| nd4 |
| ID: | 1499526956 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 392 (392) | ||
| Sequences: | 730 (207.4) | ||
| Seq/Len: | 1.862 | ||
| Nf(neff/√len): | 10.5 |
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: 1.862).
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 |
| 35_P | 267_T | 3.064 | 1.00 |
| 73_L | 92_A | 2.989 | 1.00 |
| 197_M | 255_I | 2.778 | 1.00 |
| 128_L | 156_A | 2.543 | 1.00 |
| 265_G | 334_F | 2.516 | 1.00 |
| 319_T | 326_S | 2.049 | 0.99 |
| 37_L | 79_T | 2.019 | 0.99 |
| 84_I | 133_I | 1.981 | 0.99 |
| 269_L | 331_G | 1.917 | 0.98 |
| 166_L | 363_Y | 1.892 | 0.98 |
| 317_S | 364_M | 1.811 | 0.97 |
| 32_L | 198_L | 1.780 | 0.97 |
| 253_A | 339_A | 1.766 | 0.97 |
| 84_I | 88_I | 1.748 | 0.96 |
| 254_A | 262_S | 1.726 | 0.96 |
| 128_L | 144_F | 1.708 | 0.96 |
| 40_T | 368_T | 1.701 | 0.96 |
| 250_L | 336_V | 1.633 | 0.94 |
| 11_N | 189_L | 1.632 | 0.94 |
| 198_L | 268_A | 1.631 | 0.94 |
| 309_M | 383_S | 1.621 | 0.94 |
| 231_L | 359_L | 1.607 | 0.94 |
| 226_T | 229_I | 1.601 | 0.93 |
| 236_L | 269_L | 1.582 | 0.93 |
| 3_P | 7_L | 1.581 | 0.93 |
| 156_A | 189_L | 1.562 | 0.92 |
| 11_N | 141_S | 1.557 | 0.92 |
| 306_L | 383_S | 1.547 | 0.92 |
| 1_I | 72_V | 1.457 | 0.88 |
| 231_L | 252_I | 1.455 | 0.88 |
| 130_V | 198_L | 1.448 | 0.88 |
| 358_A | 362_L | 1.444 | 0.88 |
| 292_H | 361_S | 1.430 | 0.87 |
| 240_I | 284_A | 1.401 | 0.85 |
| 216_L | 305_F | 1.392 | 0.85 |
| 231_L | 272_A | 1.373 | 0.84 |
| 161_M | 269_L | 1.368 | 0.83 |
| 236_L | 336_V | 1.357 | 0.83 |
| 37_L | 59_R | 1.341 | 0.82 |
| 53_S | 58_P | 1.332 | 0.81 |
| 128_L | 189_L | 1.320 | 0.80 |
| 36_L | 373_H | 1.311 | 0.80 |
| 48_L | 64_I | 1.305 | 0.79 |
| 132_L | 153_C | 1.305 | 0.79 |
| 225_M | 368_T | 1.304 | 0.79 |
| 132_L | 203_M | 1.294 | 0.79 |
| 131_A | 152_A | 1.290 | 0.78 |
| 111_L | 280_L | 1.286 | 0.78 |
| 361_S | 364_M | 1.281 | 0.78 |
| 67_L | 218_L | 1.275 | 0.77 |
| 249_A | 252_I | 1.275 | 0.77 |
| 189_L | 201_T | 1.265 | 0.76 |
| 292_H | 368_T | 1.264 | 0.76 |
| 36_L | 156_A | 1.261 | 0.76 |
| 129_L | 156_A | 1.256 | 0.76 |
| 11_N | 128_L | 1.253 | 0.75 |
| 234_T | 272_A | 1.251 | 0.75 |
| 161_M | 204_L | 1.247 | 0.75 |
| 287_N | 375_H | 1.246 | 0.75 |
| 263_Y | 284_A | 1.240 | 0.74 |
| 117_F | 204_L | 1.240 | 0.74 |
| 65_T | 72_V | 1.228 | 0.73 |
| 348_L | 392_A | 1.222 | 0.73 |
| 6_M | 9_P | 1.219 | 0.72 |
