| PTP1B |
| ID: | 1672055069 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 306 (278) | ||
| Sequences: | 2840 (1916.9) | ||
| Seq/Len: | 10.216 | ||
| Nf(neff/√len): | 115.0 |
HHblits Results: (2016_02)
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 |
| 109_S | 217_V | 4.284 | 1.00 |
| 88_L | 227_S | 2.990 | 1.00 |
| 49_N | 71_Y | 2.904 | 1.00 |
| 60_S | 75_S | 2.773 | 1.00 |
| 48_R | 99_H | 2.567 | 1.00 |
| 97_C | 127_A | 2.491 | 1.00 |
| 232_L | 255_L | 2.262 | 1.00 |
| 61_R | 70_D | 2.245 | 1.00 |
| 56_P | 73_N | 2.220 | 1.00 |
| 250_D | 253_K | 2.206 | 1.00 |
| 86_Y | 234_D | 2.143 | 1.00 |
| 161_R | 178_H | 2.123 | 1.00 |
| 62_I | 76_L | 2.121 | 1.00 |
| 88_L | 231_C | 2.079 | 1.00 |
| 185_P | 188_G | 2.018 | 1.00 |
| 128_Q | 132_Q | 2.003 | 1.00 |
| 103_M | 217_V | 1.993 | 1.00 |
| 104_V | 217_V | 1.967 | 1.00 |
| 105_W | 174_R | 1.941 | 1.00 |
| 101_W | 104_V | 1.939 | 1.00 |
| 224_I | 264_G | 1.936 | 1.00 |
| 93_L | 96_T | 1.878 | 1.00 |
| 129_Y | 219_H | 1.852 | 1.00 |
| 94_P | 127_A | 1.847 | 1.00 |
| 220_C | 227_S | 1.846 | 1.00 |
| 91_G | 126_C | 1.831 | 1.00 |
| 114_M | 178_H | 1.794 | 1.00 |
| 232_L | 275_S | 1.784 | 1.00 |
| 60_S | 261_F | 1.770 | 1.00 |
| 89_T | 217_V | 1.745 | 1.00 |
| 114_M | 129_Y | 1.699 | 1.00 |
| 186_D | 222_A | 1.678 | 1.00 |
| 45_N | 49_N | 1.650 | 1.00 |
| 222_A | 226_R | 1.642 | 1.00 |
| 130_W | 178_H | 1.634 | 1.00 |
| 25_Y | 28_I | 1.632 | 1.00 |
| 118_V | 128_Q | 1.620 | 1.00 |
| 233_A | 275_S | 1.620 | 1.00 |
| 222_A | 267_Q | 1.598 | 1.00 |
| 76_L | 107_Q | 1.590 | 1.00 |
| 108_K | 174_R | 1.589 | 1.00 |
| 271_Q | 274_F | 1.580 | 1.00 |
| 221_S | 226_R | 1.572 | 1.00 |
| 88_L | 265_L | 1.571 | 1.00 |
| 258_M | 265_L | 1.561 | 1.00 |
| 124_L | 127_A | 1.557 | 1.00 |
| 225_G | 267_Q | 1.551 | 1.00 |
| 56_P | 75_S | 1.549 | 1.00 |
| 233_A | 278_A | 1.540 | 1.00 |
| 40_A | 56_P | 1.532 | 1.00 |
| 39_V | 58_D | 1.530 | 1.00 |
| 162_Q | 175_E | 1.506 | 1.00 |
| 259_R | 266_I | 1.477 | 1.00 |
| 193_P | 281_E | 1.448 | 1.00 |
| 159_T | 182_T | 1.446 | 1.00 |
| 51_Y | 222_A | 1.442 | 1.00 |
| 232_L | 258_M | 1.428 | 1.00 |
| 24_I | 28_I | 1.411 | 1.00 |
| 89_T | 100_F | 1.406 | 0.99 |
| 61_R | 64_L | 1.398 | 0.99 |
| 228_G | 266_I | 1.393 | 0.99 |
| 65_H | 106_E | 1.379 | 0.99 |
| 272_L | 276_Y | 1.377 | 0.99 |
| 204_R | 234_D | 1.373 | 0.99 |
| 45_N | 48_R | 1.353 | 0.99 |
| 158_Y | 199_F | 1.347 | 0.99 |
| 162_Q | 177_L | 1.340 | 0.99 |
| 222_A | 225_G | 1.337 | 0.99 |
| 236_C | 254_V | 1.332 | 0.99 |
| 221_S | 225_G | 1.327 | 0.99 |
| 45_N | 58_D | 1.303 | 0.99 |
| 223_G | 262_R | 1.303 | 0.99 |
| 120_E | 125_K | 1.297 | 0.99 |
| 125_K | 221_S | 1.294 | 0.99 |
| 78_K | 261_F | 1.289 | 0.99 |
| 64_L | 74_A | 1.289 | 0.99 |
| 39_V | 42_L | 1.287 | 0.99 |
| 21_W | 24_I | 1.278 | 0.99 |
