| gremlindata enrich iter1 |
| ID: | 1412145799 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 310 (292) | ||
| Sequences: | 11978 (6406.2) | ||
| Seq/Len: | 41.021 | ||
| Nf(neff/√len): | 374.9 |
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: 41.021).
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 |
| 46_T | 82_A | 4.494 | 1.00 |
| 203_L | 207_R | 3.054 | 1.00 |
| 73_S | 156_W | 2.924 | 1.00 |
| 103_V | 107_I | 2.875 | 1.00 |
| 98_W | 101_G | 2.761 | 1.00 |
| 164_S | 168_L | 2.397 | 1.00 |
| 125_A | 155_V | 2.391 | 1.00 |
| 73_S | 122_H | 2.384 | 1.00 |
| 131_Y | 136_Q | 2.377 | 1.00 |
| 102_K | 106_G | 2.309 | 1.00 |
| 125_A | 151_I | 2.192 | 1.00 |
| 57_V | 72_V | 2.174 | 1.00 |
| 146_K | 150_C | 2.150 | 1.00 |
| 207_R | 210_Q | 2.148 | 1.00 |
| 110_A | 114_L | 2.141 | 1.00 |
| 33_A | 37_A | 2.137 | 1.00 |
| 114_L | 160_A | 1.994 | 1.00 |
| 283_N | 287_Y | 1.985 | 1.00 |
| 242_V | 286_I | 1.977 | 1.00 |
| 63_L | 68_N | 1.876 | 1.00 |
| 139_Y | 174_S | 1.837 | 1.00 |
| 129_D | 143_R | 1.823 | 1.00 |
| 54_V | 72_V | 1.818 | 1.00 |
| 131_Y | 135_T | 1.817 | 1.00 |
| 122_H | 152_I | 1.782 | 1.00 |
| 65_A | 68_N | 1.720 | 1.00 |
| 69_L | 152_I | 1.717 | 1.00 |
| 260_C | 263_Y | 1.712 | 1.00 |
| 205_Y | 208_I | 1.704 | 1.00 |
| 74_L | 78_D | 1.657 | 1.00 |
| 150_C | 154_I | 1.639 | 1.00 |
| 46_T | 281_S | 1.634 | 1.00 |
| 106_G | 171_D | 1.626 | 1.00 |
| 72_V | 76_T | 1.593 | 1.00 |
| 118_S | 159_S | 1.564 | 1.00 |
| 149_K | 153_V | 1.561 | 1.00 |
| 166_P | 169_S | 1.521 | 1.00 |
| 129_D | 133_S | 1.515 | 1.00 |
| 247_W | 276_G | 1.510 | 1.00 |
| 88_F | 92_N | 1.498 | 1.00 |
| 144_T | 147_R | 1.474 | 1.00 |
| 53_V | 288_T | 1.467 | 1.00 |
| 51_I | 79_I | 1.460 | 1.00 |
| 252_F | 256_L | 1.456 | 1.00 |
| 110_A | 167_L | 1.449 | 1.00 |
| 105_C | 177_C | 1.445 | 1.00 |
| 235_V | 290_F | 1.437 | 1.00 |
| 200_I | 204_V | 1.436 | 1.00 |
| 194_F | 198_C | 1.430 | 1.00 |
| 51_I | 55_I | 1.419 | 1.00 |
| 82_A | 86_M | 1.401 | 0.99 |
| 85_V | 89_S | 1.393 | 0.99 |
| 60_S | 297_A | 1.391 | 0.99 |
| 101_G | 104_W | 1.390 | 0.99 |
| 87_P | 90_L | 1.380 | 0.99 |
| 188_S | 192_A | 1.379 | 0.99 |
| 77_A | 119_S | 1.367 | 0.99 |
| 201_M | 205_Y | 1.354 | 0.99 |
| 76_T | 80_L | 1.349 | 0.99 |
| 47_V | 82_A | 1.345 | 0.99 |
| 232_F | 235_V | 1.343 | 0.99 |
| 190_S | 255_S | 1.326 | 0.99 |
| 206_I | 210_Q | 1.322 | 0.99 |
| 131_Y | 207_R | 1.315 | 0.99 |
| 132_W | 142_K | 1.313 | 0.99 |
| 237_A | 241_G | 1.306 | 0.99 |
| 117_T | 193_S | 1.301 | 0.99 |
| 133_S | 138_V | 1.300 | 0.99 |
| 133_S | 137_A | 1.295 | 0.99 |
| 151_I | 155_V | 1.291 | 0.99 |
| 278_C | 282_L | 1.269 | 0.99 |
| 202_I | 206_I | 1.263 | 0.99 |
| 86_M | 89_S | 1.261 | 0.99 |
| 121_V | 193_S | 1.254 | 0.99 |
| 248_F | 252_F | 1.252 | 0.99 |
| 70_F | 148_V | 1.250 | 0.99 |
| 120_I | 124_C | 1.249 | 0.99 |
| 53_V | 57_V | 1.247 | 0.99 |
| 244_V | 248_F | 1.243 | 0.98 |