| 94_L | 358_A | 1.219 | 0.72 |
| 267_T | 271_I | 1.218 | 0.72 |
| 198_L | 263_Y | 1.217 | 0.72 |
| 64_I | 336_V | 1.214 | 0.72 |
| 24_S | 380_I | 1.212 | 0.72 |
| 189_L | 298_L | 1.211 | 0.72 |
| 197_M | 296_M | 1.211 | 0.72 |
| 150_W | 221_W | 1.210 | 0.72 |
| 179_I | 246_S | 1.210 | 0.72 |
| 144_F | 343_S | 1.209 | 0.72 |
| 223_M | 353_N | 1.202 | 0.71 |
| 297_I | 342_W | 1.198 | 0.71 |
| 44_L | 367_M | 1.197 | 0.70 |
| 36_L | 128_L | 1.197 | 0.70 |
| 246_S | 357_T | 1.195 | 0.70 |
| 140_G | 364_M | 1.191 | 0.70 |
| 309_M | 342_W | 1.189 | 0.70 |
| 9_P | 286_S | 1.188 | 0.70 |
| 151_L | 374_T | 1.188 | 0.70 |
| 305_F | 346_T | 1.184 | 0.69 |
| 35_P | 225_M | 1.183 | 0.69 |
| 168_L | 362_L | 1.183 | 0.69 |
| 262_S | 389_A | 1.181 | 0.69 |
| 265_G | 343_S | 1.180 | 0.69 |
| 50_A | 390_L | 1.178 | 0.69 |
| 129_L | 148_F | 1.177 | 0.69 |
| 4_T | 7_L | 1.171 | 0.68 |
| 64_I | 209_E | 1.171 | 0.68 |
| 65_T | 336_V | 1.170 | 0.68 |
| 35_P | 271_I | 1.157 | 0.67 |
| 271_I | 344_N | 1.155 | 0.67 |
| 306_L | 309_M | 1.155 | 0.67 |
| 25_L | 321_L | 1.153 | 0.66 |
| 45_P | 340_F | 1.149 | 0.66 |
| 66_M | 158_L | 1.147 | 0.66 |
| 16_L | 63_Y | 1.145 | 0.66 |
| 215_F | 256_L | 1.145 | 0.66 |
| 117_F | 299_A | 1.141 | 0.65 |
| 57_E | 141_S | 1.129 | 0.64 |
| 84_I | 336_V | 1.127 | 0.64 |
| 88_I | 164_Y | 1.125 | 0.64 |
| 129_L | 189_L | 1.123 | 0.63 |
| 27_F | 55_L | 1.121 | 0.63 |
| 61_K | 115_L | 1.118 | 0.63 |
| 52_Q | 265_G | 1.117 | 0.63 |
| 156_A | 161_M | 1.113 | 0.62 |
| 89_M | 327_I | 1.106 | 0.62 |
| 154_M | 200_I | 1.104 | 0.61 |
| 276_T | 279_M | 1.104 | 0.61 |
| 135_L | 341_S | 1.104 | 0.61 |
| 123_V | 198_L | 1.101 | 0.61 |
| 92_A | 130_V | 1.101 | 0.61 |
| 266_A | 336_V | 1.100 | 0.61 |
| 23_Y | 215_F | 1.100 | 0.61 |
| 31_P | 141_S | 1.098 | 0.61 |
| 189_L | 380_I | 1.092 | 0.60 |
| 102_T | 250_L | 1.089 | 0.60 |
| 296_M | 367_M | 1.089 | 0.60 |
| 76_M | 79_T | 1.087 | 0.60 |
| 1_I | 27_F | 1.087 | 0.60 |
| 67_L | 361_S | 1.085 | 0.59 |
| 7_L | 57_E | 1.084 | 0.59 |
| 57_E | 60_K | 1.084 | 0.59 |
| 124_G | 299_A | 1.082 | 0.59 |
| 151_L | 304_I | 1.082 | 0.59 |
| 152_A | 256_L | 1.082 | 0.59 |
| 148_F | 305_F | 1.082 | 0.59 |
| 23_Y | 130_V | 1.082 | 0.59 |
| 118_L | 142_L | 1.078 | 0.59 |
| 223_M | 249_A | 1.075 | 0.58 |
| 305_F | 381_T | 1.074 | 0.58 |
| 251_V | 269_L | 1.071 | 0.58 |
| 27_F | 76_M | 1.070 | 0.58 |
