| PAK dimer |
| ID: | 1401302752 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 306 (259) | ||
| Sequences: | 43990 (30047.7) | ||
| Seq/Len: | 169.846 | ||
| Nf(neff/√len): | 1867.1 |
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: 169.846).
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 |
| 256_E | 261_K | 3.492 | 1.00 |
| 123_C | 207_A | 3.441 | 1.00 |
| 149_L | 159_T | 3.239 | 1.00 |
| 200_I | 254_C | 3.070 | 1.00 |
| 27_E | 39_T | 3.036 | 1.00 |
| 39_T | 48_E | 2.946 | 1.00 |
| 40_A | 49_V | 2.846 | 1.00 |
| 40_A | 51_I | 2.733 | 1.00 |
| 116_E | 244_S | 2.534 | 1.00 |
| 98_E | 157_K | 2.426 | 1.00 |
| 28_K | 36_T | 2.405 | 1.00 |
| 76_K | 82_N | 2.379 | 1.00 |
| 42_D | 45_T | 2.335 | 1.00 |
| 258_D | 261_K | 2.329 | 1.00 |
| 143_I | 206_M | 2.231 | 1.00 |
| 253_R | 263_G | 2.224 | 1.00 |
| 24_T | 41_M | 2.212 | 1.00 |
| 28_K | 31_Q | 2.202 | 1.00 |
| 249_D | 271_H | 2.193 | 1.00 |
| 131_E | 266_K | 2.122 | 1.00 |
| 131_E | 135_S | 2.111 | 1.00 |
| 151_G | 155_S | 2.095 | 1.00 |
| 39_T | 99_Y | 2.029 | 1.00 |
| 106_T | 146_D | 2.011 | 1.00 |
| 125_E | 155_S | 1.985 | 1.00 |
| 125_E | 156_V | 1.980 | 1.00 |
| 22_K | 42_D | 1.977 | 1.00 |
| 130_L | 203_L | 1.974 | 1.00 |
| 84_L | 98_E | 1.970 | 1.00 |
| 77_N | 132_F | 1.949 | 1.00 |
| 144_K | 180_T | 1.918 | 1.00 |
| 101_A | 152_M | 1.915 | 1.00 |
| 148_I | 156_V | 1.870 | 1.00 |
| 24_T | 43_V | 1.865 | 1.00 |
| 115_D | 118_Q | 1.823 | 1.00 |
| 254_C | 268_L | 1.811 | 1.00 |
| 127_L | 203_L | 1.807 | 1.00 |
| 185_A | 198_V | 1.785 | 1.00 |
| 104_S | 107_D | 1.782 | 1.00 |
| 130_L | 143_I | 1.781 | 1.00 |
| 127_L | 268_L | 1.761 | 1.00 |
| 126_C | 148_I | 1.725 | 1.00 |
| 51_I | 96_V | 1.704 | 1.00 |
| 179_G | 184_M | 1.697 | 1.00 |
| 82_N | 98_E | 1.692 | 1.00 |
| 129_A | 158_L | 1.661 | 1.00 |
| 41_M | 48_E | 1.648 | 1.00 |
| 204_G | 254_C | 1.617 | 1.00 |
| 26_F | 41_M | 1.612 | 1.00 |
| 200_I | 265_A | 1.590 | 1.00 |
| 183_W | 209_E | 1.587 | 1.00 |
| 211_I | 247_F | 1.578 | 1.00 |
| 148_I | 206_M | 1.536 | 1.00 |
| 119_I | 211_I | 1.519 | 1.00 |
| 145_S | 183_W | 1.513 | 1.00 |
| 122_V | 156_V | 1.512 | 1.00 |
| 37_V | 50_A | 1.489 | 1.00 |
| 49_V | 96_V | 1.472 | 1.00 |
| 28_K | 38_Y | 1.467 | 1.00 |
| 151_G | 157_K | 1.462 | 1.00 |
| 131_E | 269_I | 1.445 | 1.00 |
| 207_A | 250_F | 1.443 | 1.00 |
| 123_C | 210_M | 1.438 | 1.00 |
| 130_L | 265_A | 1.429 | 1.00 |
| 123_C | 203_L | 1.410 | 1.00 |
| 185_A | 188_V | 1.398 | 0.99 |
| 141_R | 194_Y | 1.376 | 0.99 |
| 26_F | 39_T | 1.373 | 0.99 |
| 225_A | 229_I | 1.372 | 0.99 |
| 47_Q | 84_L | 1.370 | 0.99 |
| 79_N | 128_Q | 1.361 | 0.99 |
| 250_F | 254_C | 1.340 | 0.99 |
