| srg_love_duplicate |
| ID: | 1411127800 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 320 (285) | ||
| Sequences: | 385 (315.6) | ||
| Seq/Len: | 1.351 | ||
| Nf(neff/√len): | 18.7 |
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: 1.351).
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 |
| 11_Y | 14_P | 2.051 | 0.98 |
| 270_P | 273_F | 1.997 | 0.97 |
| 88_L | 167_T | 1.920 | 0.97 |
| 38_I | 49_I | 1.862 | 0.96 |
| 112_N | 127_W | 1.840 | 0.95 |
| 15_S | 271_W | 1.761 | 0.94 |
| 133_F | 137_L | 1.723 | 0.93 |
| 46_V | 189_I | 1.546 | 0.86 |
| 274_L | 280_A | 1.541 | 0.86 |
| 2_T | 67_K | 1.531 | 0.86 |
| 143_V | 221_G | 1.516 | 0.85 |
| 11_Y | 260_Y | 1.515 | 0.85 |
| 115_S | 127_W | 1.503 | 0.84 |
| 46_V | 282_R | 1.471 | 0.82 |
| 122_T | 125_K | 1.470 | 0.82 |
| 74_L | 154_T | 1.444 | 0.81 |
| 37_F | 112_N | 1.409 | 0.78 |
| 13_I | 172_D | 1.405 | 0.78 |
| 232_V | 241_V | 1.402 | 0.78 |
| 277_S | 280_A | 1.376 | 0.76 |
| 110_S | 181_L | 1.374 | 0.76 |
| 91_F | 279_K | 1.365 | 0.75 |
| 269_H | 273_F | 1.362 | 0.75 |
| 136_I | 140_V | 1.332 | 0.73 |
| 16_M | 29_F | 1.318 | 0.72 |
| 74_L | 136_I | 1.317 | 0.72 |
| 90_V | 124_E | 1.312 | 0.71 |
| 140_V | 257_L | 1.311 | 0.71 |
| 53_F | 128_N | 1.307 | 0.71 |
| 12_S | 15_S | 1.299 | 0.70 |
| 120_S | 123_Y | 1.294 | 0.70 |
| 12_S | 267_L | 1.294 | 0.70 |
| 61_I | 281_R | 1.282 | 0.69 |
| 263_D | 270_P | 1.279 | 0.68 |
| 45_F | 273_F | 1.272 | 0.68 |
| 44_F | 224_F | 1.271 | 0.68 |
| 86_F | 214_R | 1.261 | 0.67 |
| 183_F | 187_I | 1.261 | 0.67 |
| 110_S | 220_S | 1.256 | 0.66 |
| 52_F | 267_L | 1.247 | 0.65 |
| 47_F | 57_I | 1.247 | 0.65 |
| 270_P | 281_R | 1.246 | 0.65 |
| 37_F | 40_L | 1.245 | 0.65 |
| 51_T | 262_S | 1.241 | 0.65 |
| 44_F | 272_M | 1.239 | 0.65 |
| 72_S | 257_L | 1.238 | 0.65 |
| 121_A | 186_T | 1.237 | 0.65 |
| 34_S | 224_F | 1.235 | 0.64 |
| 229_L | 282_R | 1.234 | 0.64 |
| 99_A | 265_L | 1.229 | 0.64 |
| 12_S | 52_F | 1.219 | 0.63 |
| 44_F | 109_T | 1.217 | 0.63 |
| 212_A | 254_A | 1.213 | 0.62 |
| 166_S | 232_V | 1.208 | 0.62 |
| 19_Y | 112_N | 1.206 | 0.62 |
| 52_F | 176_L | 1.197 | 0.61 |
| 191_T | 268_I | 1.195 | 0.61 |
| 258_L | 261_I | 1.195 | 0.61 |
| 38_I | 156_Y | 1.190 | 0.60 |
| 57_I | 94_I | 1.174 | 0.59 |
| 191_T | 195_N | 1.169 | 0.58 |
| 3_L | 13_I | 1.167 | 0.58 |
| 202_L | 213_E | 1.165 | 0.58 |
| 89_N | 110_S | 1.165 | 0.58 |
| 26_V | 37_F | 1.162 | 0.57 |
| 92_Y | 188_T | 1.152 | 0.56 |
| 44_F | 127_W | 1.152 | 0.56 |
| 97_Y | 260_Y | 1.152 | 0.56 |
| 265_L | 270_P | 1.147 | 0.56 |
| 102_Q | 180_L | 1.146 | 0.56 |
| 173_R | 188_T | 1.146 | 0.56 |
| 271_W | 277_S | 1.142 | 0.55 |
| 7_T | 186_T | 1.137 | 0.55 |
| 20_A | 31_K | 1.134 | 0.55 |
| 110_S | 195_N | 1.132 | 0.54 |
| 100_Y | 259_P | 1.130 | 0.54 |
| 154_T | 274_L | 1.127 | 0.54 |
| 258_L | 274_L | 1.125 | 0.54 |
| 219_M | 276_F | 1.123 | 0.54 |
| 44_F | 219_M | 1.122 | 0.53 |
| 52_F | 260_Y | 1.121 | 0.53 |
| 14_P | 55_S | 1.120 | 0.53 |
