| 1L8W |
| ID: | 1429457525 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 356 (350) | ||
| Sequences: | 549 (486.1) | ||
| Seq/Len: | 1.569 | ||
| Nf(neff/√len): | 26.0 |
Jackhmmer Results: (2015_01_07)
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: 1.569).
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 |
| 82_E | 86_T | 2.519 | 1.00 |
| 338_K | 341_D | 2.324 | 1.00 |
| 13_F | 16_F | 2.175 | 0.99 |
| 7_A | 15_V | 2.170 | 0.99 |
| 9_L | 13_F | 2.147 | 0.99 |
| 117_G | 124_E | 2.030 | 0.98 |
| 32_K | 35_Q | 2.018 | 0.98 |
| 23_V | 26_K | 1.989 | 0.98 |
| 8_I | 12_T | 1.967 | 0.98 |
| 9_L | 14_F | 1.962 | 0.98 |
| 5_S | 8_I | 1.931 | 0.98 |
| 21_S | 24_A | 1.851 | 0.97 |
| 10_L | 13_F | 1.833 | 0.96 |
| 72_T | 76_T | 1.809 | 0.96 |
| 8_I | 11_T | 1.807 | 0.96 |
| 10_L | 15_V | 1.783 | 0.96 |
| 13_F | 18_N | 1.772 | 0.95 |
| 7_A | 13_F | 1.769 | 0.95 |
| 9_L | 12_T | 1.727 | 0.95 |
| 8_I | 15_V | 1.726 | 0.95 |
| 7_A | 11_T | 1.708 | 0.94 |
| 24_A | 27_D | 1.707 | 0.94 |
| 6_S | 11_T | 1.694 | 0.94 |
| 9_L | 16_F | 1.674 | 0.93 |
| 30_T | 35_Q | 1.665 | 0.93 |
| 8_I | 13_F | 1.655 | 0.93 |
| 20_K | 23_V | 1.654 | 0.93 |
| 7_A | 10_L | 1.644 | 0.92 |
| 6_S | 9_L | 1.636 | 0.92 |
| 7_A | 16_F | 1.633 | 0.92 |
| 8_I | 16_F | 1.580 | 0.90 |
| 10_L | 14_F | 1.579 | 0.90 |
| 9_L | 15_V | 1.576 | 0.90 |
| 3_K | 7_A | 1.574 | 0.90 |
| 11_T | 14_F | 1.572 | 0.90 |
| 183_K | 186_A | 1.569 | 0.90 |
| 29_P | 32_K | 1.560 | 0.90 |
| 12_T | 16_F | 1.548 | 0.89 |
| 212_D | 215_A | 1.546 | 0.89 |
| 6_S | 13_F | 1.535 | 0.89 |
| 12_T | 17_I | 1.530 | 0.88 |
| 32_K | 37_V | 1.526 | 0.88 |
| 10_L | 16_F | 1.516 | 0.88 |
| 28_D | 31_N | 1.498 | 0.87 |
| 35_Q | 38_I | 1.498 | 0.87 |
| 6_S | 10_L | 1.485 | 0.86 |
| 66_K | 69_D | 1.480 | 0.86 |
| 90_S | 94_E | 1.480 | 0.86 |
| 4_I | 7_A | 1.480 | 0.86 |
| 78_A | 82_E | 1.473 | 0.86 |
| 28_D | 32_K | 1.471 | 0.86 |
| 75_T | 79_A | 1.469 | 0.86 |
| 13_F | 17_I | 1.468 | 0.85 |
| 21_S | 26_K | 1.466 | 0.85 |
| 6_S | 12_T | 1.460 | 0.85 |
| 78_A | 83_K | 1.456 | 0.85 |
| 15_V | 23_V | 1.453 | 0.85 |
| 7_A | 17_I | 1.452 | 0.85 |
| 69_D | 72_T | 1.447 | 0.84 |
| 109_G | 113_T | 1.446 | 0.84 |
| 12_T | 18_N | 1.443 | 0.84 |
| 32_K | 36_S | 1.425 | 0.83 |
| 194_N | 197_G | 1.417 | 0.83 |
| 11_T | 18_N | 1.413 | 0.82 |