| 41_M | 46_G | 1.311 | 0.99 |
| 138_V | 164_C | 1.306 | 0.99 |
| 121_A | 125_E | 1.306 | 0.99 |
| 81_V | 97_M | 1.285 | 0.99 |
| 263_G | 268_L | 1.276 | 0.99 |
| 81_V | 100_L | 1.268 | 0.99 |
| 250_F | 263_G | 1.268 | 0.99 |
| 249_D | 253_R | 1.268 | 0.99 |
| 142_D | 147_N | 1.255 | 0.99 |
| 203_L | 254_C | 1.240 | 0.98 |
| 205_I | 215_P | 1.238 | 0.98 |
| 135_S | 266_K | 1.232 | 0.98 |
| 264_S | 267_E | 1.226 | 0.98 |
| 126_C | 156_V | 1.220 | 0.98 |
| 38_Y | 53_Q | 1.211 | 0.98 |
| 79_N | 129_A | 1.205 | 0.98 |
| 124_R | 128_Q | 1.203 | 0.98 |
| 250_F | 268_L | 1.202 | 0.98 |
| 80_I | 133_L | 1.190 | 0.98 |
| 265_A | 268_L | 1.178 | 0.98 |
| 116_E | 119_I | 1.178 | 0.98 |
| 145_S | 206_M | 1.173 | 0.98 |
| 147_N | 160_D | 1.166 | 0.97 |
| 74_E | 136_N | 1.164 | 0.97 |
| 100_L | 149_L | 1.159 | 0.97 |
| 233_G | 257_M | 1.157 | 0.97 |
| 253_R | 267_E | 1.154 | 0.97 |
| 127_L | 265_A | 1.152 | 0.97 |
| 48_E | 99_Y | 1.147 | 0.97 |
| 209_E | 215_P | 1.143 | 0.97 |
| 31_Q | 36_T | 1.142 | 0.97 |
| 119_I | 210_M | 1.138 | 0.97 |
| 81_V | 159_T | 1.132 | 0.97 |
| 124_R | 269_I | 1.125 | 0.97 |
| 100_L | 157_K | 1.121 | 0.97 |
| 132_F | 136_N | 1.121 | 0.97 |
| 140_H | 143_I | 1.114 | 0.96 |
| 100_L | 151_G | 1.112 | 0.96 |
| 248_R | 252_N | 1.111 | 0.96 |
| 53_Q | 92_E | 1.110 | 0.96 |
| 83_Y | 95_V | 1.108 | 0.96 |
| 23_Y | 85_D | 1.103 | 0.96 |
| 197_K | 264_S | 1.100 | 0.96 |
| 32_G | 35_G | 1.094 | 0.96 |
| 109_V | 209_E | 1.091 | 0.96 |
| 163_F | 178_V | 1.087 | 0.96 |
| 49_V | 84_L | 1.063 | 0.95 |
| 102_G | 154_G | 1.062 | 0.95 |
| 127_L | 269_I | 1.055 | 0.95 |
| 141_R | 178_V | 1.053 | 0.95 |
| 253_R | 256_E | 1.053 | 0.95 |
| 71_V | 164_C | 1.040 | 0.94 |
| 137_Q | 196_P | 1.032 | 0.94 |
| 194_Y | 198_V | 1.032 | 0.94 |
| 30_G | 37_V | 1.020 | 0.93 |
| 254_C | 263_G | 1.019 | 0.93 |
| 106_T | 209_E | 1.018 | 0.93 |
| 103_G | 159_T | 1.015 | 0.93 |
| 134_H | 265_A | 1.014 | 0.93 |
| 126_C | 206_M | 1.007 | 0.93 |
| 25_R | 38_Y | 1.001 | 0.92 |
| 251_L | 255_L | 1.000 | 0.92 |
| 128_Q | 269_I | 1.000 | 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 | |
| 3fxzA | 1 | 0.9542 | 100 | 0.155 | Contact Map |
| 4fieA | 2 | 0.951 | 100 | 0.168 | Contact Map |
| 4jdiA | 1 | 0.9444 | 100 | 0.172 | Contact Map |
| 4lgdA | 4 | 0.9771 | 100 | 0.184 | Contact Map |
| 3soaA | 1 | 0.9379 | 100 | 0.207 | Contact Map |
| 1tkiA | 2 | 0.9379 | 100 | 0.211 | Contact Map |
| 3c0iA | 1 | 0.915 | 100 | 0.214 | Contact Map |
| 2x4fA | 2 | 0.8922 | 100 | 0.215 | Contact Map |
| 4ks7A | 1 | 0.9346 | 100 | 0.216 | Contact Map |
| 3q5iA | 1 | 0.9542 | 100 | 0.217 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)