| ppm1d 90-380 |
| ID: | 1485187118 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 291 (279) | ||
| Sequences: | 4035 (2314.6) | ||
| Seq/Len: | 14.462 | ||
| Nf(neff/√len): | 138.6 |
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: 14.462).
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 |
| 123_E | 233_P | 4.144 | 1.00 |
| 105_G | 127_D | 3.486 | 1.00 |
| 27_A | 186_L | 3.387 | 1.00 |
| 87_S | 106_V | 3.339 | 1.00 |
| 221_I | 236_A | 3.161 | 1.00 |
| 234_Q | 238_S | 3.080 | 1.00 |
| 27_A | 84_T | 2.865 | 1.00 |
| 95_K | 211_T | 2.829 | 1.00 |
| 57_F | 88_V | 2.683 | 1.00 |
| 227_L | 279_T | 2.619 | 1.00 |
| 105_G | 233_P | 2.619 | 1.00 |
| 223_G | 228_W | 2.582 | 1.00 |
| 89_V | 220_I | 2.538 | 1.00 |
| 95_K | 209_V | 2.492 | 1.00 |
| 136_R | 140_E | 2.474 | 1.00 |
| 11_F | 32_W | 2.463 | 1.00 |
| 139_I | 144_G | 2.391 | 1.00 |
| 26_F | 30_H | 2.356 | 1.00 |
| 221_I | 283_V | 2.223 | 1.00 |
| 137_E | 141_G | 2.183 | 1.00 |
| 126_Q | 132_L | 2.131 | 1.00 |
| 110_I | 217_H | 2.115 | 1.00 |
| 54_R | 204_E | 2.110 | 1.00 |
| 34_F | 60_C | 2.092 | 1.00 |
| 261_L | 281_A | 2.088 | 1.00 |
| 109_G | 237_I | 2.052 | 1.00 |
| 89_V | 98_V | 2.031 | 1.00 |
| 277_D | 280_S | 2.013 | 1.00 |
| 35_I | 56_G | 1.993 | 1.00 |
| 87_S | 125_T | 1.969 | 1.00 |
| 12_F | 284_I | 1.959 | 1.00 |
| 11_F | 15_C | 1.928 | 1.00 |
| 97_Y | 209_V | 1.909 | 1.00 |
| 109_G | 219_Y | 1.889 | 1.00 |
| 228_W | 236_A | 1.872 | 1.00 |
| 100_H | 125_T | 1.860 | 1.00 |
| 15_C | 86_A | 1.844 | 1.00 |
| 121_A | 234_Q | 1.833 | 1.00 |
| 227_L | 261_L | 1.821 | 1.00 |
| 231_I | 236_A | 1.781 | 1.00 |
| 264_R | 268_R | 1.733 | 1.00 |
| 15_C | 32_W | 1.715 | 1.00 |
| 85_T | 104_S | 1.710 | 1.00 |
| 84_T | 104_S | 1.698 | 1.00 |
| 13_A | 88_V | 1.692 | 1.00 |
| 220_I | 286_I | 1.687 | 1.00 |
| 133_P | 137_E | 1.680 | 1.00 |
| 128_H | 206_D | 1.659 | 1.00 |
| 127_D | 233_P | 1.650 | 1.00 |
| 219_Y | 240_C | 1.649 | 1.00 |
| 180_L | 201_V | 1.648 | 1.00 |
| 23_A | 64_M | 1.638 | 1.00 |
| 107_V | 121_A | 1.629 | 1.00 |
| 34_F | 63_A | 1.615 | 1.00 |
| 121_A | 237_I | 1.598 | 1.00 |
| 107_V | 228_W | 1.593 | 1.00 |
| 135_E | 138_R | 1.582 | 1.00 |
| 52_A | 56_G | 1.581 | 1.00 |
| 89_V | 222_L | 1.553 | 1.00 |
| 18_H | 188_D | 1.542 | 1.00 |
| 84_T | 186_L | 1.525 | 1.00 |
| 227_L | 281_A | 1.525 | 1.00 |
| 38_Q | 59_A | 1.524 | 1.00 |
| 58_L | 203_P | 1.510 | 1.00 |
| 107_V | 237_I | 1.500 | 1.00 |
| 96_M | 212_L | 1.467 | 1.00 |
| 218_K | 241_Q | 1.462 | 1.00 |
| 258_A | 283_V | 1.460 | 1.00 |
| 38_Q | 55_K | 1.452 | 1.00 |
| 50_C | 54_R | 1.439 | 1.00 |
| 49_V | 97_Y | 1.433 | 1.00 |