| 26_K | 29_P | 1.411 | 0.82 |
| 79_A | 83_K | 1.409 | 0.82 |
| 235_I | 238_A | 1.409 | 0.82 |
| 7_A | 14_F | 1.396 | 0.81 |
| 5_S | 14_F | 1.390 | 0.81 |
| 160_D | 163_S | 1.383 | 0.80 |
| 11_T | 16_F | 1.376 | 0.80 |
| 11_T | 15_V | 1.375 | 0.80 |
| 14_F | 23_V | 1.368 | 0.79 |
| 31_N | 37_V | 1.361 | 0.79 |
| 279_Q | 283_A | 1.358 | 0.79 |
| 2_K | 5_S | 1.353 | 0.78 |
| 345_A | 351_P | 1.344 | 0.78 |
| 31_N | 35_Q | 1.343 | 0.78 |
| 339_V | 343_V | 1.343 | 0.78 |
| 6_S | 15_V | 1.340 | 0.77 |
| 76_T | 79_A | 1.334 | 0.77 |
| 30_T | 37_V | 1.333 | 0.77 |
| 161_K | 165_K | 1.330 | 0.77 |
| 15_V | 21_S | 1.328 | 0.77 |
| 5_S | 12_T | 1.326 | 0.76 |
| 6_S | 16_F | 1.319 | 0.76 |
| 14_F | 17_I | 1.318 | 0.76 |
| 189_A | 192_G | 1.303 | 0.75 |
| 4_I | 11_T | 1.301 | 0.74 |
| 183_K | 188_A | 1.293 | 0.74 |
| 184_L | 188_A | 1.268 | 0.72 |
| 24_A | 29_P | 1.250 | 0.70 |
| 4_I | 13_F | 1.245 | 0.70 |
| 114_A | 117_G | 1.245 | 0.70 |
| 6_S | 14_F | 1.240 | 0.69 |
| 142_G | 145_A | 1.240 | 0.69 |
| 25_D | 29_P | 1.239 | 0.69 |
| 12_T | 15_V | 1.236 | 0.69 |
| 30_T | 38_I | 1.233 | 0.69 |
| 150_V | 154_D | 1.232 | 0.69 |
| 4_I | 9_L | 1.228 | 0.68 |
| 20_K | 24_A | 1.228 | 0.68 |
| 113_T | 116_E | 1.224 | 0.68 |
| 23_V | 27_D | 1.224 | 0.68 |
| 28_D | 35_Q | 1.223 | 0.68 |
| 17_I | 23_V | 1.221 | 0.68 |
| 79_A | 82_E | 1.219 | 0.67 |
| 111_V | 114_A | 1.216 | 0.67 |
| 16_F | 23_V | 1.214 | 0.67 |
| 3_K | 6_S | 1.204 | 0.66 |
| 16_F | 21_S | 1.204 | 0.66 |
| 183_K | 187_V | 1.200 | 0.66 |
| 135_T | 138_G | 1.198 | 0.65 |
| 31_N | 36_S | 1.193 | 0.65 |
| 31_N | 38_I | 1.189 | 0.65 |
| 301_E | 305_A | 1.188 | 0.65 |
| 5_S | 11_T | 1.187 | 0.64 |
| 9_L | 17_I | 1.186 | 0.64 |
| 11_T | 17_I | 1.183 | 0.64 |
| 24_A | 32_K | 1.176 | 0.63 |
| 10_L | 17_I | 1.175 | 0.63 |
| 17_I | 21_S | 1.175 | 0.63 |
| 38_I | 41_G | 1.175 | 0.63 |
| 42_N | 46_D | 1.175 | 0.63 |
| 117_G | 123_S | 1.173 | 0.63 |
| 113_T | 117_G | 1.169 | 0.63 |
| 35_Q | 40_L | 1.161 | 0.62 |
| 114_A | 123_S | 1.157 | 0.62 |
| 35_Q | 42_N | 1.157 | 0.62 |
| 298_K | 301_E | 1.155 | 0.61 |
| 272_D | 275_K | 1.155 | 0.61 |
| 24_A | 28_D | 1.150 | 0.61 |
| 83_K | 86_T | 1.144 | 0.60 |
| 14_F | 21_S | 1.143 | 0.60 |
| 23_V | 29_P | 1.140 | 0.60 |
| 297_V | 305_A | 1.137 | 0.59 |
| 168_A | 172_K | 1.135 | 0.59 |
| 30_T | 36_S | 1.132 | 0.59 |
