| proj |
| ID: | 1493004168 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 301 (286) | ||
| Sequences: | 720 (486.2) | ||
| Seq/Len: | 2.517 | ||
| Nf(neff/√len): | 28.7 |
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: 2.517).
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 |
| 93_T | 99_Y | 3.192 | 1.00 |
| 161_M | 178_L | 2.899 | 1.00 |
| 178_L | 241_V | 2.482 | 1.00 |
| 156_K | 217_P | 2.475 | 1.00 |
| 238_E | 259_A | 2.389 | 1.00 |
| 62_A | 83_F | 2.232 | 1.00 |
| 64_F | 90_S | 2.211 | 1.00 |
| 150_I | 218_I | 2.102 | 1.00 |
| 171_I | 245_G | 1.983 | 0.99 |
| 159_L | 180_L | 1.924 | 0.99 |
| 259_A | 264_E | 1.867 | 0.99 |
| 67_A | 112_L | 1.824 | 0.99 |
| 286_D | 290_F | 1.803 | 0.99 |
| 228_T | 231_T | 1.777 | 0.98 |
| 96_T | 100_G | 1.751 | 0.98 |
| 224_I | 227_E | 1.750 | 0.98 |
| 49_F | 134_R | 1.700 | 0.98 |
| 96_T | 99_Y | 1.669 | 0.97 |
| 124_L | 128_A | 1.665 | 0.97 |
| 13_R | 22_N | 1.611 | 0.96 |
| 145_S | 271_F | 1.572 | 0.96 |
| 97_I | 117_A | 1.569 | 0.96 |
| 93_T | 98_G | 1.557 | 0.95 |
| 13_R | 19_G | 1.552 | 0.95 |
| 180_L | 198_L | 1.542 | 0.95 |
| 125_A | 129_R | 1.531 | 0.95 |
| 186_S | 190_M | 1.489 | 0.94 |
| 178_L | 200_L | 1.468 | 0.93 |
| 182_R | 235_S | 1.415 | 0.91 |
| 52_L | 122_L | 1.387 | 0.90 |
| 141_G | 166_L | 1.373 | 0.90 |
| 46_W | 165_N | 1.344 | 0.88 |
| 259_A | 265_I | 1.342 | 0.88 |
| 159_L | 239_F | 1.335 | 0.88 |
| 287_L | 290_F | 1.328 | 0.87 |
| 93_T | 100_G | 1.314 | 0.87 |
| 177_H | 197_D | 1.308 | 0.86 |
| 219_D | 222_S | 1.299 | 0.86 |
| 109_A | 267_W | 1.297 | 0.86 |
| 158_T | 215_M | 1.293 | 0.85 |
| 266_I | 269_G | 1.279 | 0.85 |
| 165_N | 251_A | 1.275 | 0.84 |
| 61_N | 88_F | 1.265 | 0.84 |
| 161_M | 214_V | 1.265 | 0.84 |
| 74_V | 78_A | 1.261 | 0.83 |
| 46_W | 134_R | 1.256 | 0.83 |
| 32_G | 44_V | 1.250 | 0.83 |
| 106_G | 211_S | 1.231 | 0.81 |
| 92_Q | 250_F | 1.231 | 0.81 |
| 75_I | 102_L | 1.230 | 0.81 |
| 260_Y | 271_F | 1.229 | 0.81 |
| 54_T | 103_I | 1.225 | 0.81 |
| 286_D | 289_K | 1.220 | 0.81 |
| 129_R | 136_T | 1.219 | 0.80 |
| 61_N | 102_L | 1.212 | 0.80 |
| 170_Q | 174_A | 1.205 | 0.79 |
| 218_I | 223_P | 1.203 | 0.79 |
| 39_H | 43_T | 1.203 | 0.79 |
| 45_S | 48_V | 1.197 | 0.79 |
| 89_F | 99_Y | 1.196 | 0.79 |
| 176_V | 214_V | 1.193 | 0.78 |
| 216_H | 222_S | 1.182 | 0.78 |
| 63_L | 265_I | 1.178 | 0.77 |
| 92_Q | 98_G | 1.176 | 0.77 |
| 142_V | 242_L | 1.175 | 0.77 |
| 151_S | 160_M | 1.174 | 0.77 |
| 97_I | 113_V | 1.174 | 0.77 |
| 160_M | 213_T | 1.169 | 0.76 |
| 49_F | 68_Y | 1.163 | 0.76 |
| 178_L | 239_F | 1.163 | 0.76 |
| 199_T | 221_H | 1.159 | 0.76 |
| 13_R | 17_S | 1.159 | 0.76 |
| 224_I | 272_V | 1.156 | 0.75 |
| 36_D | 40_D | 1.154 | 0.75 |
| 97_I | 100_G | 1.149 | 0.75 |
