| HIFa |
| ID: | 1490983831 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 335 (334) | ||
| Sequences: | 1172 (697.7) | ||
| Seq/Len: | 3.509 | ||
| Nf(neff/√len): | 38.2 |
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: 3.509).
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 |
| 257_H | 260_D | 2.687 | 1.00 |
| 111_H | 114_D | 2.533 | 1.00 |
| 246_E | 287_K | 2.371 | 1.00 |
| 3_S | 6_T | 2.190 | 1.00 |
| 282_Y | 296_T | 2.181 | 1.00 |
| 256_Y | 264_M | 2.074 | 1.00 |
| 2_R | 6_T | 2.035 | 1.00 |
| 114_D | 146_R | 1.969 | 1.00 |
| 253_Y | 268_H | 1.947 | 1.00 |
| 260_D | 283_R | 1.901 | 1.00 |
| 30_S | 34_L | 1.874 | 1.00 |
| 69_A | 72_G | 1.709 | 0.99 |
| 27_D | 33_R | 1.609 | 0.98 |
| 29_A | 36_I | 1.602 | 0.98 |
| 59_D | 62_M | 1.599 | 0.98 |
| 54_S | 57_E | 1.570 | 0.98 |
| 25_H | 29_A | 1.537 | 0.97 |
| 1_R | 5_E | 1.533 | 0.97 |
| 17_P | 34_L | 1.508 | 0.97 |
| 257_H | 283_R | 1.501 | 0.97 |
| 28_K | 31_I | 1.492 | 0.97 |
| 30_S | 39_L | 1.477 | 0.96 |
| 1_R | 9_F | 1.472 | 0.96 |
| 70_L | 93_F | 1.452 | 0.96 |
| 141_R | 146_R | 1.449 | 0.96 |
| 87_S | 94_M | 1.444 | 0.96 |
| 303_N | 306_N | 1.436 | 0.96 |
| 110_T | 118_I | 1.435 | 0.96 |
| 58_A | 61_Q | 1.428 | 0.95 |
| 22_V | 26_L | 1.422 | 0.95 |
| 27_D | 30_S | 1.407 | 0.95 |
| 168_L | 201_C | 1.403 | 0.95 |
| 29_A | 32_M | 1.399 | 0.95 |
| 1_R | 4_K | 1.399 | 0.95 |
| 34_L | 38_F | 1.392 | 0.95 |
| 87_S | 90_I | 1.386 | 0.94 |
| 111_H | 146_R | 1.376 | 0.94 |
| 17_P | 29_A | 1.371 | 0.94 |
| 18_L | 22_V | 1.370 | 0.94 |
| 223_H | 233_D | 1.359 | 0.94 |
| 28_K | 35_A | 1.345 | 0.93 |
| 272_C | 312_I | 1.341 | 0.93 |
| 223_H | 229_F | 1.337 | 0.93 |
| 282_Y | 316_N | 1.332 | 0.93 |
| 67_L | 94_M | 1.331 | 0.93 |
| 1_R | 6_T | 1.319 | 0.92 |
| 221_S | 229_F | 1.319 | 0.92 |
| 5_E | 29_A | 1.318 | 0.92 |
| 63_D | 67_L | 1.317 | 0.92 |
| 73_F | 81_G | 1.313 | 0.92 |
| 26_L | 29_A | 1.301 | 0.92 |
| 320_S | 323_E | 1.296 | 0.91 |
| 250_R | 255_F | 1.287 | 0.91 |
| 131_G | 134_S | 1.285 | 0.91 |
| 26_L | 34_L | 1.279 | 0.91 |
| 28_K | 39_L | 1.271 | 0.90 |
| 28_K | 36_I | 1.266 | 0.90 |
| 3_S | 7_E | 1.266 | 0.90 |
| 67_L | 76_V | 1.265 | 0.90 |
| 172_G | 175_R | 1.264 | 0.90 |
| 31_I | 37_S | 1.262 | 0.90 |
