 | 0.97 |
| 85_T | 269_K | 1.684 | 0.97 |
| 284_N | 287_L | 1.655 | 0.96 |
| 276_S | 283_D | 1.604 | 0.96 |
| 238_A | 242_P | 1.586 | 0.95 |
| 127_K | 262_R | 1.585 | 0.95 |
| 115_V | 235_M | 1.557 | 0.95 |
| 181_T | 293_Y | 1.543 | 0.94 |
| 114_V | 184_F | 1.518 | 0.94 |
| 367_L | 370_L | 1.501 | 0.93 |
| 237_P | 242_P | 1.476 | 0.92 |
| 272_Q | 276_S | 1.469 | 0.92 |
| 262_R | 266_S | 1.463 | 0.92 |
| 324_S | 327_V | 1.459 | 0.92 |
| 184_F | 267_I | 1.455 | 0.92 |
| 29_I | 38_T | 1.453 | 0.91 |
| 262_R | 269_K | 1.449 | 0.91 |
| 312_P | 316_D | 1.442 | 0.91 |
| 19_Q | 56_R | 1.441 | 0.91 |
| 242_P | 264_L | 1.420 | 0.90 |
| 238_A | 275_A | 1.417 | 0.90 |
| 233_R | 272_Q | 1.414 | 0.90 |
| 266_S | 284_N | 1.394 | 0.89 |
| 30_F | 34_Q | 1.378 | 0.88 |
| 142_E | 145_T | 1.375 | 0.88 |
| 356_A | 364_H | 1.352 | 0.87 |
| 266_S | 287_L | 1.346 | 0.87 |
| 87_N | 207_K | 1.343 | 0.86 |
| 33_P | 38_T | 1.342 | 0.86 |
| 142_E | 146_G | 1.338 | 0.86 |
| 19_Q | 24_Y | 1.336 | 0.86 |
| 228_N | 276_S | 1.319 | 0.85 |
| 272_Q | 275_A | 1.316 | 0.85 |
| 281_L | 291_N | 1.315 | 0.85 |
| 177_M | 264_L | 1.313 | 0.85 |
| 106_A | 191_S | 1.313 | 0.85 |
| 182_D | 293_Y | 1.308 | 0.84 |
| 23_T | 27_K | 1.306 | 0.84 |
| 182_D | 186_S | 1.295 | 0.84 |
| 184_F | 261_R | 1.294 | 0.84 |
| 269_K | 291_N | 1.270 | 0.82 |
| 145_T | 153_Y | 1.266 | 0.82 |
| 147_E | 152_P | 1.265 | 0.82 |
| 269_K | 276_S | 1.263 | 0.82 |
| 204_K | 309_C | 1.262 | 0.81 |
| 42_D | 88_P | 1.260 | 0.81 |
| 106_A | 206_L | 1.254 | 0.81 |
| 47_T | 336_I | 1.253 | 0.81 |
| 231_Y | 240_V | 1.252 | 0.81 |
| 72_E | 269_K | 1.244 | 0.80 |
| 85_T | 111_L | 1.240 | 0.80 |
| 362_P | 369_D | 1.235 | 0.80 |
| 77_V | 348_L | 1.234 | 0.79 |
| 271_L | 298_Y | 1.219 | 0.78 |
| 312_P | 317_K | 1.218 | 0.78 |
| 138_V | 142_E | 1.213 | 0.78 |
| 10_A | 181_T | 1.212 | 0.78 |
| 193_D | 366_L | 1.201 | 0.77 |
| 129_D | 132_D | 1.201 | 0.77 |
| 22_P | 28_L | 1.200 | 0.77 |
| 155_V | 160_A | 1.199 | 0.77 |
| 58_E | 97_F | 1.197 | 0.76 |
| 65_F | 239_I | 1.190 | 0.76 |
| 85_T | 237_P | 1.189 | 0.76 |
| 348_L | 352_Q | 1.188 | 0.76 |
| 176_N | 186_S | 1.188 | 0.76 |
| 180_V | 183_K | 1.186 | 0.76 |
| 284_N | 293_Y | 1.182 | 0.75 |
| 25_L | 29_I | 1.181 | 0.75 |
| 287_L | 291_N | 1.180 | 0.75 |
| 95_V | 227_G | 1.180 | 0.75 |
