| 1EQCA |
| ID: | 1411764651 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 394 (391) | ||
| Sequences: | 592 (475.8) | ||
| Seq/Len: | 1.514 | ||
| Nf(neff/√len): | 24.1 |
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: 1.514).
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 |
| 24_M | 358_S | 3.574 | 1.00 |
| 87_I | 110_L | 3.407 | 1.00 |
| 131_A | 184_L | 2.989 | 1.00 |
| 199_Q | 203_D | 2.848 | 1.00 |
| 71_E | 120_N | 2.847 | 1.00 |
| 84_F | 355_V | 2.845 | 1.00 |
| 111_E | 169_Y | 2.710 | 1.00 |
| 20_L | 29_F | 2.669 | 1.00 |
| 71_E | 119_K | 2.634 | 1.00 |
| 131_A | 158_T | 2.516 | 1.00 |
| 17_W | 113_A | 2.490 | 1.00 |
| 10_R | 349_E | 2.489 | 1.00 |
| 80_L | 373_T | 2.402 | 1.00 |
| 289_A | 341_I | 2.212 | 0.99 |
| 111_E | 168_K | 2.204 | 0.99 |
| 87_I | 113_A | 2.111 | 0.99 |
| 74_F | 113_A | 2.062 | 0.98 |
| 90_G | 130_G | 2.060 | 0.98 |
| 77_I | 82_L | 2.023 | 0.98 |
| 305_A | 308_E | 2.007 | 0.98 |
| 63_K | 67_T | 1.964 | 0.98 |
| 125_W | 180_G | 1.926 | 0.97 |
| 117_A | 124_V | 1.903 | 0.97 |
| 76_Q | 374_Y | 1.880 | 0.97 |
| 74_F | 117_A | 1.854 | 0.96 |
| 56_A | 59_R | 1.835 | 0.96 |
| 78_S | 121_N | 1.798 | 0.96 |
| 250_Q | 340_Y | 1.737 | 0.94 |
| 19_V | 90_G | 1.718 | 0.94 |
| 129_H | 185_N | 1.700 | 0.94 |
| 133_G | 154_N | 1.674 | 0.93 |
| 71_E | 75_K | 1.666 | 0.93 |
| 341_I | 378_F | 1.645 | 0.92 |
| 72_Q | 76_Q | 1.625 | 0.91 |
| 73_D | 360_K | 1.623 | 0.91 |
| 162_L | 200_F | 1.616 | 0.91 |
| 189_G | 222_A | 1.616 | 0.91 |
| 49_T | 57_A | 1.610 | 0.91 |
| 93_A | 106_Q | 1.607 | 0.91 |
| 369_F | 373_T | 1.604 | 0.91 |
| 345_L | 378_F | 1.582 | 0.90 |
| 129_H | 357_W | 1.561 | 0.89 |
| 75_K | 79_N | 1.561 | 0.89 |
| 372_L | 377_L | 1.526 | 0.88 |
| 76_Q | 370_Q | 1.519 | 0.87 |
| 349_E | 354_W | 1.480 | 0.85 |
| 56_A | 60_I | 1.474 | 0.85 |
| 159_L | 204_G | 1.473 | 0.85 |
| 62_Q | 66_S | 1.473 | 0.85 |
| 159_L | 207_S | 1.468 | 0.85 |
| 114_L | 124_V | 1.465 | 0.85 |
| 180_G | 218_I | 1.461 | 0.84 |
| 77_I | 122_I | 1.448 | 0.84 |
| 92_W | 130_G | 1.442 | 0.83 |
| 331_D | 335_T | 1.436 | 0.83 |
| 359_W | 370_Q | 1.427 | 0.82 |
| 27_S | 362_E | 1.426 | 0.82 |
| 82_L | 369_F | 1.422 | 0.82 |
| 3_D | 6_N | 1.422 | 0.82 |
