| H3_300_sequences -force run |
| ID: | 1421763952 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 329 (322) | ||
| Sequences: | 158 (42.3) | ||
| Seq/Len: | 0.491 | ||
| Nf(neff/√len): | 2.4 |
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: 0.491).
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 |
| 37_T | 49_G | 1.751 | 0.73 |
| 17_H | 20_V | 1.715 | 0.71 |
| 15_L | 20_V | 1.698 | 0.70 |
| 317_A | 324_P | 1.637 | 0.66 |
| 76_C | 89_E | 1.560 | 0.60 |
| 314_L | 319_G | 1.557 | 0.60 |
| 317_A | 322_N | 1.512 | 0.57 |
| 52_C | 76_C | 1.510 | 0.56 |
| 76_C | 88_V | 1.497 | 0.55 |
| 90_R | 93_A | 1.495 | 0.55 |
| 48_T | 51_I | 1.494 | 0.55 |
| 321_R | 324_P | 1.478 | 0.54 |
| 237_V | 255_R | 1.470 | 0.53 |
| 17_H | 22_N | 1.437 | 0.51 |
| 31_D | 34_I | 1.429 | 0.50 |
| 240_G | 251_L | 1.422 | 0.50 |
| 14_C | 26_V | 1.420 | 0.50 |
| 38_N | 48_T | 1.419 | 0.49 |
| 65_T | 243_L | 1.415 | 0.49 |
| 89_E | 120_F | 1.408 | 0.49 |
| 17_H | 23_G | 1.398 | 0.48 |
| 77_D | 80_Q | 1.395 | 0.48 |
| 22_N | 27_K | 1.386 | 0.47 |
| 132_Q | 242_V | 1.385 | 0.47 |
| 303_G | 306_P | 1.380 | 0.47 |
| 37_T | 52_C | 1.373 | 0.46 |
| 237_V | 252_I | 1.365 | 0.45 |
| 52_C | 89_E | 1.364 | 0.45 |
| 138_A | 190_E | 1.364 | 0.45 |
| 89_E | 117_T | 1.362 | 0.45 |
| 171_N | 260_M | 1.359 | 0.45 |
| 90_R | 117_T | 1.336 | 0.43 |
| 112_V | 167_T | 1.333 | 0.43 |
| 15_L | 22_N | 1.326 | 0.42 |
| 27_K | 31_D | 1.325 | 0.42 |
| 284_P | 301_T | 1.324 | 0.42 |
| 16_G | 52_C | 1.323 | 0.42 |
| 117_T | 120_F | 1.315 | 0.42 |
| 279_S | 287_S | 1.303 | 0.41 |
| 21_P | 34_I | 1.293 | 0.40 |
| 310_K | 317_A | 1.291 | 0.40 |
| 287_S | 304_A | 1.291 | 0.40 |
| 314_L | 324_P | 1.284 | 0.39 |
| 319_G | 324_P | 1.284 | 0.39 |
| 47_S | 51_I | 1.281 | 0.39 |
| 31_D | 61_G | 1.276 | 0.39 |
| 113_A | 118_L | 1.266 | 0.38 |
| 95_S | 123_E | 1.264 | 0.38 |
| 15_L | 23_G | 1.259 | 0.37 |
| 21_P | 27_K | 1.253 | 0.37 |
| 86_L | 113_A | 1.253 | 0.37 |
| 58_I | 61_G | 1.251 | 0.37 |
| 197_Q | 230_I | 1.249 | 0.37 |
| 16_G | 76_C | 1.246 | 0.37 |
| 23_G | 33_Q | 1.243 | 0.36 |
| 148_F | 231_S | 1.241 | 0.36 |
| 43_V | 48_T | 1.240 | 0.36 |
| 52_C | 88_V | 1.239 | 0.36 |
| 89_E | 92_N | 1.235 | 0.36 |
| 233_Y | 240_G | 1.224 | 0.35 |
| 305_C | 314_L | 1.223 | 0.35 |
| 303_G | 319_G | 1.223 | 0.35 |
