| Slam 70-488 |
| ID: | 1499516668 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 419 (411) | ||
| Sequences: | 658 (599.4) | ||
| Seq/Len: | 1.601 | ||
| Nf(neff/√len): | 29.6 |
HHblits Results: (2016_02)
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: 1.601).
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 |
| 64_R | 67_E | 4.387 | 1.00 |
| 86_R | 105_Q | 2.997 | 1.00 |
| 261_W | 291_L | 2.767 | 1.00 |
| 367_D | 399_S | 2.534 | 1.00 |
| 392_L | 409_N | 2.530 | 1.00 |
| 56_G | 72_Y | 2.494 | 1.00 |
| 115_P | 118_L | 2.337 | 1.00 |
| 333_W | 340_S | 2.278 | 0.99 |
| 306_D | 326_R | 2.219 | 0.99 |
| 34_R | 62_D | 2.217 | 0.99 |
| 209_D | 236_R | 2.118 | 0.99 |
| 144_T | 171_A | 2.110 | 0.99 |
| 267_A | 285_L | 2.108 | 0.99 |
| 188_W | 218_I | 2.097 | 0.99 |
| 309_R | 352_E | 2.083 | 0.99 |
| 106_F | 125_Y | 2.078 | 0.99 |
| 110_K | 123_E | 2.050 | 0.99 |
| 397_T | 406_Y | 2.035 | 0.99 |
| 302_M | 328_A | 1.980 | 0.98 |
| 225_K | 253_F | 1.938 | 0.98 |
| 105_Q | 108_R | 1.890 | 0.97 |
| 306_D | 324_G | 1.885 | 0.97 |
| 29_N | 32_G | 1.866 | 0.97 |
| 94_F | 128_A | 1.864 | 0.97 |
| 103_A | 130_R | 1.846 | 0.97 |
| 190_T | 216_G | 1.827 | 0.96 |
| 394_H | 409_N | 1.822 | 0.96 |
| 267_A | 287_I | 1.809 | 0.96 |
| 53_Y | 84_A | 1.801 | 0.96 |
| 261_W | 293_F | 1.794 | 0.96 |
| 87_M | 90_A | 1.772 | 0.96 |
| 73_R | 93_L | 1.769 | 0.96 |
| 75_L | 85_V | 1.743 | 0.95 |
| 146_E | 408_K | 1.732 | 0.95 |
| 174_Y | 198_G | 1.723 | 0.95 |
| 103_A | 126_R | 1.718 | 0.95 |
| 351_Y | 367_D | 1.717 | 0.95 |
| 290_S | 304_G | 1.672 | 0.93 |
| 225_K | 255_R | 1.671 | 0.93 |
| 52_L | 74_E | 1.640 | 0.93 |
| 53_Y | 88_R | 1.629 | 0.92 |
| 145_R | 170_T | 1.616 | 0.92 |
| 84_A | 118_L | 1.615 | 0.92 |
| 55_Q | 71_H | 1.603 | 0.91 |
| 69_I | 89_L | 1.602 | 0.91 |
| 71_H | 74_E | 1.601 | 0.91 |
| 305_L | 323_Y | 1.596 | 0.91 |
| 86_R | 108_R | 1.581 | 0.91 |
| 299_Q | 331_Q | 1.570 | 0.90 |
| 349_R | 369_E | 1.569 | 0.90 |
| 69_I | 92_A | 1.564 | 0.90 |
| 84_A | 88_R | 1.558 | 0.90 |
| 145_R | 169_G | 1.547 | 0.89 |
| 265_S | 289_N | 1.523 | 0.88 |
| 59_A | 67_E | 1.504 | 0.88 |
| 94_F | 125_Y | 1.502 | 0.88 |
| 380_A | 388_P | 1.500 | 0.87 |
| 87_M | 118_L | 1.496 | 0.87 |
| 69_I | 147_H | 1.489 | 0.87 |
| 146_E | 410_R | 1.484 | 0.87 |
| 235_R | 242_A | 1.465 | 0.86 |
| 365_R | 401_D | 1.464 | 0.86 |
| 385_G | 388_P | 1.459 | 0.85 |
| 148_N | 399_S | 1.459 | 0.85 |
