| gk1602 |
| ID: | 1492629987 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 260 (256) | ||
| Sequences: | 17677 (10339.7) | ||
| Seq/Len: | 69.051 | ||
| Nf(neff/√len): | 646.2 |
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: 69.051).
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 |
| 102_A | 119_C | 3.250 | 1.00 |
| 124_A | 179_V | 3.149 | 1.00 |
| 129_Q | 167_R | 3.129 | 1.00 |
| 126_D | 184_P | 3.026 | 1.00 |
| 181_Y | 191_R | 2.846 | 1.00 |
| 41_Q | 92_E | 2.801 | 1.00 |
| 191_R | 194_C | 2.624 | 1.00 |
| 44_K | 97_P | 2.573 | 1.00 |
| 162_I | 210_A | 2.458 | 1.00 |
| 169_T | 172_E | 2.341 | 1.00 |
| 160_E | 166_K | 2.308 | 1.00 |
| 172_E | 175_R | 2.279 | 1.00 |
| 16_I | 193_L | 2.268 | 1.00 |
| 109_F | 131_G | 2.199 | 1.00 |
| 166_K | 198_Q | 2.174 | 1.00 |
| 136_S | 202_N | 2.153 | 1.00 |
| 13_G | 50_R | 2.066 | 1.00 |
| 16_I | 55_T | 2.056 | 1.00 |
| 123_F | 183_V | 2.044 | 1.00 |
| 157_K | 176_I | 2.024 | 1.00 |
| 25_A | 60_K | 1.983 | 1.00 |
| 31_A | 35_E | 1.954 | 1.00 |
| 6_S | 20_N | 1.914 | 1.00 |
| 15_A | 43_I | 1.904 | 1.00 |
| 103_V | 192_A | 1.890 | 1.00 |
| 25_A | 61_V | 1.880 | 1.00 |
| 37_G | 92_E | 1.863 | 1.00 |
| 18_T | 57_A | 1.837 | 1.00 |
| 18_T | 55_T | 1.820 | 1.00 |
| 221_D | 224_T | 1.810 | 1.00 |
| 93_V | 100_V | 1.808 | 1.00 |
| 52_V | 96_V | 1.786 | 1.00 |
| 44_K | 92_E | 1.778 | 1.00 |
| 20_N | 57_A | 1.764 | 1.00 |
| 122_R | 152_L | 1.757 | 1.00 |
| 116_A | 122_R | 1.695 | 1.00 |
| 160_E | 180_E | 1.690 | 1.00 |
| 15_A | 49_V | 1.679 | 1.00 |
| 34_L | 85_L | 1.652 | 1.00 |
| 124_A | 130_L | 1.649 | 1.00 |
| 19_L | 32_L | 1.643 | 1.00 |
| 127_D | 185_R | 1.636 | 1.00 |
| 126_D | 171_K | 1.625 | 1.00 |
| 247_Q | 251_E | 1.616 | 1.00 |
| 159_K | 214_I | 1.603 | 1.00 |
| 244_E | 253_R | 1.590 | 1.00 |
| 43_I | 52_V | 1.573 | 1.00 |
| 171_K | 175_R | 1.563 | 1.00 |
| 212_R | 216_S | 1.556 | 1.00 |
| 17_V | 39_L | 1.547 | 1.00 |
| 105_N | 127_D | 1.522 | 1.00 |
| 51_V | 196_A | 1.506 | 1.00 |
| 193_L | 197_Q | 1.491 | 1.00 |
| 159_K | 215_Q | 1.485 | 1.00 |
| 104_L | 116_A | 1.485 | 1.00 |
| 161_L | 168_I | 1.483 | 1.00 |
| 174_E | 182_A | 1.482 | 1.00 |
| 104_L | 108_A | 1.479 | 1.00 |
| 240_K | 260_E | 1.469 | 1.00 |
| 40_F | 96_V | 1.447 | 1.00 |
| 55_T | 105_N | 1.444 | 1.00 |
| 160_E | 181_Y | 1.442 | 1.00 |
| 103_V | 189_M | 1.430 | 1.00 |
| 123_F | 195_L | 1.428 | 1.00 |
| 166_K | 172_E | 1.424 | 1.00 |
| 157_K | 160_E | 1.411 | 1.00 |
| 8_E | 11_E | 1.410 | 1.00 |
| 37_G | 41_Q | 1.398 | 0.99 |
| 105_N | 125_A | 1.366 | 0.99 |
| 120_D | 211_K | 1.361 | 0.99 |
| 91_N | 223_E | 1.328 | 0.99 |
| 183_V | 191_R | 1.316 | 0.99 |
| 38_A | 42_E | 1.311 | 0.99 |
| 91_N | 95_K | 1.301 | 0.99 |
