| me |
| ID: | 1418102480 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 256 (256) | ||
| Sequences: | 947 (713.8) | ||
| Seq/Len: | 3.699 | ||
| Nf(neff/√len): | 44.6 |
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: 3.699).
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 |
| 52_I | 56_L | 3.623 | 1.00 |
| 30_N | 150_I | 3.603 | 1.00 |
| 142_D | 145_Q | 2.998 | 1.00 |
| 60_N | 63_R | 2.710 | 1.00 |
| 100_D | 223_R | 2.617 | 1.00 |
| 241_D | 244_S | 2.613 | 1.00 |
| 47_S | 54_D | 2.399 | 1.00 |
| 226_K | 229_Q | 2.371 | 1.00 |
| 81_L | 101_F | 2.355 | 1.00 |
| 187_E | 248_G | 2.280 | 1.00 |
| 104_A | 220_I | 2.249 | 1.00 |
| 100_D | 221_E | 2.218 | 1.00 |
| 61_A | 65_H | 2.199 | 1.00 |
| 168_I | 219_I | 2.173 | 1.00 |
| 92_Q | 95_T | 2.172 | 1.00 |
| 228_E | 231_T | 2.164 | 1.00 |
| 217_R | 221_E | 2.155 | 1.00 |
| 4_L | 167_V | 2.140 | 1.00 |
| 17_L | 77_R | 2.138 | 1.00 |
| 3_I | 219_I | 2.119 | 1.00 |
| 96_F | 100_D | 2.051 | 1.00 |
| 241_D | 253_K | 2.022 | 1.00 |
| 10_T | 84_K | 1.998 | 1.00 |
| 97_S | 100_D | 1.901 | 1.00 |
| 137_N | 140_G | 1.885 | 1.00 |
| 38_A | 64_F | 1.884 | 1.00 |
| 103_F | 107_H | 1.842 | 1.00 |
| 5_I | 216_S | 1.841 | 1.00 |
| 246_S | 249_E | 1.817 | 0.99 |
| 149_D | 153_N | 1.811 | 0.99 |
| 151_I | 178_S | 1.799 | 0.99 |
| 227_P | 250_L | 1.781 | 0.99 |
| 96_F | 101_F | 1.780 | 0.99 |
| 26_E | 154_K | 1.698 | 0.99 |
| 5_I | 108_L | 1.686 | 0.99 |
| 194_L | 253_K | 1.674 | 0.99 |
| 104_A | 216_S | 1.666 | 0.99 |
| 231_T | 250_L | 1.662 | 0.99 |
| 96_F | 217_R | 1.655 | 0.99 |
| 5_I | 87_V | 1.630 | 0.99 |
| 100_D | 220_I | 1.622 | 0.98 |
| 86_D | 206_F | 1.616 | 0.98 |
| 219_I | 224_L | 1.603 | 0.98 |
| 13_Y | 82_A | 1.594 | 0.98 |
| 59_I | 63_R | 1.574 | 0.98 |
| 46_I | 52_I | 1.567 | 0.98 |
| 244_S | 253_K | 1.525 | 0.97 |
| 105_Q | 121_L | 1.517 | 0.97 |
| 31_S | 67_W | 1.510 | 0.97 |
| 195_D | 205_S | 1.496 | 0.97 |
| 58_G | 62_A | 1.487 | 0.97 |
| 15_S | 77_R | 1.454 | 0.96 |
| 103_F | 220_I | 1.416 | 0.96 |
| 90_G | 210_K | 1.400 | 0.95 |
| 52_I | 57_A | 1.388 | 0.95 |
| 96_F | 104_A | 1.378 | 0.95 |
| 81_L | 96_F | 1.368 | 0.94 |
| 10_T | 89_T | 1.357 | 0.94 |
| 201_F | 253_K | 1.349 | 0.94 |
| 141_K | 145_Q | 1.348 | 0.94 |
