| KNL1_vertebrates -force run |
| ID: | 1517037681 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 451 (318) | ||
| Sequences: | 13121 (11921.2) | ||
| Seq/Len: | 41.261 | ||
| Nf(neff/√len): | 668.5 |
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: 41.261).
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 |
| 71_I | 74_L | 2.137 | 1.00 |
| 199_L | 202_L | 1.925 | 1.00 |
| 192_T | 195_A | 1.900 | 1.00 |
| 247_S | 250_D | 1.861 | 1.00 |
| 234_T | 238_E | 1.831 | 1.00 |
| 152_I | 156_D | 1.793 | 1.00 |
| 138_V | 142_Q | 1.782 | 1.00 |
| 145_R | 148_L | 1.760 | 1.00 |
| 152_I | 155_M | 1.736 | 1.00 |
| 159_L | 162_I | 1.733 | 1.00 |
| 206_E | 209_F | 1.724 | 1.00 |
| 215_E | 219_Q | 1.723 | 1.00 |
| 166_L | 169_V | 1.709 | 1.00 |
| 138_V | 141_A | 1.708 | 1.00 |
| 173_T | 177_E | 1.685 | 1.00 |
| 254_W | 257_D | 1.665 | 1.00 |
| 145_R | 149_Q | 1.656 | 1.00 |
| 227_I | 230_M | 1.642 | 1.00 |
| 78_A | 81_Q | 1.627 | 1.00 |
| 227_I | 231_Q | 1.602 | 1.00 |
| 66_A | 70_K | 1.597 | 1.00 |
| 234_T | 237_T | 1.590 | 1.00 |
| 199_L | 203_K | 1.564 | 1.00 |
| 229_F | 233_Q | 1.538 | 1.00 |
| 159_L | 163_D | 1.533 | 1.00 |
| 236_R | 240_L | 1.525 | 1.00 |
| 64_C | 67_R | 1.520 | 1.00 |
| 213_L | 216_L | 1.519 | 1.00 |
| 247_S | 251_V | 1.510 | 1.00 |
| 220_K | 224_L | 1.494 | 1.00 |
| 226_Q | 229_F | 1.492 | 1.00 |
| 207_E | 211_R | 1.490 | 1.00 |
| 194_T | 198_E | 1.481 | 1.00 |
| 108_G | 112_N | 1.470 | 1.00 |
| 80_N | 84_L | 1.465 | 1.00 |
| 351_C | 354_L | 1.443 | 1.00 |
| 187_E | 191_E | 1.440 | 1.00 |
| 57_I | 60_Y | 1.437 | 1.00 |
| 167_I | 170_E | 1.436 | 1.00 |
| 131_V | 134_Y | 1.431 | 1.00 |
| 225_A | 229_F | 1.428 | 1.00 |
| 73_E | 77_S | 1.417 | 1.00 |
| 104_L | 108_G | 1.407 | 0.99 |
| 124_V | 128_Q | 1.404 | 0.99 |
| 192_T | 196_E | 1.398 | 0.99 |
| 63_D | 68_R | 1.389 | 0.99 |
| 70_K | 75_K | 1.384 | 0.99 |
| 112_N | 116_S | 1.382 | 0.99 |
| 172_E | 177_E | 1.374 | 0.99 |
| 64_C | 68_R | 1.370 | 0.99 |
| 257_D | 260_V | 1.368 | 0.99 |
| 233_Q | 238_E | 1.365 | 0.99 |
| 134_Y | 138_V | 1.361 | 0.99 |
| 185_V | 188_W | 1.357 | 0.99 |
| 158_I | 161_K | 1.354 | 0.99 |
| 172_E | 175_N | 1.349 | 0.99 |
| 222_Q | 226_Q | 1.348 | 0.99 |
| 214_L | 218_V | 1.345 | 0.99 |
| 147_K | 151_K | 1.343 | 0.99 |
| 79_S | 82_D | 1.336 | 0.99 |
| 235_N | 239_E | 1.335 | 0.99 |
| 347_V | 351_C | 1.332 | 0.99 |
| 166_L | 170_E | 1.316 | 0.99 |
| 173_T | 176_L | 1.315 | 0.99 |
| 163_D | 167_I | 1.315 | 0.99 |
| 76_L | 80_N | 1.314 | 0.99 |
| 175_N | 179_E | 1.314 | 0.99 |