| 107_D | 126_R | 1.453 | 0.85 |
| 56_G | 71_H | 1.437 | 0.84 |
| 5_I | 8_E | 1.430 | 0.84 |
| 193_G | 215_S | 1.427 | 0.84 |
| 148_N | 367_D | 1.424 | 0.83 |
| 56_G | 85_V | 1.405 | 0.82 |
| 238_Y | 243_Y | 1.399 | 0.82 |
| 21_M | 40_Y | 1.396 | 0.82 |
| 351_Y | 399_S | 1.382 | 0.81 |
| 229_L | 251_L | 1.357 | 0.79 |
| 98_Q | 101_A | 1.355 | 0.79 |
| 320_F | 349_R | 1.354 | 0.79 |
| 87_M | 115_P | 1.342 | 0.78 |
| 56_G | 92_A | 1.328 | 0.77 |
| 378_H | 381_L | 1.321 | 0.77 |
| 11_L | 17_L | 1.319 | 0.76 |
| 60_Q | 95_E | 1.318 | 0.76 |
| 84_A | 87_M | 1.314 | 0.76 |
| 118_L | 121_Q | 1.303 | 0.75 |
| 73_R | 101_A | 1.295 | 0.75 |
| 304_G | 328_A | 1.295 | 0.75 |
| 141_F | 289_N | 1.293 | 0.74 |
| 7_G | 11_L | 1.291 | 0.74 |
| 90_A | 109_L | 1.288 | 0.74 |
| 346_A | 368_K | 1.287 | 0.74 |
| 41_L | 55_Q | 1.275 | 0.73 |
| 135_W | 180_K | 1.270 | 0.73 |
| 89_L | 93_L | 1.268 | 0.72 |
| 99_N | 132_R | 1.261 | 0.72 |
| 87_M | 91_A | 1.259 | 0.72 |
| 53_Y | 75_L | 1.258 | 0.72 |
| 116_P | 119_M | 1.251 | 0.71 |
| 53_Y | 85_V | 1.244 | 0.70 |
| 59_A | 71_H | 1.243 | 0.70 |
| 84_A | 121_Q | 1.241 | 0.70 |
| 24_A | 27_S | 1.237 | 0.70 |
| 394_H | 407_E | 1.230 | 0.69 |
| 142_S | 414_E | 1.230 | 0.69 |
| 171_A | 201_Y | 1.220 | 0.68 |
| 6_D | 13_N | 1.215 | 0.68 |
| 295_R | 301_W | 1.209 | 0.67 |
| 53_Y | 118_L | 1.197 | 0.66 |
| 53_Y | 87_M | 1.196 | 0.66 |
| 401_D | 404_N | 1.191 | 0.65 |
| 137_V | 178_A | 1.191 | 0.65 |
| 266_S | 288_S | 1.186 | 0.65 |
| 60_Q | 92_A | 1.178 | 0.64 |
| 65_V | 92_A | 1.177 | 0.64 |
| 110_K | 119_M | 1.173 | 0.64 |
| 229_L | 413_V | 1.170 | 0.63 |
| 224_R | 349_R | 1.168 | 0.63 |
| 338_L | 378_H | 1.164 | 0.63 |
| 87_M | 122_V | 1.158 | 0.62 |
| 106_F | 118_L | 1.154 | 0.62 |
| 205_K | 208_N | 1.147 | 0.61 |
| 5_I | 9_T | 1.147 | 0.61 |
| 53_Y | 82_A | 1.147 | 0.61 |
| 146_E | 169_G | 1.145 | 0.61 |
| 60_Q | 68_A | 1.145 | 0.61 |
| 106_F | 122_V | 1.136 | 0.60 |
| 59_A | 122_V | 1.133 | 0.60 |
| 299_Q | 329_W | 1.128 | 0.59 |
| 84_A | 115_P | 1.128 | 0.59 |
| 94_F | 129_L | 1.127 | 0.59 |
| 24_A | 36_I | 1.127 | 0.59 |
| 343_R | 373_S | 1.126 | 0.59 |
| 172_V | 227_A | 1.125 | 0.59 |
| 369_E | 397_T | 1.123 | 0.59 |
| 6_D | 9_T | 1.122 | 0.59 |
| 123_E | 303_G | 1.120 | 0.58 |
| 49_M | 75_L | 1.120 | 0.58 |
| 8_E | 12_K | 1.119 | 0.58 |
| 149_I | 169_G | 1.118 | 0.58 |
| 76_I | 86_R | 1.117 | 0.58 |
| 72_Y | 89_L | 1.114 | 0.58 |
| 5_I | 12_K | 1.114 | 0.58 |