| 113_L | 132_L | 1.291 | 0.99 |
| 135_T | 165_A | 1.275 | 0.99 |
| 30_R | 70_E | 1.261 | 0.99 |
| 159_K | 163_F | 1.261 | 0.99 |
| 21_R | 24_A | 1.241 | 0.98 |
| 155_I | 159_K | 1.238 | 0.98 |
| 42_E | 46_R | 1.238 | 0.98 |
| 52_V | 98_Q | 1.231 | 0.98 |
| 187_E | 191_R | 1.228 | 0.98 |
| 61_V | 107_S | 1.225 | 0.98 |
| 242_R | 246_L | 1.224 | 0.98 |
| 44_K | 96_V | 1.223 | 0.98 |
| 172_E | 176_I | 1.221 | 0.98 |
| 12_N | 197_Q | 1.216 | 0.98 |
| 100_V | 119_C | 1.214 | 0.98 |
| 30_R | 34_L | 1.212 | 0.98 |
| 129_Q | 169_T | 1.204 | 0.98 |
| 49_V | 98_Q | 1.201 | 0.98 |
| 35_E | 39_L | 1.200 | 0.98 |
| 168_I | 176_I | 1.191 | 0.98 |
| 29_S | 32_L | 1.175 | 0.98 |
| 196_A | 200_A | 1.174 | 0.98 |
| 19_L | 63_C | 1.169 | 0.97 |
| 126_D | 185_R | 1.168 | 0.97 |
| 14_I | 51_V | 1.154 | 0.97 |
| 154_G | 158_A | 1.144 | 0.97 |
| 113_L | 130_L | 1.135 | 0.97 |
| 199_I | 207_V | 1.132 | 0.97 |
| 63_C | 112_G | 1.131 | 0.97 |
| 104_L | 130_L | 1.124 | 0.97 |
| 94_E | 148_R | 1.120 | 0.96 |
| 220_V | 224_T | 1.120 | 0.96 |
| 153_V | 157_K | 1.118 | 0.96 |
| 187_E | 190_E | 1.118 | 0.96 |
| 147_Q | 225_G | 1.117 | 0.96 |
| 154_G | 157_K | 1.110 | 0.96 |
| 47_K | 98_Q | 1.107 | 0.96 |
| 149_L | 153_V | 1.104 | 0.96 |
| 174_E | 179_V | 1.094 | 0.96 |
| 24_A | 69_K | 1.094 | 0.96 |
| 202_N | 207_V | 1.094 | 0.96 |
| 7_F | 15_A | 1.092 | 0.96 |
| 60_K | 105_N | 1.087 | 0.96 |
| 170_A | 182_A | 1.084 | 0.96 |
| 213_A | 232_A | 1.071 | 0.95 |
| 37_G | 88_K | 1.064 | 0.95 |
| 25_A | 64_A | 1.061 | 0.95 |
| 131_G | 167_R | 1.061 | 0.95 |
| 39_L | 42_E | 1.059 | 0.95 |
| 121_I | 180_E | 1.058 | 0.95 |
| 54_L | 100_V | 1.054 | 0.95 |
| 95_K | 223_E | 1.054 | 0.95 |
| 55_T | 103_V | 1.051 | 0.94 |
| 122_R | 156_G | 1.051 | 0.94 |
| 224_T | 227_A | 1.048 | 0.94 |
| 54_L | 119_C | 1.041 | 0.94 |
| 35_E | 38_A | 1.037 | 0.94 |
| 209_Q | 235_A | 1.036 | 0.94 |
| 240_K | 258_K | 1.031 | 0.94 |
| 121_I | 195_L | 1.029 | 0.94 |
| 123_F | 181_Y | 1.028 | 0.94 |
| 125_A | 185_R | 1.024 | 0.93 |
| 205_I | 241_D | 1.024 | 0.93 |
| 17_V | 52_V | 1.020 | 0.93 |
| 16_I | 53_M | 1.001 | 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 | |
| 4jfcA | 1 | 0.9769 | 100 | 0.022 | Contact Map |
| 1nzyA | 2 | 0.9923 | 100 | 0.023 | Contact Map |
| 2ej5A | 2 | 0.9654 | 100 | 0.026 | Contact Map |
| 3sllA | 6 | 0.9808 | 100 | 0.026 | Contact Map |
| 3qxzA | 3 | 0.9885 | 100 | 0.027 | Contact Map |
| 3kqfA | 6 | 0.9923 | 100 | 0.027 | Contact Map |
| 4lk5A | 3 | 0.9577 | 100 | 0.027 | Contact Map |
| 3swxA | 3 | 0.9846 | 100 | 0.03 | Contact Map |
| 2ppyA | 6 | 0.9923 | 100 | 0.031 | Contact Map |
| 4olqA | 6 | 0.9846 | 100 | 0.032 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)