| 233_R | 269_K | 1.178 | 0.75 |
| 111_L | 236_N | 1.176 | 0.75 |
| 234_Y | 359_H | 1.176 | 0.75 |
| 99_R | 345_H | 1.175 | 0.75 |
| 36_K | 115_V | 1.175 | 0.75 |
| 63_R | 322_E | 1.173 | 0.74 |
| 63_R | 247_I | 1.172 | 0.74 |
| 85_T | 232_Y | 1.169 | 0.74 |
| 237_P | 275_A | 1.166 | 0.74 |
| 107_L | 234_Y | 1.165 | 0.74 |
| 170_L | 174_I | 1.165 | 0.74 |
| 197_Y | 318_F | 1.165 | 0.74 |
| 198_G | 204_K | 1.163 | 0.74 |
| 268_A | 274_A | 1.160 | 0.73 |
| 305_F | 308_A | 1.159 | 0.73 |
| 229_L | 247_I | 1.159 | 0.73 |
| 207_K | 309_C | 1.158 | 0.73 |
| 227_G | 305_F | 1.156 | 0.73 |
| 19_Q | 28_L | 1.150 | 0.72 |
| 269_K | 272_Q | 1.148 | 0.72 |
| 93_M | 268_A | 1.144 | 0.72 |
| 142_E | 149_S | 1.143 | 0.72 |
| 118_I | 122_K | 1.141 | 0.71 |
| 195_I | 199_M | 1.141 | 0.71 |
| 109_Q | 267_I | 1.140 | 0.71 |
| 339_G | 342_I | 1.140 | 0.71 |
| 361_D | 369_D | 1.139 | 0.71 |
| 193_D | 307_T | 1.139 | 0.71 |
| 147_E | 150_K | 1.138 | 0.71 |
| 367_L | 373_V | 1.138 | 0.71 |
| 5_R | 150_K | 1.130 | 0.70 |
| 232_Y | 272_Q | 1.129 | 0.70 |
| 15_F | 19_Q | 1.125 | 0.70 |
| 105_N | 109_Q | 1.121 | 0.70 |
| 200_R | 311_V | 1.120 | 0.69 |
| 56_R | 332_P | 1.116 | 0.69 |
| 188_I | 274_A | 1.113 | 0.69 |
| 239_I | 261_R | 1.110 | 0.68 |
| 19_Q | 57_E | 1.106 | 0.68 |
| 29_I | 32_M | 1.103 | 0.68 |
| 273_H | 287_L | 1.101 | 0.68 |
| 103_G | 107_L | 1.100 | 0.67 |
| 228_N | 232_Y | 1.096 | 0.67 |
| 266_S | 269_K | 1.093 | 0.67 |
| 181_T | 199_M | 1.092 | 0.67 |
| 238_A | 268_A | 1.091 | 0.67 |
| 133_I | 178_R | 1.088 | 0.66 |
| 20_T | 323_Y | 1.088 | 0.66 |
| 69_L | 206_L | 1.084 | 0.66 |
| 8_L | 12_Q | 1.082 | 0.66 |
| 214_F | 227_G | 1.080 | 0.65 |
| 56_R | 60_L | 1.080 | 0.65 |
| 87_N | 107_L | 1.077 | 0.65 |
| 57_E | 60_L | 1.076 | 0.65 |
| 129_D | 294_L | 1.075 | 0.65 |
| 19_Q | 133_I | 1.075 | 0.65 |
| 212_E | 308_A | 1.074 | 0.65 |
| 364_H | 370_L | 1.071 | 0.64 |
| 4_K | 157_P | 1.071 | 0.64 |
| 137_W | 151_L | 1.070 | 0.64 |
| 87_N | 275_A | 1.069 | 0.64 |
| 50_N | 97_F | 1.068 | 0.64 |
| 54_N | 325_D | 1.063 | 0.64 |
| 54_N | 337_S | 1.062 | 0.63 |
| 185_L | 227_G | 1.061 | 0.63 |
| 232_Y | 273_H | 1.054 | 0.63 |
| 51_Y | 58_E | 1.054 | 0.63 |
| 232_Y | 283_D | 1.053 | 0.63 |
| 297_S | 300_K | 1.051 | 0.62 |
| 19_Q | 134_Y | 1.051 | 0.62 |
| 302_R | 310_D | 1.050 | 0.62 |