| 190_A | 236_L | 1.119 | 0.53 |
| 103_F | 227_Q | 1.118 | 0.53 |
| 36_T | 112_N | 1.117 | 0.53 |
| 6_G | 57_I | 1.114 | 0.53 |
| 173_R | 237_N | 1.113 | 0.53 |
| 59_V | 266_T | 1.112 | 0.52 |
| 6_G | 46_V | 1.111 | 0.52 |
| 33_F | 284_F | 1.109 | 0.52 |
| 129_R | 192_A | 1.108 | 0.52 |
| 276_F | 280_A | 1.108 | 0.52 |
| 97_Y | 143_V | 1.106 | 0.52 |
| 269_H | 277_S | 1.100 | 0.51 |
| 219_M | 262_S | 1.099 | 0.51 |
| 139_I | 235_T | 1.097 | 0.51 |
| 50_I | 131_F | 1.095 | 0.51 |
| 11_Y | 267_L | 1.093 | 0.51 |
| 37_F | 91_F | 1.086 | 0.50 |
| 180_L | 262_S | 1.079 | 0.49 |
| 273_F | 280_A | 1.076 | 0.49 |
| 189_I | 232_V | 1.076 | 0.49 |
| 37_F | 127_W | 1.074 | 0.49 |
| 19_Y | 45_F | 1.074 | 0.49 |
| 69_C | 152_S | 1.074 | 0.49 |
| 165_Y | 171_V | 1.073 | 0.49 |
| 147_Y | 174_G | 1.064 | 0.48 |
| 102_Q | 177_Y | 1.064 | 0.48 |
| 55_S | 258_L | 1.064 | 0.48 |
| 3_L | 71_M | 1.061 | 0.47 |
| 73_F | 76_K | 1.061 | 0.47 |
| 221_G | 272_M | 1.059 | 0.47 |
| 33_F | 127_W | 1.057 | 0.47 |
| 95_H | 178_N | 1.057 | 0.47 |
| 146_T | 176_L | 1.055 | 0.47 |
| 10_L | 87_P | 1.055 | 0.47 |
| 111_L | 156_Y | 1.051 | 0.46 |
| 3_L | 199_F | 1.050 | 0.46 |
| 181_L | 186_T | 1.050 | 0.46 |
| 243_D | 246_K | 1.048 | 0.46 |
| 38_I | 258_L | 1.047 | 0.46 |
| 191_T | 271_W | 1.047 | 0.46 |
| 120_S | 213_E | 1.046 | 0.46 |
| 274_L | 277_S | 1.046 | 0.46 |
| 9_L | 126_A | 1.044 | 0.46 |
| 45_F | 88_L | 1.043 | 0.46 |
| 17_I | 30_S | 1.043 | 0.46 |
| 269_H | 280_A | 1.042 | 0.45 |
| 70_F | 253_I | 1.037 | 0.45 |
| 91_F | 178_N | 1.037 | 0.45 |
| 202_L | 279_K | 1.035 | 0.45 |
| 102_Q | 169_S | 1.034 | 0.45 |
| 51_T | 227_Q | 1.031 | 0.44 |
| 227_Q | 272_M | 1.028 | 0.44 |
| 164_C | 280_A | 1.028 | 0.44 |
| 41_Y | 220_S | 1.026 | 0.44 |
| 134_V | 140_V | 1.026 | 0.44 |
| 97_Y | 142_P | 1.025 | 0.44 |
| 64_N | 219_M | 1.020 | 0.43 |
| 125_K | 228_L | 1.019 | 0.43 |
| 212_A | 271_W | 1.019 | 0.43 |
| 75_F | 165_Y | 1.018 | 0.43 |
| 19_Y | 270_P | 1.015 | 0.43 |
| 105_L | 135_I | 1.014 | 0.43 |
| 110_S | 270_P | 1.012 | 0.42 |
| 122_T | 236_L | 1.009 | 0.42 |
| 193_I | 257_L | 1.009 | 0.42 |
| 15_S | 41_Y | 1.008 | 0.42 |
| 70_F | 221_G | 1.008 | 0.42 |
| 57_I | 117_I | 1.006 | 0.42 |
| 7_T | 182_P | 1.006 | 0.42 |
| 145_F | 179_Q | 1.004 | 0.42 |
| 54_N | 210_S | 1.002 | 0.41 |
| 48_N | 266_T | 1.000 | 0.41 |
| 99_A | 103_F | 1.000 | 0.41 |
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 | |
| 2z73A | 2 | 0.9187 | 98.9 | 0.836 | Contact Map |
| 4pxzA | 1 | 0.8 | 98.9 | 0.836 | Contact Map |
| 3v2yA | 1 | 0.8187 | 98.7 | 0.85 | Contact Map |
| 4mbsA | 2 | 0.8438 | 98.7 | 0.85 | Contact Map |
| 4ib4A | 1 | 0.8469 | 98.6 | 0.852 | Contact Map |
| 3vw7A | 1 | 0.8156 | 98.6 | 0.852 | Contact Map |
| 4mqsA | 1 | 0.8406 | 98.6 | 0.853 | Contact Map |
| 3oduA | 2 | 0.875 | 98.6 | 0.853 | Contact Map |
| 4ea3A | 2 | 0.8375 | 98.6 | 0.854 | Contact Map |
| 4eiyA | 1 | 0.85 | 98.6 | 0.855 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)