| 1A_CBRs -force run 350-675 |
| ID: | 1510951456 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 326 (246) | ||
| Sequences: | 578 (361.9) | ||
| Seq/Len: | 2.350 | ||
| Nf(neff/√len): | 23.1 |
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: 2.350).
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 |
| 33_S | 107_N | 2.661 | 1.00 |
| 34_F | 107_N | 2.239 | 1.00 |
| 33_S | 42_M | 1.704 | 0.97 |
| 114_L | 172_N | 1.627 | 0.96 |
| 26_S | 100_N | 1.588 | 0.95 |
| 261_N | 264_F | 1.572 | 0.95 |
| 270_D | 274_R | 1.562 | 0.95 |
| 280_L | 284_K | 1.556 | 0.95 |
| 270_D | 273_R | 1.525 | 0.94 |
| 247_T | 275_A | 1.492 | 0.93 |
| 109_S | 162_T | 1.467 | 0.92 |
| 259_M | 262_P | 1.421 | 0.90 |
| 33_S | 126_L | 1.415 | 0.90 |
| 263_P | 275_A | 1.379 | 0.89 |
| 263_P | 272_M | 1.365 | 0.88 |
| 234_G | 244_L | 1.359 | 0.88 |
| 269_V | 273_R | 1.358 | 0.88 |
| 129_L | 162_T | 1.357 | 0.88 |
| 161_E | 165_K | 1.347 | 0.87 |
| 263_P | 269_V | 1.341 | 0.87 |
| 106_A | 161_E | 1.341 | 0.87 |
| 27_N | 161_E | 1.332 | 0.86 |
| 25_V | 107_N | 1.323 | 0.86 |
| 58_L | 212_L | 1.310 | 0.85 |
| 275_A | 279_L | 1.308 | 0.85 |
| 269_V | 277_R | 1.302 | 0.85 |
| 281_A | 284_K | 1.301 | 0.84 |
| 165_K | 207_M | 1.292 | 0.84 |
| 259_M | 263_P | 1.287 | 0.84 |
| 260_Q | 263_P | 1.278 | 0.83 |
| 261_N | 270_D | 1.272 | 0.83 |
| 248_Q | 258_H | 1.271 | 0.83 |
| 246_A | 277_R | 1.259 | 0.82 |
| 263_P | 273_R | 1.256 | 0.81 |
| 105_L | 108_I | 1.251 | 0.81 |
| 274_R | 279_L | 1.248 | 0.81 |
| 249_F | 257_L | 1.237 | 0.80 |
| 42_M | 171_N | 1.235 | 0.80 |
| 249_F | 260_Q | 1.235 | 0.80 |
| 107_N | 119_E | 1.230 | 0.80 |
| 263_P | 278_A | 1.229 | 0.80 |
| 279_L | 282_L | 1.228 | 0.79 |
| 273_R | 284_K | 1.224 | 0.79 |
| 27_N | 31_S | 1.204 | 0.78 |
| 248_Q | 261_N | 1.188 | 0.76 |
| 151_A | 158_L | 1.180 | 0.76 |
| 278_A | 281_A | 1.175 | 0.75 |
| 269_V | 272_M | 1.174 | 0.75 |
| 262_P | 269_V | 1.174 | 0.75 |
| 264_F | 270_D | 1.171 | 0.75 |
| 248_Q | 259_M | 1.171 | 0.75 |
| 257_L | 281_A | 1.168 | 0.74 |
| 273_R | 276_A | 1.165 | 0.74 |
| 31_S | 90_W | 1.165 | 0.74 |
| 52_L | 101_T | 1.154 | 0.73 |
| 257_L | 260_Q | 1.152 | 0.73 |
| 258_H | 269_V | 1.151 | 0.73 |
| 58_L | 98_R | 1.149 | 0.73 |
| 276_A | 284_K | 1.145 | 0.72 |
| 246_A | 269_V | 1.142 | 0.72 |
| 153_L | 156_Q | 1.141 | 0.72 |
| 258_H | 262_P | 1.140 | 0.72 |
| 29_I | 113_D | 1.139 | 0.72 |
| 258_H | 264_F | 1.134 | 0.71 |
| 157_R | 274_R | 1.132 | 0.71 |
| 272_M | 277_R | 1.131 | 0.71 |
| 249_F | 258_H | 1.131 | 0.71 |
| 274_R | 278_A | 1.127 | 0.71 |
| 164_S | 185_L | 1.118 | 0.70 |
| 161_E | 207_M | 1.114 | 0.69 |
| 272_M | 275_A | 1.112 | 0.69 |