| 56_G | 60_C | 1.419 | 1.00 |
| 225_D | 277_D | 1.396 | 0.99 |
| 146_V | 183_A | 1.391 | 0.99 |
| 139_I | 183_A | 1.390 | 0.99 |
| 30_H | 33_G | 1.382 | 0.99 |
| 130_P | 183_A | 1.368 | 0.99 |
| 86_A | 186_L | 1.345 | 0.99 |
| 107_V | 236_A | 1.345 | 0.99 |
| 94_M | 211_T | 1.333 | 0.99 |
| 51_A | 55_K | 1.326 | 0.99 |
| 132_L | 206_D | 1.308 | 0.99 |
| 109_G | 218_K | 1.301 | 0.99 |
| 105_G | 125_T | 1.295 | 0.99 |
| 58_L | 204_E | 1.289 | 0.99 |
| 111_Q | 218_K | 1.280 | 0.99 |
| 219_Y | 237_I | 1.275 | 0.99 |
| 9_V | 92_R | 1.269 | 0.99 |
| 30_H | 63_A | 1.247 | 0.99 |
| 129_K | 229_N | 1.245 | 0.98 |
| 87_S | 222_L | 1.235 | 0.98 |
| 57_F | 86_A | 1.226 | 0.98 |
| 85_T | 225_D | 1.219 | 0.98 |
| 103_D | 225_D | 1.208 | 0.98 |
| 265_A | 279_T | 1.189 | 0.98 |
| 213_D | 216_K | 1.188 | 0.98 |
| 239_M | 264_R | 1.184 | 0.98 |
| 108_L | 217_H | 1.177 | 0.98 |
| 110_I | 122_V | 1.163 | 0.97 |
| 16_D | 20_G | 1.144 | 0.97 |
| 275_R | 278_N | 1.130 | 0.97 |
| 51_A | 54_R | 1.127 | 0.97 |
| 184_R | 187_G | 1.119 | 0.96 |
| 26_F | 64_M | 1.118 | 0.96 |
| 232_P | 235_D | 1.113 | 0.96 |
| 17_G | 20_G | 1.112 | 0.96 |
| 235_D | 268_R | 1.112 | 0.96 |
| 258_A | 265_A | 1.112 | 0.96 |
| 61_H | 65_W | 1.110 | 0.96 |
| 253_H | 256_S | 1.108 | 0.96 |
| 223_G | 236_A | 1.097 | 0.96 |
| 8_S | 93_G | 1.096 | 0.96 |
| 34_F | 37_K | 1.094 | 0.96 |
| 24_A | 84_T | 1.089 | 0.96 |
| 243_Q | 260_M | 1.086 | 0.96 |
| 258_A | 262_V | 1.085 | 0.96 |
| 262_V | 281_A | 1.083 | 0.96 |
| 59_A | 63_A | 1.079 | 0.95 |
| 126_Q | 206_D | 1.074 | 0.95 |
| 23_A | 84_T | 1.068 | 0.95 |
| 108_L | 124_V | 1.060 | 0.95 |
| 25_Q | 29_E | 1.055 | 0.95 |
| 221_I | 240_C | 1.048 | 0.94 |
| 61_H | 64_M | 1.047 | 0.94 |
| 130_P | 139_I | 1.046 | 0.94 |
| 212_L | 217_H | 1.023 | 0.93 |
| 231_I | 264_R | 1.019 | 0.93 |
| 266_L | 278_N | 1.015 | 0.93 |
| 130_P | 181_A | 1.014 | 0.93 |
| 11_F | 88_V | 1.013 | 0.93 |
| 236_A | 261_L | 1.006 | 0.93 |
| 255_Q | 259_K | 1.004 | 0.93 |
| 129_K | 183_A | 1.001 | 0.92 |
| 105_G | 123_E | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2pnqA | 2 | 0.8797 | 100 | 0.315 | Contact Map |
| 2j4oA | 1 | 0.8969 | 100 | 0.331 | Contact Map |
| 3d8kA | 4 | 0.8076 | 100 | 0.333 | Contact Map |
| 2p8eA | 2 | 0.811 | 100 | 0.333 | Contact Map |
| 2i44A | 3 | 0.8935 | 100 | 0.334 | Contact Map |
| 2irmA | 1 | 0.8763 | 100 | 0.335 | Contact Map |
| 4ra2A | 1 | 0 | 100 | 0.337 | Contact Map |
| 2i0oA | 1 | 0.811 | 100 | 0.34 | Contact Map |
| 4yzgA | 2 | 0 | 100 | 0.34 | Contact Map |
| 3qn1B | 1 | 0.8454 | 100 | 0.34 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)