| 137_W | 153_Y | 1.049 | 0.62 |
| 238_A | 264_L | 1.049 | 0.62 |
| 62_L | 201_F | 1.049 | 0.62 |
| 22_P | 27_K | 1.047 | 0.62 |
| 13_H | 206_L | 1.047 | 0.62 |
| 154_D | 158_E | 1.045 | 0.62 |
| 345_H | 371_G | 1.045 | 0.62 |
| 266_S | 286_H | 1.045 | 0.62 |
| 261_R | 264_L | 1.044 | 0.62 |
| 148_A | 366_L | 1.042 | 0.61 |
| 301_F | 331_K | 1.041 | 0.61 |
| 233_R | 345_H | 1.040 | 0.61 |
| 206_L | 305_F | 1.039 | 0.61 |
| 239_I | 374_P | 1.038 | 0.61 |
| 138_V | 165_E | 1.037 | 0.61 |
| 151_L | 163_H | 1.035 | 0.61 |
| 110_I | 234_Y | 1.035 | 0.61 |
| 145_T | 149_S | 1.033 | 0.60 |
| 61_L | 321_D | 1.032 | 0.60 |
| 106_A | 144_Q | 1.032 | 0.60 |
| 282_G | 285_A | 1.030 | 0.60 |
| 273_H | 276_S | 1.030 | 0.60 |
| 85_T | 228_N | 1.030 | 0.60 |
| 103_G | 272_Q | 1.029 | 0.60 |
| 65_F | 73_I | 1.029 | 0.60 |
| 188_I | 239_I | 1.028 | 0.60 |
| 69_L | 243_D | 1.027 | 0.60 |
| 44_V | 366_L | 1.025 | 0.59 |
| 138_V | 145_T | 1.022 | 0.59 |
| 230_L | 270_M | 1.022 | 0.59 |
| 73_I | 111_L | 1.022 | 0.59 |
| 145_T | 151_L | 1.021 | 0.59 |
| 291_N | 294_L | 1.020 | 0.59 |
| 127_K | 136_S | 1.020 | 0.59 |
| 273_H | 283_D | 1.020 | 0.59 |
| 191_S | 233_R | 1.018 | 0.59 |
| 182_D | 331_K | 1.016 | 0.58 |
| 287_L | 297_S | 1.016 | 0.58 |
| 277_N | 342_I | 1.015 | 0.58 |
| 274_A | 293_Y | 1.015 | 0.58 |
| 103_G | 269_K | 1.014 | 0.58 |
| 145_T | 150_K | 1.014 | 0.58 |
| 231_Y | 272_Q | 1.013 | 0.58 |
| 115_V | 177_M | 1.012 | 0.58 |
| 243_D | 266_S | 1.011 | 0.58 |
| 44_V | 65_F | 1.010 | 0.58 |
| 9_E | 258_T | 1.009 | 0.58 |
| 364_H | 372_E | 1.007 | 0.57 |
| 6_E | 154_D | 1.003 | 0.57 |
| 222_L | 226_I | 1.002 | 0.57 |
| 95_V | 347_L | 1.000 | 0.57 |
| 82_E | 265_G | 1.000 | 0.57 |
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 | |
| 3fayA | 1 | 0.9844 | 100 | 0.062 | Contact Map |
| 1nf1A | 1 | 0.6536 | 100 | 0.299 | Contact Map |
| 3bxjA | 2 | 0.8203 | 100 | 0.327 | Contact Map |
| 1werA | 1 | 0.8125 | 100 | 0.329 | Contact Map |
| 4m8nA | 4 | 0.901 | 73.2 | 0.953 | Contact Map |
| 1o3xA | 1 | 0.2578 | 25.8 | 0.965 | Contact Map |
| 3hm6X | 1 | 0.7708 | 18.8 | 0.967 | Contact Map |
| 1oxzA | 1 | 0.2552 | 14 | 0.969 | Contact Map |
| 1nafA | 1 | 0.237 | 13.3 | 0.97 | Contact Map |
| 3ig3A | 1 | 0.7812 | 11.6 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)