| 161_K | 165_C | 1.308 | 0.99 |
| 220_K | 223_T | 1.304 | 0.99 |
| 201_Q | 205_E | 1.303 | 0.99 |
| 183_N | 187_E | 1.302 | 0.99 |
| 185_V | 189_D | 1.300 | 0.99 |
| 68_R | 72_E | 1.300 | 0.99 |
| 221_E | 225_A | 1.297 | 0.99 |
| 200_E | 203_K | 1.296 | 0.99 |
| 193_R | 196_E | 1.292 | 0.99 |
| 58_Q | 62_Q | 1.292 | 0.99 |
| 260_V | 265_Y | 1.291 | 0.99 |
| 223_T | 227_I | 1.285 | 0.99 |
| 209_F | 213_L | 1.280 | 0.99 |
| 213_L | 217_E | 1.279 | 0.99 |
| 74_L | 78_A | 1.271 | 0.99 |
| 207_E | 210_Q | 1.252 | 0.99 |
| 127_H | 131_V | 1.250 | 0.99 |
| 228_D | 232_K | 1.239 | 0.98 |
| 143_N | 147_K | 1.236 | 0.98 |
| 94_E | 98_H | 1.234 | 0.98 |
| 204_T | 208_E | 1.230 | 0.98 |
| 259_A | 263_F | 1.229 | 0.98 |
| 253_E | 256_D | 1.228 | 0.98 |
| 239_E | 243_Q | 1.226 | 0.98 |
| 136_K | 140_S | 1.222 | 0.98 |
| 212_N | 217_E | 1.222 | 0.98 |
| 132_A | 136_K | 1.217 | 0.98 |
| 169_V | 173_T | 1.217 | 0.98 |
| 63_D | 66_A | 1.209 | 0.98 |
| 226_Q | 231_Q | 1.208 | 0.98 |
| 78_A | 82_D | 1.207 | 0.98 |
| 132_A | 135_G | 1.204 | 0.98 |
| 79_S | 83_K | 1.204 | 0.98 |
| 186_E | 189_D | 1.201 | 0.98 |
| 56_K | 60_Y | 1.200 | 0.98 |
| 124_V | 127_H | 1.199 | 0.98 |
| 193_R | 197_K | 1.194 | 0.98 |
| 154_E | 158_I | 1.190 | 0.98 |
| 206_E | 210_Q | 1.186 | 0.98 |
| 151_K | 154_E | 1.186 | 0.98 |
| 109_I | 113_K | 1.183 | 0.98 |
| 59_I | 63_D | 1.175 | 0.98 |
| 241_L | 244_L | 1.174 | 0.98 |
| 72_E | 75_K | 1.170 | 0.97 |
| 111_L | 115_K | 1.168 | 0.97 |
| 231_Q | 235_N | 1.168 | 0.97 |
| 141_A | 145_R | 1.168 | 0.97 |
| 197_K | 201_Q | 1.162 | 0.97 |
| 235_N | 238_E | 1.156 | 0.97 |
| 144_E | 149_Q | 1.156 | 0.97 |
| 350_H | 353_L | 1.154 | 0.97 |
| 77_S | 80_N | 1.149 | 0.97 |
| 70_K | 73_E | 1.146 | 0.97 |
| 261_F | 264_V | 1.141 | 0.97 |
| 174_K | 177_E | 1.140 | 0.97 |
| 363_T | 366_P | 1.135 | 0.97 |
| 128_Q | 132_A | 1.133 | 0.97 |
| 168_E | 172_E | 1.132 | 0.97 |
| 139_Q | 143_N | 1.129 | 0.97 |
| 156_D | 160_K | 1.129 | 0.97 |
| 60_Y | 64_C | 1.126 | 0.97 |
| 134_Y | 137_L | 1.126 | 0.97 |
| 221_E | 224_L | 1.125 | 0.97 |
| 70_K | 74_L | 1.125 | 0.97 |
| 195_A | 199_L | 1.121 | 0.97 |
| 189_D | 193_R | 1.121 | 0.97 |
| 240_L | 245_S | 1.119 | 0.96 |
| 357_E | 360_Y | 1.118 | 0.96 |
| 106_A | 110_Y | 1.117 | 0.96 |
| 350_H | 355_G | 1.115 | 0.96 |
| 139_Q | 142_Q | 1.115 | 0.96 |
| 344_F | 347_V | 1.112 | 0.96 |
| 146_E | 149_Q | 1.112 | 0.96 |
| 162_I | 166_L | 1.109 | 0.96 |
| 208_E | 212_N | 1.109 | 0.96 |
| 155_M | 159_L | 1.109 | 0.96 |