| 28_L | 70_D | 1.335 | 0.93 |
| 208_A | 212_R | 1.335 | 0.93 |
| 76_A | 123_L | 1.319 | 0.93 |
| 109_R | 158_A | 1.298 | 0.92 |
| 113_G | 131_M | 1.284 | 0.92 |
| 219_I | 230_L | 1.283 | 0.92 |
| 196_E | 255_Y | 1.281 | 0.91 |
| 91_L | 216_S | 1.277 | 0.91 |
| 247_N | 250_L | 1.270 | 0.91 |
| 168_I | 191_P | 1.255 | 0.90 |
| 99_D | 223_R | 1.249 | 0.90 |
| 191_P | 250_L | 1.247 | 0.90 |
| 240_F | 250_L | 1.239 | 0.90 |
| 214_L | 236_E | 1.239 | 0.90 |
| 192_V | 249_E | 1.235 | 0.89 |
| 151_I | 179_V | 1.228 | 0.89 |
| 87_V | 206_F | 1.218 | 0.88 |
| 26_E | 158_A | 1.217 | 0.88 |
| 31_S | 146_F | 1.213 | 0.88 |
| 196_E | 256_E | 1.211 | 0.88 |
| 149_D | 180_K | 1.204 | 0.88 |
| 207_Y | 254_R | 1.178 | 0.86 |
| 224_L | 229_Q | 1.176 | 0.86 |
| 8_A | 11_L | 1.174 | 0.86 |
| 37_E | 135_L | 1.173 | 0.86 |
| 84_K | 89_T | 1.151 | 0.84 |
| 95_T | 217_R | 1.129 | 0.83 |
| 2_L | 165_N | 1.125 | 0.82 |
| 84_K | 94_E | 1.100 | 0.80 |
| 42_T | 45_Q | 1.099 | 0.80 |
| 22_Y | 73_P | 1.095 | 0.80 |
| 62_A | 66_D | 1.089 | 0.80 |
| 35_I | 114_L | 1.083 | 0.79 |
| 4_L | 155_L | 1.082 | 0.79 |
| 87_V | 204_I | 1.079 | 0.79 |
| 37_E | 41_L | 1.078 | 0.79 |
| 239_F | 255_Y | 1.062 | 0.77 |
| 27_L | 196_E | 1.061 | 0.77 |
| 216_S | 220_I | 1.058 | 0.77 |
| 131_M | 175_Y | 1.048 | 0.76 |
| 250_L | 253_K | 1.048 | 0.76 |
| 18_T | 81_L | 1.044 | 0.75 |
| 221_E | 235_S | 1.042 | 0.75 |
| 95_T | 221_E | 1.040 | 0.75 |
| 158_A | 163_G | 1.030 | 0.74 |
| 12_D | 82_A | 1.028 | 0.74 |
| 148_G | 151_I | 1.027 | 0.74 |
| 173_D | 190_K | 1.023 | 0.73 |
| 113_G | 130_E | 1.023 | 0.73 |
| 79_A | 88_Y | 1.013 | 0.72 |
| 77_R | 82_A | 1.007 | 0.72 |
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 | |
| 3eyiA | 2 | 0.2422 | 14.8 | 0.966 | Contact Map |
| 4glxA | 1 | 0.3281 | 8.7 | 0.969 | Contact Map |
| 4a1qA | 2 | 0.2617 | 8.2 | 0.97 | Contact Map |
| 1wrdA | 1 | 0.2734 | 7.4 | 0.97 | Contact Map |
| 3hixA | 3 | 0.3359 | 6.7 | 0.971 | Contact Map |
| 2duyA | 1 | 0.25 | 6.6 | 0.971 | Contact Map |
| 2yfvC | 1 | 0.2266 | 5.4 | 0.972 | Contact Map |
| 1wgrA | 1 | 0.2812 | 4.9 | 0.973 | Contact Map |
| 4tp8B | 1 | 0.457 | 4.7 | 0.973 | Contact Map |
| 2v1lA | 1 | 0.3359 | 4.7 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)