| 305_C | 319_G | 1.223 | 0.35 |
| 303_G | 314_L | 1.223 | 0.35 |
| 17_H | 21_P | 1.218 | 0.35 |
| 92_N | 118_L | 1.216 | 0.34 |
| 76_C | 87_F | 1.216 | 0.34 |
| 191_Q | 250_N | 1.216 | 0.34 |
| 303_G | 308_Y | 1.215 | 0.34 |
| 89_E | 122_T | 1.215 | 0.34 |
| 305_C | 308_Y | 1.215 | 0.34 |
| 39_A | 122_T | 1.215 | 0.34 |
| 265_S | 293_P | 1.214 | 0.34 |
| 70_L | 301_T | 1.214 | 0.34 |
| 317_A | 321_R | 1.199 | 0.33 |
| 182_V | 214_I | 1.198 | 0.33 |
| 199_S | 214_I | 1.196 | 0.33 |
| 38_N | 51_I | 1.193 | 0.33 |
| 37_T | 76_C | 1.191 | 0.33 |
| 151_L | 251_L | 1.190 | 0.33 |
| 145_S | 237_V | 1.188 | 0.33 |
| 20_V | 23_G | 1.187 | 0.32 |
| 38_N | 43_V | 1.183 | 0.32 |
| 270_S | 291_D | 1.180 | 0.32 |
| 306_P | 319_G | 1.179 | 0.32 |
| 306_P | 314_L | 1.179 | 0.32 |
| 13_L | 34_I | 1.178 | 0.32 |
| 42_L | 315_K | 1.170 | 0.31 |
| 88_V | 122_T | 1.166 | 0.31 |
| 316_L | 323_V | 1.161 | 0.31 |
| 56_H | 182_V | 1.155 | 0.30 |
| 87_F | 93_A | 1.147 | 0.30 |
| 292_K | 328_T | 1.146 | 0.30 |
| 294_F | 308_Y | 1.144 | 0.30 |
| 115_S | 118_L | 1.143 | 0.30 |
| 38_N | 47_S | 1.129 | 0.29 |
| 203_T | 252_I | 1.127 | 0.29 |
| 87_F | 120_F | 1.125 | 0.28 |
| 77_D | 90_R | 1.121 | 0.28 |
| 11_A | 95_S | 1.118 | 0.28 |
| 15_L | 21_P | 1.118 | 0.28 |
| 298_N | 302_Y | 1.116 | 0.28 |
| 320_M | 325_E | 1.114 | 0.28 |
| 16_G | 89_E | 1.110 | 0.28 |
| 23_G | 27_K | 1.109 | 0.27 |
| 65_T | 212_T | 1.106 | 0.27 |
| 63_D | 230_I | 1.103 | 0.27 |
| 80_Q | 120_F | 1.101 | 0.27 |
| 145_S | 199_S | 1.100 | 0.27 |
| 15_L | 33_Q | 1.095 | 0.27 |
| 65_T | 230_I | 1.094 | 0.27 |
| 201_G | 246_N | 1.093 | 0.26 |
| 296_N | 308_Y | 1.091 | 0.26 |
| 42_L | 292_K | 1.087 | 0.26 |
| 298_N | 313_T | 1.086 | 0.26 |
| 158_G | 290_N | 1.086 | 0.26 |
| 35_E | 38_N | 1.083 | 0.26 |
| 14_C | 28_T | 1.082 | 0.26 |
| 234_W | 249_G | 1.079 | 0.26 |
| 235_T | 243_L | 1.079 | 0.26 |
| 132_Q | 151_L | 1.078 | 0.26 |
| 315_K | 325_E | 1.078 | 0.26 |
| 316_L | 319_G | 1.077 | 0.26 |
| 17_H | 27_K | 1.077 | 0.26 |
| 282_I | 289_P | 1.075 | 0.25 |
| 156_K | 159_S | 1.072 | 0.25 |
| 147_F | 153_W | 1.072 | 0.25 |
| 232_I | 251_L | 1.070 | 0.25 |
| 294_F | 314_L | 1.069 | 0.25 |
| 294_F | 319_G | 1.069 | 0.25 |
| 91_S | 159_S | 1.068 | 0.25 |
| 65_T | 245_I | 1.064 | 0.25 |