| 240_I | 247_L | 1.244 | 0.89 |
| 330_S | 333_Q | 1.242 | 0.89 |
| 36_I | 42_H | 1.238 | 0.89 |
| 5_E | 9_F | 1.238 | 0.89 |
| 3_S | 9_F | 1.229 | 0.88 |
| 302_Y | 309_P | 1.222 | 0.88 |
| 14_H | 31_I | 1.221 | 0.88 |
| 296_T | 314_C | 1.219 | 0.88 |
| 154_R | 159_N | 1.217 | 0.87 |
| 57_E | 61_Q | 1.212 | 0.87 |
| 301_I | 304_P | 1.207 | 0.87 |
| 225_M | 309_P | 1.204 | 0.87 |
| 28_K | 32_M | 1.203 | 0.87 |
| 4_K | 17_P | 1.202 | 0.87 |
| 32_M | 36_I | 1.201 | 0.87 |
| 110_T | 147_M | 1.195 | 0.86 |
| 284_M | 294_L | 1.189 | 0.86 |
| 33_R | 39_L | 1.188 | 0.86 |
| 73_F | 85_F | 1.184 | 0.85 |
| 17_P | 33_R | 1.175 | 0.85 |
| 73_F | 98_Q | 1.174 | 0.85 |
| 13_A | 28_K | 1.171 | 0.85 |
| 25_H | 32_M | 1.164 | 0.84 |
| 236_I | 292_V | 1.163 | 0.84 |
| 8_V | 11_E | 1.161 | 0.84 |
| 242_Y | 287_K | 1.160 | 0.84 |
| 275_G | 296_T | 1.160 | 0.84 |
| 15_E | 20_H | 1.159 | 0.84 |
| 59_D | 63_D | 1.159 | 0.84 |
| 165_W | 201_C | 1.159 | 0.84 |
| 13_A | 23_S | 1.158 | 0.84 |
| 67_L | 71_E | 1.154 | 0.83 |
| 2_R | 5_E | 1.153 | 0.83 |
| 2_R | 9_F | 1.153 | 0.83 |
| 252_A | 256_Y | 1.151 | 0.83 |
| 91_S | 97_T | 1.151 | 0.83 |
| 16_L | 22_V | 1.147 | 0.83 |
| 76_V | 81_G | 1.147 | 0.83 |
| 19_P | 24_S | 1.145 | 0.83 |
| 13_A | 31_I | 1.141 | 0.82 |
| 17_P | 26_L | 1.140 | 0.82 |
| 223_H | 296_T | 1.139 | 0.82 |
| 201_C | 219_F | 1.135 | 0.82 |
| 130_F | 133_K | 1.134 | 0.82 |
| 9_F | 25_H | 1.130 | 0.82 |
| 168_L | 172_G | 1.130 | 0.82 |
| 4_K | 9_F | 1.128 | 0.81 |
| 256_Y | 284_M | 1.127 | 0.81 |
| 239_L | 249_G | 1.127 | 0.81 |
| 30_S | 33_R | 1.125 | 0.81 |
| 49_C | 53_E | 1.124 | 0.81 |
| 301_I | 310_Q | 1.124 | 0.81 |
| 241_G | 246_E | 1.123 | 0.81 |
| 168_L | 174_V | 1.120 | 0.81 |
| 110_T | 115_H | 1.115 | 0.80 |
| 118_I | 124_L | 1.111 | 0.80 |
| 10_Y | 19_P | 1.104 | 0.80 |
| 285_L | 290_G | 1.100 | 0.79 |
| 90_I | 101_L | 1.098 | 0.79 |
| 242_Y | 246_E | 1.096 | 0.79 |
| 63_D | 66_Y | 1.095 | 0.79 |
| 28_K | 33_R | 1.095 | 0.79 |
| 3_S | 24_S | 1.093 | 0.79 |
| 19_P | 22_V | 1.093 | 0.79 |
| 2_R | 12_L | 1.093 | 0.79 |
| 16_L | 19_P | 1.088 | 0.78 |
| 257_H | 291_Y | 1.086 | 0.78 |
| 281_Q | 295_E | 1.083 | 0.78 |
| 27_D | 31_I | 1.083 | 0.78 |
| 56_A | 59_D | 1.078 | 0.77 |
| 173_Q | 201_C | 1.074 | 0.77 |