| 77_A | 118_S | 1.235 | 0.98 |
| 84_L | 87_P | 1.228 | 0.98 |
| 297_A | 300_K | 1.223 | 0.98 |
| 75_A | 78_D | 1.220 | 0.98 |
| 194_F | 250_F | 1.215 | 0.98 |
| 47_V | 79_I | 1.211 | 0.98 |
| 54_V | 57_V | 1.199 | 0.98 |
| 121_V | 158_I | 1.198 | 0.98 |
| 85_V | 88_F | 1.197 | 0.98 |
| 84_L | 88_F | 1.190 | 0.98 |
| 73_S | 152_I | 1.180 | 0.98 |
| 34_S | 38_L | 1.179 | 0.98 |
| 57_V | 64_K | 1.174 | 0.98 |
| 286_I | 290_F | 1.170 | 0.97 |
| 184_W | 188_S | 1.169 | 0.97 |
| 194_F | 248_F | 1.160 | 0.97 |
| 265_I | 268_T | 1.157 | 0.97 |
| 44_L | 48_V | 1.155 | 0.97 |
| 139_Y | 173_I | 1.152 | 0.97 |
| 80_L | 115_F | 1.150 | 0.97 |
| 186_I | 189_S | 1.142 | 0.97 |
| 288_T | 291_N | 1.140 | 0.97 |
| 123_L | 201_M | 1.138 | 0.97 |
| 153_V | 157_L | 1.121 | 0.97 |
| 110_A | 160_A | 1.121 | 0.97 |
| 134_V | 138_V | 1.119 | 0.96 |
| 58_L | 72_V | 1.119 | 0.96 |
| 215_R | 219_I | 1.115 | 0.96 |
| 87_P | 91_A | 1.113 | 0.96 |
| 250_F | 254_Y | 1.111 | 0.96 |
| 90_L | 93_E | 1.111 | 0.96 |
| 113_V | 163_S | 1.110 | 0.96 |
| 207_R | 211_V | 1.103 | 0.96 |
| 119_S | 246_C | 1.102 | 0.96 |
| 194_F | 251_F | 1.102 | 0.96 |
| 233_T | 239_V | 1.100 | 0.96 |
| 201_M | 240_M | 1.094 | 0.96 |
| 120_I | 197_P | 1.092 | 0.96 |
| 143_R | 148_V | 1.091 | 0.96 |
| 49_G | 75_A | 1.088 | 0.96 |
| 52_L | 56_A | 1.084 | 0.96 |
| 216_K | 219_I | 1.081 | 0.95 |
| 69_L | 73_S | 1.079 | 0.95 |
| 229_E | 233_T | 1.078 | 0.95 |
| 209_Y | 233_T | 1.064 | 0.95 |
| 88_F | 104_W | 1.061 | 0.95 |
| 296_R | 299_Q | 1.056 | 0.95 |
| 209_Y | 213_K | 1.055 | 0.95 |
| 209_Y | 212_A | 1.053 | 0.95 |
| 54_V | 76_T | 1.052 | 0.95 |
| 71_L | 293_D | 1.052 | 0.95 |
| 111_L | 115_F | 1.051 | 0.94 |
| 238_V | 286_I | 1.050 | 0.94 |
| 56_A | 294_F | 1.041 | 0.94 |
| 53_V | 283_N | 1.040 | 0.94 |
| 60_S | 63_L | 1.032 | 0.94 |
| 19_A | 97_Y | 1.032 | 0.94 |
| 66_P | 70_F | 1.032 | 0.94 |
| 118_S | 122_H | 1.028 | 0.94 |
| 198_C | 244_V | 1.027 | 0.94 |
| 190_S | 195_F | 1.026 | 0.94 |
| 246_C | 249_P | 1.019 | 0.93 |
| 127_S | 236_L | 1.017 | 0.93 |
| 162_I | 165_P | 1.014 | 0.93 |
| 299_Q | 303_C | 1.013 | 0.93 |
| 280_S | 283_N | 1.010 | 0.93 |
| 122_H | 155_V | 1.008 | 0.93 |
| 34_S | 37_A | 1.007 | 0.93 |
| 89_S | 93_E | 1.007 | 0.93 |
| 54_V | 75_A | 1.006 | 0.93 |
| 156_W | 279_N | 1.003 | 0.93 |
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 | |
| 4iarA | 1 | 0.9 | 100 | 0.159 | Contact Map |
| 1u19A | 2 | 1 | 100 | 0.17 | Contact Map |
| 2r4rA | 1 | 0.6742 | 100 | 0.182 | Contact Map |
| 4buoA | 2 | 0.929 | 100 | 0.192 | Contact Map |
| 2rh1A | 1 | 0.8903 | 100 | 0.205 | Contact Map |
| 4bvnA | 1 | 0.8742 | 100 | 0.207 | Contact Map |
| 3uonA | 1 | 0.8871 | 100 | 0.208 | Contact Map |
| 4grvA | 1 | 0.8903 | 100 | 0.21 | Contact Map |
| 4phuA | 1 | 0.8226 | 100 | 0.211 | Contact Map |
| 4pxzA | 1 | 0.8613 | 100 | 0.213 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)