| 330_I | 347_I | 1.070 | 0.58 |
| 180_A | 266_A | 1.069 | 0.58 |
| 161_M | 179_I | 1.067 | 0.57 |
| 128_L | 269_L | 1.066 | 0.57 |
| 9_P | 117_F | 1.066 | 0.57 |
| 200_I | 215_F | 1.066 | 0.57 |
| 336_V | 343_S | 1.065 | 0.57 |
| 129_L | 269_L | 1.063 | 0.57 |
| 388_H | 391_M | 1.062 | 0.57 |
| 317_S | 361_S | 1.061 | 0.57 |
| 133_I | 299_A | 1.056 | 0.56 |
| 140_G | 207_L | 1.056 | 0.56 |
| 297_I | 361_S | 1.056 | 0.56 |
| 36_L | 229_I | 1.054 | 0.56 |
| 189_L | 269_L | 1.053 | 0.56 |
| 268_A | 272_A | 1.052 | 0.56 |
| 123_V | 130_V | 1.052 | 0.56 |
| 232_R | 261_W | 1.051 | 0.56 |
| 236_L | 250_L | 1.050 | 0.56 |
| 102_T | 111_L | 1.047 | 0.55 |
| 151_L | 352_T | 1.046 | 0.55 |
| 92_A | 148_F | 1.045 | 0.55 |
| 23_Y | 61_K | 1.044 | 0.55 |
| 152_A | 197_M | 1.044 | 0.55 |
| 251_V | 331_G | 1.043 | 0.55 |
| 1_I | 12_S | 1.042 | 0.55 |
| 131_A | 382_P | 1.039 | 0.54 |
| 84_I | 189_L | 1.035 | 0.54 |
| 156_A | 198_L | 1.035 | 0.54 |
| 7_L | 309_M | 1.032 | 0.54 |
| 73_L | 158_L | 1.030 | 0.53 |
| 184_V | 297_I | 1.030 | 0.53 |
| 224_I | 266_A | 1.029 | 0.53 |
| 345_P | 352_T | 1.026 | 0.53 |
| 155_M | 310_A | 1.024 | 0.53 |
| 250_L | 353_N | 1.024 | 0.53 |
| 201_T | 211_M | 1.023 | 0.53 |
| 267_T | 344_N | 1.022 | 0.53 |
| 131_A | 303_Q | 1.022 | 0.53 |
| 15_L | 268_A | 1.020 | 0.52 |
| 164_Y | 339_A | 1.018 | 0.52 |
| 18_L | 48_L | 1.017 | 0.52 |
| 15_L | 111_L | 1.016 | 0.52 |
| 261_W | 362_L | 1.015 | 0.52 |
| 63_Y | 100_I | 1.014 | 0.52 |
| 95_I | 240_I | 1.013 | 0.52 |
| 102_T | 189_L | 1.013 | 0.52 |
| 94_L | 282_C | 1.011 | 0.51 |
| 215_F | 298_L | 1.010 | 0.51 |
| 214_P | 343_S | 1.008 | 0.51 |
| 80_A | 228_S | 1.008 | 0.51 |
| 9_P | 32_L | 1.008 | 0.51 |
| 75_I | 284_A | 1.003 | 0.51 |
| 117_F | 124_G | 1.000 | 0.50 |
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 | |
| 3rkoM | 2 | 0.9974 | 100 | 0.648 | Contact Map |
| 4he8M | 2 | 0.9668 | 100 | 0.672 | Contact Map |
| 3rkoN | 2 | 0.9847 | 100 | 0.71 | Contact Map |
| 4he8N | 2 | 0.9413 | 100 | 0.717 | Contact Map |
| 3rkoL | 2 | 0.9796 | 100 | 0.717 | Contact Map |
| 4he8L | 2 | 0.9821 | 100 | 0.728 | Contact Map |
| 2l0nA | 1 | 0.0765 | 3.2 | 0.989 | Contact Map |
| 1hznA | 1 | 0.0561 | 3 | 0.989 | Contact Map |
| 2jo4A | 4 | 0.051 | 1.4 | 0.991 | Contact Map |
| 5bxvB | 2 | 0 | 1.1 | 0.991 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)