| 253_S | 256_E | 1.417 | 0.82 |
| 43_V | 144_R | 1.409 | 0.81 |
| 360_K | 370_Q | 1.403 | 0.81 |
| 75_K | 120_N | 1.393 | 0.80 |
| 185_N | 357_W | 1.389 | 0.80 |
| 69_I | 358_S | 1.386 | 0.80 |
| 187_P | 197_L | 1.377 | 0.79 |
| 107_V | 111_E | 1.368 | 0.79 |
| 256_E | 259_R | 1.360 | 0.78 |
| 16_G | 25_T | 1.349 | 0.77 |
| 125_W | 218_I | 1.339 | 0.76 |
| 289_A | 356_F | 1.338 | 0.76 |
| 208_L | 217_V | 1.333 | 0.76 |
| 204_G | 217_V | 1.328 | 0.76 |
| 260_N | 263_D | 1.319 | 0.75 |
| 100_D | 157_V | 1.289 | 0.73 |
| 269_C | 391_C | 1.287 | 0.72 |
| 15_G | 21_E | 1.286 | 0.72 |
| 154_N | 368_S | 1.277 | 0.72 |
| 129_H | 186_E | 1.276 | 0.71 |
| 341_I | 345_L | 1.272 | 0.71 |
| 46_Y | 102_Y | 1.271 | 0.71 |
| 11_G | 21_E | 1.260 | 0.70 |
| 134_S | 141_S | 1.251 | 0.69 |
| 69_I | 359_W | 1.245 | 0.69 |
| 2_W | 5_D | 1.240 | 0.68 |
| 136_N | 141_S | 1.235 | 0.68 |
| 134_S | 137_G | 1.232 | 0.68 |
| 62_Q | 108_Q | 1.228 | 0.67 |
| 304_G | 310_A | 1.220 | 0.66 |
| 67_T | 70_T | 1.212 | 0.66 |
| 370_Q | 374_Y | 1.210 | 0.66 |
| 86_R | 247_H | 1.206 | 0.65 |
| 90_G | 181_I | 1.196 | 0.64 |
| 94_F | 107_V | 1.193 | 0.64 |
| 197_L | 201_F | 1.190 | 0.64 |
| 129_H | 286_E | 1.189 | 0.64 |
| 105_G | 140_N | 1.187 | 0.63 |
| 220_H | 223_F | 1.184 | 0.63 |
| 112_K | 126_I | 1.180 | 0.63 |
| 287_W | 354_W | 1.179 | 0.63 |
| 186_E | 249_Y | 1.179 | 0.63 |
| 183_L | 204_G | 1.176 | 0.62 |
| 186_E | 357_W | 1.175 | 0.62 |
| 43_V | 47_H | 1.175 | 0.62 |
| 48_W | 60_I | 1.168 | 0.62 |
| 346_D | 385_R | 1.164 | 0.61 |
| 16_G | 24_M | 1.155 | 0.60 |
| 307_Y | 323_L | 1.140 | 0.59 |
| 77_I | 359_W | 1.139 | 0.59 |
| 15_G | 357_W | 1.138 | 0.59 |
| 109_Y | 112_K | 1.136 | 0.58 |
| 249_Y | 286_E | 1.135 | 0.58 |
| 49_T | 61_L | 1.135 | 0.58 |
| 250_Q | 268_A | 1.135 | 0.58 |
| 128_L | 344_Q | 1.135 | 0.58 |
| 78_S | 120_N | 1.129 | 0.58 |
| 23_Y | 181_I | 1.128 | 0.58 |
| 76_Q | 359_W | 1.123 | 0.57 |
| 118_R | 172_N | 1.120 | 0.57 |
| 75_K | 119_K | 1.120 | 0.57 |
| 65_W | 90_G | 1.116 | 0.56 |
| 186_E | 286_E | 1.115 | 0.56 |
| 359_W | 373_T | 1.107 | 0.55 |
| 22_P | 359_W | 1.106 | 0.55 |
| 344_Q | 348_F | 1.105 | 0.55 |
| 68_W | 358_S | 1.104 | 0.55 |
| 15_G | 129_H | 1.103 | 0.55 |