| 249_W | 253_E | 1.109 | 0.96 |
| 148_L | 152_I | 1.108 | 0.96 |
| 345_S | 349_N | 1.103 | 0.96 |
| 56_K | 59_I | 1.103 | 0.96 |
| 165_C | 168_E | 1.102 | 0.96 |
| 184_L | 187_E | 1.102 | 0.96 |
| 174_K | 178_D | 1.101 | 0.96 |
| 358_I | 361_L | 1.099 | 0.96 |
| 167_I | 171_I | 1.098 | 0.96 |
| 198_E | 203_K | 1.096 | 0.96 |
| 72_E | 76_L | 1.090 | 0.96 |
| 224_L | 228_D | 1.090 | 0.96 |
| 44_E | 48_L | 1.088 | 0.96 |
| 126_T | 130_K | 1.088 | 0.96 |
| 203_K | 207_E | 1.088 | 0.96 |
| 186_E | 190_S | 1.088 | 0.96 |
| 182_D | 186_E | 1.085 | 0.96 |
| 246_V | 250_D | 1.082 | 0.96 |
| 69_Q | 73_E | 1.078 | 0.95 |
| 58_Q | 61_R | 1.071 | 0.95 |
| 125_F | 128_Q | 1.069 | 0.95 |
| 352_R | 356_E | 1.068 | 0.95 |
| 171_I | 175_N | 1.064 | 0.95 |
| 140_S | 144_E | 1.064 | 0.95 |
| 144_E | 147_K | 1.064 | 0.95 |
| 202_L | 205_E | 1.062 | 0.95 |
| 219_Q | 222_Q | 1.058 | 0.95 |
| 184_L | 189_D | 1.054 | 0.95 |
| 347_V | 350_H | 1.053 | 0.95 |
| 214_L | 217_E | 1.053 | 0.95 |
| 238_E | 242_D | 1.052 | 0.95 |
| 256_D | 260_V | 1.051 | 0.94 |
| 135_G | 139_Q | 1.051 | 0.94 |
| 61_R | 65_E | 1.051 | 0.94 |
| 342_Q | 346_L | 1.051 | 0.94 |
| 230_M | 234_T | 1.051 | 0.94 |
| 157_K | 160_K | 1.051 | 0.94 |
| 130_K | 133_L | 1.050 | 0.94 |
| 252_V | 256_D | 1.050 | 0.94 |
| 209_F | 212_N | 1.048 | 0.94 |
| 149_Q | 153_D | 1.045 | 0.94 |
| 74_L | 77_S | 1.041 | 0.94 |
| 334_Q | 338_P | 1.035 | 0.94 |
| 205_E | 210_Q | 1.032 | 0.94 |
| 212_N | 215_E | 1.031 | 0.94 |
| 260_V | 263_F | 1.031 | 0.94 |
| 55_P | 58_Q | 1.030 | 0.94 |
| 223_T | 226_Q | 1.029 | 0.94 |
| 205_E | 208_E | 1.027 | 0.94 |
| 81_Q | 84_L | 1.026 | 0.94 |
| 78_A | 85_L | 1.024 | 0.93 |
| 360_Y | 364_W | 1.018 | 0.93 |
| 262_T | 266_D | 1.015 | 0.93 |
| 125_F | 129_G | 1.014 | 0.93 |
| 198_E | 201_Q | 1.012 | 0.93 |
| 111_L | 114_I | 1.003 | 0.93 |
| 83_K | 87_D | 1.003 | 0.93 |
| 77_S | 82_D | 1.002 | 0.92 |
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 | |
| 4nfaA | 1 | 0.4501 | 99.6 | 0.666 | Contact Map |
| 1i84S | 2 | 0.2616 | 98.9 | 0.77 | Contact Map |
| 3vkgA | 2 | 0.9512 | 98.4 | 0.809 | Contact Map |
| 1c1gA | 4 | 0.6297 | 98.2 | 0.817 | Contact Map |
| 2dfsA | 2 | 0.3902 | 97.1 | 0.854 | Contact Map |
| 4uxvA | 1 | 0.8115 | 97 | 0.856 | Contact Map |
| 2v71A | 2 | 0.3548 | 96.6 | 0.864 | Contact Map |
| 4linA | 12 | 0.6098 | 96.4 | 0.867 | Contact Map |
| 3tnuB | 1 | 0.2106 | 96.2 | 0.87 | Contact Map |
| 3tnuA | 1 | 0.1996 | 96.1 | 0.87 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)