| 105_Y | 235_T | 1.064 | 0.25 |
| 319_G | 322_N | 1.063 | 0.25 |
| 314_L | 322_N | 1.063 | 0.25 |
| 23_G | 35_E | 1.062 | 0.25 |
| 68_D | 100_Y | 1.059 | 0.25 |
| 314_L | 317_A | 1.058 | 0.24 |
| 34_I | 44_Q | 1.056 | 0.24 |
| 135_G | 140_K | 1.056 | 0.24 |
| 31_D | 44_Q | 1.056 | 0.24 |
| 237_V | 242_V | 1.055 | 0.24 |
| 204_V | 220_R | 1.053 | 0.24 |
| 196_V | 230_I | 1.052 | 0.24 |
| 151_L | 179_I | 1.050 | 0.24 |
| 55_P | 61_G | 1.048 | 0.24 |
| 146_G | 149_S | 1.048 | 0.24 |
| 22_N | 34_I | 1.046 | 0.24 |
| 11_A | 34_I | 1.043 | 0.24 |
| 208_R | 227_S | 1.042 | 0.24 |
| 109_R | 218_G | 1.039 | 0.23 |
| 88_V | 120_F | 1.036 | 0.23 |
| 295_Q | 326_K | 1.036 | 0.23 |
| 62_R | 236_V | 1.032 | 0.23 |
| 207_R | 245_I | 1.031 | 0.23 |
| 112_V | 265_S | 1.031 | 0.23 |
| 29_I | 218_G | 1.027 | 0.23 |
| 308_Y | 319_G | 1.027 | 0.23 |
| 308_Y | 314_L | 1.027 | 0.23 |
| 80_Q | 87_F | 1.025 | 0.23 |
| 303_G | 324_P | 1.023 | 0.23 |
| 305_C | 324_P | 1.023 | 0.23 |
| 62_R | 206_T | 1.021 | 0.22 |
| 190_E | 226_Q | 1.017 | 0.22 |
| 206_T | 209_S | 1.017 | 0.22 |
| 61_G | 68_D | 1.017 | 0.22 |
| 28_T | 36_V | 1.016 | 0.22 |
| 138_A | 210_Q | 1.014 | 0.22 |
| 308_Y | 322_N | 1.014 | 0.22 |
| 311_Q | 320_M | 1.014 | 0.22 |
| 27_K | 32_D | 1.013 | 0.22 |
| 300_I | 327_Q | 1.013 | 0.22 |
| 40_T | 51_I | 1.011 | 0.22 |
| 295_Q | 300_I | 1.010 | 0.22 |
| 87_F | 122_T | 1.008 | 0.22 |
| 230_I | 279_S | 1.007 | 0.22 |
| 40_T | 47_S | 1.005 | 0.22 |
| 164_L | 171_N | 1.004 | 0.22 |
| 89_E | 123_E | 1.004 | 0.22 |
| 20_V | 33_Q | 1.004 | 0.22 |
| 20_V | 35_E | 1.003 | 0.21 |
| 43_V | 299_K | 1.002 | 0.21 |
| 233_Y | 251_L | 1.001 | 0.21 |
| 115_S | 122_T | 1.000 | 0.21 |
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 | |
| 4o5nA | 1 | 0.9635 | 100 | 0.037 | Contact Map |
| 3ku3A | 1 | 0.9666 | 100 | 0.042 | Contact Map |
| 4fqiA | 1 | 0.9635 | 100 | 0.043 | Contact Map |
| 3eykA | 1 | 0.9635 | 100 | 0.043 | Contact Map |
| 4gxxA | 3 | 0.9635 | 100 | 0.047 | Contact Map |
| 2yp5A | 1 | 0.9726 | 100 | 0.048 | Contact Map |
| 4lvhA | 4 | 0.6535 | 100 | 0.049 | Contact Map |
| 2wr1A | 3 | 0.9605 | 100 | 0.052 | Contact Map |
| 4cyvA | 3 | 0.9574 | 100 | 0.052 | Contact Map |
| 4bsgA | 1 | 0.9514 | 100 | 0.054 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)