| 78_K | 85_S | 1.249 | 0.99 |
| 223_G | 226_R | 1.245 | 0.98 |
| 235_T | 254_V | 1.238 | 0.98 |
| 57_F | 73_N | 1.228 | 0.98 |
| 255_L | 266_I | 1.227 | 0.98 |
| 151_S | 162_Q | 1.224 | 0.98 |
| 102_E | 106_E | 1.222 | 0.98 |
| 140_F | 147_L | 1.219 | 0.98 |
| 64_L | 70_D | 1.216 | 0.98 |
| 111_G | 179_F | 1.215 | 0.98 |
| 237_L | 282_G | 1.214 | 0.98 |
| 223_G | 228_G | 1.212 | 0.98 |
| 66_Q | 102_E | 1.208 | 0.98 |
| 40_A | 45_N | 1.204 | 0.98 |
| 114_M | 126_C | 1.199 | 0.98 |
| 71_Y | 74_A | 1.192 | 0.98 |
| 272_L | 275_S | 1.190 | 0.98 |
| 196_F | 233_A | 1.189 | 0.98 |
| 150_I | 164_E | 1.188 | 0.98 |
| 196_F | 200_L | 1.187 | 0.98 |
| 94_P | 124_L | 1.183 | 0.98 |
| 104_V | 112_V | 1.180 | 0.98 |
| 72_I | 89_T | 1.177 | 0.98 |
| 255_L | 265_L | 1.172 | 0.98 |
| 225_G | 229_T | 1.163 | 0.97 |
| 184_W | 190_P | 1.159 | 0.97 |
| 181_Y | 195_S | 1.156 | 0.97 |
| 178_H | 219_H | 1.142 | 0.97 |
| 62_I | 103_M | 1.134 | 0.97 |
| 57_F | 75_S | 1.131 | 0.97 |
| 225_G | 228_G | 1.131 | 0.97 |
| 252_K | 272_L | 1.127 | 0.97 |
| 54_V | 224_I | 1.127 | 0.97 |
| 115_L | 128_Q | 1.125 | 0.97 |
| 179_F | 203_V | 1.122 | 0.97 |
| 45_N | 50_R | 1.116 | 0.96 |
| 221_S | 267_Q | 1.112 | 0.96 |
| 166_E | 173_T | 1.105 | 0.96 |
| 148_T | 164_E | 1.104 | 0.96 |
| 251_I | 276_Y | 1.102 | 0.96 |
| 219_H | 227_S | 1.101 | 0.96 |
| 63_K | 70_D | 1.099 | 0.96 |
| 91_G | 116_N | 1.096 | 0.96 |
| 109_S | 214_G | 1.095 | 0.96 |
| 161_R | 180_H | 1.088 | 0.96 |
| 255_L | 259_R | 1.085 | 0.96 |
| 60_S | 258_M | 1.078 | 0.95 |
| 104_V | 109_S | 1.071 | 0.95 |
| 56_P | 263_M | 1.069 | 0.95 |
| 236_C | 239_L | 1.065 | 0.95 |
| 164_E | 173_T | 1.063 | 0.95 |
| 259_R | 262_R | 1.059 | 0.95 |
| 79_M | 85_S | 1.053 | 0.95 |
| 231_C | 265_L | 1.049 | 0.94 |
| 225_G | 266_I | 1.045 | 0.94 |
| 125_K | 186_D | 1.038 | 0.94 |
| 99_H | 102_E | 1.030 | 0.94 |
| 255_L | 275_S | 1.026 | 0.94 |
| 54_V | 264_G | 1.024 | 0.93 |
| 218_V | 230_F | 1.021 | 0.93 |
| 271_Q | 276_Y | 1.012 | 0.93 |
| 203_V | 230_F | 1.012 | 0.93 |
| 116_N | 125_K | 1.007 | 0.93 |
| 165_L | 201_F | 1.004 | 0.93 |
| 113_V | 230_F | 1.004 | 0.93 |
| 148_T | 166_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
- 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 | |
| 4bjoA | 2 | 0.9346 | 100 | -0.009 | Contact Map |
| 2cm2A | 1 | 0.9248 | 100 | 0.024 | Contact Map |
| 1l8kA | 1 | 0.8922 | 100 | 0.039 | Contact Map |
| 3ps5A | 1 | 0.9183 | 100 | 0.1 | Contact Map |
| 1larA | 2 | 0.8595 | 100 | 0.106 | Contact Map |
| 2b3oA | 1 | 0.8889 | 100 | 0.107 | Contact Map |
| 2shpA | 2 | 0.8529 | 100 | 0.109 | Contact Map |
| 2oc3A | 1 | 0.8627 | 100 | 0.109 | Contact Map |
| 2jjdA | 6 | 0.8366 | 100 | 0.112 | Contact Map |
| 1ygrA | 2 | 0.9706 | 100 | 0.115 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)