| 1f88 |
| ID: | 1406128786 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 348 (318) | ||
| Sequences: | 13894 (8700.5) | ||
| Seq/Len: | 43.692 | ||
| Nf(neff/√len): | 487.9 |
Jackhmmer Results: (2014_04_16)
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: 43.692).
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 |
| 51_G | 87_V | 6.241 | 1.00 |
| 136_Y | 141_K | 3.619 | 1.00 |
| 221_F | 225_Q | 3.503 | 1.00 |
| 103_F | 106_G | 3.327 | 1.00 |
| 108_T | 112_L | 3.096 | 1.00 |
| 78_N | 161_W | 3.073 | 1.00 |
| 78_N | 127_S | 3.009 | 1.00 |
| 130_V | 160_T | 2.798 | 1.00 |
| 68_L | 73_N | 2.465 | 1.00 |
| 107_P | 111_N | 2.462 | 1.00 |
| 265_W | 295_A | 2.381 | 1.00 |
| 62_T | 77_L | 2.358 | 1.00 |
| 59_L | 77_L | 2.349 | 1.00 |
| 38_S | 42_A | 2.250 | 1.00 |
| 130_V | 156_G | 2.165 | 1.00 |
| 115_F | 119_L | 2.151 | 1.00 |
| 225_Q | 228_F | 2.060 | 1.00 |
| 74_Y | 157_V | 2.029 | 1.00 |
| 260_A | 305_I | 1.977 | 1.00 |
| 151_N | 155_M | 1.972 | 1.00 |
| 123_I | 164_A | 1.959 | 1.00 |
| 56_F | 84_L | 1.953 | 1.00 |
| 56_F | 60_Y | 1.950 | 1.00 |
| 216_L | 262_L | 1.944 | 1.00 |
| 119_L | 165_L | 1.908 | 1.00 |
| 52_F | 87_V | 1.902 | 1.00 |
| 155_M | 159_F | 1.892 | 1.00 |
| 218_V | 222_C | 1.890 | 1.00 |
| 136_Y | 225_Q | 1.858 | 1.00 |
| 224_G | 228_F | 1.850 | 1.00 |
| 75_I | 153_A | 1.780 | 1.00 |
| 253_M | 309_M | 1.744 | 1.00 |
| 110_C | 187_C | 1.734 | 1.00 |
| 35_W | 39_M | 1.731 | 1.00 |
| 169_A | 173_V | 1.713 | 1.00 |
| 266_L | 270_G | 1.682 | 1.00 |
| 127_S | 157_V | 1.635 | 1.00 |
| 206_Y | 210_V | 1.635 | 1.00 |
| 270_G | 274_Y | 1.629 | 1.00 |
| 128_L | 219_I | 1.612 | 1.00 |
| 70_T | 73_N | 1.609 | 1.00 |
| 208_F | 213_I | 1.605 | 1.00 |
| 136_Y | 140_C | 1.604 | 1.00 |
| 228_F | 232_E | 1.588 | 1.00 |
| 278_H | 281_S | 1.587 | 1.00 |
| 171_P | 174_G | 1.576 | 1.00 |
| 115_F | 172_L | 1.559 | 1.00 |
| 220_F | 224_G | 1.552 | 1.00 |
| 60_Y | 320_T | 1.527 | 1.00 |
| 96_Y | 105_F | 1.515 | 1.00 |
| 51_G | 300_V | 1.500 | 1.00 |
| 156_G | 160_T | 1.482 | 1.00 |
| 48_I | 95_L | 1.474 | 1.00 |
| 78_N | 157_V | 1.474 | 1.00 |
| 212_F | 266_L | 1.472 | 1.00 |
| 268_Y | 272_A | 1.469 | 1.00 |
| 83_D | 302_N | 1.452 | 1.00 |
| 77_L | 81_V | 1.452 | 1.00 |
| 136_Y | 221_F | 1.446 | 1.00 |
| 154_I | 158_A | 1.445 | 1.00 |
| 271_V | 291_P | 1.444 | 1.00 |
| 65_H | 316_C | 1.440 | 1.00 |
| 54_I | 300_V | 1.432 | 1.00 |
| 227_V | 251_T | 1.431 | 1.00 |
| 134_E | 138_V | 1.429 | 1.00 |
| 133_I | 222_C | 1.427 | 1.00 |
| 149_G | 152_H | 1.406 | 0.99 |
| 115_F | 165_L | 1.380 | 0.99 |
| 262_L | 266_L | 1.378 | 0.99 |
| 202_S | 206_Y | 1.369 | 0.99 |
| 225_Q | 229_T | 1.348 | 0.99 |
| 53_P | 56_F | 1.333 | 0.99 |
| 62_T | 68_L | 1.326 | 0.99 |
| 41_A | 99_L | 1.319 | 0.99 |
| 41_A | 95_L | 1.318 | 0.99 |
| 122_E | 211_H | 1.313 | 0.99 |
| 82_A | 123_I | 1.311 | 0.99 |
| 297_T | 301_Y | 1.306 | 0.99 |
| 58_T | 62_T | 1.305 | 0.99 |
| 124_A | 298_S | 1.301 | 0.99 |
| 129_V | 218_V | 1.297 | 0.99 |
| 205_I | 277_T | 1.294 | 0.99 |
| 52_F | 84_L | 1.294 | 0.99 |
| 287_F | 291_P | 1.293 | 0.99 |
| 106_G | 109_G | 1.275 | 0.99 |
| 211_H | 215_P | 1.270 | 0.99 |
| 41_A | 45_F | 1.262 | 0.99 |