| 262_P | 270_D | 1.111 | 0.69 |
| 259_M | 270_D | 1.110 | 0.69 |
| 258_H | 277_R | 1.106 | 0.69 |
| 261_N | 273_R | 1.105 | 0.69 |
| 33_S | 172_N | 1.099 | 0.68 |
| 246_A | 273_R | 1.097 | 0.68 |
| 264_F | 269_V | 1.094 | 0.67 |
| 201_N | 242_D | 1.093 | 0.67 |
| 249_F | 277_R | 1.093 | 0.67 |
| 109_S | 119_E | 1.092 | 0.67 |
| 25_V | 66_K | 1.091 | 0.67 |
| 260_Q | 273_R | 1.090 | 0.67 |
| 197_S | 209_V | 1.083 | 0.66 |
| 277_R | 281_A | 1.082 | 0.66 |
| 6_T | 9_C | 1.080 | 0.66 |
| 41_E | 44_K | 1.078 | 0.66 |
| 246_A | 261_N | 1.073 | 0.65 |
| 152_V | 276_A | 1.072 | 0.65 |
| 100_N | 164_S | 1.071 | 0.65 |
| 248_Q | 260_Q | 1.064 | 0.64 |
| 15_Q | 18_L | 1.063 | 0.64 |
| 248_Q | 269_V | 1.062 | 0.64 |
| 6_T | 11_L | 1.060 | 0.64 |
| 52_L | 112_L | 1.059 | 0.64 |
| 186_E | 191_T | 1.059 | 0.64 |
| 157_R | 270_D | 1.055 | 0.63 |
| 128_G | 132_W | 1.054 | 0.63 |
| 270_D | 284_K | 1.053 | 0.63 |
| 264_F | 272_M | 1.051 | 0.63 |
| 237_L | 244_L | 1.050 | 0.63 |
| 247_T | 258_H | 1.048 | 0.63 |
| 258_H | 273_R | 1.048 | 0.63 |
| 237_L | 241_E | 1.047 | 0.62 |
| 247_T | 284_K | 1.047 | 0.62 |
| 269_V | 275_A | 1.046 | 0.62 |
| 41_E | 135_C | 1.044 | 0.62 |
| 10_T | 196_L | 1.042 | 0.62 |
| 7_P | 260_Q | 1.041 | 0.62 |
| 152_V | 247_T | 1.041 | 0.62 |
| 95_E | 99_E | 1.038 | 0.61 |
| 272_M | 278_A | 1.032 | 0.61 |
| 24_C | 27_N | 1.032 | 0.61 |
| 7_P | 259_M | 1.028 | 0.60 |
| 260_Q | 269_V | 1.028 | 0.60 |
| 222_A | 226_I | 1.027 | 0.60 |
| 235_N | 238_G | 1.026 | 0.60 |
| 264_F | 278_A | 1.026 | 0.60 |
| 108_I | 229_Q | 1.024 | 0.60 |
| 257_L | 277_R | 1.024 | 0.60 |
| 259_M | 269_V | 1.023 | 0.60 |
| 229_Q | 234_G | 1.023 | 0.60 |
| 91_W | 130_L | 1.019 | 0.59 |
| 247_T | 259_M | 1.019 | 0.59 |
| 246_A | 249_F | 1.019 | 0.59 |
| 152_V | 264_F | 1.019 | 0.59 |
| 269_V | 281_A | 1.016 | 0.59 |
| 240_L | 262_P | 1.014 | 0.59 |
| 55_L | 101_T | 1.011 | 0.58 |
| 124_P | 132_W | 1.008 | 0.58 |
| 130_L | 177_L | 1.004 | 0.58 |
| 48_L | 187_K | 1.004 | 0.58 |
| 245_A | 248_Q | 1.000 | 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 | |
| 3nmwA | 2 | 0.7699 | 98 | 0.888 | Contact Map |
| 3nmzA | 2 | 0.7822 | 97.5 | 0.898 | Contact Map |
| 4ev8A | 1 | 0.7055 | 97.3 | 0.902 | Contact Map |
| 2z6gA | 1 | 0.7393 | 97.2 | 0.904 | Contact Map |
| 2z6hA | 1 | 0.727 | 96.7 | 0.911 | Contact Map |
| 4r0zA | 1 | 0 | 96.6 | 0.912 | Contact Map |
| 3tt9A | 1 | 0.6564 | 96.6 | 0.912 | Contact Map |
| 4i2zA | 1 | 0.7239 | 96.2 | 0.915 | Contact Map |
| 3opbA | 2 | 0.7853 | 95.9 | 0.917 | Contact Map |
| 1xm9A | 1 | 0.4816 | 95.7 | 0.919 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)