| 92_Q | 100_G | 1.148 | 0.75 |
| 92_Q | 255_H | 1.140 | 0.74 |
| 65_A | 276_T | 1.140 | 0.74 |
| 88_F | 102_L | 1.139 | 0.74 |
| 71_C | 106_G | 1.137 | 0.74 |
| 115_L | 197_D | 1.136 | 0.74 |
| 258_H | 264_E | 1.135 | 0.73 |
| 275_F | 283_R | 1.132 | 0.73 |
| 72_G | 112_L | 1.132 | 0.73 |
| 49_F | 130_L | 1.132 | 0.73 |
| 46_W | 87_F | 1.131 | 0.73 |
| 61_N | 106_G | 1.117 | 0.72 |
| 15_L | 22_N | 1.116 | 0.72 |
| 71_C | 112_L | 1.107 | 0.71 |
| 121_M | 161_M | 1.105 | 0.71 |
| 55_G | 59_V | 1.104 | 0.70 |
| 71_C | 108_L | 1.104 | 0.70 |
| 169_E | 248_E | 1.102 | 0.70 |
| 53_I | 127_A | 1.102 | 0.70 |
| 68_Y | 113_V | 1.100 | 0.70 |
| 112_L | 168_I | 1.096 | 0.70 |
| 83_F | 90_S | 1.095 | 0.70 |
| 88_F | 92_Q | 1.094 | 0.69 |
| 50_I | 55_G | 1.091 | 0.69 |
| 31_R | 142_V | 1.087 | 0.69 |
| 43_T | 141_G | 1.087 | 0.69 |
| 244_T | 255_H | 1.086 | 0.69 |
| 186_S | 189_G | 1.084 | 0.68 |
| 44_V | 52_L | 1.083 | 0.68 |
| 188_E | 192_F | 1.083 | 0.68 |
| 125_A | 132_Y | 1.083 | 0.68 |
| 92_Q | 110_N | 1.079 | 0.68 |
| 175_D | 204_R | 1.075 | 0.68 |
| 181_V | 267_W | 1.070 | 0.67 |
| 148_M | 238_E | 1.069 | 0.67 |
| 63_L | 115_L | 1.066 | 0.67 |
| 171_I | 174_A | 1.064 | 0.66 |
| 174_A | 177_H | 1.063 | 0.66 |
| 55_G | 115_L | 1.063 | 0.66 |
| 122_L | 208_F | 1.056 | 0.66 |
| 49_F | 56_L | 1.055 | 0.65 |
| 47_P | 139_T | 1.050 | 0.65 |
| 255_H | 259_A | 1.045 | 0.64 |
| 94_M | 116_E | 1.042 | 0.64 |
| 207_I | 243_F | 1.041 | 0.64 |
| 171_I | 287_L | 1.037 | 0.63 |
| 236_H | 267_W | 1.033 | 0.63 |
| 19_G | 22_N | 1.031 | 0.63 |
| 162_R | 198_L | 1.030 | 0.63 |
| 148_M | 159_L | 1.029 | 0.63 |
| 19_G | 23_I | 1.026 | 0.62 |
| 143_L | 291_H | 1.026 | 0.62 |
| 82_S | 85_D | 1.024 | 0.62 |
| 238_E | 241_V | 1.024 | 0.62 |
| 58_L | 185_I | 1.024 | 0.62 |
| 216_H | 245_G | 1.024 | 0.62 |
| 68_Y | 251_A | 1.023 | 0.62 |
| 135_F | 247_H | 1.021 | 0.62 |
| 224_I | 241_V | 1.019 | 0.61 |
| 147_R | 266_I | 1.016 | 0.61 |
| 68_Y | 91_V | 1.016 | 0.61 |
| 32_G | 36_D | 1.015 | 0.61 |
| 166_L | 274_V | 1.011 | 0.61 |
| 211_S | 238_E | 1.005 | 0.60 |
| 117_A | 129_R | 1.003 | 0.60 |
| 71_C | 109_A | 1.003 | 0.60 |
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 | |
| 4lp8A | 1 | 0.9402 | 100 | 0.221 | Contact Map |
| 3syaA | 1 | 0.9601 | 100 | 0.24 | Contact Map |
| 3spcA | 1 | 0.9468 | 100 | 0.247 | Contact Map |
| 1p7bA | 2 | 0.8571 | 100 | 0.267 | Contact Map |
| 2qksA | 2 | 0.9535 | 100 | 0.309 | Contact Map |
| 2xkyI | 4 | 0.7442 | 100 | 0.477 | Contact Map |
| 2gixA | 4 | 0.6113 | 100 | 0.481 | Contact Map |
| 1n9pA | 1 | 0.5814 | 100 | 0.485 | Contact Map |
| 3vsqA | 1 | 0.6013 | 100 | 0.488 | Contact Map |
| 1u4fA | 4 | 0.5947 | 100 | 0.488 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)