| 279_S | 282_Y | 1.072 | 0.77 |
| 249_G | 314_C | 1.071 | 0.77 |
| 57_E | 60_Q | 1.068 | 0.76 |
| 305_R | 311_C | 1.068 | 0.76 |
| 151_V | 211_D | 1.067 | 0.76 |
| 57_E | 62_M | 1.065 | 0.76 |
| 71_E | 88_E | 1.065 | 0.76 |
| 169_H | 173_Q | 1.064 | 0.76 |
| 33_R | 41_T | 1.064 | 0.76 |
| 30_S | 38_F | 1.063 | 0.76 |
| 1_R | 11_E | 1.063 | 0.76 |
| 265_T | 268_H | 1.063 | 0.76 |
| 3_S | 10_Y | 1.061 | 0.76 |
| 10_Y | 16_L | 1.060 | 0.76 |
| 5_E | 8_V | 1.059 | 0.75 |
| 73_F | 90_I | 1.059 | 0.75 |
| 328_V | 333_Q | 1.058 | 0.75 |
| 325_N | 332_D | 1.056 | 0.75 |
| 185_S | 188_G | 1.053 | 0.75 |
| 72_G | 94_M | 1.051 | 0.75 |
| 29_A | 35_A | 1.050 | 0.75 |
| 130_F | 134_S | 1.049 | 0.74 |
| 276_Q | 290_G | 1.048 | 0.74 |
| 311_C | 315_V | 1.046 | 0.74 |
| 167_V | 170_C | 1.044 | 0.74 |
| 46_S | 49_C | 1.044 | 0.74 |
| 229_F | 284_M | 1.043 | 0.74 |
| 178_N | 181_P | 1.042 | 0.74 |
| 4_K | 15_E | 1.041 | 0.74 |
| 34_L | 95_G | 1.039 | 0.73 |
| 219_F | 271_L | 1.039 | 0.73 |
| 296_T | 316_N | 1.035 | 0.73 |
| 222_R | 231_Y | 1.032 | 0.73 |
| 71_E | 94_M | 1.029 | 0.72 |
| 29_A | 38_F | 1.028 | 0.72 |
| 15_E | 34_L | 1.028 | 0.72 |
| 10_Y | 14_H | 1.026 | 0.72 |
| 13_A | 20_H | 1.024 | 0.72 |
| 197_L | 201_C | 1.023 | 0.72 |
| 9_F | 14_H | 1.020 | 0.72 |
| 129_G | 132_K | 1.018 | 0.71 |
| 218_T | 227_M | 1.016 | 0.71 |
| 106_I | 110_T | 1.016 | 0.71 |
| 103_G | 316_N | 1.016 | 0.71 |
| 171_T | 174_V | 1.015 | 0.71 |
| 204_I | 208_S | 1.014 | 0.71 |
| 219_F | 222_R | 1.013 | 0.71 |
| 60_Q | 63_D | 1.011 | 0.71 |
| 223_H | 227_M | 1.011 | 0.71 |
| 331_M | 334_T | 1.006 | 0.70 |
| 144_F | 171_T | 1.003 | 0.70 |
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 | |
| 4f3lA | 1 | 0.9075 | 100 | 0.291 | Contact Map |
| 4f3lB | 1 | 0.8448 | 100 | 0.299 | Contact Map |
| 3rtyA | 8 | 0.6567 | 100 | 0.525 | Contact Map |
| 3gdiA | 2 | 0.7373 | 100 | 0.526 | Contact Map |
| 4dj3A | 2 | 0.7463 | 100 | 0.598 | Contact Map |
| 4dj2A | 4 | 0.7045 | 100 | 0.617 | Contact Map |
| 3ewkA | 1 | 0.6358 | 99.9 | 0.65 | Contact Map |
| 1oj5A | 1 | 0.2985 | 99.9 | 0.674 | Contact Map |
| 4hh3A | 2 | 0.6746 | 99.9 | 0.684 | Contact Map |
| 4hh2A | 4 | 0.8269 | 99.9 | 0.69 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)