| 208_F | 273_F | 1.259 | 0.99 |
| 141_K | 144_S | 1.257 | 0.99 |
| 187_C | 192_Y | 1.250 | 0.99 |
| 82_A | 124_A | 1.245 | 0.98 |
| 118_T | 168_A | 1.239 | 0.98 |
| 86_M | 299_A | 1.239 | 0.98 |
| 93_T | 109_G | 1.235 | 0.98 |
| 256_I | 305_I | 1.234 | 0.98 |
| 119_L | 168_A | 1.233 | 0.98 |
| 255_I | 259_I | 1.227 | 0.98 |
| 138_V | 142_P | 1.218 | 0.98 |
| 187_C | 191_Y | 1.216 | 0.98 |
| 50_L | 300_V | 1.193 | 0.98 |
| 126_W | 163_M | 1.184 | 0.98 |
| 48_I | 87_V | 1.177 | 0.98 |
| 82_A | 161_W | 1.170 | 0.97 |
| 90_G | 94_T | 1.169 | 0.97 |
| 265_W | 302_N | 1.168 | 0.97 |
| 129_V | 222_C | 1.167 | 0.97 |
| 59_L | 84_L | 1.166 | 0.97 |
| 85_F | 120_G | 1.165 | 0.97 |
| 47_L | 297_T | 1.163 | 0.97 |
| 248_K | 252_R | 1.162 | 0.97 |
| 201_E | 277_T | 1.161 | 0.97 |
| 230_V | 233_A | 1.145 | 0.97 |
| 80_A | 302_N | 1.139 | 0.97 |
| 212_F | 261_F | 1.133 | 0.97 |
| 144_S | 147_R | 1.130 | 0.97 |
| 123_I | 127_S | 1.128 | 0.97 |
| 281_S | 284_G | 1.125 | 0.97 |
| 59_L | 80_A | 1.125 | 0.97 |
| 151_N | 154_I | 1.123 | 0.97 |
| 155_M | 158_A | 1.116 | 0.96 |
| 54_I | 80_A | 1.114 | 0.96 |
| 140_C | 229_T | 1.114 | 0.96 |
| 71_P | 153_A | 1.114 | 0.96 |
| 117_A | 296_K | 1.106 | 0.96 |
| 59_L | 81_V | 1.104 | 0.96 |
| 318_V | 322_C | 1.103 | 0.96 |
| 286_I | 290_I | 1.102 | 0.96 |
| 58_T | 303_P | 1.102 | 0.96 |
| 138_V | 143_M | 1.099 | 0.96 |
| 302_N | 310_N | 1.096 | 0.96 |
| 171_P | 175_W | 1.085 | 0.96 |
| 127_S | 161_W | 1.083 | 0.96 |
| 230_V | 248_K | 1.079 | 0.95 |
| 58_T | 307_I | 1.076 | 0.95 |
| 96_Y | 100_H | 1.074 | 0.95 |
| 316_C | 319_T | 1.071 | 0.95 |
| 45_F | 99_L | 1.070 | 0.95 |
| 247_E | 251_T | 1.069 | 0.95 |
| 79_L | 127_S | 1.066 | 0.95 |
| 62_T | 69_R | 1.064 | 0.95 |
| 107_P | 176_S | 1.062 | 0.95 |
| 170_P | 203_F | 1.052 | 0.95 |
| 129_V | 219_I | 1.051 | 0.94 |
| 219_I | 258_V | 1.048 | 0.94 |
| 125_L | 261_F | 1.046 | 0.94 |
| 74_Y | 154_I | 1.045 | 0.94 |
| 132_A | 222_C | 1.042 | 0.94 |
| 305_I | 309_M | 1.039 | 0.94 |
| 230_V | 259_I | 1.034 | 0.94 |
| 198_T | 202_S | 1.034 | 0.94 |
| 58_T | 302_N | 1.033 | 0.94 |
| 58_T | 306_Y | 1.030 | 0.94 |
| 50_L | 53_P | 1.023 | 0.93 |
| 125_L | 129_V | 1.019 | 0.93 |
| 127_S | 160_T | 1.019 | 0.93 |
| 219_I | 223_Y | 1.015 | 0.93 |
| 260_A | 301_Y | 1.013 | 0.93 |
| 137_V | 141_K | 1.011 | 0.93 |
| 227_V | 231_K | 1.009 | 0.93 |
| 229_T | 232_E | 1.007 | 0.93 |
| 231_K | 235_A | 1.006 | 0.93 |
| 87_V | 299_A | 1.004 | 0.93 |
| 71_P | 75_I | 1.003 | 0.93 |
| 212_F | 262_L | 1.003 | 0.93 |
| 131_L | 254_V | 1.002 | 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 | |
| 1u19A | 2 | 1 | 100 | 0.207 | Contact Map |
| 4iarA | 1 | 0.8075 | 100 | 0.273 | Contact Map |
| 2r4rA | 1 | 0.6006 | 100 | 0.289 | Contact Map |
| 4pxzA | 1 | 0.7989 | 100 | 0.29 | Contact Map |
| 2rh1A | 1 | 0.8276 | 100 | 0.291 | Contact Map |
| 4grvA | 1 | 0.8218 | 100 | 0.292 | Contact Map |
| 4bvnA | 1 | 0.8161 | 100 | 0.303 | Contact Map |
| 3vw7A | 1 | 0.8132 | 100 | 0.305 | Contact Map |
| 4buoA | 2 | 0.8563 | 100 | 0.307 | Contact Map |
| 3uonA | 1 | 0.8103 | 100 | 0.31 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)