| 290_S | 306_D | 1.111 | 0.57 |
| 143_V | 170_T | 1.105 | 0.57 |
| 76_I | 115_P | 1.099 | 0.56 |
| 340_S | 376_L | 1.099 | 0.56 |
| 169_G | 204_N | 1.092 | 0.56 |
| 380_A | 385_G | 1.090 | 0.55 |
| 103_A | 107_D | 1.085 | 0.55 |
| 123_E | 127_K | 1.085 | 0.55 |
| 325_L | 346_A | 1.084 | 0.55 |
| 153_P | 165_K | 1.081 | 0.54 |
| 25_V | 30_I | 1.076 | 0.54 |
| 151_Q | 237_T | 1.074 | 0.54 |
| 88_R | 91_A | 1.074 | 0.54 |
| 354_P | 364_R | 1.071 | 0.53 |
| 355_G | 363_E | 1.070 | 0.53 |
| 76_I | 85_V | 1.065 | 0.53 |
| 91_A | 95_E | 1.064 | 0.53 |
| 4_Q | 8_E | 1.064 | 0.53 |
| 31_A | 34_R | 1.063 | 0.52 |
| 384_K | 388_P | 1.061 | 0.52 |
| 246_T | 270_G | 1.060 | 0.52 |
| 94_F | 99_N | 1.058 | 0.52 |
| 148_N | 365_R | 1.053 | 0.51 |
| 65_V | 260_K | 1.044 | 0.50 |
| 87_M | 121_Q | 1.038 | 0.50 |
| 13_N | 16_L | 1.036 | 0.50 |
| 88_R | 274_N | 1.036 | 0.50 |
| 9_T | 12_K | 1.036 | 0.50 |
| 385_G | 417_K | 1.035 | 0.50 |
| 53_Y | 90_A | 1.034 | 0.49 |
| 81_D | 147_H | 1.034 | 0.49 |
| 171_A | 248_G | 1.029 | 0.49 |
| 103_A | 129_L | 1.027 | 0.49 |
| 57_I | 72_Y | 1.025 | 0.48 |
| 257_Q | 263_T | 1.025 | 0.48 |
| 169_G | 388_P | 1.022 | 0.48 |
| 108_R | 332_E | 1.021 | 0.48 |
| 4_Q | 12_K | 1.018 | 0.48 |
| 229_L | 249_A | 1.016 | 0.48 |
| 125_Y | 128_A | 1.015 | 0.47 |
| 59_A | 90_A | 1.015 | 0.47 |
| 142_S | 176_L | 1.014 | 0.47 |
| 132_R | 141_F | 1.014 | 0.47 |
| 389_R | 414_E | 1.011 | 0.47 |
| 294_Y | 300_Y | 1.011 | 0.47 |
| 127_K | 251_L | 1.010 | 0.47 |
| 30_I | 33_I | 1.010 | 0.47 |
| 75_L | 171_A | 1.010 | 0.47 |
| 32_G | 35_V | 1.009 | 0.47 |
| 133_D | 183_S | 1.007 | 0.47 |
| 64_R | 96_N | 1.006 | 0.46 |
| 198_G | 210_M | 1.005 | 0.46 |
| 307_F | 321_N | 1.005 | 0.46 |
| 24_A | 32_G | 1.004 | 0.46 |
| 69_I | 73_R | 1.001 | 0.46 |
| 351_Y | 400_N | 1.000 | 0.46 |
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 | |
| 2xevA | 3 | 0.2816 | 99.2 | 0.816 | Contact Map |
| 3gyzA | 2 | 0.2983 | 99.1 | 0.829 | Contact Map |
| 4j8fA | 1 | 0.3437 | 99 | 0.83 | Contact Map |
| 4nrhB | 2 | 0.3007 | 99 | 0.832 | Contact Map |
| 3rkvA | 1 | 0.3055 | 99 | 0.833 | Contact Map |
| 3upvA | 1 | 0.2888 | 99 | 0.833 | Contact Map |
| 2dbaA | 1 | 0.3126 | 99 | 0.833 | Contact Map |
| 1ihgA | 1 | 0.3198 | 99 | 0.834 | Contact Map |
| 2fbnA | 2 | 0.3174 | 99 | 0.834 | Contact Map |
| 2if4A | 1 | 0.2625 | 99 | 0.835 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)