| 7_A | 23_V | 1.129 | 0.59 |
| 17_I | 22_Q | 1.128 | 0.59 |
| 33_F | 41_G | 1.122 | 0.58 |
| 5_S | 13_F | 1.121 | 0.58 |
| 16_F | 25_D | 1.121 | 0.58 |
| 16_F | 26_K | 1.120 | 0.58 |
| 248_K | 251_E | 1.118 | 0.58 |
| 179_G | 183_K | 1.117 | 0.57 |
| 345_A | 350_T | 1.110 | 0.57 |
| 298_K | 305_A | 1.107 | 0.56 |
| 7_A | 12_T | 1.106 | 0.56 |
| 9_L | 24_A | 1.105 | 0.56 |
| 34_Y | 38_I | 1.104 | 0.56 |
| 8_I | 14_F | 1.104 | 0.56 |
| 29_P | 40_L | 1.101 | 0.56 |
| 78_A | 85_K | 1.101 | 0.56 |
| 35_Q | 39_Q | 1.101 | 0.56 |
| 116_E | 123_S | 1.101 | 0.56 |
| 278_D | 281_A | 1.099 | 0.56 |
| 266_G | 269_F | 1.096 | 0.55 |
| 2_K | 10_L | 1.096 | 0.55 |
| 344_K | 350_T | 1.095 | 0.55 |
| 257_A | 260_I | 1.093 | 0.55 |
| 4_I | 15_V | 1.088 | 0.54 |
| 4_I | 10_L | 1.082 | 0.54 |
| 254_N | 257_A | 1.079 | 0.54 |
| 346_A | 350_T | 1.079 | 0.54 |
| 83_K | 90_S | 1.079 | 0.54 |
| 15_V | 24_A | 1.076 | 0.53 |
| 197_G | 218_K | 1.065 | 0.52 |
| 33_F | 38_I | 1.063 | 0.52 |
| 320_V | 350_T | 1.061 | 0.52 |
| 5_S | 10_L | 1.054 | 0.51 |
| 14_F | 25_D | 1.053 | 0.51 |
| 2_K | 14_F | 1.050 | 0.51 |
| 307_G | 310_K | 1.045 | 0.50 |
| 301_E | 312_A | 1.045 | 0.50 |
| 2_K | 8_I | 1.040 | 0.49 |
| 108_T | 112_G | 1.036 | 0.49 |
| 108_T | 113_T | 1.034 | 0.49 |
| 28_D | 39_Q | 1.032 | 0.49 |
| 97_D | 103_G | 1.032 | 0.49 |
| 17_I | 24_A | 1.029 | 0.48 |
| 32_K | 38_I | 1.029 | 0.48 |
| 37_V | 41_G | 1.022 | 0.48 |
| 288_G | 313_A | 1.021 | 0.47 |
| 10_L | 18_N | 1.019 | 0.47 |
| 43_G | 46_D | 1.015 | 0.47 |
| 184_L | 187_V | 1.011 | 0.46 |
| 331_A | 334_S | 1.007 | 0.46 |
| 192_G | 197_G | 1.004 | 0.46 |
| 25_D | 28_D | 1.004 | 0.46 |
| 2_K | 9_L | 1.003 | 0.46 |
| 165_K | 169_K | 1.000 | 0.45 |
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 | |
| 1l8wA | 4 | 0.8567 | 100 | 0.217 | Contact Map |
| 2kvpA | 1 | 0.3287 | 32.6 | 0.969 | Contact Map |
| 2b0hA | 1 | 0.3287 | 20.7 | 0.972 | Contact Map |
| 2wtgA | 1 | 0.236 | 20.1 | 0.972 | Contact Map |
| 2wxfA | 1 | 0.1713 | 14.4 | 0.974 | Contact Map |
| 4lunU | 1 | 0.4101 | 14.2 | 0.974 | Contact Map |
| 2y3aA | 1 | 0.191 | 11.7 | 0.975 | Contact Map |
| 4cemA | 2 | 0.382 | 10.5 | 0.976 | Contact Map |
| 2wvrC | 1 | 0 | 10 | 0.976 | Contact Map |
| 4aurA | 1 | 0.264 | 9.9 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)