| dhc_fl 375-660 |
| ID: | 1509422457 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 286 (275) | ||
| Sequences: | 642 (532.1) | ||
| Seq/Len: | 2.335 | ||
| Nf(neff/√len): | 32.1 |
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: 2.335).
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 |
| 232_V | 264_R | 2.470 | 1.00 |
| 249_S | 274_M | 2.460 | 1.00 |
| 177_M | 243_G | 2.290 | 1.00 |
| 20_T | 38_V | 2.224 | 1.00 |
| 225_K | 258_Q | 2.092 | 1.00 |
| 37_G | 40_S | 2.080 | 1.00 |
| 178_M | 255_V | 2.070 | 0.99 |
| 32_I | 35_D | 2.010 | 0.99 |
| 47_V | 58_L | 1.909 | 0.99 |
| 182_T | 245_F | 1.819 | 0.98 |
| 246_S | 273_D | 1.795 | 0.98 |
| 241_M | 268_G | 1.795 | 0.98 |
| 235_Q | 240_L | 1.771 | 0.98 |
| 179_A | 185_I | 1.754 | 0.98 |
| 232_V | 240_L | 1.750 | 0.98 |
| 254_E | 257_R | 1.726 | 0.97 |
| 33_V | 72_L | 1.721 | 0.97 |
| 176_Y | 240_L | 1.702 | 0.97 |
| 232_V | 262_L | 1.648 | 0.96 |
| 174_P | 198_M | 1.624 | 0.96 |
| 187_T | 245_F | 1.622 | 0.96 |
| 62_F | 72_L | 1.584 | 0.95 |
| 254_E | 258_Q | 1.570 | 0.95 |
| 262_L | 272_I | 1.551 | 0.95 |
| 178_M | 251_V | 1.539 | 0.94 |
| 12_I | 50_V | 1.523 | 0.94 |
| 188_Y | 245_F | 1.516 | 0.94 |
| 61_T | 65_E | 1.497 | 0.93 |
| 128_D | 131_F | 1.495 | 0.93 |
| 257_R | 261_A | 1.492 | 0.93 |
| 14_D | 18_K | 1.489 | 0.93 |
| 224_A | 254_E | 1.479 | 0.92 |
| 129_Q | 132_T | 1.473 | 0.92 |
| 15_S | 50_V | 1.461 | 0.92 |
| 224_A | 255_V | 1.449 | 0.91 |
| 180_D | 188_Y | 1.446 | 0.91 |
| 179_A | 206_P | 1.416 | 0.90 |
| 115_A | 118_L | 1.389 | 0.89 |
| 176_Y | 238_G | 1.383 | 0.89 |
| 107_E | 111_M | 1.368 | 0.88 |
| 113_D | 118_L | 1.365 | 0.88 |
| 8_L | 76_F | 1.361 | 0.88 |
| 228_V | 232_V | 1.349 | 0.87 |
| 183_G | 254_E | 1.347 | 0.87 |
| 107_E | 114_T | 1.343 | 0.87 |
| 16_I | 38_V | 1.328 | 0.86 |
| 205_S | 227_I | 1.323 | 0.86 |
| 114_T | 118_L | 1.321 | 0.86 |
| 66_H | 75_A | 1.317 | 0.85 |
| 20_T | 33_V | 1.314 | 0.85 |
| 230_A | 233_T | 1.303 | 0.84 |
| 237_T | 240_L | 1.301 | 0.84 |
| 179_A | 227_I | 1.301 | 0.84 |
| 16_I | 20_T | 1.298 | 0.84 |
| 180_D | 245_F | 1.294 | 0.84 |
| 176_Y | 235_Q | 1.289 | 0.84 |
| 59_P | 62_F | 1.276 | 0.83 |
| 111_M | 114_T | 1.273 | 0.83 |
| 178_M | 231_L | 1.271 | 0.82 |
| 219_G | 222_G | 1.268 | 0.82 |
| 250_I | 276_C | 1.262 | 0.82 |
| 161_I | 166_G | 1.258 | 0.81 |
| 250_I | 277_P | 1.246 | 0.81 |
| 240_L | 264_R | 1.243 | 0.80 |
| 228_V | 240_L | 1.242 | 0.80 |
| 176_Y | 231_L | 1.239 | 0.80 |
| 146_G | 149_D | 1.239 | 0.80 |
| 107_E | 110_S | 1.238 | 0.80 |
| 235_Q | 238_G | 1.230 | 0.79 |
| 33_V | 63_V | 1.213 | 0.78 |
| 23_D | 26_E | 1.208 | 0.78 |
| 179_A | 247_A | 1.199 | 0.77 |