| 156_Q | 160_N | 1.101 | 0.55 |
| 389_N | 392_G | 1.100 | 0.55 |
| 118_R | 176_D | 1.098 | 0.54 |
| 129_H | 142_G | 1.096 | 0.54 |
| 356_F | 372_L | 1.089 | 0.54 |
| 174_Y | 192_L | 1.085 | 0.53 |
| 11_G | 15_G | 1.083 | 0.53 |
| 154_N | 157_V | 1.083 | 0.53 |
| 107_V | 168_K | 1.078 | 0.52 |
| 384_D | 389_N | 1.078 | 0.52 |
| 267_V | 356_F | 1.077 | 0.52 |
| 95_Q | 157_V | 1.076 | 0.52 |
| 30_E | 296_K | 1.075 | 0.52 |
| 53_G | 103_V | 1.067 | 0.51 |
| 116_W | 205_Y | 1.061 | 0.51 |
| 8_V | 83_N | 1.061 | 0.51 |
| 142_G | 185_N | 1.056 | 0.50 |
| 14_L | 18_F | 1.054 | 0.50 |
| 52_L | 103_V | 1.054 | 0.50 |
| 313_N | 317_I | 1.052 | 0.50 |
| 166_F | 208_L | 1.051 | 0.50 |
| 326_I | 378_F | 1.049 | 0.49 |
| 27_S | 85_V | 1.048 | 0.49 |
| 74_F | 120_N | 1.040 | 0.48 |
| 341_I | 368_S | 1.040 | 0.48 |
| 156_Q | 159_L | 1.035 | 0.48 |
| 268_A | 343_A | 1.035 | 0.48 |
| 16_G | 358_S | 1.035 | 0.48 |
| 52_L | 372_L | 1.035 | 0.48 |
| 361_T | 368_S | 1.032 | 0.48 |
| 90_G | 106_Q | 1.029 | 0.47 |
| 78_S | 117_A | 1.029 | 0.47 |
| 13_N | 245_D | 1.029 | 0.47 |
| 152_G | 156_Q | 1.026 | 0.47 |
| 75_K | 78_S | 1.024 | 0.47 |
| 95_Q | 161_V | 1.024 | 0.47 |
| 307_Y | 317_I | 1.024 | 0.47 |
| 299_N | 306_R | 1.023 | 0.47 |
| 59_R | 63_K | 1.021 | 0.46 |
| 2_W | 303_R | 1.019 | 0.46 |
| 49_T | 103_V | 1.019 | 0.46 |
| 15_G | 185_N | 1.011 | 0.45 |
| 199_Q | 270_N | 1.010 | 0.45 |
| 10_R | 354_W | 1.009 | 0.45 |
| 295_A | 364_A | 1.006 | 0.45 |
| 165_I | 265_I | 1.006 | 0.45 |
| 53_G | 90_G | 1.006 | 0.45 |
| 14_L | 19_V | 1.004 | 0.45 |
| 126_I | 165_I | 1.001 | 0.44 |
| 286_E | 357_W | 1.000 | 0.44 |
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 | |
| 1h4pA | 2 | 1 | 100 | 0.256 | Contact Map |
| 1ceoA | 1 | 0.7234 | 100 | 0.728 | Contact Map |
| 3zmrA | 2 | 0.8096 | 100 | 0.731 | Contact Map |
| 3w0kA | 2 | 0.7234 | 100 | 0.733 | Contact Map |
| 1edgA | 1 | 0.802 | 100 | 0.736 | Contact Map |
| 3ncoA | 2 | 0.6954 | 100 | 0.74 | Contact Map |
| 3l55A | 2 | 0.7893 | 100 | 0.74 | Contact Map |
| 3aofA | 2 | 0.698 | 100 | 0.743 | Contact Map |
| 1vjzA | 1 | 0.7183 | 100 | 0.747 | Contact Map |
| 3ayrA | 1 | 0.7919 | 100 | 0.753 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)