| 112_S | 115_A | 1.197 | 0.77 |
| 177_M | 180_D | 1.187 | 0.76 |
| 107_E | 113_D | 1.186 | 0.76 |
| 29_D | 73_R | 1.183 | 0.76 |
| 58_L | 62_F | 1.178 | 0.75 |
| 224_A | 251_V | 1.176 | 0.75 |
| 248_G | 256_T | 1.174 | 0.75 |
| 29_D | 69_I | 1.174 | 0.75 |
| 175_F | 277_P | 1.172 | 0.75 |
| 13_L | 76_F | 1.159 | 0.74 |
| 122_L | 126_E | 1.149 | 0.73 |
| 131_F | 135_P | 1.140 | 0.72 |
| 41_I | 203_I | 1.134 | 0.71 |
| 182_T | 275_C | 1.132 | 0.71 |
| 38_V | 42_M | 1.130 | 0.71 |
| 34_A | 38_V | 1.124 | 0.70 |
| 31_T | 38_V | 1.121 | 0.70 |
| 225_K | 229_D | 1.102 | 0.68 |
| 179_A | 245_F | 1.099 | 0.68 |
| 17_S | 24_P | 1.089 | 0.67 |
| 110_S | 115_A | 1.089 | 0.67 |
| 110_S | 114_T | 1.084 | 0.66 |
| 182_T | 188_Y | 1.082 | 0.66 |
| 174_P | 199_P | 1.078 | 0.66 |
| 35_D | 58_L | 1.077 | 0.65 |
| 44_I | 48_A | 1.075 | 0.65 |
| 13_L | 27_F | 1.075 | 0.65 |
| 98_S | 101_P | 1.070 | 0.65 |
| 179_A | 269_L | 1.067 | 0.64 |
| 112_S | 116_S | 1.067 | 0.64 |
| 31_T | 42_M | 1.057 | 0.63 |
| 221_P | 258_Q | 1.053 | 0.63 |
| 250_I | 278_R | 1.048 | 0.62 |
| 38_V | 59_P | 1.047 | 0.62 |
| 237_T | 264_R | 1.043 | 0.62 |
| 220_I | 251_V | 1.042 | 0.62 |
| 109_T | 112_S | 1.041 | 0.62 |
| 252_A | 273_D | 1.040 | 0.61 |
| 45_E | 179_A | 1.039 | 0.61 |
| 201_Y | 205_S | 1.039 | 0.61 |
| 178_M | 242_I | 1.037 | 0.61 |
| 71_D | 74_R | 1.037 | 0.61 |
| 174_P | 201_Y | 1.036 | 0.61 |
| 207_F | 214_L | 1.036 | 0.61 |
| 180_D | 204_D | 1.034 | 0.61 |
| 31_T | 35_D | 1.032 | 0.61 |
| 251_V | 255_V | 1.027 | 0.60 |
| 244_G | 249_S | 1.025 | 0.60 |
| 8_L | 17_S | 1.024 | 0.60 |
| 182_T | 247_A | 1.024 | 0.60 |
| 158_T | 224_A | 1.024 | 0.60 |
| 163_L | 166_G | 1.021 | 0.59 |
| 220_I | 250_I | 1.017 | 0.59 |
| 205_S | 243_G | 1.017 | 0.59 |
| 33_V | 39_D | 1.017 | 0.59 |
| 33_V | 64_L | 1.016 | 0.59 |
| 177_M | 192_P | 1.014 | 0.59 |
| 116_S | 123_V | 1.013 | 0.58 |
| 253_Y | 257_R | 1.013 | 0.58 |
| 19_A | 22_S | 1.013 | 0.58 |
| 27_F | 49_T | 1.010 | 0.58 |
| 174_P | 238_G | 1.007 | 0.58 |
| 122_L | 128_D | 1.005 | 0.58 |
| 44_I | 159_V | 1.002 | 0.57 |
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 | |
| 2vz8A | 2 | 0 | 100 | 0.395 | Contact Map |
| 3tejA | 2 | 0.7168 | 100 | 0.48 | Contact Map |
| 2vsqA | 1 | 0.6643 | 100 | 0.513 | Contact Map |
| 2px6A | 2 | 0.4266 | 99.8 | 0.678 | Contact Map |
| 2cb9A | 1 | 0.4056 | 99.8 | 0.696 | Contact Map |
| 1jmkC | 2 | 0.4161 | 99.7 | 0.699 | Contact Map |
| 1kezA | 3 | 0.5769 | 99.7 | 0.705 | Contact Map |
| 3ilsA | 1 | 0.465 | 99.7 | 0.713 | Contact Map |
| 4oqjA | 1 | 0 | 99.6 | 0.732 | Contact Map |
| 4r0mB | 2 | 0.2622 | 99.6 | 0.736 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)